Seal Phase4AE same-precision GPU numerical gate and audit limits
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# 当前研究状态 — Phase 4AD
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# 当前研究状态 — Phase 4AE
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已按用户授权建立独立分支 `codex/lif-author-semantics-lab`。
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正式状态：**COMPLETE-ORACLE-VALIDATED-LAB-ONLY**。
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学习仍未达到可用标准；不替换任何旧候选，不把实现检查PASS当作学习PASS。
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独立新模型分支：`codex/lif-author-semantics-lab`。
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正式状态：**PASS-ISOLATED-GPU-NUMERICAL-GATE**。
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尚未完成新动力学全脑验证或conditioning，学习仍未达到可用标准。
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- [关键结果、限制与下一步](docs/progress/phase4ad-interpretation.md)
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- [完整实验报告](docs/progress/phase4ad-author-semantics.md)
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- [实验预声明](models/male-cns-lif/author-semantics-lab-v1/PROTOCOL.md)
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- [新产物封存核验](registry/phase4ad-author-semantics/seal-verification.json)
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- [此前全脑输入背景复核](docs/progress/feedback-context-review-20260930.md)
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- [本轮关键结果、限制和下一步](docs/progress/phase4ae-interpretation.md)
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- [完整数值实验](docs/progress/phase4ae-author-runtime.md)
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- [预先声明的协议](models/male-cns-lif/author-runtime-lab-v1/PROTOCOL.md)
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- [交叉精度差异](registry/phase4ae-author-runtime/cross-precision-description.json)
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- [校验与来源](registry/phase4ae-author-runtime/seal-verification.json)
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- [上轮持续循环发现](docs/progress/phase4ad-interpretation.md)
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## 关键发现
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## 已完成
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固定作者代码在Brian2 2.5.1实际运行。16项单元检查、10组真实回路/精度对照及其重复通过；58/58审计项通过。
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恢复作者完整动力学后，五节点真实回路1秒放电从1,483降到610，但后500ms仍有306次。
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因此不能认为“修g reset/不应期就解决学习问题”；持续循环仍存在，低活跃度不是晋级条件。
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12组固定小图/压力case、两种精度、各重复3次，共72次GPU执行。
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每次GPU与同精度实际Brian2参考的完整V/g history逐bit相同、最大误差0；事件、计数、不应期、请求送达及到达顺序/guard也一致。
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旧五组全脑参考回归和原230,239项及后续封存产物hash再次通过。
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下一步先做独立GPU实现的高入度/累加顺序与短时全图对照，再检验固定DoOR嗅觉输入是否保留区别；尚未开始conditioning。
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输入请求、不应期拒绝和实际放电必须分开统计。后续学习必须执行真实无调制/冻结/随机奖励对照和等待期，而非复用标签。
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float64与float32在临界阈值夹具分别放电4次/3次，因此不能把32位版本直接称为64位等价优化。
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旧模型、base CSR、原synapse count、W_syn、transmitter signs、APL校准、eligibility-v2和14,232 mask均未修改。
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## 冻结与服务
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## 下一步
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原230,239项以及4AA/4AB/4AC与背景复核封存文件前后校验不变。
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旧deterministic-v2五组全脑参考重新运行，事件、计数、最终电压和g精确一致。
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base CSR、raw counts、W_syn、transmitter signs、APL参数、eligibility-v2、14,232-edge mask未修改。
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只在独立实验环境安装作者版本依赖；未停用或修改ComfyUI。
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没有游戏、RL、decoder、视觉输入或权重训练，没有生成新的learned candidate。
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先用float64做完整图的10/50ms固定数值对照，再进行固定DoOR嗅觉信息保持测试。
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全部通过才进入真实学习验收：至少5个training seeds、独立evaluation、刺激特异性MBON/downstream，以及真正运行的对照和保持期。
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未训练、未进入游戏/RL/decoder/视觉接口。ComfyUI保持原样。
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代码、小报告、来源和校验清单进入Git；大数据及完整实验轨迹保留服务器，不等于完整异机备份。
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Git仅同步源码、小报告和校验清单；大数据与完整实验轨迹在服务器，不等于完整异机备份。
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# Phase 4AE GPU作者语义数值门禁
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状态：`PASS-ISOLATED-GPU-NUMERICAL-GATE`。
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仅验证固定小网络，尚未证明全脑等价、生物学正确或学习可用。未训练、未修改冻结输入或旧模型。
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| case | precision | events | max V/g error V | exact whole history | pass |
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|---|---|---:|---:|---|---|
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| fanin_bursts | float64 | 1539 | 0.0 | True | True |
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| fanin_bursts | float32 | 1539 | 0.0 | True | True |
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| highest_indegree | float64 | 101 | 0.0 | True | True |
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| highest_indegree | float32 | 101 | 0.0 | True | True |
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| mixed_high_indegree | float64 | 106 | 0.0 | True | True |
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| mixed_high_indegree | float32 | 106 | 0.0 | True | True |
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| motif_feedforward | float64 | 3 | 0.0 | True | True |
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| motif_feedforward | float32 | 3 | 0.0 | True | True |
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| motif_five | float64 | 60 | 0.0 | True | True |
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| motif_five | float32 | 60 | 0.0 | True | True |
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| motif_no_input | float64 | 0 | 0.0 | True | True |
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| motif_no_input | float32 | 0 | 0.0 | True | True |
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| motif_pair | float64 | 22 | 0.0 | True | True |
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| motif_pair | float32 | 22 | 0.0 | True | True |
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| motif_trio | float64 | 45 | 0.0 | True | True |
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| motif_trio | float32 | 45 | 0.0 | True | True |
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| ordered_cancellation | float64 | 32 | 0.0 | True | True |
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| ordered_cancellation | float32 | 32 | 0.0 | True | True |
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| release_selfloop | float64 | 8 | 0.0 | True | True |
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| release_selfloop | float32 | 8 | 0.0 | True | True |
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| signed_random | float64 | 400 | 0.0 | True | True |
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| signed_random | float32 | 400 | 0.0 | True | True |
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| threshold_rounding | float64 | 4 | 0.0 | True | True |
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| threshold_rounding | float32 | 3 | 0.0 | True | True |
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每项GPU执行3次，检查原始事件、输入请求实际送达、逐目标到达顺序及guard、计数、不应期和完整状态。
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大整数、随机图、重复/零边属于纯数值夹具，不是新增MaleCNS连接或生理假设。真实子图使用全部既有诱导边、原contact count与冻结transmitter sign。
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原始冻结完整性与旧五组全脑deterministic-v2回归再次核验；该旧回归PASS不等于新动力学全脑PASS。
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没有根据活动强度选择参数；尚须短时全图对照及嗅觉信息保持测试。
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# Phase 4AE：独立GPU后端通过固定数值压力集
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状态：`PASS-ISOLATED-GPU-NUMERICAL-GATE`。独立分支仍为 `codex/lif-author-semantics-lab`。
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这不是 learned candidate，也不是全脑或长期动力学等价声明。
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## 具体推进
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- 新增双精度CUDA后端，按已验证作者表达式逐次舍入，禁用FMA和fast-math。
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- 保留精确18-step delay与22-step refractory；只展开当时放电源的真实出边，不逐步扫描全部edge。
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- 突触从目标当前g开始逐条累加，不能先求边权和再加；刚放电的目标拒绝同tick输入。
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- 将实际请求、允许注入、不应期拒绝分开统计。没有采用作者poi接口的rfc=0策略。
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- Brian2实际队列由只读代理观测；每个oracle再做无代理复跑，证明观测工具没有改变输出。
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固定12组case × float64/float32 × 3次GPU执行，**72/72通过**。
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全部状态history逐bit一致，V/g最大绝对差为0；事件、计数、不应期、请求送达、逐目标到达顺序和接受标记均一致。
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三次GPU重复逐数组相同，24组Brian oracle的观测/无观测对照均通过。
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这些是整个短轨迹的对照，不是仅比较总spike数或末态。
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## 覆盖范围和未覆盖项
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5个合成夹具覆盖有序正负抵消、256源fan-in、同tick输入与不应期释放、自环/队列回绕、阈值可表示数邻域，以及固定seed随机有符号网络。
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极大整数、重复/零边只用于明确标记的数值夹具，不是真实MaleCNS新连接或生理参数。
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2个真实128-neuron诱导子图按入度和原contact count选取，保持所有真实内部边与sign。
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两者中心都是全图最高入度节点neuron_idx=5/body_id=10009/type=CT1，入度11,526；伙伴组成不同。
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这是数值压力测试，不是两个独立中心的证据，也不是视觉编码实验。
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另有原4AD五个固定真实motif的100ms前缀。还没有覆盖所有全图累加场景和长时间反馈。
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## 精度差异不能隐藏
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作者float64与作者float32在阈值临界夹具产生4次和3次事件，首次分歧在tick0。
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两套GPU分别精确复制了各自参考，但**float32不能因此称为float64的等价加速**。
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本轮没有放宽事件门槛，没有根据活动强度选模型。下一次全图首先使用作者默认float64，以减少精度混淆。
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[完整交叉精度记录](../../registry/phase4ae-author-runtime/cross-precision-description.json)。
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## 下一步与学习门槛
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下一关：166,700节点/25,582,938边完整图的短时float64逐步对照：无输入10ms、固定单seed50ms、固定五seed50ms。
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采用连续运行和流式状态记录，不保存dense spike矩阵；比较实际队列摘要及所有细胞的每tick状态。
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通过后才进行固定DoOR嗅觉CAL，并独立审计原graded APL与新语义的组合。
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只有信息保持、held-out区分和真实conditioning功能/对照通过，才能讨论学习候选；不能从本轮数值PASS跳到学习PASS。
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## 完整性与运行信息
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原230,239项及4AA–4AD、背景复核前后hash检查通过，旧五个deterministic-v2全脑参考再次精确一致。
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新模型11个payload、新实验916个payload独立封存。ComfyUI未修改，科学环境未升级。
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72次GPU诊断总wall约15.93s；诊断峰值allocated VRAM约5.45MB。
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这些数值来自小图并包含诊断同步，**不是全脑性能或实时性承诺**；旧全脑回归峰值约286MB也不是新动力学性能。
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大数据/完整状态只留服务器；Git同步源码、小报告、出处与checksum，不等于完整异机备份。
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详见[完整实验报告](phase4ae-author-runtime.md)、[预声明](../../models/male-cns-lif/author-runtime-lab-v1/PROTOCOL.md)、[封存校验](../../registry/phase4ae-author-runtime/seal-verification.json)。
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# Phase 4AE — GPU author-semantics numerical gate
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User authorized an independent model branch. This is not conditioning and does
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not replace any Phase 1–4AD candidate/artifact. Learning remains unachieved.
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The fixed author equations and all physical parameters come from the validated
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4AD oracle, with dt=.1ms, delay=18 steps, refractory=22 steps and W=.275mV.
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Canonical CSR, raw contact counts and frozen transmitter signs are read-only.
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## Predeclared tests
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Five synthetic numerical fixtures: ordered cancellation (including deliberately
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nonphysiological large signed integers), 256-source fan-in bursts, refractory
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release/self-loop collisions, representable threshold neighbours, and a fixed
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seed signed random graph. Synthetic negative node labels are NOT MaleCNS IDs;
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duplicate/zero edges occur only in labelled numerical fixtures.
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Two 128-neuron real induced graphs are selected before simulation: the highest
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in-degree target and its 127 largest-contact presynaptic partners; separately the
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highest-in-degree target with >=64 positive and >=63 negative presynaptic inputs,
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64 positive and 63 negative largest-contact partners. Ties break by canonical
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neuron_idx. Include every existing edge within the selected node set, without
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changing raw counts/signs or adding edges. This is numerical stress, not an input
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interface or a physiological validation. Preserve identities and selection audit.
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Also run the same five 4AD motifs for 100ms with one common seed request (or no
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request for no_input). Report every outcome; do not select by activity/separability.
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These tests do not exhaust all full-brain numerical corner cases.
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## Exact arithmetic and schedule
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Execute unchanged pinned author create_model in Brian2 2.5.1/NumPy1.22.3 using
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the isolated 4AD environment. Export raw SI variables, actual coefficients and
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weights. GPU float32 coefficients round to float32 before each multiply/add;
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float64 uses double. No FMA or fast-math. Match generated expression order.
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Update refractory and integrate; apply only currently permitted voltage seed
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requests; strict threshold closes write access immediately; then accept delayed
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anatomical arrivals in author order within each target, external synthetic input,
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and reset. A fused reset is equivalent only if all arrivals reject current spikes.
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Never replace sequential g+=w with g+sum(w). A queue proxy observes real Brian
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arrival order without changing values; compare proxy and unwrapped runs exactly.
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Use an exact spike ring buffer, no approximated delay or dense edge scan.
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Before-threshold requests use the existing common requested-event convention,
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not the author's distinct poi interface that changes target refractory to zero.
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Report requested/accepted/rejected input separately. No graded APL in these isolated
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tests; its future integration and frozen coefficients require explicit audit.
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For each case/precision compare GPU to the same-precision real Brian oracle:
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exact events, counts, refractory, input delivery and per-target arrival order/guard;
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report full-history max/mean V/g error and bitwise state comparison. Fixed tolerance
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is 1e-11V float64 / 1e-6V float32. Any event divergence fails, regardless of tolerance.
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Each GPU case repeats three times with all arrays exactly equal. Cross-precision
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differences are separately descriptive, not grounds to change thresholds.
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## Integrity and progression
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Preregister sources, old input hashes and deterministic fixture hashes before any
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model execution. Preserve failures; use a separately recorded new attempt for
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implementation repairs. Do not change frozen artifacts. Save manifests/SHA-256.
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Old five deterministic-v2 full-brain reference regressions must pass again.
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Only then consider a short full-graph author comparison, followed by DoOR CAL;
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never claim full-brain equivalence or learning from isolated test PASS.
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Author source/license/provenance are inherited read-only from 4AD. Supporting
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primary documentation: https://numpy.org/doc/1.22/reference/generated/numpy.ufunc.at.html
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and https://brian2.readthedocs.io/en/2.5.1/user/refractoriness.html . The fixed
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generated source and actual boundary fixtures, not simplified prose, define timing.
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#include <torch/extension.h>
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void author_state_cuda(torch::Tensor v, torch::Tensor g, torch::Tensor ref,
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torch::Tensor requests, torch::Tensor spikes, torch::Tensor counts,
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double gd, double c0, double cg, double cv, double threshold,
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double reset, double seed_volt, int64_t refractory_steps);
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void author_fill_edges_cuda(torch::Tensor indptr, torch::Tensor sources,
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torch::Tensor offsets, torch::Tensor output);
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void author_arrivals_cuda(torch::Tensor edges, torch::Tensor starts, torch::Tensor targets,
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torch::Tensor weights, torch::Tensor g, torch::Tensor ref);
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void author_external_cuda(torch::Tensor external, torch::Tensor g, torch::Tensor ref);
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PYBIND11_MODULE(TORCH_EXTENSION_NAME, m) {
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m.def("state_step", &author_state_cuda, "Author NumPy-ordered integration/threshold/reset");
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m.def("fill_edges", &author_fill_edges_cuda, "Expand only active-source canonical CSR edges");
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m.def("apply_arrivals", &author_arrivals_cuda, "Sequential per-target arrival additions");
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m.def("apply_external", &author_external_cuda, "Post-anatomical external arrival additions");
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}
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#include <torch/extension.h>
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#include <ATen/cuda/CUDAContext.h>
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#include <c10/cuda/CUDAGuard.h>
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#include <c10/cuda/CUDAException.h>
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#include <cuda.h>
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#include <cuda_runtime.h>
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#include <cmath>
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#include <cstdint>
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#include <limits>
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namespace {
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constexpr int BLOCK = 128;
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void check_tensor(const torch::Tensor& x, const torch::Tensor& like,
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at::ScalarType dtype, const char* name) {
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TORCH_CHECK(x.is_cuda() && x.is_contiguous() && x.dim() == 1,
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name, " must be a contiguous CUDA vector");
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TORCH_CHECK(x.device() == like.device(), name, " is on a different CUDA device");
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TORCH_CHECK(x.scalar_type() == dtype, name, " has the wrong dtype");
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}
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void check_state(const torch::Tensor& g, const torch::Tensor& ref) {
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TORCH_CHECK(g.scalar_type() == torch::kFloat32 || g.scalar_type() == torch::kFloat64,
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"state must be float32 or float64");
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check_tensor(g, g, g.scalar_type(), "g");
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check_tensor(ref, g, torch::kInt32, "ref");
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TORCH_CHECK(g.numel() == ref.numel(), "g/ref length mismatch");
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TORCH_CHECK(g.numel() <= std::numeric_limits<int>::max(), "too many neurons");
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}
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void index_range(const torch::Tensor& x, int64_t upper, const char* name) {
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if (x.numel()) {
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TORCH_CHECK(x.min().item<int64_t>() >= 0 && x.max().item<int64_t>() < upper,
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name, " index out of bounds");
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}
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}
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template <typename T> __device__ __forceinline__ T add_rn(T a, T b);
|
||||
template <> __device__ __forceinline__ float add_rn(float a, float b) { return __fadd_rn(a, b); }
|
||||
template <> __device__ __forceinline__ double add_rn(double a, double b) { return __dadd_rn(a, b); }
|
||||
template <typename T> __device__ __forceinline__ T mul_rn(T a, T b);
|
||||
template <> __device__ __forceinline__ float mul_rn(float a, float b) { return __fmul_rn(a, b); }
|
||||
template <> __device__ __forceinline__ double mul_rn(double a, double b) { return __dmul_rn(a, b); }
|
||||
|
||||
template <typename T>
|
||||
__global__ void state_kernel(T* v, T* g, int32_t* ref, const uint8_t* requests,
|
||||
uint8_t* spikes, int32_t* counts, int n, T gd, T c0,
|
||||
T cg, T cv, T threshold, T reset, T seed_volt, int ref_steps) {
|
||||
const int i = blockIdx.x * blockDim.x + threadIdx.x;
|
||||
if (i >= n) return;
|
||||
int r = ref[i];
|
||||
r = r > 0 ? r - 1 : 0;
|
||||
const bool available = r == 0;
|
||||
T vi = v[i];
|
||||
if (available) {
|
||||
const T oldg = g[i];
|
||||
const T oldv = vi;
|
||||
// Match NumPy float-array expression evaluation: each operation rounds in T.
|
||||
g[i] = mul_rn(gd, oldg);
|
||||
const T driven = mul_rn(cg, oldg);
|
||||
const T leaked = mul_rn(cv, oldv);
|
||||
vi = add_rn(c0, add_rn(driven, leaked));
|
||||
if (requests[i]) vi = seed_volt;
|
||||
}
|
||||
const bool fired = available && vi > threshold;
|
||||
if (fired) {
|
||||
vi = reset;
|
||||
g[i] = T(0);
|
||||
r = ref_steps;
|
||||
counts[i] += 1;
|
||||
}
|
||||
// Nonavailable neurons retain V/g. Resetting fired cells before arrivals is
|
||||
// equivalent to reset-after-arrivals because all their arrivals are rejected.
|
||||
v[i] = vi;
|
||||
ref[i] = r;
|
||||
spikes[i] = fired ? 1 : 0;
|
||||
}
|
||||
|
||||
__global__ void fill_kernel(const int64_t* indptr, const int64_t* sources,
|
||||
const int64_t* offsets, int64_t* output, int n) {
|
||||
const int i = blockIdx.x * blockDim.x + threadIdx.x;
|
||||
if (i >= n) return;
|
||||
const int64_t source = sources[i];
|
||||
const int64_t begin = indptr[source];
|
||||
const int64_t end = indptr[source + 1];
|
||||
for (int64_t j = begin; j < end; ++j) output[offsets[i] + j - begin] = j;
|
||||
}
|
||||
|
||||
template <typename T>
|
||||
__global__ void arrival_kernel(const int64_t* edges, const int64_t* starts,
|
||||
const int32_t* targets, const T* weights, T* g,
|
||||
const int32_t* ref, int segments, int64_t edge_count) {
|
||||
const int segment = blockIdx.x * blockDim.x + threadIdx.x;
|
||||
if (segment >= segments) return;
|
||||
const int target = targets[segment];
|
||||
if (ref[target] != 0) return;
|
||||
const int64_t end = segment + 1 < segments ? starts[segment + 1] : edge_count;
|
||||
// Start at existing g, never sum weights separately: cancellation can differ.
