From f2de8797372b2d7558a0547e450928fdc231b860 Mon Sep 17 00:00:00 2001 From: Digital Drosophila Archive Date: Thu, 1 Oct 2026 15:45:19 +0800 Subject: [PATCH] Preserve CPU and GPU acceleration plans, evidence and LFS archives; mark research paused --- .gitattributes | 1 + .gitignore | 2 + CURRENT.md | 19 +- README.md | 16 +- artifacts/acceleration-20261001/gpu.tar.zst | 3 + .../acceleration-20261001/pipeline.tar.zst | 3 + docs/40-operations/branches-20261001.md | 23 + registry/acceleration-20261001/README.md | 43 + registry/acceleration-20261001/gpu/RESULTS.md | 29 + registry/acceleration-20261001/gpu/SHA256SUMS | 660 ++ .../gpu/artifact-manifest.json | 2662 +++++ .../gpu/final-summary.json | 160 + .../pack-verification.json | 21 + .../acceleration-20261001/pipeline/RESULTS.md | 31 + .../acceleration-20261001/pipeline/SHA256SUMS | 1072 ++ .../pipeline/artifact-manifest.json | 4303 ++++++++ .../pipeline/final-summary.json | 532 + .../publication-catalog.json | 8734 +++++++++++++++++ .../archive_results.py | 183 + .../verify_delivery.py | 68 + tools/lfs-publication/lan_lfs_transfer.py | 336 + .../lfs-publication/test_lan_lfs_transfer.py | 286 + 22 files changed, 19177 insertions(+), 10 deletions(-) create mode 100644 artifacts/acceleration-20261001/gpu.tar.zst create mode 100644 artifacts/acceleration-20261001/pipeline.tar.zst create mode 100644 docs/40-operations/branches-20261001.md create mode 100644 registry/acceleration-20261001/README.md create mode 100644 registry/acceleration-20261001/gpu/RESULTS.md create mode 100644 registry/acceleration-20261001/gpu/SHA256SUMS create mode 100644 registry/acceleration-20261001/gpu/artifact-manifest.json create mode 100644 registry/acceleration-20261001/gpu/final-summary.json create mode 100644 registry/acceleration-20261001/pack-verification.json create mode 100644 registry/acceleration-20261001/pipeline/RESULTS.md create mode 100644 registry/acceleration-20261001/pipeline/SHA256SUMS create mode 100644 registry/acceleration-20261001/pipeline/artifact-manifest.json create mode 100644 registry/acceleration-20261001/pipeline/final-summary.json create mode 100644 registry/acceleration-20261001/publication-catalog.json create mode 100644 tools/acceleration-publication/archive_results.py create mode 100644 tools/acceleration-publication/verify_delivery.py create mode 100644 tools/lfs-publication/lan_lfs_transfer.py create mode 100644 tools/lfs-publication/test_lan_lfs_transfer.py diff --git a/.gitattributes b/.gitattributes index cfc7ca6..137fff0 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,3 +1,4 @@ # Preserve historical source bytes and SHA-256 across platforms. No EOL conversion. * -text *.jsonl.gz binary +artifacts/acceleration-20261001/*.tar.zst filter=lfs diff=lfs merge=lfs -text diff --git a/.gitignore b/.gitignore index e43b590..4f9485e 100644 --- a/.gitignore +++ b/.gitignore @@ -34,3 +34,5 @@ id_ed25519* /registry/verification-runs/ # Historical learned deltas/checkpoints are not source files. /models/learned/ +# Explicit, audited experiment exports only; original data stay ignored. +!/artifacts/acceleration-20261001/*.tar.zst diff --git a/CURRENT.md b/CURRENT.md index c66c039..a023d67 100644 --- a/CURRENT.md +++ b/CURRENT.md @@ -1,8 +1,23 @@ # Digital Drosophila — 当前状态 -更新：2026-10-01。独立分支：`codex/lif-author-semantics-lab`。 +更新：2026-10-01。成果保存分支：`codex/v100-conditioning-acceleration`。 -## 最新状态（取代下方历史摘要的“当前／下一步”表述） +## 最新状态：暂停研究，CPU/GPU 两套方案保留 + +用户要求保存并上传现有成果，以后再继续。没有恢复训练、没有启动新实验，没有切换正式科学实现。 + +- Phase 4AR 按真实已提交账本停在 **1,033/30,000 轮训练及 CPU 校验、138/3,920 probes**；末个未完成提交不算完成，也不自动重试。 +- 原科学登记 SHA 为 `b63e6281b6505ca3b60acb467dd0b3fae274cf513dcbfd653649ba52e9ba9740`，注册源码为 `80aeb2093db655329774eff7b32fb6e417b8b40b`。 +- CPU 原方案、独立 CPU 校验和常驻进程方案全部保留；GPU eligibility/update 原型在两张 V100 与 4090 的固定回放上通过逐位比较，没有替换原 CPU 代码。 +- 全脑常驻回放保持原 4090 环境、原始数学与 fresh state，42/42 次逐位一致。13 组稳态配对：原运行函数中位 5.9825 → 3.7222 秒，配对倍率中位 1.6201×；不是整轮训练加速，也不是学习成功。 +- 原实验 64,034 文件/16 源码、前一轮 659 产物/13 源码均保持一致。完整历史 Phase 1–4AQ 没有重跑。 +- 公开原始/参考数据已在独立 LFS 发布分支保存；本次另保存 CPU/GPU 科学回放结果，不包含环境、编译缓存或未确认许可的软件包。 + +[CPU/GPU 方案、结果、恢复与限制](registry/acceleration-20261001/README.md) · [为什么有多个分支](docs/40-operations/branches-20261001.md) + +以下全部是历史状态，不能据此恢复任务或认为仍在运行。 + +## 2026-10-01 00:09 的历史快照（已被上文停止状态取代） Phase 4AQ 已封存为 **PASS-EXACT-UPDATED-BOUNDARY-ENGINEERING-NOT-LEARNING**。Phase 4AR 的普通嗅觉 acquisition 已登记并启动，仍在执行；学习成功尚未判定，没有新 learned candidate。 diff --git a/README.md b/README.md index 393d3a9..d770a57 100644 --- a/README.md +++ b/README.md @@ -3,9 +3,9 @@ 面向 MaleCNS v1.0 的可审计连接组、LIF 模型、感觉接口与局部可塑性机制研究。 **这是研究工程仓库，不是已经实现自主学习或游戏控制的果蝇。** -截至 2026-10-01 00:09（Asia/Shanghai），最新封存阶段是 **Phase 4AQ：PASS-EXACT-UPDATED-BOUNDARY-ENGINEERING-NOT-LEARNING**。 -**Phase 4AR 普通嗅觉 acquisition 正在执行，科学结论未判定**：采样时已提交 411/30,000 轮训练及 CPU 校验、62/3,920 次独立 probe；不是实时自动更新计数。 -最新研发分支为 `codex/lif-author-semantics-lab`，远端默认分支仍为初始化分支。本页状态不表示已完成分支合并。 +截至 2026-10-01，最新正式封存科学阶段仍是 **Phase 4AQ：PASS-EXACT-UPDATED-BOUNDARY-ENGINEERING-NOT-LEARNING**。 +**Phase 4AR 已按用户要求停止，暂不恢复**：已提交 1,033/30,000 轮训练及 CPU 校验、138/3,920 次独立 probe；执行尚未完成，学习成功未判定。 +本分支 `codex/v100-conditioning-acceleration` 同时保留 CPU 与 GPU 方案及两轮独立性能回放。它不是已升级的生产运行时；原登记实验和权重没有改动。远端默认分支仍为初始化分支，见[分支说明](docs/40-operations/branches-20261001.md)。 项目顶层验收口径为 **5/10（50%）**；这不是生物学逼真度、工作量完成率或剩余工期。 最新正式候选运行时为 `MaleCNS-LIF-runtime-v2-deterministic-candidate`。 `MaleCNS-TemporalEligibility-v2-candidate` 与 `MaleCNS-OlfactoryEncoder-v1-candidate` 保留。 @@ -15,7 +15,7 @@ | 主题 | 文档 | |---|---| -| 最新运行状态、证据与下一步 | [当前状态](CURRENT.md)、[本次同步说明](docs/progress/repository-sync-20261001.md) | +| 最新运行状态、证据与下一步 | [当前状态](CURRENT.md)、[CPU/GPU 保存说明](registry/acceleration-20261001/README.md) | | 顶层验收比例与历史基线 | [项目状态](docs/00-overview/status.md) | | 目录和数据流 | [架构与目录](docs/00-overview/architecture.md) | | 科学数据定义和来源 | [数据契约](docs/10-data/data-contract.md)、[来源登记](docs/10-data/provenance.md) | @@ -38,17 +38,17 @@ 服务器项目根目录：`/data/digital-drosophila/`。 远程：`ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git`。 -初始化／当前远端默认分支：`codex/project-bootstrap`；最新研发分支：`codex/lif-author-semantics-lab`。 +初始化／当前远端默认分支：`codex/project-bootstrap`；注册科学源码分支：`codex/lif-author-semantics-lab`；最新独立加速成果：`codex/v100-conditioning-acceleration`。 Git 保存源代码、配置、文档、书目、阶段证据副本和逐文件哈希清单。 -**Git 不保存原始 SWC/Feather、CSR、完整事件/状态、模型 checkpoint、虚拟环境或大型压缩包。** +普通 Git 不直接保存大型科学二进制。获准公开再分发的原始/参考数据已在 `codex/lfs-public-resources` 通过 **Git LFS** 归档；本分支另通过 LFS 保存本次 CPU/GPU 回放的科学结果。没有上传虚拟环境、SDK 编译缓存、凭据或其他服务的数据。 原项目实占约 29.72 GB（十进制、初始化前统计），不会因为初始化 Git 被删除、搬移或重写。 -仅 clone 本仓库不能恢复全数据；按[恢复说明](docs/30-reproducibility/restore.md)配置单独的数据副本。 +只取得 Git pointer 不能恢复全数据；需下载对应分支的 LFS 对象并验证内部成员。本次恢复说明见 [CPU/GPU 发布入口](registry/acceleration-20261001/README.md)。这不是全服务器灾备。 ## 安全的首次检查 ```bash -git clone --branch codex/lif-author-semantics-lab ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git +GIT_LFS_SKIP_SMUDGE=1 git clone --branch codex/v100-conditioning-acceleration ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git cd digital-drosophila python3 -B tools/repo_guard.py ``` diff --git a/artifacts/acceleration-20261001/gpu.tar.zst b/artifacts/acceleration-20261001/gpu.tar.zst new file mode 100644 index 0000000..0f185c4 --- /dev/null +++ b/artifacts/acceleration-20261001/gpu.tar.zst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:50acdc85342a2c79c3516e50ee4542b909813d179518451edaaf2d94150c534b +size 1679158 diff --git a/artifacts/acceleration-20261001/pipeline.tar.zst b/artifacts/acceleration-20261001/pipeline.tar.zst new file mode 100644 index 0000000..65ddc7b --- /dev/null +++ b/artifacts/acceleration-20261001/pipeline.tar.zst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fdc39013d71fb7d14313d8249c929601a8a7050cc2eac88b733d692bbe1b6b42 +size 74767927 diff --git a/docs/40-operations/branches-20261001.md b/docs/40-operations/branches-20261001.md new file mode 100644 index 0000000..6560a74 --- /dev/null +++ b/docs/40-operations/branches-20261001.md @@ -0,0 +1,23 @@ +# 分支用途与当前入口 + +2026-10-01 只读审计。此次只保存/推送已存在的加速实验分支，不删除分支、不强推、不合并、不更改默认分支。 + +所有名称均带 `codex/` 前缀。 + +| 分支 | 用途 | +|---|---| +| project-bootstrap | 最初项目归档、数据索引、论文与来源；当前远端默认入口 | +| apl-pn-scope-audit | APL→PN 实际接触位置审计 | +| terminal-scope-diagnostic | PN calyx 接触范围诊断 | +| lif-semantics-audit | 冻结 LIF 语义与反馈回路审计 | +| lif-author-semantics-lab | 独立模型及正式 Phase 4AR/CPU 实现，当前科学现场的分支 | +| lfs-public-resources | 获准公开再分发的大数据、作者资源及实际远端恢复验证 | +| v100-conditioning-acceleration | CPU 常驻、独立校验、V100 更新原型、4090 常驻回放；本次最新保存入口 | + +前五个主要是同一条提交历史上的阶段指针，并不是五份独立完整数据。它们线性继承至 `09187e4`，之后分为 LFS 资源发布和加速实验两条路线。Git/LFS 会按内容地址保存对象；多个分支名不意味着同一文件被完整复制多份。 + +加速分支原已在本地存在，本次推送后远端共 7 个分支。CPU/GPU 两套实现放在同一加速分支的不同目录，不再各建分支。LFS 资源分支仍独立，不能把这次发布描述为已经合并全部数据。 + +默认仍为最早的 bootstrap，所以网页默认看到的内容较旧。这是入口未整理，不是后续工作丢失。 + +后续可在用户确认后统一主入口、给历史阶段打保留标签，再整理旧分支。集成 LFS 时需核对属性、状态文档、许可说明和自动下载开销；不得把工程实验分支直接视为通过科学验收的正式运行时。 diff --git a/registry/acceleration-20261001/README.md b/registry/acceleration-20261001/README.md new file mode 100644 index 0000000..150a2cb --- /dev/null +++ b/registry/acceleration-20261001/README.md @@ -0,0 +1,43 @@ +# CPU / GPU 方案保存 — 2026-10-01 + +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。** + +## 保存内容 + +| 方案 | 代码 | 状态 | +|---|---|---| +| 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 | +| 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 | +| 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 | + +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。 + +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。 + +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。 + +## 来源、许可与排除 + +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。 + +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。 + +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。 + +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。 + +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。 + +## 恢复与验证（不运行模型） + +在新目录 clone 本分支，安装 Git LFS，执行： + +```sh +git lfs pull --include='artifacts/acceleration-20261001/**' +python3 -B tools/acceleration-publication/archive_results.py verify +``` + +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。 +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。 + +`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。 