Preserve CPU and GPU acceleration plans, evidence and LFS archives; mark research paused
This commit is contained in:
Digital Drosophila Archive
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# CPU / GPU 方案保存 — 2026-10-01
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用户要求保存当前方案并上传，之后再继续。**原 Phase4AR 保持停止，未训练、未安装新权重，未进入下一科学阶段。**
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## 保存内容
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| 方案 | 代码 | 状态 |
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|---|---|---|
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| 原 CPU 更新与独立验证 | `models/male-cns-lif/olfactory-conditioning-lab-v1/`、`conditioning-interface-v2/` | 注册实现保留，未替换 |
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| V100/4090 eligibility 更新原型 | `models/male-cns-lif/conditioning-acceleration-v1/` | 固定案例逐位回放 PASS，不是全脑已迁移到 V100 |
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| CPU 常驻与 4090 全脑常驻 | `models/male-cns-lif/conditioning-pipeline-acceleration-v1/` | 42 次全脑精确回放 PASS，不是已验收生产运行时 |
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本目录的 `gpu/`、`pipeline/` 保存原报告、manifest 与完整性说明的原字节副本；`publication-catalog.json` 逐项记录公开归档成员和有意排除项。完整数值回放、请求、状态和诊断回执封装在 `artifacts/acceleration-20261001/` 的两个 Git LFS 归档中。
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代码版本：GPU 核心 `221e1f13f758ebe8d9f188bab976c361f7cacf45`；常驻回放封存 `018f038c7857c7e0236dd7408a680458520d92ce`。原科学登记源码 `80aeb2093db655329774eff7b32fb6e417b8b40b` 不变。
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原科学现场停在 1,033 轮已提交且 CPU 校验的训练、138 个已提交 probe。完整科学执行、独立学习 gate 未完成；本次性能成果不代表学会关联记忆。
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## 来源、许可与排除
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MaleCNS v1.0 原数据来源为 [官方数据页](https://male-cns.janelia.org/download/)，既有许可审计为 CC BY 4.0。署名保留 Male CNS collaboration：FlyEM/HHMI Janelia、University of Cambridge、MRC Laboratory of Molecular Biology、Google Research 及原论文作者。本项目进行了既有 neuron-only 过滤/重编号和模型模拟；本次只原字节复制已生成的回放数据，不重新推导或修改科学数值。
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嗅觉输入来源链中的 DoOR.data 2.0.1（commit `eea72d64b42a4e91dafe822cf0b5204de33f8d34`）维持 CC BY-SA 4.0，作者 Daniel Münch、C. Giovanni Galizia、Shouwen Ma、Martin Strauch、Anja Nissler。涉及其派生输入的成员保留此 ShareAlike/署名约束；不将其许可泛化至无关代码。[DoOR 论文](https://doi.org/10.1038/srep21841)。Shiu 作者源码维持其原 MIT 声明；本项目是 adapted dynamics，不是严格原模型复现。
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原资源许可证据及上游 notices 在 `codex/lfs-public-resources` 的 `registry/publication-20261001/`，固定发布提交 `5b1d1b7`。本次没有打包 NVIDIA SDK、CuPy/PyTorch 环境、FlyVis、论文全文或其他服务。软件没有被擅自统一换证，仍适用仓库 NOTICE 和各上游声明。
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明确排除：虚拟环境、CUDA 编译缓存/中间产物/二进制、安装下载日志。完整原实验（包括失败与编译诊断）仍原样留在服务器；原 sealed manifest 包含未上传缓存的哈希。因此公开归档应使用 **publication-catalog.json** 校验，不能要求原始全目录 SHA 清单在省略缓存的副本中全部通过。没有丢弃科学失败案例。
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旧原始/参考大数据不重复上传，它们在 `codex/lfs-public-resources`。本次发布不是全服务器或全部历史科学目录灾备，也没有打包已停止 AR 的所有 64,034 个现场文件。
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## 恢复与验证（不运行模型）
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在新目录 clone 本分支，安装 Git LFS，执行：
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```sh
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git lfs pull --include='artifacts/acceleration-20261001/**'
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python3 -B tools/acceleration-publication/archive_results.py verify
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```
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验证器只读流式校验归档 SHA、成员集合、每个成员字节数与 SHA，不解包、不运行模型。
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如需解包，只解到新建空目录；不得覆盖 `/data/digital-drosophila` 或直接运行旧封存脚本。性能原型依赖固定科学源与历史输入，不能只 clone 就自动恢复正式训练。
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`delivery.json` 只在真实远端 push、独立新 LFS store 下载和完整成员验证成功后写入。没有该回执时，不能把打包完成称为异机恢复已通过。
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# V100 conditioning acceleration — engineering replay result
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Status: **PASS-ELIGIBILITY-UPDATE-REPLAY-EQUIVALENCE**. This is not a learning result or a production-training promotion.