|
||||
T accumulator = g[target];
|
||||
for (int64_t j = starts[segment]; j < end; ++j)
|
||||
accumulator = add_rn(accumulator, weights[edges[j]]);
|
||||
g[target] = accumulator;
|
||||
}
|
||||
|
||||
template <typename T>
|
||||
__global__ void external_kernel(const T* external, T* g, const int32_t* ref, int n) {
|
||||
const int i = blockIdx.x * blockDim.x + threadIdx.x;
|
||||
if (i < n && ref[i] == 0 && external[i] != T(0))
|
||||
g[i] = add_rn(g[i], external[i]);
|
||||
}
|
||||
} // namespace
|
||||
|
||||
void author_state_cuda(torch::Tensor v, torch::Tensor g, torch::Tensor ref,
|
||||
torch::Tensor requests, torch::Tensor spikes, torch::Tensor counts,
|
||||
double gd, double c0, double cg, double cv, double threshold,
|
||||
double reset, double seed_volt, int64_t refractory_steps) {
|
||||
check_state(g, ref);
|
||||
const c10::cuda::CUDAGuard guard(g.device());
|
||||
check_tensor(v, g, g.scalar_type(), "v");
|
||||
check_tensor(requests, g, torch::kUInt8, "requests");
|
||||
check_tensor(spikes, g, torch::kUInt8, "spikes");
|
||||
check_tensor(counts, g, torch::kInt32, "counts");
|
||||
const int64_t n = g.numel();
|
||||
TORCH_CHECK(v.numel() == n && requests.numel() == n && spikes.numel() == n && counts.numel() == n,
|
||||
"state vector length mismatch");
|
||||
TORCH_CHECK(refractory_steps > 0 && refractory_steps <= std::numeric_limits<int>::max(),
|
||||
"invalid refractory length");
|
||||
for (double x : {gd, c0, cg, cv, threshold, reset, seed_volt})
|
||||
TORCH_CHECK(std::isfinite(x), "nonfinite coefficient");
|
||||
if (!n) return;
|
||||
const auto stream = at::cuda::getCurrentCUDAStream(g.get_device());
|
||||
AT_DISPATCH_FLOATING_TYPES(g.scalar_type(), "author_state", [&] {
|
||||
state_kernel<scalar_t><<<(n + BLOCK - 1) / BLOCK, BLOCK, 0, stream>>>(
|
||||
v.data_ptr<scalar_t>(), g.data_ptr<scalar_t>(), ref.data_ptr<int32_t>(),
|
||||
requests.data_ptr<uint8_t>(), spikes.data_ptr<uint8_t>(), counts.data_ptr<int32_t>(),
|
||||
static_cast<int>(n), static_cast<scalar_t>(gd), static_cast<scalar_t>(c0),
|
||||
static_cast<scalar_t>(cg), static_cast<scalar_t>(cv), static_cast<scalar_t>(threshold),
|
||||
static_cast<scalar_t>(reset), static_cast<scalar_t>(seed_volt), static_cast<int>(refractory_steps));
|
||||
});
|
||||
C10_CUDA_KERNEL_LAUNCH_CHECK();
|
||||
}
|
||||
|
||||
void author_fill_edges_cuda(torch::Tensor indptr, torch::Tensor sources,
|
||||
torch::Tensor offsets, torch::Tensor output) {
|
||||
check_tensor(indptr, indptr, torch::kInt64, "indptr");
|
||||
const c10::cuda::CUDAGuard guard(indptr.device());
|
||||
check_tensor(sources, indptr, torch::kInt64, "sources");
|
||||
check_tensor(offsets, indptr, torch::kInt64, "offsets");
|
||||
check_tensor(output, indptr, torch::kInt64, "output");
|
||||
TORCH_CHECK(indptr.numel() >= 1 && sources.numel() == offsets.numel(), "CSR shape mismatch");
|
||||
TORCH_CHECK(sources.numel() <= std::numeric_limits<int>::max(), "too many sources");
|
||||
TORCH_CHECK(indptr[0].item<int64_t>() == 0, "CSR indptr must begin at zero");
|
||||
if (indptr.numel() > 1)
|
||||
TORCH_CHECK((indptr.slice(0, 1) >= indptr.slice(0, 0, -1)).all().item<bool>(), "CSR indptr not monotonic");
|
||||
index_range(sources, indptr.numel() - 1, "source");
|
||||
if (!sources.numel()) {
|
||||
TORCH_CHECK(output.numel() == 0, "nonempty expansion for no active sources");
|
||||
return;
|
||||
}
|
||||
const auto degrees = indptr.index_select(0, sources + 1) - indptr.index_select(0, sources);
|
||||
const auto expected_offsets = degrees.cumsum(0) - degrees;
|
||||
TORCH_CHECK(torch::equal(offsets, expected_offsets), "incorrect output offsets");
|
||||
TORCH_CHECK(degrees.sum().item<int64_t>() == output.numel(), "incorrect expansion length");
|
||||
const auto stream = at::cuda::getCurrentCUDAStream(indptr.get_device());
|
||||
fill_kernel<<<(sources.numel() + BLOCK - 1) / BLOCK, BLOCK, 0, stream>>>(
|
||||
indptr.data_ptr<int64_t>(), sources.data_ptr<int64_t>(), offsets.data_ptr<int64_t>(),
|
||||
output.data_ptr<int64_t>(), static_cast<int>(sources.numel()));
|
||||
C10_CUDA_KERNEL_LAUNCH_CHECK();
|
||||
}
|
||||
|
||||
void author_arrivals_cuda(torch::Tensor edges, torch::Tensor starts, torch::Tensor targets,
|
||||
torch::Tensor weights, torch::Tensor g, torch::Tensor ref) {
|
||||
check_state(g, ref);
|
||||
const c10::cuda::CUDAGuard guard(g.device());
|
||||
check_tensor(edges, g, torch::kInt64, "edges");
|
||||
check_tensor(starts, g, torch::kInt64, "starts");
|
||||
check_tensor(targets, g, torch::kInt32, "targets");
|
||||
check_tensor(weights, g, g.scalar_type(), "weights");
|
||||
TORCH_CHECK(starts.numel() == targets.numel(), "segment count mismatch");
|
||||
TORCH_CHECK(starts.numel() <= std::numeric_limits<int>::max(), "too many target segments");
|
||||
if (!starts.numel()) {
|
||||
TORCH_CHECK(!edges.numel(), "edges without target segments");
|
||||
return;
|
||||
}
|
||||
index_range(edges, weights.numel(), "edge");
|
||||
index_range(starts, edges.numel(), "segment start");
|
||||
index_range(targets, g.numel(), "target");
|
||||
TORCH_CHECK(starts[0].item<int64_t>() == 0, "first segment must start at zero");
|
||||
if (starts.numel() > 1) {
|
||||
TORCH_CHECK((starts.slice(0, 1) > starts.slice(0, 0, -1)).all().item<bool>(), "segment starts not increasing");
|
||||
TORCH_CHECK((targets.slice(0, 1) > targets.slice(0, 0, -1)).all().item<bool>(), "targets must be unique and increasing");
|
||||
}
|
||||
const auto stream = at::cuda::getCurrentCUDAStream(g.get_device());
|
||||
AT_DISPATCH_FLOATING_TYPES(g.scalar_type(), "author_arrivals", [&] {
|
||||
arrival_kernel<scalar_t><<<(starts.numel() + BLOCK - 1) / BLOCK, BLOCK, 0, stream>>>(
|
||||
edges.data_ptr<int64_t>(), starts.data_ptr<int64_t>(), targets.data_ptr<int32_t>(),
|
||||
weights.data_ptr<scalar_t>(), g.data_ptr<scalar_t>(), ref.data_ptr<int32_t>(),
|
||||
static_cast<int>(starts.numel()), edges.numel());
|
||||
});
|
||||
C10_CUDA_KERNEL_LAUNCH_CHECK();
|
||||
}
|
||||
|
||||
void author_external_cuda(torch::Tensor external, torch::Tensor g, torch::Tensor ref) {
|
||||
check_state(g, ref);
|
||||
const c10::cuda::CUDAGuard guard(g.device());
|
||||
check_tensor(external, g, g.scalar_type(), "external");
|
||||
TORCH_CHECK(external.numel() == g.numel(), "external/state length mismatch");
|
||||
if (!g.numel()) return;
|
||||
const auto stream = at::cuda::getCurrentCUDAStream(g.get_device());
|
||||
AT_DISPATCH_FLOATING_TYPES(g.scalar_type(), "author_external", [&] {
|
||||
external_kernel<scalar_t><<<(g.numel() + BLOCK - 1) / BLOCK, BLOCK, 0, stream>>>(
|
||||
external.data_ptr<scalar_t>(), g.data_ptr<scalar_t>(), ref.data_ptr<int32_t>(), static_cast<int>(g.numel()));
|
||||
});
|
||||
C10_CUDA_KERNEL_LAUNCH_CHECK();
|
||||
}
|
||||
@@ -0,0 +1,12 @@
|
||||
72601f46dde3202d62e71161958f620a3ce5b8f9c24cf1f5b7158289b5f9a3f0 PROTOCOL.md
|
||||
208a937d17bbb041b9bf6b25b89264ee566830b60609e58491b44583d8541f15 author_ext.cpp
|
||||
669f166e18ce9a3f63fc723db8b0a8b74f7fa4757194b1bd65b4cf6008a7787e author_ext.cu
|
||||
356b6161576f6f6d79745af1927bb43b12a7c3d50922bf9e1bd29e473fcf2106 config.json
|
||||
9eea9a592241cab7f4303850e969def7887eee3f4ec18421103605cafd258cf8 context.py
|
||||
cb75d512ddf9a5ff344f3ac82eefb112406593bf7b414dfac79d7c5d730371ee finalize.py
|
||||
03758d07572f4b44d272059d9308fac534268ad201b57bdd77d69fee95e67278 gpu_backend.py
|
||||
32eb1c42383068ce52701d2139a376ce155ad7072cde019949f8ca2d55492409 oracle_stress.py
|
||||
2519eaa2c50b2d91fd0c4f623aeabd6f5d212c5b537951d0a66bc81c569db78c prepare.py
|
||||
92733a48921f95c3c0935bf16a704634b89b6540352f31cc1169ec6d3211b57a run_suite.py
|
||||
720d04b379b6f1f64cae28a2203444a6d4c4e72ecb121cc69e93c2740fae69ab verify_frozen.py
|
||||
7e8b0ac4adcd48eceabca7c9cc4f2c42a8746ebc673aee4490bae5a4746bbe12 manifest.json
|
||||
@@ -0,0 +1,19 @@
|
||||
{
|
||||
"phase": "4AE",
|
||||
"name": "author-runtime-lab-v1",
|
||||
"human_authorization": "允许独立新模型分支测试动力学假设",
|
||||
"seed": 410301,
|
||||
"gpu_uuid": "GPU-79f3a85d-adce-7833-7003-6488140ca596",
|
||||
"precisions": ["float64", "float32"],
|
||||
"gpu_repeats": 3,
|
||||
"max_abs_volt": {"float64": 1e-11, "float32": 1e-6},
|
||||
"exact_events_required": true,
|
||||
"exact_refractory_required": true,
|
||||
"exact_arrival_order_per_tick_target_required": true,
|
||||
"training": false,
|
||||
"whole_brain_author_backend_claimed": false,
|
||||
"candidate_generation": false,
|
||||
"synthetic_cases": ["ordered_cancellation", "fanin_bursts", "release_selfloop", "threshold_rounding", "signed_random"],
|
||||
"real_cases": ["highest_indegree", "mixed_high_indegree"],
|
||||
"prior_motifs": ["pair", "trio", "five", "feedforward", "no_input"]
|
||||
}
|
||||
@@ -0,0 +1,40 @@
|
||||
import hashlib
|
||||
import json
|
||||
from pathlib import Path
|
||||
|
||||
MODEL=Path(__file__).resolve().parent
|
||||
ROOT=Path('/data/digital-drosophila')
|
||||
EXP=ROOT/'experiments/phase4ae-author-runtime'
|
||||
AD=ROOT/'experiments/phase4ad-author-semantics'
|
||||
CFG=json.loads((MODEL/'config.json').read_text())
|
||||
|
||||
def digest(path):
|
||||
h=hashlib.sha256()
|
||||
with Path(path).open('rb') as f:
|
||||
for b in iter(lambda:f.read(8<<20),b''):h.update(b)
|
||||
return h.hexdigest()
|
||||
|
||||
def save(path,value):
|
||||
path=Path(path);path.parent.mkdir(parents=True,exist_ok=True)
|
||||
with path.open('x',encoding='utf-8') as f:json.dump(value,f,indent=2,ensure_ascii=False,allow_nan=False);f.write('\n')
|
||||
|
||||
def sources():
|
||||
return {p.name:digest(p) for p in sorted(MODEL.iterdir()) if p.is_file() and p.name not in ('manifest.json','checksums.sha256')}
|
||||
|
||||
def check():
|
||||
p=json.loads((EXP/'protocol/preregistered.json').read_text())
|
||||
assert sources()==p['sources'],'Source changed after preregistration'
|
||||
for row in p['inputs']:assert digest(ROOT/row['path'])==row['sha256'],row['path']
|
||||
for row in json.loads((EXP/'protocol/case-hashes.json').read_text()):assert digest(EXP/row['path'])==row['sha256'],row['path']
|
||||
return p
|
||||
|
||||
def integrity():
|
||||
import sys
|
||||
sys.path.insert(0,str(ROOT/'models/male-cns-lif/lif-semantics-audit-v1'))
|
||||
import audit_semantics as old
|
||||
r=old.integrity()
|
||||
for rel in ('models/male-cns-lif/lif-semantics-audit-v1','experiments/phase4ac-lif-semantics',
|
||||
'registry/feedback-context-review-20260930','models/male-cns-lif/author-semantics-lab-v1','experiments/phase4ad-author-semantics'):
|
||||
r[rel]=old.manifest_check(ROOT/rel,digest)
|
||||
assert all(x['pass'] for x in r.values())
|
||||
return r
|
||||
@@ -0,0 +1,52 @@
|
||||
"""Gate the diagnostic prototype, never promote it as learned/full-brain runtime."""
|
||||
import json
|
||||
from pathlib import Path
|
||||
import sys
|
||||
from context import ROOT,EXP,MODEL,CFG,save,check,integrity,digest
|
||||
from run_suite import load,compare
|
||||
|
||||
def seal(root):
|
||||
rows=[]
|
||||
for p in sorted(root.rglob('*')):
|
||||
if '__pycache__' in p.parts or '.venv' in p.parts:continue
|
||||
if p.is_file():rows.append(dict(path=str(p.relative_to(root)),bytes=p.stat().st_size,sha256=digest(p)))
|
||||
assert not (root/'manifest.json').exists() and not (root/'checksums.sha256').exists()
|
||||
save(root/'manifest.json',dict(root=str(root),files=rows))
|
||||
with (root/'checksums.sha256').open('x') as f:
|
||||
for r in rows:f.write(r['sha256']+' '+r['path']+'\n')
|
||||
f.write(digest(root/'manifest.json')+' manifest.json\n')
|
||||
|
||||
def main():
|
||||
check();after=integrity();save(EXP/'regression/old-integrity-after.json',after)
|
||||
summary=json.loads((EXP/'regression/gpu-complete.json').read_text());ref=json.loads((EXP/'regression/frozen-five.json').read_text())
|
||||
expected=(len(CFG['synthetic_cases'])+len(CFG['real_cases'])+len(CFG['prior_motifs']))*len(CFG['precisions'])*CFG['gpu_repeats']
|
||||
assert len(summary['trials'])==expected
|
||||
rows=[]
|
||||
for record in summary['trials']:
|
||||
name=record['case'];precision=record['precision'];repeat=record['repeat'];case=EXP/'cases'/name
|
||||
oracle=load(EXP/'oracle'/(name+'-'+precision)/'state.npz');gpu=load(EXP/'gpu'/(name+'-'+precision+f'-r{repeat}')/'state.npz')
|
||||
actual=compare(oracle,gpu,case,precision);assert actual==record['comparison'],'Stored report differs from raw states'
|
||||
first=load(EXP/'gpu'/(name+'-'+precision+'-r0')/'state.npz')
|
||||
import numpy as np
|
||||
equal={k:bool(np.array_equal(v,gpu[k])) for k,v in first.items()};assert equal==record['repeat_arrays']
|
||||
rows.append(record)
|
||||
passed=all(r['pass_all'] for r in rows) and ref['pass_all'] and all(x['pass'] for x in after.values())
|
||||
status='PASS-ISOLATED-GPU-NUMERICAL-GATE' if passed else 'FAIL-ISOLATED-GPU-NUMERICAL-GATE'
|
||||
save(EXP/'audit/final-status.json',dict(status=status,pass_all=passed,cases=expected//6,gpu_runs=expected,
|
||||
full_brain_author_equivalence=False,conditioning=False,learning_achieved=False,candidate_generated=False,
|
||||
next_gate='Short full-graph same-precision author comparison, then fixed DoOR CAL only if numerical gates pass'))
|
||||
lines=['# Phase 4AE GPU作者语义数值门禁','',f'状态：`{status}`。','',
|
||||
'仅验证固定小网络，尚未证明全脑等价、生物学正确或学习可用。未训练、未修改冻结输入或旧模型。','',
|
||||
'| case | precision | events | max V/g error V | exact whole history | pass |','|---|---|---:|---:|---|---|']
|
||||
for r in rows:
|
||||
if r['repeat']:continue
|
||||
c=r['comparison'];lines.append(f"| {r['case']} | {r['precision']} | {c['oracle_events']} | {c['max_abs_volt']} | {c['bitwise_history']} | {r['pass_all']} |")
|
||||
lines+=['','每项GPU执行3次，检查原始事件、输入请求实际送达、逐目标到达顺序及guard、计数、不应期和完整状态。',
|
||||
'大整数、随机图、重复/零边属于纯数值夹具，不是新增MaleCNS连接或生理假设。真实子图使用全部既有诱导边、原contact count与冻结transmitter sign。',
|
||||
'原始冻结完整性与旧五组全脑deterministic-v2回归再次核验；该旧回归PASS不等于新动力学全脑PASS。',
|
||||
'没有根据活动强度选择参数；尚须短时全图对照及嗅觉信息保持测试。','']
|
||||
with (EXP/'REPORT.md').open('x',encoding='utf-8') as f:f.write('\n'.join(lines))
|
||||
check();seal(MODEL);seal(EXP);print(status,flush=True)
|
||||
if not passed:raise SystemExit(1)
|
||||
|
||||
if __name__=='__main__':main()
|
||||
@@ -0,0 +1,275 @@
|
||||
"""Small-case diagnostic CUDA backend; SI states, explicit dtype rounding.
|
||||
|
||||
run_gpu is serial, records CPU diagnostics, and is not a performance runtime.
|
||||
Coefficients and optional weights must come from the same-precision Brian2 oracle.