diff --git a/registry/acceleration-20261001/gpu/RESULTS.md b/registry/acceleration-20261001/gpu/RESULTS.md new file mode 100644 index 0000000..2a43fb9 --- /dev/null +++ b/registry/acceleration-20261001/gpu/RESULTS.md @@ -0,0 +1,29 @@ +# V100 conditioning acceleration — engineering replay result + +Status: **PASS-ELIGIBILITY-UPDATE-REPLAY-EQUIVALENCE**. This is not a learning result or a production-training promotion. + +Benchmark code commit: `221e1f13f758ebe8d9f188bab976c361f7cacf45`. + +| Device | Real-fixture replay median (prep + transfers + comparison) | Resident CUDA kernel median | +|---|---:|---:| +| Tesla V100-SXM2-16GB (v100a-02) | 3.430 ms | 0.122 ms | +| Tesla V100-SXM2-16GB (v100b-01) | 3.344 ms | 0.122 ms | +| NVIDIA GeForce RTX 4090 (rtx4090-01) | 3.327 ms | 0.074 ms | + +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. + +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. + +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. + +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. + +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. + +Phase4AR remains stopped at1033/30000CPU-verified epochs and138/3920probes. No weights were installed and no training was resumed. + +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. + +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. + +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). diff --git a/registry/acceleration-20261001/gpu/SHA256SUMS b/registry/acceleration-20261001/gpu/SHA256SUMS new file mode 100644 index 0000000..5d087e1 --- /dev/null +++ b/registry/acceleration-20261001/gpu/SHA256SUMS @@ -0,0 +1,660 @@ +b63b6d799a83f46c3c69805cfbec316537b06ae7f8e4b63703c9b02575c11cc1 RESULTS.md +e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 candidate-freeze.stderr.log +8ddcbb332825939eb1e091d87a6f73459de707defedb93654727662a0d4e2f0e candidate-freeze.stdout.log +e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 create-venv.stderr.log +e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 create-venv.stdout.log 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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 +} \ No newline at end of file diff --git a/registry/acceleration-20261001/pack-verification.json b/registry/acceleration-20261001/pack-verification.json new file mode 100644 index 0000000..346e019 --- /dev/null +++ b/registry/acceleration-20261001/pack-verification.json @@ -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" +} diff --git a/registry/acceleration-20261001/pipeline/RESULTS.md b/registry/acceleration-20261001/pipeline/RESULTS.md new file mode 100644 index 0000000..cadec55 --- /dev/null +++ b/registry/acceleration-20261001/pipeline/RESULTS.md @@ -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。 diff --git a/registry/acceleration-20261001/pipeline/SHA256SUMS b/registry/acceleration-20261001/pipeline/SHA256SUMS new file mode 100644 index 0000000..6ee8cff --- /dev/null +++ b/registry/acceleration-20261001/pipeline/SHA256SUMS @@ -0,0 +1,1072 @@ +5dabdfd53837793b898335e67f0282fde8270243f9fd48937383f5ecdcbeab28 RESULTS.md 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source packing and streamed verification for exact replay evidence.""" +import argparse +from datetime import datetime, timezone +import hashlib +import io +import json +from pathlib import Path +import re +import shutil +import subprocess +import tarfile + +SOURCE_CODE = Path('/home/qishizhe/digital-drosophila-v100-acceleration/models/male-cns-lif') +GROUPS = { + 'gpu': (Path('/home/qishizhe/phase4ar-v100-acceleration-20261001'), + '6efdec34c96cdc79f786b91bd7a99b0e8ef64d0c4dcfa525646c82659a77d44f', + 'conditioning-acceleration-v1'), + 'pipeline': (Path('/home/qishizhe/phase4ar-pipeline-acceleration-20261001'), + '4c598f51e927b3145891db42d9bb345c52d4aaa3b3a05ac257b207fff90cace4', + 'conditioning-pipeline-acceleration-v1'), +} +REGISTRY = Path('registry/acceleration-20261001') +ARTIFACTS = Path('artifacts/acceleration-20261001') +INSTALL_LOGS = { + 'create-venv.stdout.log', 'create-venv.stderr.log', + 'install-candidate.stdout.log', 'install-candidate.stderr.log', + 'install-candidate-attempt-02.stdout.log', 'install-candidate-attempt-02.stderr.log', + 'upgrade-candidate-pip.stdout.log', 'upgrade-candidate-pip.stderr.log', +} +SECRET_RULES = [ + rb'-----BEGIN (?:OPENSSH |RSA |EC )?PRIVATE KEY-----', + rb'(?:gh[pousr]_[A-Za-z0-9]{30,}|github_pat_[A-Za-z0-9_]{30,}|AKIA[A-Z0-9]{16})', + rb'https?://[^\s/]+:[^\s/@]+@', +] + + +def require(value, message): + if not value: + raise ValueError(message) + + +def sha(path): + digest = hashlib.sha256() + with path.open('rb') as stream: + for block in iter(lambda: stream.read(8 << 20), b''): + digest.update(block) + return digest.hexdigest() + + +def ident(path): + return dict(bytes=path.stat().st_size, sha256=sha(path)) + + +def save(path, obj): + with path.open('x') as stream: + json.dump(obj, stream, indent=2, sort_keys=True, allow_nan=False) + stream.write('\n') + + +def excluded(name): + if name.startswith(('cupy-cache-', 'brain-replay/build/')): + return 'Rebuildable compiler cache/SDK intermediates, not a scientific result' + if name in INSTALL_LOGS: + return 'Environment installation output; versions and wheel report retained' + return None + + +def scan_text(path): + if path.suffix.lower() not in ('.json', '.jsonl', '.log', '.md', '.txt', '.csv', '.py', '.cu', '.diff'): + return + require(path.stat().st_size <= 25 * (1 << 20), 'Oversized text requires manual review') + data = path.read_bytes() + for rule in SECRET_RULES: + require(not re.search(rule, data), 'Potential credential marker: ' + path.name) + + +def pack(root): + require(root == Path('/home/qishizhe/digital-drosophila-acceleration-publication-20261001'), 'Independent publication clone required') + require((root / '.git').is_dir() and not root.is_symlink(), 'Ordinary independent clone required') + registry, artifacts = root / REGISTRY, root / ARTIFACTS + registry.mkdir(parents=True, exist_ok=True) + artifacts.mkdir(parents=True, exist_ok=False) + catalog = dict(schema='acceleration-publication-v1', created_utc=datetime.now(timezone.utc).isoformat(), + numerical_changes=False, training_resumed=False, complete_training_restore=False, + scope='Two completed independent engineering experiments, not the full stopped scientific run', groups={}) + for group, (source, expected_manifest, code_dir) in GROUPS.items(): + require(sha(source / 'artifact-manifest.json') == expected_manifest, 'Sealed source manifest changed') + manifest = json.loads((source / 'artifact-manifest.json').read_text()) + for name, expected in manifest['source_files'].items(): + require(sha(SOURCE_CODE / code_dir / name) == expected, 'Sealed source code changed') + require(sha(root / 'models/male-cns-lif' / code_dir / name) == expected, 'Published source differs') + members, omitted = {}, {} + for name, expected in manifest['files'].items(): + path = source / name + require(path.resolve().is_relative_to(source) and not path.is_symlink(), 'Unsafe source path') + require(ident(path) == expected, 'Sealed input file changed: ' + name) + reason = excluded(name) + if reason: + omitted[name] = dict(expected, reason=reason) + else: + scan_text(path) + members[group + '/' + name] = dict(expected, source_relative=name) + for name in ('artifact-manifest.json', 'SHA256SUMS'): + require(group + '/' + name not in members, 'Duplicate source control file') + members[group + '/' + name] = dict(ident(source / name), source_relative=name) + archive = artifacts / (group + '.tar.zst') + with archive.open('xb') as destination: + compressor = subprocess.Popen(['zstd', '-q', '-T2', '-3', '-c'], stdin=subprocess.PIPE, stdout=destination) + try: + with tarfile.open(fileobj=compressor.stdin, mode='w|', format=tarfile.PAX_FORMAT) as tar: + for name, item in sorted(members.items()): + path = source / item['source_relative'] + info = tarfile.TarInfo(name) + info.size, info.mode, info.mtime = item['bytes'], 0o644, 0 + with path.open('rb') as stream: + tar.addfile(info, stream) + require(ident(path) == {k: item[k] for k in ('bytes', 'sha256')}, 'Input changed during packing') + compressor.stdin.close() + require(compressor.wait(timeout=120) == 0, 'Compression failed') + finally: + if compressor.poll() is None: + compressor.kill() + compressor.wait() + target = registry / group + target.mkdir(exist_ok=False) + for name in ('RESULTS.md', 'final-summary.json', 'artifact-manifest.json', 'SHA256SUMS'): + shutil.copyfile(source / name, target / name) + require(sha(source / name) == sha(target / name), 'Summary copy differs') + catalog['groups'][group] = dict(source_root=str(source), source_manifest_sha256=expected_manifest, + source_files=manifest['source_files'], archive=str(archive.relative_to(root)), **ident(archive), + member_count=len(members), member_bytes=sum(x['bytes'] for x in members.values()), + members=members, excluded=omitted, excluded_count=len(omitted)) + save(registry / 'publication-catalog.json', catalog) + result = verify(root) + save(registry / 'pack-verification.json', result) + print(json.dumps(dict(complete=True, groups=result['groups'], source_files_modified=False), indent=2)) + + +def verify(root): + catalog_path = root / REGISTRY / 'publication-catalog.json' + catalog = json.loads(catalog_path.read_text()) + require(catalog['schema'] == 'acceleration-publication-v1', 'Wrong publication catalog') + results = {} + for group, info in catalog['groups'].items(): + archive = root / info['archive'] + require(archive.resolve().is_relative_to(root / ARTIFACTS) and not archive.is_symlink(), 'Unsafe archive path') + require(ident(archive) == {k: info[k] for k in ('bytes', 'sha256')}, 'Archive identity mismatch') + decoder = subprocess.Popen(['zstd', '-q', '-d', '-c', str(archive)], stdout=subprocess.PIPE) + found, total = set(), 0 + try: + with tarfile.open(fileobj=decoder.stdout, mode='r|') as tar: + for entry in tar: + require(entry.isfile() and entry.name in info['members'] and entry.name not in found, 'Unexpected/duplicate member') + expected = info['members'][entry.name] + require(entry.size == expected['bytes'], 'Member size mismatch') + h, count = hashlib.sha256(), 0 + with tar.extractfile(entry) as stream: + for block in iter(lambda: stream.read(8 << 20), b''): + h.update(block) + count += len(block) + require(count == entry.size and h.hexdigest() == expected['sha256'], 'Member hash mismatch') + found.add(entry.name) + total += count + while decoder.stdout.read(1 << 20): + pass + require(decoder.wait(timeout=30) == 0 and found == set(info['members']), 'Archive truncated or member set differs') + finally: + decoder.stdout.close() + if decoder.poll() is None: + decoder.kill() + decoder.wait() + results[group] = dict(files=len(found), original_bytes=total, archive_bytes=info['bytes'], sha256=info['sha256'], verified=True) + return dict(pass_all=True, groups=results, catalog_sha256=sha(catalog_path), verification='Full streamed members, no