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Benchmark code commit: `221e1f13f758ebe8d9f188bab976c361f7cacf45`.
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| Device | Real-fixture replay median (prep + transfers + comparison) | Resident CUDA kernel median |
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|---|---:|---:|
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| Tesla V100-SXM2-16GB (v100a-02) | 3.430 ms | 0.122 ms |
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| Tesla V100-SXM2-16GB (v100b-01) | 3.344 ms | 0.122 ms |
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| NVIDIA GeForce RTX 4090 (rtx4090-01) | 3.327 ms | 0.074 ms |
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Each GPU passed14sealed real fixtures +16fixed synthetic cases, with sampled trace, final trace, allUS snapshots and delta byte-identical to the original independent CPU oracle. Six invalid inputs were rejected on each GPU.
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CPU warm reference includes the original API's repeated provenance checks and AST parsing; it is only one warm sample perfixture. GPU authenticates the source and complete anatomical mapping once. Therefore ratios in JSON describe API implementation replay, not pure hardware acceleration.
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The CUDA kernels preserve every timestep, float32 separate round-to-nearest operations, exact US timing, noUS zeros, compartment/frozen/D0 identity and the depression floor. No gain/learning-rate/tau/threshold/connectome/sign changes. No dense time×neuron matrix.
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A new candidate-only CuPy environment and explicit CUDA12.6 nvcc compilation are used. Original science and ComfyUI environments are unchanged. All three ComfyUI queues were checked before each fixture; no services were stopped.
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Integrity: 64034 saved files, 3103901058 bytes, 16 registered source files checked; no mismatch. This is the saved Phase4AR inventory, not a new Phase1–4AQ numerical regression.
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Phase4AR remains stopped at1033/30000CPU-verified epochs and138/3920probes. No weights were installed and no training was resumed.
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Next: a separately validated persistent-worker pipeline and end-to-end benchmark. This local optimization does not justify dividing the9-day estimate by the kernel speedup. Independent-seed V100 parallelism is not yet measured.
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Preserved failures: candidate packaging incompatibility (--report unsupported bypip22); first CuPy compile FTZ flag conflict (before any kernel ran). Both were corrected only in the independent branch.
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Compiler references: [CuPy precompiled RawModule](https://docs.cupy.dev/en/v13.6.0/reference/generated/cupy.RawModule.html), [CUDA12.6 compiler options](https://docs.nvidia.com/cuda/archive/12.6.3/cuda-compiler-driver-nvcc/index.html).
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b63b6d799a83f46c3c69805cfbec316537b06ae7f8e4b63703c9b02575c11cc1 RESULTS.md
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e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 candidate-freeze.stderr.log
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8ddcbb332825939eb1e091d87a6f73459de707defedb93654727662a0d4e2f0e candidate-freeze.stdout.log
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e3cc62cc576238a0d08ebbcfcfb151ba5c6f4bfe4891c3b46c39f66e1ccd5d21 create-worktree.stderr.log
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8960fa67e787f4103b0ae3dfb1d17d6133754ae9c97244877b148ebba1a302af create-worktree.stdout.log
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06df3158d0329dc925ecd7ceabe47f7c83ee8974f4fd959516411e82ed0dc34b environment-authority.json
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794855bb5509c4773378f7023219574f90e1bc393d48570161c9e024a91e7eb9 final-summary.json
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b5b896ac413d5fcbd8510e553993884a3e941d10f2a4bbbf25f7ccb4bc263781 fixtures/00-cs_only/authority.json
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9dfe7afae9438a9df33f32ab8f982d1e24ed5d9a5c72329cfedd65403d25dbe9 fixtures/00-cs_only/fixture.json
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6e4f6c0ccdad03049c75e056a4222e87c7b1f1d3f90bffb59a1b77ec4b363843 fixtures/00-cs_only/fixture.npz
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2a8d5e9b0072e40d69e46258ff8ced3379f3e72bd9d86e49caaa74918a00be42 fixtures/00-cs_only/inputs.npz