|
||||
"""
|
||||
from functools import lru_cache
|
||||
import hashlib
|
||||
import json
|
||||
import math
|
||||
import os
|
||||
from pathlib import Path
|
||||
import time
|
||||
import traceback
|
||||
|
||||
import numpy as np
|
||||
import torch
|
||||
from torch.utils.cpp_extension import load
|
||||
|
||||
|
||||
SOURCE_ROOT = Path(__file__).resolve().parent
|
||||
COEFFICIENT_NAMES = ("gd", "c0", "cg", "cv", "threshold", "reset", "seed_volt")
|
||||
|
||||
|
||||
def require(condition, message):
|
||||
if not condition:
|
||||
raise ValueError(message)
|
||||
|
||||
|
||||
def write_json(path, data):
|
||||
with Path(path).open("x", encoding="utf-8") as output:
|
||||
json.dump(data, output, indent=2, allow_nan=False)
|
||||
output.write("\n")
|
||||
|
||||
|
||||
def digest(path):
|
||||
checksum = hashlib.sha256()
|
||||
with Path(path).open("rb") as source:
|
||||
for block in iter(lambda: source.read(1 << 20), b""):
|
||||
checksum.update(block)
|
||||
return checksum.hexdigest()
|
||||
|
||||
|
||||
@lru_cache(maxsize=None)
|
||||
def _load_extension(build_path, signature):
|
||||
build = Path(build_path) / ("author_cuda_" + signature[:16])
|
||||
build.mkdir(parents=True, exist_ok=True)
|
||||
module = load(name="author_cuda_" + signature[:16],
|
||||
sources=[str(SOURCE_ROOT / "author_ext.cpp"), str(SOURCE_ROOT / "author_ext.cu")],
|
||||
build_directory=str(build), extra_cflags=["-O2"],
|
||||
extra_cuda_cflags=["-O2", "--fmad=false", "--ftz=false", "--prec-div=true", "--prec-sqrt=true"],
|
||||
verbose=False)
|
||||
return module
|
||||
|
||||
|
||||
def build_extension(build_root):
|
||||
provenance = {"sources": {name: digest(SOURCE_ROOT / name)
|
||||
for name in ("author_ext.cpp", "author_ext.cu")},
|
||||
"torch": torch.__version__, "torch_cuda": torch.version.cuda,
|
||||
"arch_list": os.environ.get("TORCH_CUDA_ARCH_LIST"),
|
||||
"cuda_flags": ["-O2", "--fmad=false", "--ftz=false", "--prec-div=true", "--prec-sqrt=true"]}
|
||||
signature = hashlib.sha256(json.dumps(provenance, sort_keys=True).encode()).hexdigest()
|
||||
return _load_extension(str(Path(build_root).resolve()), signature), provenance
|
||||
|
||||
|
||||
def read_case(case_dir, precision, coefficients, weights):
|
||||
case_dir = Path(case_dir)
|
||||
require(precision in ("float32", "float64"), "precision must be float32 or float64")
|
||||
dtype = np.dtype(precision)
|
||||
with (case_dir / "spec.json").open(encoding="utf-8") as source:
|
||||
spec = json.load(source)
|
||||
for key in ("dt_ms", "steps", "duration_ms", "model"):
|
||||
require(key in spec, "Missing spec field: " + key)
|
||||
model = spec["model"]
|
||||
for key in ("threshold_mv", "reset_potential_mv", "resting_potential_mv",
|
||||
"synaptic_delay_ms", "refractory_ms", "w_syn_mv_per_anatomical_synapse"):
|
||||
require(key in model and math.isfinite(float(model[key])), "Missing/nonfinite model field: " + key)
|
||||
steps = spec["steps"]
|
||||
require(type(steps) is int and 0 < steps < np.iinfo(np.int32).max, "Invalid step count")
|
||||
dt = float(spec["dt_ms"])
|
||||
require(math.isfinite(dt) and dt > 0, "Invalid dt")
|
||||
require(math.isfinite(float(spec["duration_ms"])) and
|
||||
round(float(spec["duration_ms"]) / dt) == steps, "Duration/steps mismatch")
|
||||
delay = round(float(model["synaptic_delay_ms"]) / dt)
|
||||
refractory = round(float(model["refractory_ms"]) / dt)
|
||||
require(delay == 18 and refractory == 22, "This declared backend requires delay=18 and refractory=22")
|
||||
require(float(model["w_syn_mv_per_anatomical_synapse"]) == 0.275, "W_syn differs from frozen value")
|
||||
coeff = {}
|
||||
for key in COEFFICIENT_NAMES:
|
||||
require(key in coefficients and math.isfinite(float(coefficients[key])), "Missing/nonfinite coefficient: " + key)
|
||||
coeff[key] = float(coefficients[key])
|
||||
require(bool(np.isfinite(dtype.type(coeff[key]))), "Coefficient overflows requested dtype: " + key)
|
||||
require(dtype.type(coeff["threshold"]) == dtype.type(float(model["threshold_mv"]) * .001),
|
||||
"Oracle threshold differs from case spec")
|
||||
require(dtype.type(coeff["reset"]) == dtype.type(float(model["reset_potential_mv"]) * .001),
|
||||
"Oracle reset differs from case spec")
|
||||
with np.load(case_dir / "arrays.npz", allow_pickle=False) as inputs:
|
||||
arrays = {key: inputs[key].copy() for key in inputs.files}
|
||||
required_types = {"nodes": "int32", "edge_id": "int64", "src": "int32", "dst": "int32",
|
||||
"signed_raw": "int64", "requests": "uint8", "external_mv": "float64",
|
||||
"initial_v_mv": "float64", "initial_g_mv": "float64"}
|
||||
for key, expected in required_types.items():
|
||||
require(key in arrays and arrays[key].dtype == np.dtype(expected), "Missing/wrong array dtype: " + key)
|
||||
nodes = arrays["nodes"]
|
||||
require(nodes.ndim == 1 and len(np.unique(nodes)) == len(nodes), "Invalid neuron identities")
|
||||
n = len(nodes)
|
||||
require(n < 512, "This diagnostic backend is restricted to fewer than 512 cells")
|
||||
edge_id = arrays["edge_id"]
|
||||
require(edge_id.ndim == 1 and len(np.unique(edge_id)) == len(edge_id), "Invalid edge identities")
|
||||
e = len(edge_id)
|
||||
for key in ("src", "dst", "signed_raw"):
|
||||
require(arrays[key].shape == (e,), "Edge vector shape mismatch: " + key)
|
||||
for key in ("src", "dst"):
|
||||
require(bool(np.all((arrays[key] >= 0) & (arrays[key] < n))), "Local edge endpoint out of bounds")
|
||||
require(np.array_equal(np.lexsort((edge_id, arrays["src"])), np.arange(e)),
|
||||
"Edges must already be canonical source/edge_id sorted; indices will not be silently reordered")
|
||||
for key in ("requests", "external_mv"):
|
||||
require(arrays[key].shape == (steps, n), "Trial array shape mismatch: " + key)
|
||||
require(bool(np.all(arrays["requests"] <= 1)), "Request array is not Boolean uint8")
|
||||
for key in ("initial_v_mv", "initial_g_mv"):
|
||||
require(arrays[key].shape == (n,), "Initial state shape mismatch: " + key)
|
||||
for key in ("external_mv", "initial_v_mv", "initial_g_mv"):
|
||||
require(bool(np.isfinite(arrays[key]).all()), "Nonfinite case array: " + key)
|
||||
if weights is None:
|
||||
weight_array = np.asarray(arrays["signed_raw"] * (.275 * .001), dtype=dtype)
|
||||
weight_origin = "signed_raw * (0.275 * 0.001), then cast to requested dtype"
|
||||
else:
|
||||
weight_array = np.asarray(weights, dtype=dtype)
|
||||
weight_origin = "caller supplied oracle SI weight array"
|
||||
require(weight_array.shape == (e,) and bool(np.isfinite(weight_array).all()), "Invalid SI weights")
|
||||
for key in ("initial_v_mv", "initial_g_mv", "external_mv"):
|
||||
converted = np.asarray(arrays[key] * .001, dtype=dtype)
|
||||
require(bool(np.isfinite(converted).all()), "Conversion overflow: " + key)
|
||||
return spec, arrays, coeff, np.ascontiguousarray(weight_array), weight_origin
|
||||
|
||||
|
||||
def run_gpu(case_dir, out_dir, precision, coefficients, build_root, weights=None):
|
||||
"""Run one case; return state dict and save SI state plus GPU-selected arrivals.
|
||||
|
||||
``weights`` is optional SI volts in the original arrays.npz edge-row order.
|
||||
Repeated calls share a cached extension; each needs a new exclusive out_dir.
|
||||
"""
|
||||
case_dir, out_dir = Path(case_dir), Path(out_dir)
|
||||
require(not out_dir.exists(), "Refusing existing output directory: " + str(out_dir))
|
||||
spec, arrays, coeff, weight_array, weight_origin = read_case(case_dir, precision, coefficients, weights)
|
||||
require(torch.cuda.is_available(), "CUDA unavailable")
|
||||
require(torch.cuda.device_count() == 1 and "4090" in torch.cuda.get_device_name(), "Only the single declared RTX4090 is permitted")
|
||||
out_dir.mkdir(parents=True, exist_ok=False)
|
||||
start = time.perf_counter()
|
||||
try:
|
||||
ext, build_provenance = build_extension(build_root)
|
||||
build_done = time.perf_counter()
|
||||
device = torch.device("cuda", torch.cuda.current_device())
|
||||
torch.cuda.reset_peak_memory_stats(device)
|
||||
dtype = torch.float32 if precision == "float32" else torch.float64
|
||||
numpy_dtype = np.dtype(precision)
|
||||
n, steps = len(arrays["nodes"]), spec["steps"]
|
||||
|
||||
def upload(value, target_dtype=None):
|
||||
return torch.as_tensor(np.ascontiguousarray(value), device=device, dtype=target_dtype).contiguous()
|
||||
|
||||
v = upload(np.asarray(arrays["initial_v_mv"] * .001, dtype=numpy_dtype), dtype)
|
||||
g = upload(np.asarray(arrays["initial_g_mv"] * .001, dtype=numpy_dtype), dtype)
|
||||
ref = torch.zeros(n, dtype=torch.int32, device=device)
|
||||
counts = torch.zeros(n, dtype=torch.int32, device=device)
|
||||
requests = upload(arrays["requests"], torch.uint8)
|
||||
accepted_requests = torch.empty_like(requests)
|
||||
rejected_requests = torch.empty_like(requests)
|
||||
external = upload(np.asarray(arrays["external_mv"] * .001, dtype=numpy_dtype), dtype)
|
||||
synaptic_weights = upload(weight_array, dtype)
|
||||
dst = upload(arrays["dst"], torch.int32)
|
||||
degrees_np = np.bincount(arrays["src"], minlength=n).astype(np.int64)
|
||||
indptr_np = np.concatenate((np.zeros(1, np.int64), np.cumsum(degrees_np, dtype=np.int64)))
|
||||
indptr = upload(indptr_np, torch.int64)
|
||||
ring = torch.zeros((19, n), dtype=torch.uint8, device=device)
|
||||
history = torch.empty((steps, 3, n), dtype=dtype, device=device)
|
||||
event_steps, event_nodes = [], []
|
||||
arrival_steps, arrival_indices, arrival_accepted = [], [], []
|
||||
torch.cuda.synchronize(device)
|
||||
simulation_start = time.perf_counter()
|
||||
for step in range(steps):
|
||||
spikes = ring[step % 19]
|
||||
# The state kernel decrements refractory before considering a request.
|
||||
# These diagnostics use that exact pre-kernel eligibility on the GPU.
|
||||
available_after_decrement = ref <= 1
|
||||
accepted_requests[step].copy_(requests[step] & available_after_decrement.to(torch.uint8))
|
||||
rejected_requests[step].copy_(requests[step] & (~available_after_decrement).to(torch.uint8))
|
||||
ext.state_step(v, g, ref, requests[step], spikes, counts,
|
||||
*[coeff[key] for key in COEFFICIENT_NAMES], 22)
|
||||
if step >= 18:
|
||||
due = ring[(step - 18) % 19]
|
||||
sources = torch.nonzero(due, as_tuple=False).flatten().contiguous()
|
||||
if sources.numel():
|
||||
degrees = indptr[sources + 1] - indptr[sources]
|
||||
offsets = (torch.cumsum(degrees, dim=0) - degrees).contiguous()
|
||||
edge_count = int(degrees.sum().item())
|
||||
expanded = torch.empty(edge_count, device=device, dtype=torch.int64)
|
||||
ext.fill_edges(indptr, sources, offsets, expanded)
|
||||
if edge_count:
|
||||
destination = dst[expanded]
|
||||
order = torch.argsort(destination, stable=True)
|
||||
edge_indices = expanded[order].contiguous()
|
||||
ordered_targets = destination[order]
|
||||
boundary = torch.ones(edge_count, dtype=torch.bool, device=device)
|
||||
boundary[1:] = ordered_targets[1:] != ordered_targets[:-1]
|
||||
starts = torch.nonzero(boundary, as_tuple=False).flatten().contiguous()
|
||||
targets = ordered_targets[starts].contiguous()
|
||||
accepted = (ref[ordered_targets.long()] == 0).to(torch.uint8)
|
||||
# Capture the actual CUDA-expanded and GPU-stable-sorted edge stream.
|
||||
arrival_steps.append(np.full(edge_count, step, dtype=np.int32))
|
||||
arrival_indices.append(edge_indices.cpu().numpy().copy())
|
||||
arrival_accepted.append(accepted.cpu().numpy().copy())
|
||||
ext.apply_arrivals(edge_indices, starts, targets, synaptic_weights, g, ref)
|
||||
ext.apply_external(external[step], g, ref)
|
||||
history[step, 0].copy_(v)
|
||||
history[step, 1].copy_(g)
|
||||
history[step, 2].copy_(ref)
|
||||
fired = torch.nonzero(spikes, as_tuple=False).flatten().cpu().numpy()
|
||||
if len(fired):
|
||||
event_steps.append(np.full(len(fired), step, dtype=np.int32))
|
||||
event_nodes.append(arrays["nodes"][fired])
|
||||
torch.cuda.synchronize(device)
|
||||
simulation_done = time.perf_counter()
|
||||
|
||||
def joined(chunks, dt):
|
||||
return np.concatenate(chunks).astype(dt, copy=False) if chunks else np.empty(0, dtype=dt)
|
||||
|
||||
result = {"nodes": arrays["nodes"], "history": history.cpu().numpy(),
|
||||
"counts": counts.cpu().numpy(), "v": v.cpu().numpy(), "g": g.cpu().numpy(),
|
||||
"ref": ref.cpu().numpy(), "weights": synaptic_weights.cpu().numpy(),
|
||||
"step": joined(event_steps, np.int32), "neuron_idx": joined(event_nodes, np.int32),
|
||||
"request_attempted": arrays["requests"].copy(),
|
||||
"request_accepted": accepted_requests.cpu().numpy(),
|
||||
"request_rejected": rejected_requests.cpu().numpy()}
|
||||
arrival_index = joined(arrival_indices, np.int64)
|
||||
arrivals = {"step": joined(arrival_steps, np.int32), "edge_index": arrival_index,
|
||||
"edge_id": arrays["edge_id"][arrival_index],
|
||||
"target_local": arrays["dst"][arrival_index],
|
||||
"accepted": joined(arrival_accepted, np.uint8)}
|
||||
result.update(arrival_step=arrivals["step"], arrival_edge_index=arrivals["edge_index"],
|
||||
arrival_accepted=arrivals["accepted"])
|
||||
with (out_dir / "state.npz").open("xb") as target:
|
||||
np.savez_compressed(target, **result)
|
||||
with (out_dir / "arrival-order.npz").open("xb") as target:
|
||||
np.savez_compressed(target, **arrivals)
|
||||
finite = bool(all(np.isfinite(value).all() for value in result.values()))
|
||||
metrics = {"precision": precision, "state_units": "SI volts; refractory is steps",
|
||||
"coefficients_double_input": coeff,
|
||||
"coefficients_effective_dtype": {key: float(numpy_dtype.type(value)) for key, value in coeff.items()},
|
||||
"weights_origin": weight_origin, "nodes": n, "edges": len(weight_array), "steps": steps,
|
||||
"total_spikes": len(result["step"]), "arriving_edges": len(arrival_index),
|
||||
"accepted_arriving_edges": int(np.count_nonzero(arrivals["accepted"])),
|
||||
"requested": int(np.count_nonzero(result["request_attempted"])),
|
||||
"accepted_requests": int(np.count_nonzero(result["request_accepted"])),
|
||||
"rejected_requests": int(np.count_nonzero(result["request_rejected"])),
|
||||
"all_finite": finite, "delay_steps": 18, "refractory_steps": 22,
|
||||
"build_or_cache_seconds": build_done - start,
|
||||
"diagnostic_simulation_seconds": simulation_done - simulation_start,
|
||||
"wall_seconds": time.perf_counter() - start,
|
||||
"gpu": torch.cuda.get_device_name(device), "device": str(device),
|
||||
"peak_allocated_vram_bytes": int(torch.cuda.max_memory_allocated(device)),
|
||||
"peak_reserved_vram_bytes": int(torch.cuda.max_memory_reserved(device)),
|
||||
"build": build_provenance,
|
||||
"input_sha256": {name: digest(case_dir / name) for name in ("spec.json", "arrays.npz")},
|
||||
"arrival_order_scope": "GPU expanded edges, stable target grouping; compare relative order per tick and target",
|
||||
"performance_runtime_claim": False, "oracle_validation_claim": False,
|
||||
"whole_brain_run": False, "learning": False,
|
||||
"cpu_transfer_each_step_for_diagnostics": True}
|
||||
write_json(out_dir / "metrics.json", metrics)
|
||||
require(finite, "Nonfinite GPU state; raw trace preserved")
|
||||
return result
|
||||
except Exception as error:
|
||||
write_json(out_dir / "error.json", {"type": type(error).__name__, "message": str(error),
|
||||
"traceback": traceback.format_exc(), "precision": precision,
|
||||
"validation_pass": False})
|
||||
raise
|
||||
@@ -0,0 +1,60 @@
|
||||
{
|
||||
"root": "/data/digital-drosophila/models/male-cns-lif/author-runtime-lab-v1",
|
||||
"files": [
|
||||
{
|
||||
"path": "PROTOCOL.md",
|
||||
"bytes": 4188,
|
||||
"sha256": "72601f46dde3202d62e71161958f620a3ce5b8f9c24cf1f5b7158289b5f9a3f0"
|
||||
},
|
||||
{
|
||||
"path": "author_ext.cpp",
|
||||
"bytes": 1203,
|
||||
"sha256": "208a937d17bbb041b9bf6b25b89264ee566830b60609e58491b44583d8541f15"
|
||||
},
|
||||
{
|
||||
"path": "author_ext.cu",
|
||||
"bytes": 10422,
|
||||
"sha256": "669f166e18ce9a3f63fc723db8b0a8b74f7fa4757194b1bd65b4cf6008a7787e"
|
||||
},
|
||||
{
|
||||
"path": "config.json",
|
||||
"bytes": 805,
|
||||
"sha256": "356b6161576f6f6d79745af1927bb43b12a7c3d50922bf9e1bd29e473fcf2106"
|
||||
},
|
||||
{
|
||||
"path": "context.py",
|
||||
"bytes": 1707,
|
||||
"sha256": "9eea9a592241cab7f4303850e969def7887eee3f4ec18421103605cafd258cf8"
|
||||
},
|
||||
{
|
||||
"path": "finalize.py",
|
||||
"bytes": 3814,
|
||||
"sha256": "cb75d512ddf9a5ff344f3ac82eefb112406593bf7b414dfac79d7c5d730371ee"
|
||||
},
|
||||
{
|
||||
"path": "gpu_backend.py",
|
||||
"bytes": 16277,
|
||||
"sha256": "03758d07572f4b44d272059d9308fac534268ad201b57bdd77d69fee95e67278"
|
||||
},
|
||||
{
|
||||
"path": "oracle_stress.py",
|
||||
"bytes": 29235,
|
||||
"sha256": "32eb1c42383068ce52701d2139a376ce155ad7072cde019949f8ca2d55492409"
|
||||
},
|
||||
{
|
||||
"path": "prepare.py",
|
||||
"bytes": 8828,
|
||||
"sha256": "2519eaa2c50b2d91fd0c4f623aeabd6f5d212c5b537951d0a66bc81c569db78c"
|
||||
},
|
||||
{
|
||||
"path": "run_suite.py",
|
||||
"bytes": 5318,
|
||||
"sha256": "92733a48921f95c3c0935bf16a704634b89b6540352f31cc1169ec6d3211b57a"
|
||||
},
|
||||
{
|
||||
"path": "verify_frozen.py",
|
||||
"bytes": 2157,
|
||||
"sha256": "720d04b379b6f1f64cae28a2203444a6d4c4e72ecb121cc69e93c2740fae69ab"
|
||||
}
|
||||
]
|
||||
}
|
||||
@@ -0,0 +1,502 @@
|
||||
"""Small, fixed-input Brian2 2.5.1 stress oracle for Phase 4AE.
|
||||
|
||||
The archived author source, equations, reset, parameters, and synapses are left
|
||||
unchanged. Diagnostic initial states and the old common request interface are
|
||||
explicit inputs. This file does not install packages or run whole-brain cases.
|
||||
"""
|
||||
from __future__ import annotations
|
||||
|
||||
import hashlib
|
||||
import importlib.metadata
|
||||
import json
|
||||
import platform
|
||||
import sys
|
||||
import types
|
||||
from pathlib import Path
|
||||
|
||||
import numpy as np
|
||||
import pandas as pd
|
||||
|
||||
|
||||
AUTHOR_PATH = Path("/data/digital-drosophila/experiments/phase4ad-author-semantics/external-resources/model.py")
|
||||
AUTHOR_SHA256 = "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e"
|
||||
AUTHOR_COMMIT = "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960"
|
||||
LIO_NAMES = {"gd": "_lio_2", "c0": "_lio_8", "cg": "_lio_9", "cv": "_lio_10"}
|
||||
|
||||
|
||||
def _save(path: Path, value) -> None:
|
||||
with path.open("x", encoding="utf-8") as handle:
|
||||
json.dump(value, handle, indent=2, sort_keys=True, allow_nan=False)
|
||||
handle.write("\n")
|
||||
|
||||
|
||||
def _save_arrays(path: Path, arrays: dict) -> None:
|
||||
with path.open("xb") as handle:
|
||||
np.savez_compressed(handle, **arrays)
|
||||
|
||||
|
||||
def _digest(path: Path) -> str:
|
||||
h = hashlib.sha256()
|
||||
with path.open("rb") as handle:
|
||||
for block in iter(lambda: handle.read(8 << 20), b""):
|
||||
h.update(block)
|
||||
return h.hexdigest()
|
||||
|
||||
|
||||
def _check(condition, message: str) -> None:
|
||||
if not condition:
|
||||
raise ValueError(message)
|
||||
|
||||
|
||||
def _load_case(case_dir: Path) -> tuple[dict, dict]:
|
||||
spec = json.loads((case_dir / "spec.json").read_text(encoding="utf-8"))
|
||||
with np.load(case_dir / "arrays.npz", allow_pickle=False) as archive:
|
||||
arrays = {name: archive[name].copy() for name in archive.files}
|
||||
expected_types = {"nodes": "int32", "edge_id": "int64", "src": "int32",
|
||||
"dst": "int32", "signed_raw": "int64", "requests": "uint8",
|
||||
"external_mv": "float64", "initial_v_mv": "float64",
|
||||
"initial_g_mv": "float64"}
|
||||
for name, dtype in expected_types.items():
|
||||
_check(name in arrays, f"Missing input array: {name}")
|
||||
_check(arrays[name].dtype == np.dtype(dtype), f"{name} must have dtype {dtype}")
|
||||
nodes = arrays["nodes"]
|
||||
_check(nodes.ndim == 1 and 1 <= len(nodes) <= 512, "Stress cases require 1..512 nodes")
|
||||
_check(np.all(np.diff(nodes.astype(np.int64)) > 0), "nodes must be sorted and unique")
|
||||
steps = int(spec["steps"])
|
||||
_check(steps == spec["steps"] and 1 <= steps <= 1000, "steps must be an integer in 1..1000")
|
||||
_check(float(spec["dt_ms"]) == .1, "The fixed stress protocol requires dt_ms=0.1")
|
||||
if "duration_ms" in spec:
|
||||
_check(np.isclose(float(spec["duration_ms"]), steps * .1, rtol=0, atol=1e-12),
|
||||
"duration_ms disagrees with steps and dt_ms")
|
||||
if "dt_ms" in spec["model"]:
|
||||
_check(float(spec["model"]["dt_ms"]) == .1, "model dt_ms disagrees with case dt_ms")
|
||||
edge_count = len(arrays["edge_id"])
|
||||
# The unchanged author calls Synapses.connect(i=[], j=[]), which Brian2
|
||||
# 2.5.1 does not support. Empty-network fixtures must explicitly provide
|
||||
# a documented zero-weight synthetic edge in the input case.
|
||||
_check(edge_count > 0, "Use an explicit zero-weight fixture edge instead of empty connectivity")
|
||||
for name in ("edge_id", "src", "dst", "signed_raw"):
|
||||
_check(arrays[name].shape == (edge_count,), f"{name} has an inconsistent shape")
|
||||
_check(len(np.unique(arrays["edge_id"])) == edge_count, "edge_id must be unique")
|
||||
for name in ("src", "dst"):
|
||||
_check(np.all((arrays[name] >= 0) & (arrays[name] < len(nodes))), f"{name} is out of local range")
|
||||
_check(np.array_equal(np.lexsort((arrays["edge_id"], arrays["src"])), np.arange(edge_count)),
|
||||
"Edges must be in canonical source-then-edge order")
|
||||
for name in ("requests", "external_mv"):
|
||||
_check(arrays[name].shape == (steps, len(nodes)), f"{name} must have shape (steps, N)")
|
||||
_check(np.all(arrays["requests"] <= 1), "requests must contain only 0 or 1")
|
||||
for name in ("initial_v_mv", "initial_g_mv"):
|
||||
_check(arrays[name].shape == (len(nodes),), f"{name} must have shape (N,)")
|
||||
for name in ("external_mv", "initial_v_mv", "initial_g_mv"):
|
||||
_check(np.isfinite(arrays[name]).all(), f"{name} contains a nonfinite value")
|
||||
return spec, arrays
|
||||
|
||||
|
||||
def _code_records(network) -> list:
|
||||
records = []
|
||||
for obj in network.sorted_objects:
|
||||
row = {"name": obj.name, "type": type(obj).__name__,
|
||||
"when": obj.when, "order": int(obj.order), "active": bool(obj.active)}
|
||||
if hasattr(obj, "abstract_code"):
|
||||
abstract = obj.abstract_code
|
||||
row["abstract_code"] = abstract if isinstance(abstract, (str, dict)) else str(abstract)
|
||||
row["code_objects"] = [
|
||||
{"name": code.name, "generated_code": str(code.code)}
|
||||
for code in getattr(obj, "code_objects", ())]
|
||||
records.append(row)
|
||||
return records
|
||||
|
||||
|
||||
class _QueueReadProxy:
|
||||
"""Forward the queue unchanged; copy only observations from peek()."""
|
||||
|
||||
def __init__(self, queue, get_tick, get_available, targets, observations, counters):
|
||||
self._original_queue = queue
|
||||
self._get_tick = get_tick
|
||||
self._get_available = get_available
|
||||
self._targets = targets
|
||||
self._observations = observations
|
||||
self._counters = counters
|
||||
|
||||
def peek(self, *args, **kwargs):
|
||||
value = self._original_queue.peek(*args, **kwargs)
|
||||
edge_indices = np.asarray(value, dtype=np.int64).copy()
|
||||
if np.any(edge_indices < 0) or np.any(edge_indices >= len(self._targets)):
|
||||
raise AssertionError("The anatomical queue returned an invalid local edge index")
|
||||
tick = self._get_tick()
|
||||
accepted = np.asarray(self._get_available(), dtype=bool)[self._targets[edge_indices]].astype(np.uint8)
|
||||
self._observations.append((tick, edge_indices, accepted))
|
||||
self._counters["peek_calls"] += 1
|
||||
return value
|
||||
|
||||
def advance(self, *args, **kwargs):
|
||||
self._counters["advance_calls"] += 1
|
||||
return self._original_queue.advance(*args, **kwargs)
|
||||
|
||||
def __getattr__(self, name):
|
||||
return getattr(self._original_queue, name)
|
||||
|
||||
|
||||
def _scalar_namespace(code_runner, name: str):
|
||||
for code in getattr(code_runner, "code_objects", ()):
|
||||
if name in code.namespace:
|
||||
value = np.asarray(code.namespace[name])
|
||||
if value.ndim == 0 and np.isfinite(value):
|
||||
return float(value), {"source": "CodeObject.namespace", "code_object": code.name,
|
||||
"name": name, "namespace_dtype": str(value.dtype)}
|
||||
return None, None
|
||||
|
||||
|
||||
def _coefficients(neu, parameters, b2, dt_seconds: float) -> dict:
|
||||
generated = "\n".join(str(code.code) for code in neu.state_updater.code_objects)
|
||||
_check("_lio_2 * g" in generated and
|
||||
"_lio_8 + ((_lio_9 * g) + (_lio_10 * v))" in generated,
|
||||
"Generated state expression changed; the recorded _lio-to-GPU mapping is not valid")
|
||||
dt = np.float64(dt_seconds)
|
||||
tau = np.float64(parameters["tau"] / b2.second)
|
||||
membrane = np.float64(parameters["t_mbr"] / b2.second)
|
||||
rest = np.float64(parameters["v_0"] / b2.volt)
|
||||
# This is the actual scalar expression order emitted by the pinned Brian
|
||||
# state updater, not an algebraically rearranged analytic solution.
|
||||
lio_1 = (-dt) / tau
|
||||
lio_3 = tau / (membrane - tau)
|
||||
lio_4 = dt / membrane
|
||||
lio_5 = dt / tau
|
||||
lio_6 = (-dt) / membrane
|
||||
fallback = {
|
||||
"gd": np.exp(lio_1), "c0": rest - (rest * np.exp(lio_6)),
|
||||
"cg": ((lio_3 * ((-np.exp(lio_4)) + np.exp(lio_5))) * np.exp(lio_6)) * np.exp(lio_1),
|
||||
"cv": np.exp(lio_6),
|
||||
}
|
||||
result, provenance = {}, {}
|
||||
for key, name in LIO_NAMES.items():
|
||||
value, record = _scalar_namespace(neu.state_updater, name)
|
||||
if value is None:
|
||||
value = float(fallback[key])
|
||||
record = {"source": "same generated scalar expression evaluated with numpy.float64", "name": name}
|
||||
result[key], provenance[key] = value, record
|
||||
for key, runner, name, author_key in (
|
||||
("threshold", neu.thresholder["spike"], "v_th", "v_th"),
|
||||
("reset", neu.resetter["spike"], "v_rst", "v_rst"),
|
||||
):
|
||||
value, record = _scalar_namespace(runner, name)
|
||||
if value is None:
|
||||
value = float(parameters[author_key] / b2.volt)
|
||||
record = {"source": "unchanged author parameter", "name": name}
|
||||
result[key], provenance[key] = value, record
|
||||
result["seed_volt"] = float((parameters["v_th"] + 1 * b2.mV) / b2.volt)
|
||||
provenance["seed_volt"] = {"source": "common request interface: unchanged v_th + 1 mV"}
|
||||
result["metadata"] = {
|
||||
"units": "SI volts and dimensionless coefficients", "names": LIO_NAMES,
|
||||
"provenance": provenance, "hex": {key: value.hex() for key, value in result.items()},
|
||||
"voltage_expression": "c0 + ((cg * old_g) + (cv * old_v))",
|
||||
"g_expression": "gd * old_g",
|
||||
"constant_values_are_double": True,
|
||||
"float32_execution_note": "Brian NumPy scalar/array promotion and operation order must be matched separately; double coefficients alone do not assert float64 intermediate array arithmetic.",
|
||||
}
|
||||
return result
|
||||
|
||||
|
||||
def _parameters_match(parameters, model, b2) -> dict:
|
||||
rows = {}
|
||||
for config_key, author_key, unit in (
|
||||
("membrane_tau_ms", "t_mbr", b2.ms), ("synaptic_tau_ms", "tau", b2.ms),
|
||||
("refractory_ms", "t_rfc", b2.ms), ("synaptic_delay_ms", "t_dly", b2.ms),
|
||||
("resting_potential_mv", "v_0", b2.mV), ("reset_potential_mv", "v_rst", b2.mV),
|
||||
("threshold_mv", "v_th", b2.mV), ("w_syn_mv_per_anatomical_synapse", "w_syn", b2.mV),
|
||||
):
|
||||
requested, actual = float(model[config_key]), float(parameters[author_key] / unit)
|
||||
_check(np.isfinite(requested) and np.isclose(requested, actual, rtol=0, atol=1e-12),
|
||||
f"Model parameter {config_key} differs from the archived author")
|
||||
rows[config_key] = {"case": requested, "author": actual}
|
||||
return rows
|
||||
|
||||
|
||||
def _run_once(spec, arrays, precision, output, source_bytes, trace_queue):
|
||||
import brian2 as b2
|
||||
from brian2.core.base import BrianObject
|
||||
|
||||
output.mkdir(parents=True, exist_ok=False)
|
||||
saved = {key: b2.prefs[key] for key in (
|
||||
"codegen.target", "core.default_float_dtype", "legacy.refractory_timing")}
|
||||
old_dt = b2.defaultclock.dt
|
||||
dtype = np.dtype(precision)
|
||||
steps, nodes = int(spec["steps"]), arrays["nodes"]
|
||||
dt_ms, dt_seconds = float(spec["dt_ms"]), float(spec["dt_ms"]) * .001
|
||||
try:
|
||||
b2.start_scope()
|
||||
b2.prefs["codegen.target"] = "numpy"
|
||||
b2.prefs["core.default_float_dtype"] = dtype.type
|
||||
b2.prefs["legacy.refractory_timing"] = False
|
||||
b2.defaultclock.dt = dt_ms * b2.ms
|
||||
author = types.ModuleType("phase4ae_author_" + precision)
|
||||
author.__file__ = str(AUTHOR_PATH)
|
||||
exec(compile(source_bytes, str(AUTHOR_PATH), "exec"), author.__dict__)
|
||||
parameters = dict(author.default_params)
|
||||
parameter_checks = _parameters_match(parameters, spec["model"], b2)
|
||||
completeness = pd.DataFrame({"local_index": np.arange(len(nodes), dtype=np.int32)},
|
||||
index=pd.Index(nodes, name="global_neuron_idx"))
|
||||
connectivity = pd.DataFrame({
|
||||
"Presynaptic_Index": arrays["src"], "Postsynaptic_Index": arrays["dst"],
|
||||
"Excitatory x Connectivity": arrays["signed_raw"], "edge_id": arrays["edge_id"],
|
||||
"source_neuron_idx": nodes[arrays["src"]], "target_neuron_idx": nodes[arrays["dst"]],
|
||||
})
|
||||
comp_path, con_path = output / "completeness.csv", output / "connectivity.parquet"
|
||||
completeness.to_csv(comp_path)
|
||||
connectivity.to_parquet(con_path, engine="pyarrow", index=False)
|
||||
neu, syn, spikes = author.create_model(comp_path, con_path, parameters)
|
||||
_check(np.dtype(neu.variables["v"].dtype) == dtype and np.dtype(neu.variables["g"].dtype) == dtype,
|
||||
"Brian state dtype disagrees with the precision arm")
|
||||
_check(np.dtype(syn.variables["w"].dtype) == dtype, "Brian synaptic weight dtype disagrees")
|
||||
np.testing.assert_array_equal(np.asarray(syn.i[:]), arrays["src"])
|
||||
np.testing.assert_array_equal(np.asarray(syn.j[:]), arrays["dst"])
|
||||
neu.v = arrays["initial_v_mv"] * b2.mV
|
||||
neu.g = arrays["initial_g_mv"] * b2.mV
|
||||
initial_v = np.asarray(neu.v_[:], dtype=dtype).copy()
|
||||
initial_g = np.asarray(neu.g_[:], dtype=dtype).copy()
|
||||
attempted = arrays["requests"].copy()
|
||||
accepted = np.zeros_like(attempted)
|
||||
rejected = np.zeros_like(attempted)
|
||||
request_slots_seen = np.zeros(steps, dtype=np.uint8)
|
||||
|
||||
def current_tick():
|
||||
return int(round(float(neu.clock.t / b2.second) / dt_seconds))
|
||||
|
||||
def requests_before_thresholds():
|
||||
tick = current_tick()
|
||||
if tick < 0 or tick >= steps or request_slots_seen[tick]:
|
||||
raise AssertionError("Common request operation executed outside its unique tick")
|
||||
request_slots_seen[tick] = 1
|
||||
request = attempted[tick].astype(bool)
|
||||
available = np.asarray(neu.not_refractory[:], dtype=bool)
|
||||
permitted = request & available
|
||||
accepted[tick] = permitted
|
||||
rejected[tick] = request & ~available
|
||||
if permitted.any():
|
||||
neu.v[np.flatnonzero(permitted)] = parameters["v_th"] + 1 * b2.mV
|
||||
|
||||
request_op = b2.NetworkOperation(requests_before_thresholds, clock=neu.clock,
|
||||
when="before_thresholds", order=0, name="oracle_common_requests")
|
||||
objects = [neu, syn, spikes, request_op]
|
||||
ext_ticks, ext_targets = np.nonzero(arrays["external_mv"])
|
||||
external_weights = np.empty(0, dtype=dtype)
|
||||
if len(ext_ticks):
|
||||
ext_ids = np.arange(len(ext_ticks), dtype=np.int32)
|
||||
ext_source = b2.SpikeGeneratorGroup(len(ext_ticks), ext_ids,
|
||||
ext_ticks.astype(np.float64) * dt_ms * b2.ms, sorted=True,
|
||||
clock=neu.clock, name="zz_external_sources")
|
||||
ext_syn = b2.Synapses(ext_source, neu, "w : volt", on_pre="g_post += w",
|
||||
delay=0 * b2.ms, name="zz_external_arrivals")
|
||||
ext_syn.connect(i=ext_ids, j=ext_targets)
|
||||
ext_syn.w = arrays["external_mv"][ext_ticks, ext_targets] * b2.mV
|
||||
ext_syn.pre.order = 0
|
||||
_check(syn.pre.when == ext_syn.pre.when == "synapses" and syn.pre.order < 0,
|
||||
"External delivery must follow the original anatomical pathway")
|
||||
external_weights = np.asarray(ext_syn.w_[:], dtype=dtype).copy()
|
||||
objects.extend([ext_source, ext_syn])
|
||||
|
||||
observations = []
|
||||
queue_counters = {"peek_calls": 0, "advance_calls": 0, "installations": []}
|
||||
if trace_queue:
|
||||
class QueueInstaller(BrianObject):
|
||||
def __init__(self):
|
||||
super().__init__(clock=neu.clock, when="end", order=1_000_000,
|
||||
name="zz_oracle_queue_installer")
|
||||
|
||||
def before_run(self, run_namespace):