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df5b094bd8d43b0705637dafdc3091b1e98e4c6bc331fed6279b6662e883f157 fixtures/00-cs_only/reference-sources.json
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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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|
||||
"Original9.07-day estimate is not replaced by this component benchmark"
|
||||
],
|
||||
"next_work": "Separately validate persistent training/update/verification workers and complete chain timing before authorizing a new scientific execution version",
|
||||
"original_experiment_resumed": false,
|
||||
"report_code_commit": "221e1f13f758ebe8d9f188bab976c361f7cacf45",
|
||||
"scientific_experiment_status": "STOPPED, unchanged:1033/30000 CPU-verified training epochs and138/3920 probes",
|
||||
"status": "PASS-ELIGIBILITY-UPDATE-REPLAY-EQUIVALENCE",
|
||||
"weights_installed": false
|
||||
}
|
||||
@@ -0,0 +1,21 @@
|
||||
{
|
||||
"catalog_sha256": "28071f276848ea60149f21a9794653486b404670a58b34d97b1aaae742095245",
|
||||
"groups": {
|
||||
"gpu": {
|
||||
"archive_bytes": 1679158,
|
||||
"files": 614,
|
||||
"original_bytes": 13242628,
|
||||
"sha256": "50acdc85342a2c79c3516e50ee4542b909813d179518451edaaf2d94150c534b",
|
||||
"verified": true
|
||||
},
|
||||
"pipeline": {
|
||||
"archive_bytes": 74767927,
|
||||
"files": 1066,
|
||||
"original_bytes": 103062185,
|
||||
"sha256": "fdc39013d71fb7d14313d8249c929601a8a7050cc2eac88b733d692bbe1b6b42",
|
||||
"verified": true
|
||||
}
|
||||
},
|
||||
"pass_all": true,
|
||||
"verification": "Full streamed members, no extraction or model execution"
|
||||
}
|
||||
@@ -0,0 +1,31 @@
|
||||
# 常驻进程工程回放结果
|
||||
|
||||
状态：`PASS-PERSISTENT-REPLAY-EQUIVALENCE`。仅限这次固定回放，不代表学习成功或正式运行时升级。
|
||||
|
||||
## 实测
|
||||
|
||||
| 测量范围 | 新进程 | 常驻进程 | 说明 |
|
||||
|---|---:|---:|---|
|
||||
| 原始 CPU 更新 API | 1.3480 s | 0.1182 s | 新进程首次 API 包含导入等开销 |
|
||||
| 完整更新 API，同一固定案例 | 3.7089 s | 2.3424 s | 仅一组冷启动对照 |
|
||||
| 全脑原始运行函数，13 组配对中位数 | 5.9825 s | 3.7222 s | 含原有输出；排除固定首例的初始化 |
|
||||
|
||||
完整更新常驻 14 组中位耗时：2.3483 s。
|
||||
完整独立验证仍需：3.6435 s（14 组中位数）。
|
||||
全脑运行函数同案例配对倍率中位数：1.620×，不是整轮训练加速倍率。
|
||||
|
||||
## 一致性与保护
|
||||
|
||||
- 17 项主机测试通过。
|
||||
- CPU：14 次冷启动更新、42 次独立双进程更新/重算、29 次完整更新、14 次完整独立验证通过。
|
||||
- 全脑：14 次新进程、正序 14 次与逆序 14 次常驻回放；所有脉冲、状态、延迟队列和请求等一致，10 个数组逐位相同。
|
||||
- 64,034 个原实验文件与 16 个注册源码重新校验通过；之前 659 个加速产物和 13 个源码保持不变。
|
||||
- 原 Phase4AR 仍停止于 1,033 轮 CPU 校验训练与 138 次 probe，没有新增训练或安装新权重。
|
||||
|
||||
## 边界与下一步
|
||||
|
||||
本次全脑测试使用原 RTX 4090 环境，没有证明全脑已能迁移到 V100。此前 V100 约 3.4 ms 的成绩仅属于 eligibility/update 模块。
|
||||
常驻进程复用的是解释器、模块和 CUDA 上下文；每轮神经状态仍由原始函数重新分配。
|
||||
当前仍保留完整验证、图和权重上传、记录写盘。下一步应在新的可审计流水线中验证整轮开销，不能把本报告的独立阶段相加当作实测训练速度。
|
||||
|
||||
源码提交：`018f038c7857c7e0236dd7408a680458520d92ce`。完整逐例耗时、实际进程退出、来源校验见 `final-summary.json` 和各 lane 报告。
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,532 @@
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||||
{
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"fixture_id": "06-frozen",
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||||
"fixture_id": "07-frozen",
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{
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"fixture_id": "08-paired",
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"fixture_id": "09-paired",
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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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|
||||
"fixture_id": "11-random_reward",
|
||||
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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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||||
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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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|
||||
"cpu_regression": {
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
},
|
||||
"cpu_summary": {
|
||||
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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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||||
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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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"discover",
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"-s",
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"/home/qishizhe/digital-drosophila-v100-acceleration/models/male-cns-lif/conditioning-pipeline-acceleration-v1",
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"-p",
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"--output",
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}
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||||
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user