|
||||
# Network.before_run traverses sorted objects. All original
|
||||
# code runners have compiled before this last end-slot object.
|
||||
installed = []
|
||||
for code in syn.pre.code_objects:
|
||||
if "_queue" not in code.namespace or "_queue.peek()" not in str(code.code):
|
||||
continue
|
||||
original = code.namespace["_queue"]
|
||||
if isinstance(original, _QueueReadProxy):
|
||||
original = original._original_queue
|
||||
code.namespace["_queue"] = _QueueReadProxy(
|
||||
original, current_tick, lambda: neu.not_refractory[:],
|
||||
arrays["dst"], observations, queue_counters)
|
||||
installed.append(code.name)
|
||||
if len(installed) != 1:
|
||||
raise AssertionError(f"Expected exactly one anatomical queue consumer, got {installed}")
|
||||
queue_counters["installations"].append(installed[0])
|
||||
|
||||
objects.append(QueueInstaller())
|
||||
|
||||
trace = b2.StateMonitor(neu, ["v", "g", "lastspike", "not_refractory"],
|
||||
record=True, when="end", order=0, name="oracle_end_state")
|
||||
objects.append(trace)
|
||||
network = b2.Network(*objects)
|
||||
_save(output / "schedule.json", {"schedule": list(network.schedule),
|
||||
"summary": str(network.scheduling_summary())})
|
||||
_save(output / "input-audit.json", {
|
||||
"source_sha256": AUTHOR_SHA256, "parameter_checks": parameter_checks,
|
||||
"source_parameters_modified": False, "precision": precision,
|
||||
"dt_ms": dt_ms, "steps": steps, "request_interface": "before_thresholds; v=v_th+1mV only if not_refractory",
|
||||
"poisson_helper_used": False, "all_neurons_keep_original_rfc": True,
|
||||
"queue_trace_enabled": trace_queue, "state_units": "SI volts, original dtype",
|
||||
"completeness_sha256": _digest(comp_path), "connectivity_sha256": _digest(con_path),
|
||||
})
|
||||
network.run(0 * b2.ms, namespace={})
|
||||
_save(output / "compiled-code.json", _code_records(network))
|
||||
if request_slots_seen.any() or observations:
|
||||
raise AssertionError("Zero-duration compilation unexpectedly advanced the case")
|
||||
network.run(steps * dt_ms * b2.ms, namespace={})
|
||||
_save(output / "generated-code.json", _code_records(network))
|
||||
_check(np.all(request_slots_seen == 1), "Not every request tick was observed exactly once")
|
||||
|
||||
event_float = np.asarray(spikes.t[:] / b2.second, dtype=np.float64) / dt_seconds
|
||||
event_ticks = np.rint(event_float).astype(np.int32)
|
||||
_check(np.allclose(event_float, event_ticks, rtol=0, atol=1e-6), "Spike time is off the integer clock")
|
||||
local_indices = np.asarray(spikes.i[:], dtype=np.int32).copy()
|
||||
order = np.lexsort((nodes[local_indices], event_ticks))
|
||||
event_ticks, local_indices = event_ticks[order], local_indices[order]
|
||||
fired = np.zeros_like(attempted)
|
||||
fired[event_ticks, local_indices] = 1
|
||||
counts = np.asarray(spikes.count[:], dtype=np.int32).copy()
|
||||
_check(np.array_equal(fired.sum(axis=0), counts), "Events and per-neuron counts disagree")
|
||||
_check(not np.any(accepted & ~fired), "An applicable common request did not produce a real spike")
|
||||
_check(np.array_equal(attempted, accepted + rejected), "Request accounting is incomplete")
|
||||
state_ticks = np.asarray(trace.t[:] / b2.second, dtype=np.float64) / dt_seconds
|
||||
_check(state_ticks.shape == (steps,) and np.allclose(state_ticks, np.arange(steps), rtol=0, atol=1e-6),
|
||||
"StateMonitor does not cover the exact requested ticks")
|
||||
voltage = np.asarray(trace.v_, dtype=dtype).T.copy()
|
||||
conductance = np.asarray(trace.g_, dtype=dtype).T.copy()
|
||||
last = np.asarray(trace.lastspike_, dtype=np.float64).T
|
||||
seen = np.isfinite(last) & (last >= 0)
|
||||
last_ticks = np.zeros(last.shape, dtype=np.int64)
|
||||
last_ticks[seen] = np.rint(last[seen] / dt_seconds).astype(np.int64)
|
||||
refractory_steps = int(round(float(parameters["t_rfc"] / b2.ms) / dt_ms))
|
||||
remaining = np.where(seen, np.maximum(refractory_steps - (np.arange(steps)[:, None] - last_ticks), 0), 0).astype(np.int32)
|
||||
available_end = np.asarray(trace.not_refractory, dtype=bool).T
|
||||
_check(np.array_equal(remaining == 0, available_end), "Refractory flag and integer countdown disagree")
|
||||
history = np.stack([voltage, conductance, remaining.astype(dtype)], axis=1)
|
||||
_check(np.isfinite(history).all(), "Author state became nonfinite")
|
||||
arrival_step = np.empty(0, dtype=np.int32)
|
||||
arrival_edge = np.empty(0, dtype=np.int64)
|
||||
arrival_accepted = np.empty(0, dtype=np.uint8)
|
||||
if trace_queue:
|
||||
_check(queue_counters["peek_calls"] == steps and queue_counters["advance_calls"] == steps,
|
||||
"Queue proxy did not observe exactly one peek and advance per tick")
|
||||
_check([entry[0] for entry in observations] == list(range(steps)), "Queue peek ticks are not complete and ordered")
|
||||
arrival_step = np.concatenate([np.full(len(ids), tick, dtype=np.int32) for tick, ids, _ in observations])
|
||||
arrival_edge = np.concatenate([ids for _, ids, _ in observations]).astype(np.int64, copy=False)
|
||||
arrival_accepted = np.concatenate([mask for _, _, mask in observations]).astype(np.uint8, copy=False)
|
||||
delay_steps = int(round(float(parameters["t_dly"] / b2.ms) / dt_ms))
|
||||
if len(arrival_step):
|
||||
_check(np.all(arrival_step >= delay_steps), "An anatomical event arrived before the fixed delay")
|
||||
_check(np.all(fired[arrival_step - delay_steps, arrays["src"][arrival_edge]]),
|
||||
"A queued arrival has no matching presynaptic spike at the author delay")
|
||||
_check(np.array_equal(arrival_accepted,
|
||||
available_end[arrival_step, arrays["dst"][arrival_edge]].astype(np.uint8)),
|
||||
"Observed arrival gating disagrees with the post-threshold refractory state")
|
||||
source_counts_due = fired[:max(0, steps - delay_steps)].sum(axis=0, dtype=np.int64)
|
||||
expected_arrivals = int(source_counts_due[arrays["src"]].sum(dtype=np.int64))
|
||||
_check(len(arrival_edge) == expected_arrivals, "Queue trace omitted or duplicated an anatomical arrival")
|
||||
result = {
|
||||
"nodes": nodes.copy(), "step": event_ticks, "local_idx": local_indices,
|
||||
"neuron_idx": nodes[local_indices], "counts": counts,
|
||||
"v": voltage[-1].copy(), "g": conductance[-1].copy(), "ref": remaining[-1].copy(),
|
||||
"history": history, "ref_history": remaining,
|
||||
"not_refractory": available_end.astype(np.uint8),
|
||||
"weights": np.asarray(syn.w_[:], dtype=dtype).copy(),
|
||||
"initial_v": initial_v, "initial_g": initial_g,
|
||||
"request_attempted": attempted, "request_accepted": accepted, "request_rejected": rejected,
|
||||
"request_count": attempted.sum(axis=1, dtype=np.int32),
|
||||
"applicable_count": accepted.sum(axis=1, dtype=np.int32),
|
||||
"rejected_count": rejected.sum(axis=1, dtype=np.int32), "fired": fired,
|
||||
"arrival_step": arrival_step, "arrival_edge_index": arrival_edge,
|
||||
"arrival_accepted": arrival_accepted,
|
||||
"external_step": ext_ticks.astype(np.int32), "external_target": ext_targets.astype(np.int32),
|
||||
"external_weights": external_weights,
|
||||
"external_accepted": available_end[ext_ticks, ext_targets].astype(np.uint8),
|
||||
}
|
||||
coefficients = _coefficients(neu, parameters, b2, dt_seconds)
|
||||
_save(output / "coefficients.json", coefficients)
|
||||
_save(output / "queue-audit.json", {
|
||||
**queue_counters, "trace_enabled": trace_queue, "due_events": len(arrival_edge),
|
||||
"accepted_due_events": int(arrival_accepted.sum()),
|
||||
"all_due_events_preserved": True if trace_queue else None,
|
||||
"ordering": "raw anatomical queue.peek local edge-index sequence; no sorting or filtering",
|
||||
"proxy_contract": "peek returns original object; advance and all other methods forward unchanged",
|
||||
})
|
||||
_save_arrays(output / "state.npz", result)
|
||||
return result, coefficients
|
||||
except Exception as error:
|
||||
_save(output / "error.json", {"type": type(error).__name__, "message": str(error)})
|
||||
raise
|
||||
finally:
|
||||
for key, value in saved.items():
|
||||
b2.prefs[key] = value
|
||||
b2.defaultclock.dt = old_dt
|
||||
|
||||
|
||||
def run_case(case_dir: Path, out_dir: Path, precision: str) -> dict:
|
||||
"""Run one <=512-node, <=1000-step fixed case with exclusive outputs.
|
||||
|
||||
Main outputs are ``state.npz`` and ``coefficients.json``. Queue tracing is
|
||||
enabled by default. ``spec.trace_queue`` can disable it; when enabled,
|
||||
``spec.validate_queue_proxy`` defaults to True and repeats the same case
|
||||
without instrumentation. That repeat must match every non-arrival array
|
||||
exactly. An opt-out is recorded as unverified, never as a successful check.
|
||||
This function changes global Brian preferences temporarily; run it serially.
|
||||
"""
|
||||
_check(precision in ("float64", "float32"), "precision must be float64 or float32")
|
||||
case_dir, out_dir = Path(case_dir).resolve(strict=True), Path(out_dir).resolve()
|
||||
spec, arrays = _load_case(case_dir)
|
||||
source_bytes = AUTHOR_PATH.read_bytes()
|
||||
source_hash = hashlib.sha256(source_bytes).hexdigest()
|
||||
_check(source_hash == AUTHOR_SHA256, "Archived author source hash mismatch")
|
||||
trace_queue = spec.get("trace_queue", True)
|
||||
validate_proxy = spec.get("validate_queue_proxy", trace_queue)
|
||||
_check(isinstance(trace_queue, bool) and isinstance(validate_proxy, bool), "Queue switches must be JSON booleans")
|
||||
_check(not validate_proxy or trace_queue, "Proxy validation requires queue tracing")
|
||||
out_dir.mkdir(parents=True, exist_ok=False)
|
||||
try:
|
||||
versions = {}
|
||||
for name in ("brian2", "numpy", "pandas", "scipy", "pyarrow", "sympy", "cython"):
|
||||
versions[name] = importlib.metadata.version(name)
|
||||
_save(out_dir / "environment.json", {"python": sys.version, "platform": platform.platform(),
|
||||
"packages": versions, "backend": "Brian2 numpy runtime"})
|
||||
_check(versions["brian2"] == "2.5.1", "The stress oracle requires Brian2 2.5.1")
|
||||
_check(versions["numpy"] == "1.22.3", "The stress oracle requires the recorded NumPy 1.22.3 promotion rules")
|
||||
_save(out_dir / "case.json", {"spec": spec, "precision": precision,
|
||||
"author_path": str(AUTHOR_PATH), "author_commit": AUTHOR_COMMIT, "author_sha256": source_hash,
|
||||
"case_spec_sha256": _digest(case_dir / "spec.json"), "case_arrays_sha256": _digest(case_dir / "arrays.npz"),
|
||||
"trace_queue": trace_queue, "validate_queue_proxy": validate_proxy,
|
||||
"common_interface_preserved": True, "original_poi_interface_adopted": False,
|
||||
"whole_brain": False, "learning": False})
|
||||
result, coefficients = _run_once(spec, arrays, precision, out_dir / "instrumented",
|
||||
source_bytes, trace_queue)
|
||||
# Preserve the primary result even if the independent proxy check fails.
|
||||
_save_arrays(out_dir / "state.npz", result)
|
||||
_save(out_dir / "coefficients.json", coefficients)
|
||||
validation = {"performed": False, "pass": None,
|
||||
"reason": "Disabled by explicit case switch" if not validate_proxy else None}
|
||||
if validate_proxy:
|
||||
baseline, baseline_coefficients = _run_once(spec, arrays, precision, out_dir / "unwrapped-audit",
|
||||
source_bytes, False)
|
||||
checks = {key: bool(np.array_equal(value, baseline[key]))
|
||||
for key, value in result.items() if not key.startswith("arrival_")}
|
||||
coefficient_keys = ["gd", "c0", "cg", "cv", "threshold", "reset", "seed_volt"]
|
||||
checks["coefficients"] = all(coefficients[key] == baseline_coefficients[key] for key in coefficient_keys)
|
||||
validation = {"performed": True, "pass": bool(all(checks.values())),
|
||||
"exact_arrays": checks,
|
||||
"arrival_arrays_excluded": "An unwrapped queue is deliberately not observed"}
|
||||
_save(out_dir / "proxy-validation.json", validation)
|
||||
_check(not validate_proxy or validation["pass"], "Queue proxy changed an author result")
|
||||
_check(_digest(AUTHOR_PATH) == source_hash, "Author source changed during the stress case")
|
||||
summary = {"name": spec["name"], "precision": precision, "steps": int(spec["steps"]),
|
||||
"nodes": len(arrays["nodes"]), "edges": len(arrays["edge_id"]),
|
||||
"spikes": len(result["step"]), "requests": int(result["request_count"].sum()),
|
||||
"applicable_requests": int(result["applicable_count"].sum()),
|
||||
"rejected_requests": int(result["rejected_count"].sum()),
|
||||
"due_arrivals": len(result["arrival_step"]),
|
||||
"queue_trace_enabled": trace_queue, "queue_proxy_validated": validation["pass"],
|
||||
"source_unchanged": True, "state_file": str(out_dir / "state.npz"),
|
||||
"coefficient_file": str(out_dir / "coefficients.json"), "complete": True}
|
||||
_save(out_dir / "summary.json", summary)
|
||||
return {"arrays": result, "coefficients": coefficients, "summary": summary}
|
||||
except Exception as error:
|
||||
_save(out_dir / "error.json", {"type": type(error).__name__, "message": str(error)})
|
||||
raise
|
||||
@@ -0,0 +1,103 @@
|
||||
"""Read-only selection and deterministic fixtures, before observing any dynamics."""
|
||||
from datetime import datetime,timezone
|
||||
import json
|
||||
import subprocess
|
||||
import numpy as np
|
||||
import pandas as pd
|
||||
import yaml
|
||||
from context import MODEL,ROOT,EXP,AD,CFG,digest,save,sources,integrity
|
||||
|
||||
M=json.loads((AD/'protocol/preregistered.json').read_text())['config']['model']
|
||||
|
||||
def put(name,nodes,src,dst,raw,steps,description,edge_id=None,requests=None,external=None,v=None,g=None,metadata=None):
|
||||
n=len(nodes);src=np.asarray(src,np.int32);dst=np.asarray(dst,np.int32);raw=np.asarray(raw,np.int64)
|
||||
eid=np.arange(len(src),dtype=np.int64) if edge_id is None else np.asarray(edge_id,np.int64)
|
||||
order=np.lexsort((eid,src));src,dst,raw,eid=src[order],dst[order],raw[order],eid[order]
|
||||
assert len(src) and len(src)==len(dst)==len(raw) and np.all((src>=0)&(src<n)) and np.all((dst>=0)&(dst<n))
|
||||
arrays=dict(nodes=np.asarray(nodes,np.int32),src=src,dst=dst,signed_raw=raw,edge_id=eid,
|
||||
requests=np.zeros((steps,n),np.uint8) if requests is None else requests,
|
||||
external_mv=np.zeros((steps,n),np.float64) if external is None else external,
|
||||
initial_v_mv=np.full(n,M['resting_potential_mv'],np.float64) if v is None else v,
|
||||
initial_g_mv=np.zeros(n,np.float64) if g is None else g)
|
||||
folder=EXP/'cases'/name;folder.mkdir()
|
||||
np.savez_compressed(folder/'arrays.npz',**arrays)
|
||||
save(folder/'spec.json',dict(name=name,dt_ms=M['dt_ms'],steps=steps,duration_ms=steps*M['dt_ms'],model=M,
|
||||
description=description,trace_queue=True,validate_queue_proxy=True,selection=metadata))
|
||||
|
||||
def synthetic():
|
||||
n=33;t=160;raw=np.array([16777216,1,-16777216,1]+[(-1 if i%2 else 1)*(i+1) for i in range(28)],np.int64)
|
||||
req=np.zeros((t,n),np.uint8);req[0,:32]=1;g=np.zeros(n);g[-1]=.123
|
||||
put('ordered_cancellation',np.arange(-n,0),np.arange(32),np.full(32,32),raw,t,
|
||||
'Pure synthetic numerical cancellation; huge counts are nonphysiological; nonzero initial g.',requests=req,g=g)
|
||||
n=257;t=600;src=np.r_[np.arange(256),0,256];dst=np.full(258,256);raw=np.r_[np.where(np.arange(256)%2,-1,1)*(np.arange(256)%17+1)*13,19,11]
|
||||
req=np.zeros((t,n),np.uint8)
|
||||
for step in (0,21,22,40,62,101,150,300):req[step,:256]=1
|
||||
req[0,256]=1;ext=np.zeros((t,n));ext[[0,21,22,23,300],256]=[1,1,1,-1,.5]
|
||||
put('fanin_bursts',np.arange(-n,0),src,dst,raw,t,'256-source signed fan-in, labelled duplicate/loop; refractory requests and external writes.',requests=req,external=ext)
|
||||
n=4;t=160;req=np.zeros((t,n),np.uint8);req[0,[0,1,2]]=1;req[22,2]=1;req[44,[0,1]]=1
|
||||
ext=np.zeros((t,n));ext[[0,21,22,23,43,44,45],2]=[2,2,2,2,-1,1,1]
|
||||
put('release_selfloop',np.arange(-n,0),[0,1,2,2,3],[2,2,2,3,2],[1,400,10,100,-1],t,'Release at22 with same-tick force/arrival, loops and ring wraps.',requests=req,external=ext)
|
||||
dt=.0001;tm=.020;ts=.005;rest=-.052;th=-.045;cv=np.exp(-dt/tm);c0=rest-rest*cv
|
||||
center=(th-c0)/cv;vals=[np.nextafter(center,-np.inf),center,np.nextafter(center,np.inf)]
|
||||
center32=np.float32((np.float32(th)-np.float32(c0))/np.float32(cv));x=center32
|
||||
for _ in range(3):x=np.nextafter(x,np.float32(-np.inf))
|
||||
for _ in range(7):vals.append(float(x));x=np.nextafter(x,np.float32(np.inf))
|
||||
n=len(vals);put('threshold_rounding',np.arange(-n,0),[0],[0],[0],100,
|
||||
'Preintegration voltages bracket strict-threshold landing in both precisions; inert zero fixture edge.',v=np.asarray(vals)*1000)
|
||||
rng=np.random.default_rng(CFG['seed']);n=128;t=400;src=np.repeat(np.arange(n),8);dst=rng.integers(0,n,len(src),dtype=np.int32)
|
||||
raw=rng.integers(1,601,len(src),dtype=np.int64)*np.where(src%3==0,-1,1)
|
||||
req=(rng.random((t,n))<.001).astype(np.uint8);req[200:]=0
|
||||
g=rng.uniform(-1,1,n);ext=np.zeros((t,n));ext[::37]=rng.uniform(-.5,.5,(len(ext[::37]),n))
|
||||
put('signed_random',np.arange(-n,0),src,dst,raw,t,'Fixed seed128-cell signed random fixture; forcing stops at20ms; signs assigned per synthetic source.',requests=req,external=ext,g=g)
|
||||
|
||||
def real():
|
||||
can=ROOT/'datasets/male-cns-v1.0/processed/neuron-only';ptr=np.load(can/'gpu/csr-indptr.int64.npy',mmap_mode='r');dst=np.load(can/'gpu/csr-indices.int32.npy',mmap_mode='r');raw=np.load(can/'gpu/csr-weights.int64.npy',mmap_mode='r')
|
||||
meta=pd.read_parquet(can/'neuron-index/unified-metadata.parquet').sort_values('neuron_idx').reset_index(drop=True)
|
||||
assert np.array_equal(meta.neuron_idx,np.arange(166700)) and len(dst)==25582938 and int(raw.sum())==124177617
|
||||
pol=yaml.safe_load((ROOT/'models/male-cns-lif/runtime-v1/phase4c.yaml').read_text())['sign_policy']
|
||||
signs=[]
|
||||
for nt in meta.neurotransmitter:
|
||||
s='' if pd.isna(nt) else str(nt).strip().lower()
|
||||
signs.append(pol['unknown_sign'] if not s else pol['unclear_sign'] if s=='unclear' else pol['neurotransmitter_sign'][s])
|
||||
signs=np.asarray(signs,np.int8);src=np.repeat(np.arange(166700,dtype=np.int32),np.diff(ptr))
|
||||
degree=np.bincount(dst,minlength=166700);pos=np.bincount(dst[signs[src]>0],minlength=166700);neg=np.bincount(dst[signs[src]<0],minlength=166700)
|
||||
ranked=np.lexsort((np.arange(166700),-degree));targets=[int(ranked[0]),int(next(i for i in ranked if pos[i]>=64 and neg[i]>=63))]
|
||||
for name,target in zip(CFG['real_cases'],targets):
|
||||
incoming=np.flatnonzero((dst==target)&(src!=target));incoming=incoming[np.lexsort((src[incoming],-raw[incoming]))]
|
||||
if name=='highest_indegree':chosen=incoming[:127]
|
||||
else:
|
||||
pp=incoming[signs[src[incoming]]>0][:64];nn=incoming[signs[src[incoming]]<0][:63]
|
||||
assert len(pp)==64 and len(nn)==63,'Insufficient mixed partners for predeclared graph'
|
||||
chosen=np.r_[pp,nn]
|
||||
nodes=np.sort(np.unique(np.r_[src[chosen],target])).astype(np.int32);assert len(nodes)==128
|
||||
lookup=np.full(166700,-1,np.int32);lookup[nodes]=np.arange(len(nodes),dtype=np.int32)
|
||||
ids=np.concatenate([np.arange(ptr[s],ptr[s+1],dtype=np.int64) for s in nodes]);ids=ids[lookup[dst[ids]]>=0]
|
||||
local_src=lookup[src[ids]];local_dst=lookup[dst[ids]];signed=raw[ids]*signs[src[ids]]
|
||||
req=np.zeros((500,len(nodes)),np.uint8);stim=np.sort(src[chosen[:16]])
|
||||
for tick in (0,25,50,100,150,200):req[tick,lookup[stim]]=1
|
||||
put(name,nodes,local_src,local_dst,signed,500,'Deterministically selected real induced graph; canonical edge IDs/counts and frozen signs.',edge_id=ids,requests=req,
|
||||
metadata=dict(target_neuron_idx=target,target_body_id=int(meta.body_id.iloc[target]),global_in_degree=int(degree[target]),positive_in_edges=int(pos[target]),negative_in_edges=int(neg[target]),stimulated_neuron_idx=stim.tolist()))
|
||||
meta.iloc[nodes][['neuron_idx','body_id','annotation_type','neurotransmitter']].to_csv(EXP/'cases'/name/'identities.csv',index=False)
|
||||
pd.DataFrame(dict(edge_id=ids,source_neuron_idx=src[ids],target_neuron_idx=dst[ids],raw_count=raw[ids],source_sign=signs[src[ids]],signed_raw=signed)).to_csv(EXP/'cases'/name/'anatomical-edges.csv',index=False)
|
||||
ac=ROOT/'experiments/phase4ac-lif-semantics'
|
||||
for name in CFG['prior_motifs']:
|
||||
e=pd.read_csv(ac/'motifs'/f'{name}-edges.csv');nodes=np.load(ac/'motifs'/f'{name}-state.npz')['nodes'];look={int(v):i for i,v in enumerate(nodes)}
|
||||
req=np.zeros((1000,len(nodes)),np.uint8)
|
||||
if name!='no_input':req[0,look[1381]]=1
|
||||
put('motif_'+name,nodes,[look[int(x)] for x in e.source_neuron_idx],[look[int(x)] for x in e.target_neuron_idx],e.raw_count.to_numpy()*signs[e.source_neuron_idx],1000,
|
||||
'Same selected4AC/4AD motif,100ms prefix; no new edge or weight.',edge_id=e.edge_id.to_numpy(),requests=req)
|
||||
|
||||
def main():
|
||||
assert not (EXP/'protocol').exists()
|
||||
for d in ('protocol','cases','oracle','gpu','regression','audit','performance'):(EXP/d).mkdir()
|
||||
can=ROOT/'datasets/male-cns-v1.0/processed/neuron-only'
|
||||
inputs=[can/'gpu/csr-indptr.int64.npy',can/'gpu/csr-indices.int32.npy',can/'gpu/csr-weights.int64.npy',can/'neuron-index/unified-metadata.parquet',ROOT/'models/male-cns-lif/runtime-v1/phase4c.yaml',AD/'external-resources/model.py',AD/'manifest.json']
|
||||
save(EXP/'protocol/preregistered.json',dict(timestamp_utc=datetime.now(timezone.utc).isoformat(),config=CFG,sources=sources(),
|
||||
inputs=[dict(path=str(p.relative_to(ROOT)),sha256=digest(p)) for p in inputs],before_model_execution=True,
|
||||
parent_commit=subprocess.check_output(['git','-C',str(ROOT),'rev-parse','HEAD'],text=True).strip()))
|
||||
save(EXP/'regression/old-integrity-before.json',integrity())
|
||||
synthetic();real()
|
||||
save(EXP/'protocol/case-hashes.json',[dict(path=str(p.relative_to(EXP)),sha256=digest(p)) for p in sorted((EXP/'cases').rglob('*')) if p.is_file()])
|
||||
print('PREPARED',len(list((EXP/'cases').iterdir())),'fixed cases; old integrity PASS',flush=True)
|
||||
|
||||
if __name__=='__main__':main()
|
||||
@@ -0,0 +1,87 @@
|
||||
"""Fixed Brian/GPU stress suite, with source-checked immutable inputs."""
|
||||
import argparse
|
||||
import json
|
||||
import os
|
||||
from pathlib import Path
|
||||
import sys
|
||||
import time
|
||||
import numpy as np
|
||||
from context import ROOT,MODEL,EXP,CFG,save,check
|
||||
|
||||
def load(path):
|
||||
with np.load(path,allow_pickle=False) as f:return {k:f[k].copy() for k in f.files}
|
||||
|
||||
def compare(a,b,case,precision):
|
||||
checks={k:bool(np.array_equal(a[k],b[k])) for k in ('step','neuron_idx','counts','ref')}
|
||||
ah=np.asarray(a['history'],np.float64);bh=np.asarray(b['history'],np.float64)
|
||||
assert ah.shape==bh.shape
|
||||
delta=np.abs(ah[:,:2]-bh[:,:2]);limit=CFG['max_abs_volt'][precision]
|
||||
checks['history_ref_exact']=bool(np.array_equal(ah[:,2],bh[:,2]))
|
||||
checks['finite_states']=bool(np.isfinite(ah).all() and np.isfinite(bh).all())
|
||||
checks['state_tolerance']=bool(delta.max()<=limit)
|
||||
checks['weights_exact']=bool(np.array_equal(a['weights'],b['weights']))
|
||||
# Distinguish logical event requests from realised requests after refractory.
|
||||
for key in ('request_attempted','request_accepted','request_rejected'):
|
||||
checks[key+'_exact']=bool(key in a and key in b and np.array_equal(a[key],b[key]))
|
||||
data=load(case/'arrays.npz');targets=data['dst']
|
||||
def arrival_sequence(result):
|
||||
tick=result['arrival_step'];eid=result['arrival_edge_index'];guard=result['arrival_accepted']
|
||||
assert tick.shape==eid.shape==guard.shape
|
||||
# Different targets can interleave; order of writes to one target cannot.
|
||||
order=np.lexsort((np.arange(len(eid)),targets[eid],tick))
|
||||
return np.stack((tick[order],eid[order],guard[order]),axis=1)
|
||||
aa=arrival_sequence(a);bb=arrival_sequence(b)
|
||||
checks['arrival_order_and_guard_exact']=bool(np.array_equal(aa,bb))
|
||||
first=None
|
||||
for t in range(len(ah)):
|
||||
if not np.array_equal(a['neuron_idx'][a['step']==t],b['neuron_idx'][b['step']==t]):first=t;break
|
||||
bits_equal=a['history'].dtype==b['history'].dtype and np.array_equal(np.ascontiguousarray(a['history']).view(np.uint8),np.ascontiguousarray(b['history']).view(np.uint8))
|
||||
return dict(pass_all=all(checks.values()),checks=checks,bitwise_history=bool(bits_equal),
|
||||
max_abs_volt=float(delta.max()),mean_abs_volt=float(delta.mean()),fixed_limit_volt=limit,
|
||||
first_event_divergence_step=first,oracle_events=int(len(a['step'])),gpu_events=int(len(b['step'])),
|
||||
due_edges=int(len(aa)),accepted_edges=int(a['arrival_accepted'].sum()),
|
||||
attempted_requests=int(a['request_attempted'].sum()),accepted_requests=int(a['request_accepted'].sum()))
|
||||
|
||||
def oracle():
|
||||
from oracle_stress import run_case
|
||||
t0=time.perf_counter();rows=[]
|
||||
for case in sorted((EXP/'cases').iterdir()):
|
||||
for precision in CFG['precisions']:
|
||||
output=EXP/'oracle'/(case.name+'-'+precision)
|
||||
run_case(case,output,precision)
|
||||
r=load(output/'state.npz');assert np.isfinite(r['history']).all()
|
||||
rows.append(dict(case=case.name,precision=precision,events=len(r['step'])))
|
||||
print(json.dumps(rows[-1]),flush=True)
|
||||
save(EXP/'regression/oracle-complete.json',dict(cases=rows,wall_seconds=time.perf_counter()-t0))
|
||||
|
||||
def gpu():
|
||||
assert (EXP/'regression/oracle-complete.json').exists(),'No complete oracle suite'
|
||||
os.environ['CUDA_VISIBLE_DEVICES']=CFG['gpu_uuid'];os.environ['CUDA_HOME']='/usr/local/cuda'
|
||||
os.environ['PATH']=str(ROOT/'models/male-cns-lif/.venv/bin')+':/usr/local/cuda/bin:'+os.environ['PATH']
|
||||
os.environ['MAX_JOBS']='2';os.environ['TORCH_CUDA_ARCH_LIST']='8.9'
|
||||
sys.path.insert(0,str(ROOT/'models/male-cns-lif/terminal-scope-diagnostic-v1'))
|
||||
from diagnostic import queues
|
||||
queues()
|
||||
from gpu_backend import run_gpu
|
||||
t0=time.perf_counter();rows=[]
|
||||
for case in sorted((EXP/'cases').iterdir()):
|
||||
for precision in CFG['precisions']:
|
||||
queues();refdir=EXP/'oracle'/(case.name+'-'+precision)
|
||||
reference=load(refdir/'state.npz');coeff=json.loads((refdir/'coefficients.json').read_text());first=None
|
||||
for repeat in range(CFG['gpu_repeats']):
|
||||
out=EXP/'gpu'/(case.name+'-'+precision+f'-r{repeat}')
|
||||
run_gpu(case,out,precision,coeff,EXP/'extension-build',weights=reference['weights'])
|
||||
result=load(out/'state.npz');cmp=compare(reference,result,case,precision)
|
||||
if first is None:first=result
|
||||
rep={k:bool(np.array_equal(v,result[k])) for k,v in first.items()}
|
||||
row=dict(case=case.name,precision=precision,repeat=repeat,comparison=cmp,repeat_arrays=rep,
|
||||
pass_all=cmp['pass_all'] and all(rep.values()))
|
||||
save(out/'comparison.json',row);rows.append(row)
|
||||
print(json.dumps(dict(case=case.name,precision=precision,repeat=repeat,pass_all=row['pass_all'],
|
||||
error_volt=cmp['max_abs_volt'],events=cmp['oracle_events'],bitwise_history=cmp['bitwise_history'])),flush=True)
|
||||
save(EXP/'regression/gpu-complete.json',dict(pass_all=all(x['pass_all'] for x in rows),trials=rows,
|
||||
wall_seconds=time.perf_counter()-t0,whole_brain_tested=False,learning_achieved=False))
|
||||
|
||||
if __name__=='__main__':
|
||||
p=argparse.ArgumentParser();p.add_argument('mode',choices=['oracle','gpu']);args=p.parse_args()
|
||||
check();globals()[args.mode]()
|
||||
@@ -0,0 +1,33 @@
|
||||
"""Run old frozen trials into new output only; no author-model equivalence claim."""
|
||||
import os
|
||||
import sys
|
||||
import time
|
||||
import numpy as np
|
||||
import pandas as pd
|
||||
import yaml
|
||||
from context import ROOT,EXP,CFG,save,check
|
||||
|
||||
def main():
|
||||
check();assert not (EXP/'regression/frozen-five.json').exists()
|
||||
rtpath=ROOT/'models/male-cns-lif/deterministic-runtime-v2';pc=yaml.safe_load((rtpath/'phase4p.yaml').read_text())
|
||||
os.environ['CUDA_VISIBLE_DEVICES']=CFG['gpu_uuid'];os.environ['CUDA_HOME']='/usr/local/cuda'
|
||||
os.environ['PATH']=str(ROOT/'models/male-cns-lif/.venv/bin')+':/usr/local/cuda/bin:'+os.environ['PATH']
|
||||
os.environ['MAX_JOBS']='2';os.environ['TORCH_CUDA_ARCH_LIST']='8.9'
|
||||
sys.path.insert(0,str(ROOT/'models/male-cns-lif/terminal-scope-diagnostic-v1'))
|
||||
from diagnostic import queues
|
||||
queues();sys.path.insert(0,str(ROOT/'models/male-cns-lif'));sys.path.insert(0,str(rtpath))
|
||||
import torch,phase4p
|
||||
assert torch.cuda.mem_get_info()[0]>2*1024**3
|
||||
torch.cuda.reset_peak_memory_stats();t0=time.perf_counter();rt=phase4p.CanonicalRuntime(pc,rtpath,EXP);rows=[]
|
||||
for spec in pc['reference_trials']:
|
||||
queues();base=ROOT/'experiments/phase4p-deterministic-runtime/phase4c-v2/reference'/spec['name']
|
||||
ev=pd.read_parquet(base/'spike-events.parquet')
|
||||
ref=dict(step=ev.step.to_numpy(),neuron_idx=ev.neuron_idx.to_numpy(),counts=np.load(base/'per-neuron-spike-counts.int32.npy'),v=np.load(base/'final-voltage.float32.npy'),g=np.load(base/'final-g.float32.npy'))
|
||||
r=rt.run(np.flatnonzero(rt.pops[spec['population']]),spec['rate_hz'],spec['seed'],spec['duration_ms'])
|
||||
row=dict(trial=spec['name'],exact={k:bool(np.array_equal(v,r[k])) for k,v in ref.items()},wall_seconds=r['metrics']['wall_seconds'])
|
||||
rows.append(row);print(row,flush=True)
|
||||
save(EXP/'regression/frozen-five.json',dict(pass_all=all(all(r['exact'].values()) for r in rows),trials=rows,
|
||||
wall_seconds=time.perf_counter()-t0,peak_allocated_vram=int(torch.cuda.max_memory_allocated()),oracle='old frozen deterministic-v2 only'))
|
||||
assert all(all(r['exact'].values()) for r in rows)
|
||||
|
||||
if __name__=='__main__':main()
|
||||
@@ -0,0 +1,149 @@
|
||||
{
|
||||
"cases": [
|
||||
{
|
||||
"case": "fanin_bursts",
|
||||
"event_equal": true,
|
||||
"events_float64": 1539,
|
||||
"events_float32": 1539,
|
||||
"first_event_divergence_step": null,
|
||||
"max_vg_abs_volt": 1.538265524056448e-07,
|
||||
"input_hashes": {
|
||||
"experiments/phase4ae-author-runtime/oracle/fanin_bursts-float64/state.npz": "48d4cf57a0fd4cd83dfad8497042063022a3a6b2214106080da69deaaaf5fa9e",
|
||||
"experiments/phase4ae-author-runtime/oracle/fanin_bursts-float32/state.npz": "660c10c905097d76d91bea09c67ca861534196fc720d0e12102bac074a8525f5"
|
||||
}
|
||||
},
|
||||
{
|
||||
"case": "highest_indegree",
|
||||
"event_equal": true,
|
||||
"events_float64": 101,
|
||||
"events_float32": 101,
|
||||
"first_event_divergence_step": null,
|
||||
"max_vg_abs_volt": 2.132226918638569e-07,
|
||||
"input_hashes": {
|
||||
"experiments/phase4ae-author-runtime/oracle/highest_indegree-float64/state.npz": "768d39cdeaa17a8b0fa7a64be5ffbe771e4d00c8db2709c4c5cdb0749f6c3455",
|
||||
"experiments/phase4ae-author-runtime/oracle/highest_indegree-float32/state.npz": "11de500da330704334d9ce2d128aa2bba32decef851c75bc720a59f91fe534d2"
|
||||
}
|
||||
},
|
||||
{
|
||||
"case": "mixed_high_indegree",
|
||||
"event_equal": true,
|
||||
"events_float64": 106,
|
||||
"events_float32": 106,
|
||||
"first_event_divergence_step": null,
|
||||
"max_vg_abs_volt": 2.1416214047303983e-07,
|
||||
"input_hashes": {
|
||||
"experiments/phase4ae-author-runtime/oracle/mixed_high_indegree-float64/state.npz": "c267e765682525fce86a72d5a86eb921c2d1cef4200172cdc48d1fb41634d727",
|
||||
"experiments/phase4ae-author-runtime/oracle/mixed_high_indegree-float32/state.npz": "5df4b542b303e747bbbfbdb057da15e522465e54d6617349ee99f7192e1603f9"
|
||||
}
|
||||
},
|
||||
{
|
||||
"case": "motif_feedforward",
|
||||
"event_equal": true,
|
||||
"events_float64": 3,
|
||||
"events_float32": 3,
|
||||
"first_event_divergence_step": null,
|
||||
"max_vg_abs_volt": 2.0734813362816018e-07,
|
||||
"input_hashes": {
|
||||
"experiments/phase4ae-author-runtime/oracle/motif_feedforward-float64/state.npz": "21f5487f461f02c60c8b23be2f7def85c52d54f95fd00dbcd9b5f1d16d933c3a",
|
||||
"experiments/phase4ae-author-runtime/oracle/motif_feedforward-float32/state.npz": "e24ef4caddd186832c767df704c0073253735a6bbfa4381d76a23614ef7c0f8f"
|
||||
}
|
||||
},
|
||||
{
|
||||
"case": "motif_five",
|
||||
"event_equal": true,
|
||||
"events_float64": 60,
|
||||
"events_float32": 60,
|
||||
"first_event_divergence_step": null,
|
||||
"max_vg_abs_volt": 1.8507321130484256e-07,
|
||||
"input_hashes": {
|
||||
"experiments/phase4ae-author-runtime/oracle/motif_five-float64/state.npz": "cf6ac75da0a75ccdd5ab6ac1b282fae8b8a07128f3e0a3f0106739348f75dfbb",
|
||||
"experiments/phase4ae-author-runtime/oracle/motif_five-float32/state.npz": "3463e35fa10471d5abfd8090db1967fd5c2046364ef4e6b7974b710eb225fff2"
|
||||
}
|
||||
},
|
||||
{
|
||||
"case": "motif_no_input",
|
||||
"event_equal": true,
|
||||
"events_float64": 0,
|
||||
"events_float32": 0,
|
||||
"first_event_divergence_step": null,
|
||||
"max_vg_abs_volt": 1.0728836014051168e-09,
|
||||
"input_hashes": {
|
||||
"experiments/phase4ae-author-runtime/oracle/motif_no_input-float64/state.npz": "4f8b98d81b6b91aeccdf59788e7cfa6a770fe1ac59753fa8c4777776e559fbe1",
|
||||
"experiments/phase4ae-author-runtime/oracle/motif_no_input-float32/state.npz": "fbf19ad2fa292ecfcfbf893047ed0ee1dc411fd7825f728b21147349085177ad"
|
||||
}
|
||||
},
|
||||
{
|
||||
"case": "motif_pair",
|
||||
"event_equal": true,
|
||||
"events_float64": 22,
|
||||
"events_float32": 22,
|
||||
"first_event_divergence_step": null,
|
||||
"max_vg_abs_volt": 3.596376418196767e-08,
|
||||
"input_hashes": {
|
||||
"experiments/phase4ae-author-runtime/oracle/motif_pair-float64/state.npz": "236fcb984139a2e376b026fe33e5fb079a1c3a9a4f1090925fbe2643c92fa31b",
|
||||
"experiments/phase4ae-author-runtime/oracle/motif_pair-float32/state.npz": "016d9e6cd2e38e3ac4bf5dcd4526771f30885a7152b77e703bfa6debbed047f1"
|
||||
}
|
||||
},
|
||||
{
|
||||
"case": "motif_trio",
|
||||
"event_equal": true,
|
||||
"events_float64": 45,
|
||||
"events_float32": 45,
|
||||
"first_event_divergence_step": null,
|
||||
"max_vg_abs_volt": 3.596376418196767e-08,
|
||||
"input_hashes": {
|
||||
"experiments/phase4ae-author-runtime/oracle/motif_trio-float64/state.npz": "bf670c8bc344163408fb96baf2df5d0fab9804f134fdd9011205ff6873d2084a",
|
||||
"experiments/phase4ae-author-runtime/oracle/motif_trio-float32/state.npz": "ce04a18d25df422285be6ee80d36c949da506ebc885a87d31e109ee3d31f292b"
|
||||
}
|
||||
},
|
||||
{
|
||||
"case": "ordered_cancellation",
|
||||
"event_equal": true,
|
||||
"events_float64": 32,
|
||||
"events_float32": 32,
|
||||
"first_event_divergence_step": null,
|
||||
"max_vg_abs_volt": 0.00012916631594562123,
|
||||
"input_hashes": {
|
||||
"experiments/phase4ae-author-runtime/oracle/ordered_cancellation-float64/state.npz": "1ad4991463a440d466ec28bc32bb35572f84b351716a8150ed6360d90d36942b",
|
||||
"experiments/phase4ae-author-runtime/oracle/ordered_cancellation-float32/state.npz": "c937b1ec1e1ec63d1f0aedd3ab91b506f745849f3b66d8223d0d831bd9a689b0"
|
||||
}
|
||||
},
|
||||
{
|
||||
"case": "release_selfloop",
|
||||
"event_equal": true,
|
||||
"events_float64": 8,
|
||||
"events_float32": 8,
|
||||
"first_event_divergence_step": null,
|
||||
"max_vg_abs_volt": 3.4269942050801916e-08,
|
||||
"input_hashes": {
|
||||
"experiments/phase4ae-author-runtime/oracle/release_selfloop-float64/state.npz": "2615645c5ae1bea1d9ba279c6639e35209907e4e103db6d10c05ad23dc11919d",
|
||||
"experiments/phase4ae-author-runtime/oracle/release_selfloop-float32/state.npz": "dd8c3ac01e4d8035d94d0772efbb81948ba427f5ef66caf8d104f4819845a3cc"
|
||||
}
|
||||
},
|
||||
{
|
||||
"case": "signed_random",
|
||||
"event_equal": true,
|
||||
"events_float64": 400,
|
||||
"events_float32": 400,
|
||||
"first_event_divergence_step": null,
|
||||
"max_vg_abs_volt": 1.4282541487831146e-06,
|
||||
"input_hashes": {
|
||||
"experiments/phase4ae-author-runtime/oracle/signed_random-float64/state.npz": "148f6098bb58c952afe07b680a79355091cfb7d6c21e2fc49fc4c902a191cafd",
|
||||
"experiments/phase4ae-author-runtime/oracle/signed_random-float32/state.npz": "8657a63c2ea9703b8e37b0339eb63c24f31c597cf20cf214bb5e088312489d4a"
|
||||
}
|
||||
},
|
||||
{
|
||||
"case": "threshold_rounding",
|
||||
"event_equal": false,
|
||||
"events_float64": 4,
|
||||
"events_float32": 3,
|
||||
"first_event_divergence_step": 0,
|
||||
"max_vg_abs_volt": 0.006999998211860661,
|
||||
"input_hashes": {
|
||||
"experiments/phase4ae-author-runtime/oracle/threshold_rounding-float64/state.npz": "2b7071d125814ce8855806157f8ff5b778f554076e6ab8f2488ad99fd8b447e0",
|
||||
"experiments/phase4ae-author-runtime/oracle/threshold_rounding-float32/state.npz": "e225d3b95c5455cfb5f850e8fc3b3c97e99b4bd87bbfce6c2e6f764f32432a44"
|
||||
}
|
||||
}
|
||||
],
|
||||
"meaning": "Descriptive only; no changed tolerances, no variant selected by activity. Each GPU arm is validated against its own precision Brian oracle."
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,37 @@
|
||||
# Phase 4AE GPU作者语义数值门禁
|
||||
|
||||
状态：`PASS-ISOLATED-GPU-NUMERICAL-GATE`。
|
||||
|
||||
仅验证固定小网络，尚未证明全脑等价、生物学正确或学习可用。未训练、未修改冻结输入或旧模型。
|
||||
|
||||
| case | precision | events | max V/g error V | exact whole history | pass |
|
||||
|---|---|---:|---:|---|---|
|
||||
| fanin_bursts | float64 | 1539 | 0.0 | True | True |
|
||||
| fanin_bursts | float32 | 1539 | 0.0 | True | True |
|
||||
| highest_indegree | float64 | 101 | 0.0 | True | True |
|
||||
| highest_indegree | float32 | 101 | 0.0 | True | True |
|
||||
| mixed_high_indegree | float64 | 106 | 0.0 | True | True |
|
||||
| mixed_high_indegree | float32 | 106 | 0.0 | True | True |
|
||||
| motif_feedforward | float64 | 3 | 0.0 | True | True |
|
||||
| motif_feedforward | float32 | 3 | 0.0 | True | True |
|
||||
| motif_five | float64 | 60 | 0.0 | True | True |
|
||||
| motif_five | float32 | 60 | 0.0 | True | True |
|
||||
| motif_no_input | float64 | 0 | 0.0 | True | True |
|
||||
| motif_no_input | float32 | 0 | 0.0 | True | True |
|
||||
| motif_pair | float64 | 22 | 0.0 | True | True |
|
||||
| motif_pair | float32 | 22 | 0.0 | True | True |
|
||||
| motif_trio | float64 | 45 | 0.0 | True | True |
|
||||
| motif_trio | float32 | 45 | 0.0 | True | True |
|
||||
| ordered_cancellation | float64 | 32 | 0.0 | True | True |
|
||||
| ordered_cancellation | float32 | 32 | 0.0 | True | True |
|
||||
| release_selfloop | float64 | 8 | 0.0 | True | True |
|
||||
| release_selfloop | float32 | 8 | 0.0 | True | True |
|
||||
| signed_random | float64 | 400 | 0.0 | True | True |
|
||||
| signed_random | float32 | 400 | 0.0 | True | True |
|
||||
| threshold_rounding | float64 | 4 | 0.0 | True | True |
|
||||
| threshold_rounding | float32 | 3 | 0.0 | True | True |
|
||||
|
||||
每项GPU执行3次，检查原始事件、输入请求实际送达、逐目标到达顺序及guard、计数、不应期和完整状态。
|
||||
大整数、随机图、重复/零边属于纯数值夹具，不是新增MaleCNS连接或生理假设。真实子图使用全部既有诱导边、原contact count与冻结transmitter sign。
|
||||
原始冻结完整性与旧五组全脑deterministic-v2回归再次核验；该旧回归PASS不等于新动力学全脑PASS。
|
||||
没有根据活动强度选择参数；尚须短时全图对照及嗅觉信息保持测试。
|
||||
@@ -0,0 +1,11 @@
|
||||
{
|
||||
"status": "PASS-ISOLATED-GPU-NUMERICAL-GATE",
|
||||
"pass_all": true,
|
||||
"cases": 12,
|
||||
"gpu_runs": 72,
|
||||
"full_brain_author_equivalence": false,
|
||||
"conditioning": false,
|
||||
"learning_achieved": false,
|
||||
"candidate_generated": false,
|
||||
"next_gate": "Short full-graph same-precision author comparison, then fixed DoOR CAL only if numerical gates pass"
|
||||
}
|
||||
@@ -0,0 +1,21 @@
|
||||
{
|
||||
"name": "fanin_bursts",
|
||||
"dt_ms": 0.1,
|
||||
"steps": 600,
|
||||
"duration_ms": 60.0,
|
||||
"model": {
|
||||
"dt_ms": 0.1,
|
||||
"membrane_tau_ms": 20.0,
|
||||
"synaptic_tau_ms": 5.0,
|
||||
"refractory_ms": 2.2,
|
||||
"resting_potential_mv": -52.0,
|
||||
"reset_potential_mv": -52.0,
|
||||
"threshold_mv": -45.0,
|
||||
"synaptic_delay_ms": 1.8,
|
||||
"w_syn_mv_per_anatomical_synapse": 0.275
|
||||
},
|
||||
"description": "256-source signed fan-in, labelled duplicate/loop; refractory requests and external writes.",
|
||||
"trace_queue": true,
|
||||
"validate_queue_proxy": true,
|
||||
"selection": null
|
||||
}
|
||||
+321
@@ -0,0 +1,321 @@
|
||||
edge_id,source_neuron_idx,target_neuron_idx,raw_count,source_sign,signed_raw
|
||||
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|
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||||
21607353,137444,62795,1,-1,-1
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||||
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||||
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||||
21607400,137444,64443,1,-1,-1
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||||
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|
||||
21607440,137444,66003,1,-1,-1
|
||||
21607475,137444,67373,2,-1,-2
|
||||
21607506,137444,68199,2,-1,-2
|
||||
21607518,137444,68617,1,-1,-1
|
||||
21607582,137444,69966,1,-1,-1
|
||||
21607588,137444,70036,1,-1,-1
|
||||
21607623,137444,70626,1,-1,-1
|
||||
21607633,137444,70897,3,-1,-3
|
||||
21607657,137444,71346,1,-1,-1
|
||||
21607714,137444,72578,1,-1,-1
|
||||
21607833,137444,74495,1,-1,-1
|
||||
21607852,137444,74818,2,-1,-2
|
||||
21609321,137444,91986,1,-1,-1
|
||||
21610281,137444,101566,1,-1,-1
|
||||
21610534,137444,105260,1,-1,-1
|
||||
21934630,140350,5,45,1,45
|
||||
|
@@ -0,0 +1,129 @@
|
||||
neuron_idx,body_id,annotation_type,neurotransmitter
|
||||
5,10009,CT1,gaba
|
||||
21,10029,LoVC16,glutamate
|
||||
494,10532,MeVC26,acetylcholine
|
||||
775,10836,OLVC3,acetylcholine
|
||||
1572,11684,MeVPLp2,glutamate
|
||||
52515,70245,Tm9,acetylcholine
|
||||
57252,76118,Tm9,acetylcholine
|
||||
59937,79501,Tm9,acetylcholine
|
||||
60155,79781,Tm9,acetylcholine
|
||||
60450,80142,Tm9,acetylcholine
|
||||
60737,80501,Tm9,acetylcholine
|
||||
61164,81041,Tm9,acetylcholine
|
||||
61387,81301,Tm9,acetylcholine
|
||||
61721,81734,Tm9,acetylcholine
|
||||
61804,81831,Tm9,acetylcholine
|
||||
61941,82003,Tm9,acetylcholine
|
||||
62257,82394,Tm9,acetylcholine
|
||||
62700,82937,Tm9,acetylcholine
|
||||
62734,82979,Tm9,acetylcholine
|
||||
62795,83060,Tm9,acetylcholine
|
||||
62888,83185,Tm9,acetylcholine
|
||||
63041,83375,Tm9,acetylcholine
|
||||
63106,83462,Tm9,acetylcholine
|
||||
63173,83545,Tm9,acetylcholine
|
||||
63287,83686,Tm9,acetylcholine
|
||||
63339,83753,Tm9,acetylcholine
|
||||
63918,84478,Tm9,acetylcholine
|
||||
64210,84851,Tm9,acetylcholine
|
||||
64233,84878,Tm9,acetylcholine
|
||||
64443,85140,Tm9,acetylcholine
|
||||
64514,85236,Tm9,acetylcholine
|
||||
65001,85889,Tm9,acetylcholine
|
||||
65235,86195,Tm9,acetylcholine
|
||||
65262,86232,Tm9,acetylcholine
|
||||
65374,86371,Tm9,acetylcholine
|
||||
65565,86617,Tm9,acetylcholine
|
||||
65691,86786,Tm9,acetylcholine
|
||||
65742,86856,Tm9,acetylcholine
|
||||
66003,87208,Tm9,acetylcholine
|
||||
66127,87381,Tm9,acetylcholine
|
||||
66225,87504,Tm9,acetylcholine
|
||||
66237,87520,Tm9,acetylcholine
|
||||
66541,87925,Tm9,acetylcholine
|
||||
66598,87994,Tm9,acetylcholine
|
||||
66843,88320,Tm9,acetylcholine
|
||||
66958,88475,Tm9,acetylcholine
|
||||
67072,88621,Tm9,acetylcholine
|
||||
67135,88713,Tm9,acetylcholine
|
||||
67241,88850,Tm9,acetylcholine
|
||||
67284,88907,Tm9,acetylcholine
|
||||
67324,88959,Tm9,acetylcholine
|
||||
67373,89023,Tm9,acetylcholine
|
||||
67453,89138,Tm9,acetylcholine
|
||||
67483,89177,Tm9,acetylcholine
|
||||
67537,89251,Tm9,acetylcholine
|
||||
67594,89319,Tm9,acetylcholine
|
||||
68056,89933,Tm9,acetylcholine
|
||||
68074,89954,Tm9,acetylcholine
|
||||
68192,90120,Tm9,acetylcholine
|
||||
68199,90133,Tm9,acetylcholine
|
||||
68355,90340,Tm9,acetylcholine
|
||||
68543,90590,Tm9,acetylcholine
|
||||
68617,90688,Tm9,acetylcholine
|
||||
68656,90733,Tm9,acetylcholine
|
||||
68838,90991,Tm9,acetylcholine
|
||||
68856,91014,Tm9,acetylcholine
|
||||
68869,91034,Tm9,acetylcholine
|
||||
69139,91392,Tm9,acetylcholine
|
||||
69415,91766,Tm9,acetylcholine
|
||||
69516,91900,Tm9,acetylcholine
|
||||
69540,91933,Tm9,acetylcholine
|
||||
69809,92279,Tm9,acetylcholine
|
||||
69860,92356,Tm9,acetylcholine
|
||||
69966,92497,Tm9,acetylcholine
|
||||
69982,92521,Tm9,acetylcholine
|
||||
70036,92592,Tm9,acetylcholine
|
||||
70202,92805,Tm9,acetylcholine
|
||||
70316,92954,Tm9,acetylcholine
|
||||
70561,93271,Tm9,acetylcholine
|
||||
70626,93347,Tm9,acetylcholine
|
||||
70744,93499,Tm9,acetylcholine
|
||||
70783,93556,Tm9,acetylcholine
|
||||
70897,93720,Tm9,acetylcholine
|
||||
70977,93824,Tm9,acetylcholine
|
||||
70995,93845,Tm9,acetylcholine
|
||||
71060,93923,Tm9,acetylcholine
|
||||
71120,94000,Tm9,acetylcholine
|
||||
71215,94133,Tm9,acetylcholine
|
||||
71267,94199,Tm9,acetylcholine
|
||||
71346,94296,Tm9,acetylcholine
|
||||
71440,94423,Tm9,acetylcholine
|
||||
71456,94443,Tm9,acetylcholine
|
||||
71738,94831,Tm9,acetylcholine
|
||||
72060,95260,Tm9,acetylcholine
|
||||
72219,95470,Tm9,acetylcholine
|
||||
72322,95604,Tm9,acetylcholine
|
||||
72365,95658,Tm9,acetylcholine
|
||||
72473,95798,Tm9,acetylcholine
|
||||
72485,95813,Tm9,acetylcholine
|
||||
72578,95937,Tm9,acetylcholine
|
||||
73026,96565,Tm9,acetylcholine
|
||||
73221,96845,Tm9,acetylcholine
|
||||
73544,97254,Tm9,acetylcholine
|
||||
73653,97408,Tm9,acetylcholine
|
||||
73903,97731,Tm9,acetylcholine
|
||||
74495,98585,Tm9,acetylcholine
|
||||
74818,99046,Tm9,acetylcholine
|
||||
74995,99268,Tm9,acetylcholine
|
||||
75925,100512,Tm9,acetylcholine
|
||||
76961,101957,Tm9,acetylcholine
|
||||
77090,102126,Tm9,acetylcholine
|
||||
77291,102421,Tm9,acetylcholine
|
||||
77444,102619,Tm9,acetylcholine
|
||||
78506,104080,Tm9,acetylcholine
|
||||
78574,104167,Tm9,acetylcholine
|
||||
80691,107094,Tm9,acetylcholine
|
||||
85419,113692,Tm9,acetylcholine
|
||||
91986,123393,Tm9,acetylcholine
|
||||
97175,131756,Tm9,acetylcholine
|
||||
98515,134011,Tm9,acetylcholine
|
||||
101566,139750,Tm9,acetylcholine
|
||||
102237,141068,Tm9,acetylcholine
|
||||
104598,145922,Tm9,acetylcholine
|
||||
105190,147208,Tm9,acetylcholine
|
||||
105260,147382,Tm9,acetylcholine
|
||||
106136,149457,Tm9,acetylcholine
|
||||
137444,537032,LT33,gaba
|
||||
140350,546479,Tm9,acetylcholine
|
||||
|
@@ -0,0 +1,45 @@
|
||||
{
|
||||
"name": "highest_indegree",
|
||||
"dt_ms": 0.1,
|
||||
"steps": 500,
|
||||
"duration_ms": 50.0,
|
||||
"model": {
|
||||
"dt_ms": 0.1,
|
||||
"membrane_tau_ms": 20.0,
|
||||
"synaptic_tau_ms": 5.0,
|
||||
"refractory_ms": 2.2,
|
||||
"resting_potential_mv": -52.0,
|
||||
"reset_potential_mv": -52.0,
|
||||
"threshold_mv": -45.0,
|
||||
"synaptic_delay_ms": 1.8,
|
||||
"w_syn_mv_per_anatomical_synapse": 0.275
|
||||
},
|
||||
"description": "Deterministically selected real induced graph; canonical edge IDs/counts and frozen signs.",
|
||||
"trace_queue": true,
|
||||
"validate_queue_proxy": true,
|
||||
"selection": {
|
||||
"target_neuron_idx": 5,
|
||||
"target_body_id": 10009,
|
||||
"global_in_degree": 11526,
|
||||
"positive_in_edges": 10076,
|
||||
"negative_in_edges": 1403,
|
||||
"stimulated_neuron_idx": [
|
||||
494,
|
||||
775,
|
||||
1572,
|
||||
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|
||||
62257,
|
||||
62700,
|
||||
62795,
|
||||
63041,
|
||||
65262,
|
||||
66225,
|
||||
66237,
|
||||
67241,
|
||||
67324,
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||||
68856,
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||||
70626,
|
||||
137444
|
||||
]
|
||||
}
|
||||
}
|
||||
+267
@@ -0,0 +1,267 @@
|
||||
edge_id,source_neuron_idx,target_neuron_idx,raw_count,source_sign,signed_raw
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4897,5,21,2,-1,-2
|
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4899,5,44,4,-1,-4
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6312,5,60182,1,-1,-1
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6412,5,62700,12,-1,-12
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6435,5,63041,12,-1,-12
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6448,5,63287,7,-1,-7
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6452,5,63339,10,-1,-10
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6491,5,63918,13,-1,-13
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6505,5,64210,13,-1,-13
|
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6508,5,64233,9,-1,-9
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6529,5,64514,14,-1,-14
|
||||
6569,5,65262,12,-1,-12
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6636,5,66225,10,-1,-10
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6637,5,66237,9,-1,-9
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6660,5,66541,8,-1,-8
|
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6666,5,66598,14,-1,-14
|
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6714,5,67072,14,-1,-14
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6738,5,67241,15,-1,-15
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6743,5,67284,13,-1,-13
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7569,5,73026,6,-1,-6
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7930,5,74995,12,-1,-12
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36732,21,72473,1,-1,-1
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758405,494,137444,51,1,51
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1000652,775,44,2,1,2
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1000681,775,494,1,1,1
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1000776,775,6667,7,1,7
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1001593,775,137444,344,1,344
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1598110,1572,5,83,-1,-83
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1598130,1572,494,2,-1,-2
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1598393,1572,18811,1,-1,-1
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1598691,1572,59164,1,-1,-1
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3758873,6667,5,7,-1,-7
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3758874,6667,21,5,-1,-5
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3758876,6667,44,1,-1,-1
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10569176,40937,5,8,-1,-8
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11899194,49809,5,7,-1,-7
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11998296,50455,5,9,-1,-9
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12038629,50734,5,7,-1,-7
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12091997,51102,5,8,-1,-8
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12099494,51157,5,10,-1,-10
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12252801,52222,5,9,-1,-9
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12271215,52352,5,12,-1,-12
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12293012,52494,5,9,-1,-9
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12856017,56539,5,8,-1,-8
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12955015,57252,5,42,1,42
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13005488,57612,5,9,-1,-9
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13212934,59164,5,10,-1,-10
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13212942,59164,1572,1,-1,-1
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13545470,61707,5,12,-1,-12
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13557213,61804,5,50,1,50
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13615444,62257,5,55,1,55
|
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13674106,62700,5,46,1,46
|
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13674108,62700,6667,1,1,1
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||||
13674164,62700,137444,3,1,3
|
||||
13678358,62734,5,42,1,42
|
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13685724,62795,5,51,1,51
|
||||
13715954,63041,5,47,1,47
|
||||
13732392,63173,5,41,1,41
|
||||
13747092,63287,5,42,1,42
|
||||
13752625,63339,5,42,1,42
|
||||
13752679,63339,137444,1,1,1
|
||||
13826190,63918,5,41,1,41
|
||||
13862959,64210,5,45,1,45
|
||||
13865226,64233,5,44,1,44
|
||||
13879186,64335,5,10,-1,-10
|
||||
13902952,64514,5,42,1,42
|
||||
13998219,65262,5,47,1,47
|
||||
14070553,65848,5,9,-1,-9
|
||||
14115991,66225,5,49,1,49
|
||||
14116044,66225,137444,1,1,1
|
||||
14117243,66237,5,46,1,46
|
||||
14154260,66541,5,41,1,41
|
||||
14160491,66598,5,41,1,41
|
||||
14216589,67072,5,45,1,45
|
||||
14235496,67241,5,49,1,49
|
||||
14241113,67284,5,43,1,43
|
||||
14245371,67324,5,46,1,46
|
||||
14245378,67324,49476,2,1,2
|
||||
14251187,67373,5,46,1,46
|
||||
14251198,67373,53324,2,1,2
|
||||
14259668,67453,5,45,1,45
|
||||
14259716,67453,137444,3,1,3
|
||||
14269476,67537,5,42,1,42
|
||||
14275638,67594,5,41,1,41
|
||||
14330661,68074,5,44,1,44
|
||||
14344600,68199,5,46,1,46
|
||||
14379230,68506,5,8,-1,-8
|
||||
14392791,68617,5,45,1,45
|
||||
14396678,68656,5,43,1,43
|
||||
14412757,68785,5,9,-1,-9
|
||||
14420756,68856,5,50,1,50
|
||||
14450763,69139,5,42,1,42
|
||||
14486521,69462,5,10,-1,-10
|
||||
14492363,69516,5,41,1,41
|
||||
14525565,69809,5,43,1,43
|
||||
14531569,69860,5,41,1,41
|
||||
14531613,69860,137444,4,1,4
|
||||
14534259,69887,5,8,-1,-8
|
||||
14581777,70316,5,44,1,44
|
||||
14618088,70626,5,52,1,52
|
||||
14622283,70662,5,8,-1,-8
|
||||
14647714,70897,5,41,1,41
|
||||
14654473,70959,5,8,-1,-8
|
||||
14658186,70995,5,46,1,46
|
||||
14664944,71060,5,41,1,41
|
||||
14664945,71060,494,1,1,1
|
||||
14680828,71215,5,43,1,43
|
||||
14685821,71267,5,42,1,42
|
||||
14703808,71440,5,41,1,41
|
||||
14705510,71456,5,44,1,44
|
||||
14705563,71456,137444,1,1,1
|
||||
14771140,72060,5,41,1,41
|
||||
14794365,72275,5,11,-1,-11
|
||||
14799628,72322,5,45,1,45
|
||||
14804288,72365,5,42,1,42
|
||||
14815151,72473,5,41,1,41
|
||||
14815152,72473,21,1,1,1
|
||||
14816101,72485,5,43,1,43
|
||||
14816111,72485,51102,2,1,2
|
||||
14872749,73026,5,41,1,41
|
||||
14926968,73544,5,45,1,45
|
||||
15064838,74878,5,9,-1,-9
|
||||
15076955,74995,5,42,1,42
|
||||
15077006,74995,137444,1,1,1
|
||||
15316989,77390,5,8,-1,-8
|
||||
15430092,78506,5,44,1,44
|
||||
16053751,84964,5,9,-1,-9
|
||||
16298962,87611,5,9,-1,-9
|
||||
16407272,88823,5,15,-1,-15
|
||||
16448785,89271,5,10,-1,-10
|
||||
16448792,89271,1572,1,-1,-1
|
||||
16690249,91986,5,44,1,44
|
||||
17112927,96731,5,12,-1,-12
|
||||
17128837,96909,5,8,-1,-8
|
||||
17152556,97175,5,43,1,43
|
||||
17840952,104999,5,8,-1,-8
|
||||
17861992,105260,5,43,1,43
|
||||
21606907,137444,5,126,-1,-126
|
||||
21606909,137444,21,3,-1,-3
|
||||
21606916,137444,494,1,-1,-1
|
||||
21606921,137444,775,6,-1,-6
|
||||
21607331,137444,61721,1,-1,-1
|
||||
21607352,137444,62734,1,-1,-1
|
||||
21607353,137444,62795,1,-1,-1
|
||||
21607365,137444,63173,1,-1,-1
|
||||
21607366,137444,63287,1,-1,-1
|
||||
21607475,137444,67373,2,-1,-2
|
||||
21607506,137444,68199,2,-1,-2
|
||||
21607518,137444,68617,1,-1,-1
|
||||
21607623,137444,70626,1,-1,-1
|
||||
21607633,137444,70897,3,-1,-3
|
||||
21609321,137444,91986,1,-1,-1
|
||||
21610534,137444,105260,1,-1,-1
|
||||
21934630,140350,5,45,1,45
|
||||
|
@@ -0,0 +1,129 @@
|
||||
neuron_idx,body_id,annotation_type,neurotransmitter
|
||||
5,10009,CT1,gaba
|
||||
21,10029,LoVC16,glutamate
|
||||
44,10053,LoVC16,glutamate
|
||||
494,10532,MeVC26,acetylcholine
|
||||
775,10836,OLVC3,acetylcholine
|
||||
1572,11684,MeVPLp2,glutamate
|
||||
6667,17289,Li29,gaba
|
||||
15460,27130,TmY15,gaba
|
||||
18811,30896,TmY15,gaba
|
||||
40937,56248,Mi9,glutamate
|
||||
41813,57306,Mi9,glutamate
|
||||
42005,57537,Mi9,glutamate
|
||||
45077,61192,Mi9,glutamate
|
||||
45449,61642,Mi9,glutamate
|
||||
47004,63517,Mi9,glutamate
|
||||
47028,63547,Mi9,glutamate
|
||||
47491,64100,Mi9,glutamate
|
||||
47754,64418,Mi9,glutamate
|
||||
47782,64451,Mi9,glutamate
|
||||
48155,64903,Mi9,glutamate
|
||||
48221,64984,Mi9,glutamate
|
||||
48947,65851,Mi9,glutamate
|
||||
49476,66497,Mi9,glutamate
|
||||
49706,66780,Mi9,glutamate
|
||||
49809,66902,Mi9,glutamate
|
||||
50350,67574,Mi9,glutamate
|
||||
50455,67707,Mi9,glutamate
|
||||
50561,67843,Mi9,glutamate
|
||||
50622,67918,Mi9,glutamate
|
||||
50734,68057,Mi9,glutamate
|
||||
51102,68508,Mi9,glutamate
|
||||
51157,68577,Mi9,glutamate
|
||||
51608,69132,Mi9,glutamate
|
||||
52222,69881,Mi9,glutamate
|
||||
52352,70046,Mi9,glutamate
|
||||
52494,70216,Mi9,glutamate
|
||||
52515,70245,Tm9,acetylcholine
|
||||
53063,70927,Mi9,glutamate
|
||||
53324,71249,Mi9,glutamate
|
||||
54010,72095,Mi9,glutamate
|
||||
55100,73466,Mi9,glutamate
|
||||
56539,75256,Mi9,glutamate
|
||||
57201,76059,Mi9,glutamate
|
||||
57252,76118,Tm9,acetylcholine
|
||||
57612,76551,Mi9,glutamate
|
||||
59164,78522,Mi9,glutamate
|
||||
59365,78774,Mi9,glutamate
|
||||
60182,79818,Mi9,glutamate
|
||||
60450,80142,Tm9,acetylcholine
|
||||
61164,81041,Tm9,acetylcholine
|
||||
61707,81713,Mi9,glutamate
|
||||
61721,81734,Tm9,acetylcholine
|
||||
61804,81831,Tm9,acetylcholine
|
||||
62257,82394,Tm9,acetylcholine
|
||||
62700,82937,Tm9,acetylcholine
|
||||
62734,82979,Tm9,acetylcholine
|
||||
62795,83060,Tm9,acetylcholine
|
||||
63041,83375,Tm9,acetylcholine
|
||||
63173,83545,Tm9,acetylcholine
|
||||
63287,83686,Tm9,acetylcholine
|
||||
63339,83753,Tm9,acetylcholine
|
||||
63918,84478,Tm9,acetylcholine
|
||||
64210,84851,Tm9,acetylcholine
|
||||
64233,84878,Tm9,acetylcholine
|
||||
64335,85004,Mi9,glutamate
|
||||
64514,85236,Tm9,acetylcholine
|
||||
65262,86232,Tm9,acetylcholine
|
||||
65848,86983,Mi9,glutamate
|
||||
66225,87504,Tm9,acetylcholine
|
||||
66237,87520,Tm9,acetylcholine
|
||||
66541,87925,Tm9,acetylcholine
|
||||
66598,87994,Tm9,acetylcholine
|
||||
67072,88621,Tm9,acetylcholine
|
||||
67241,88850,Tm9,acetylcholine
|
||||
67284,88907,Tm9,acetylcholine
|
||||
67324,88959,Tm9,acetylcholine
|
||||
67373,89023,Tm9,acetylcholine
|
||||
67453,89138,Tm9,acetylcholine
|
||||
67537,89251,Tm9,acetylcholine
|
||||
67594,89319,Tm9,acetylcholine
|
||||
68074,89954,Tm9,acetylcholine
|
||||
68199,90133,Tm9,acetylcholine
|
||||
68506,90541,Mi9,glutamate
|
||||
68617,90688,Tm9,acetylcholine
|
||||
68656,90733,Tm9,acetylcholine
|
||||
68785,90917,Mi9,glutamate
|
||||
68856,91014,Tm9,acetylcholine
|
||||
69139,91392,Tm9,acetylcholine
|
||||
69462,91829,Mi9,glutamate
|
||||
69516,91900,Tm9,acetylcholine
|
||||
69809,92279,Tm9,acetylcholine
|
||||
69860,92356,Tm9,acetylcholine
|
||||
69887,92394,Mi9,glutamate
|
||||
70316,92954,Tm9,acetylcholine
|
||||
70626,93347,Tm9,acetylcholine
|
||||
70662,93393,Mi9,glutamate
|
||||
70897,93720,Tm9,acetylcholine
|
||||
70959,93800,Mi9,glutamate
|
||||
70995,93845,Tm9,acetylcholine
|
||||
71060,93923,Tm9,acetylcholine
|
||||
71215,94133,Tm9,acetylcholine
|
||||
71267,94199,Tm9,acetylcholine
|
||||
71440,94423,Tm9,acetylcholine
|
||||
71456,94443,Tm9,acetylcholine
|
||||
72060,95260,Tm9,acetylcholine
|
||||
72275,95544,Mi9,glutamate
|
||||
72322,95604,Tm9,acetylcholine
|
||||
72365,95658,Tm9,acetylcholine
|
||||
72473,95798,Tm9,acetylcholine
|
||||
72485,95813,Tm9,acetylcholine
|
||||
73026,96565,Tm9,acetylcholine
|
||||
73544,97254,Tm9,acetylcholine
|
||||
74878,99133,Mi9,glutamate
|
||||
74995,99268,Tm9,acetylcholine
|
||||
77390,102542,Mi9,glutamate
|
||||
78506,104080,Tm9,acetylcholine
|
||||
84964,113050,Mi9,glutamate
|
||||
87611,116890,Mi9,glutamate
|
||||
88823,118635,Mi9,glutamate
|
||||
89271,119289,Mi9,glutamate
|
||||
91986,123393,Tm9,acetylcholine
|
||||
96731,131072,Mi9,glutamate
|
||||
96909,131351,Mi9,glutamate
|
||||
97175,131756,Tm9,acetylcholine
|
||||
104999,146808,Mi9,glutamate
|
||||
105260,147382,Tm9,acetylcholine
|
||||
137444,537032,LT33,gaba
|
||||
140350,546479,Tm9,acetylcholine
|
||||
|
@@ -0,0 +1,45 @@
|
||||
{
|
||||
"name": "mixed_high_indegree",
|
||||
"dt_ms": 0.1,
|
||||
"steps": 500,
|
||||
"duration_ms": 50.0,
|
||||
"model": {
|
||||
"dt_ms": 0.1,
|
||||
"membrane_tau_ms": 20.0,
|
||||
"synaptic_tau_ms": 5.0,
|
||||
"refractory_ms": 2.2,
|
||||
"resting_potential_mv": -52.0,
|
||||
"reset_potential_mv": -52.0,
|
||||
"threshold_mv": -45.0,
|
||||
"synaptic_delay_ms": 1.8,
|
||||
"w_syn_mv_per_anatomical_synapse": 0.275
|
||||
},
|
||||
"description": "Deterministically selected real induced graph; canonical edge IDs/counts and frozen signs.",
|
||||
"trace_queue": true,
|
||||
"validate_queue_proxy": true,
|
||||
"selection": {
|
||||
"target_neuron_idx": 5,
|
||||
"target_body_id": 10009,
|
||||
"global_in_degree": 11526,
|
||||
"positive_in_edges": 10076,
|
||||
"negative_in_edges": 1403,
|
||||
"stimulated_neuron_idx": [
|
||||
494,
|
||||
775,
|
||||
61804,
|
||||
62257,
|
||||
62700,
|
||||
62795,
|
||||
63041,
|
||||
65262,
|
||||
66225,
|
||||
66237,
|
||||
67241,
|
||||
67324,
|
||||
67373,
|
||||
68199,
|
||||
68856,
|
||||
70626
|
||||
]
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,21 @@
|
||||
{
|
||||
"name": "motif_feedforward",
|
||||
"dt_ms": 0.1,
|
||||
"steps": 1000,
|
||||
"duration_ms": 100.0,
|
||||
"model": {
|
||||
"dt_ms": 0.1,
|
||||
"membrane_tau_ms": 20.0,
|
||||
"synaptic_tau_ms": 5.0,
|
||||
"refractory_ms": 2.2,
|
||||
"resting_potential_mv": -52.0,
|
||||
"reset_potential_mv": -52.0,
|
||||
"threshold_mv": -45.0,
|
||||
"synaptic_delay_ms": 1.8,
|
||||
"w_syn_mv_per_anatomical_synapse": 0.275
|
||||
},
|
||||
"description": "Same selected4AC/4AD motif,100ms prefix; no new edge or weight.",
|
||||
"trace_queue": true,
|
||||
"validate_queue_proxy": true,
|
||||
"selection": null
|
||||
}
|
||||
@@ -0,0 +1,21 @@
|
||||
{
|
||||
"name": "motif_five",
|
||||
"dt_ms": 0.1,
|
||||
"steps": 1000,
|
||||
"duration_ms": 100.0,
|
||||
"model": {
|
||||
"dt_ms": 0.1,
|
||||
"membrane_tau_ms": 20.0,
|
||||
"synaptic_tau_ms": 5.0,
|
||||
"refractory_ms": 2.2,
|
||||
"resting_potential_mv": -52.0,
|
||||
"reset_potential_mv": -52.0,
|
||||
"threshold_mv": -45.0,
|
||||
"synaptic_delay_ms": 1.8,
|
||||
"w_syn_mv_per_anatomical_synapse": 0.275
|
||||
},
|
||||
"description": "Same selected4AC/4AD motif,100ms prefix; no new edge or weight.",
|
||||
"trace_queue": true,
|
||||
"validate_queue_proxy": true,
|
||||
"selection": null
|
||||
}
|
||||
@@ -0,0 +1,21 @@
|
||||
{
|
||||
"name": "motif_no_input",
|
||||
"dt_ms": 0.1,
|
||||
"steps": 1000,
|
||||
"duration_ms": 100.0,
|
||||
"model": {
|
||||
"dt_ms": 0.1,
|
||||
"membrane_tau_ms": 20.0,
|
||||
"synaptic_tau_ms": 5.0,
|
||||
"refractory_ms": 2.2,
|
||||
"resting_potential_mv": -52.0,
|
||||
"reset_potential_mv": -52.0,
|
||||
"threshold_mv": -45.0,
|
||||
"synaptic_delay_ms": 1.8,
|
||||
"w_syn_mv_per_anatomical_synapse": 0.275
|
||||
},
|
||||
"description": "Same selected4AC/4AD motif,100ms prefix; no new edge or weight.",
|
||||
"trace_queue": true,
|
||||
"validate_queue_proxy": true,
|
||||
"selection": null
|
||||
}
|
||||
@@ -0,0 +1,21 @@
|
||||
{
|
||||
"name": "motif_pair",
|
||||
"dt_ms": 0.1,
|
||||
"steps": 1000,
|
||||
"duration_ms": 100.0,
|
||||
"model": {
|
||||
"dt_ms": 0.1,
|
||||
"membrane_tau_ms": 20.0,
|
||||
"synaptic_tau_ms": 5.0,
|
||||
"refractory_ms": 2.2,
|
||||
"resting_potential_mv": -52.0,
|
||||
"reset_potential_mv": -52.0,
|
||||
"threshold_mv": -45.0,
|
||||
"synaptic_delay_ms": 1.8,
|
||||
"w_syn_mv_per_anatomical_synapse": 0.275
|
||||
},
|
||||
"description": "Same selected4AC/4AD motif,100ms prefix; no new edge or weight.",
|
||||
"trace_queue": true,
|
||||
"validate_queue_proxy": true,
|
||||
"selection": null
|
||||
}
|
||||
@@ -0,0 +1,21 @@
|
||||
{
|
||||
"name": "motif_trio",
|
||||
"dt_ms": 0.1,
|
||||
"steps": 1000,
|
||||
"duration_ms": 100.0,
|
||||
"model": {
|
||||
"dt_ms": 0.1,
|
||||
"membrane_tau_ms": 20.0,
|
||||
"synaptic_tau_ms": 5.0,
|
||||
"refractory_ms": 2.2,
|
||||
"resting_potential_mv": -52.0,
|
||||
"reset_potential_mv": -52.0,
|
||||
"threshold_mv": -45.0,
|
||||
"synaptic_delay_ms": 1.8,
|
||||
"w_syn_mv_per_anatomical_synapse": 0.275
|
||||
},
|
||||
"description": "Same selected4AC/4AD motif,100ms prefix; no new edge or weight.",
|
||||
"trace_queue": true,
|
||||
"validate_queue_proxy": true,
|
||||
"selection": null
|
||||
}
|
||||
@@ -0,0 +1,21 @@
|
||||
{
|
||||
"name": "ordered_cancellation",
|
||||
"dt_ms": 0.1,
|
||||
"steps": 160,
|
||||
"duration_ms": 16.0,
|
||||
"model": {
|
||||
"dt_ms": 0.1,
|
||||
"membrane_tau_ms": 20.0,
|
||||
"synaptic_tau_ms": 5.0,
|
||||
"refractory_ms": 2.2,
|
||||
"resting_potential_mv": -52.0,
|
||||
"reset_potential_mv": -52.0,
|
||||
"threshold_mv": -45.0,
|
||||
"synaptic_delay_ms": 1.8,
|
||||
"w_syn_mv_per_anatomical_synapse": 0.275
|
||||
},
|
||||
"description": "Pure synthetic numerical cancellation; huge counts are nonphysiological; nonzero initial g.",
|
||||
"trace_queue": true,
|
||||
"validate_queue_proxy": true,
|
||||
"selection": null
|
||||
}
|
||||
@@ -0,0 +1,21 @@
|
||||
{
|
||||
"name": "release_selfloop",
|
||||
"dt_ms": 0.1,
|
||||
"steps": 160,
|
||||
"duration_ms": 16.0,
|
||||
"model": {
|
||||
"dt_ms": 0.1,
|
||||
"membrane_tau_ms": 20.0,
|
||||
"synaptic_tau_ms": 5.0,
|
||||
"refractory_ms": 2.2,
|
||||
"resting_potential_mv": -52.0,
|
||||
"reset_potential_mv": -52.0,
|
||||
"threshold_mv": -45.0,
|
||||
"synaptic_delay_ms": 1.8,
|
||||
"w_syn_mv_per_anatomical_synapse": 0.275
|
||||
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||||
@@ -0,0 +1,68 @@
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||||
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+51
@@ -0,0 +1,51 @@
|
||||
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||||
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||||
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||||
+68
@@ -0,0 +1,68 @@
|
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@@ -0,0 +1,51 @@
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@@ -0,0 +1,68 @@
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@@ -0,0 +1,51 @@
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@@ -0,0 +1,68 @@
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|
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+51
@@ -0,0 +1,51 @@
|
||||
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|
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|
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+68
@@ -0,0 +1,68 @@
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@@ -0,0 +1,51 @@
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@@ -0,0 +1,68 @@
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@@ -0,0 +1,51 @@
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@@ -0,0 +1,68 @@
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@@ -0,0 +1,51 @@
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@@ -0,0 +1,68 @@
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@@ -0,0 +1,68 @@
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|
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+68
@@ -0,0 +1,68 @@
|
||||
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|
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+51
@@ -0,0 +1,51 @@
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||||
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+68
@@ -0,0 +1,68 @@
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+51
@@ -0,0 +1,51 @@
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@@ -0,0 +1,68 @@
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@@ -0,0 +1,51 @@
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@@ -0,0 +1,68 @@
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+51
@@ -0,0 +1,51 @@
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+68
@@ -0,0 +1,68 @@
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@@ -0,0 +1,51 @@
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@@ -0,0 +1,68 @@
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@@ -0,0 +1,51 @@
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@@ -0,0 +1,68 @@
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@@ -0,0 +1,51 @@
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@@ -0,0 +1,68 @@
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
},
|
||||
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|
||||
}
|
||||
@@ -0,0 +1,68 @@
|
||||
{
|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
||||
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|
||||
@@ -0,0 +1,51 @@
|
||||
{
|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
@@ -0,0 +1,68 @@
|
||||
{
|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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@@ -0,0 +1,51 @@
|
||||
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|
||||
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||||
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||||
@@ -0,0 +1,68 @@
|
||||
{
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||||
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||||
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||||
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||||
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+51
@@ -0,0 +1,51 @@
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||||
{
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||||
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|
||||
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||||
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||||
@@ -0,0 +1,68 @@
|
||||
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|
||||
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||||
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|
||||
"torch": "2.14.0+cu130",
|
||||
"torch_cuda": "13.0",
|
||||
"arch_list": "8.9",
|
||||
"cuda_flags": [
|
||||
"-O2",
|
||||
"--fmad=false",
|
||||
"--ftz=false",
|
||||
"--prec-div=true",
|
||||
"--prec-sqrt=true"
|
||||
]
|
||||
},
|
||||
"input_sha256": {
|
||||
"spec.json": "02adfcd0717aa2d98eb571107136eae7186166ce1c7d7eb87df23bedb452fbd9",
|
||||
"arrays.npz": "3e3f7c2bd477e097761d3e34745f88fb215636c74d89a9e77a2b9a5f2fc738c3"
|
||||
},
|
||||
"arrival_order_scope": "GPU expanded edges, stable target grouping; compare relative order per tick and target",
|
||||
"performance_runtime_claim": false,
|
||||
"oracle_validation_claim": false,
|
||||
"whole_brain_run": false,
|
||||
"learning": false,
|
||||
"cpu_transfer_each_step_for_diagnostics": true
|
||||
}
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user