extraction or model execution') + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('mode', choices=('pack', 'verify')) + args = parser.parse_args() + if args.mode == 'pack': + pack(Path.cwd()) + else: + print(json.dumps(verify(Path.cwd()), indent=2)) diff --git a/tools/acceleration-publication/verify_delivery.py b/tools/acceleration-publication/verify_delivery.py new file mode 100644 index 0000000..5e4a57f --- /dev/null +++ b/tools/acceleration-publication/verify_delivery.py @@ -0,0 +1,68 @@ +"""Actual fresh-store remote retrieval; no scientific execution or retries.""" +import argparse +from datetime import datetime, timezone +import json +from pathlib import Path +import subprocess +import time + +import archive_results as archives + +REMOTE = 'ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git' +BRANCH = 'codex/v100-conditioning-acceleration' + + +def cmd(args, output=False): + result = subprocess.run(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + archives.require(result.returncode == 0, 'Git/LFS command failed; no automatic retry; diagnostic output not published') + return result.stdout.decode().strip() if output else result.returncode + + +def run(expected, receipt): + root = Path.cwd() + archives.require(root == Path('/home/qishizhe/digital-drosophila-acceleration-verify-20261001') + and (root / '.git').is_dir(), 'New independent verification clone required') + archives.require(cmd(['git', 'rev-parse', 'HEAD'], True) == expected, 'Unexpected checkout commit') + archives.require(cmd(['git', 'remote', 'get-url', 'origin'], True) == REMOTE, 'Unexpected remote') + remote_ref = cmd(['git', 'ls-remote', 'origin', 'refs/heads/' + BRANCH], True) + archives.require(remote_ref.split()[0] == expected, 'Remote branch does not identify data commit') + archives.require(not cmd(['git', 'status', '--porcelain'], True), 'Unclean initial checkout') + objects = root / '.git/lfs/objects' + before = list(p for p in objects.rglob('*') if p.is_file()) if objects.exists() else [] + archives.require(not before, 'Fresh LFS object store must contain no prior object') + archives.require(not receipt.exists() and receipt.parent.is_dir() + and receipt.parent == Path('/home/qishizhe/digital-drosophila-acceleration-publication-20261001/registry/acceleration-20261001'), + 'Exclusive publication receipt required') + start = time.perf_counter() + pull = cmd(['git', 'lfs', 'pull', '--include=artifacts/acceleration-20261001/**', '--exclude=', 'origin']) + fsck = cmd(['git', 'lfs', 'fsck', '--dry-run']) + report = archives.verify(root) + catalog = json.loads((root / archives.REGISTRY / 'publication-catalog.json').read_text()) + source_count = 0 + for group, info in catalog['groups'].items(): + directory = archives.GROUPS[group][2] + for name, expected_sha in info['source_files'].items(): + archives.require(archives.sha(root / 'models/male-cns-lif' / directory / name) == expected_sha, + 'Published source differs from sealed version') + source_count += 1 + stored = [p for p in objects.rglob('*') if p.is_file()] + archives.require(len(stored) == 2 and not cmd(['git', 'status', '--porcelain'], True), 'Incomplete LFS store or changed checkout') + archives.require(cmd(['git', 'rev-parse', 'HEAD'], True) == expected, 'Checkout changed during verification') + report.update(schema='acceleration-fresh-remote-delivery-v1', verified_utc=datetime.now(timezone.utc).isoformat(), + remote=REMOTE, branch=BRANCH, data_commit=expected, fresh_download_proven=True, + initial_LFS_objects=0, downloaded_LFS_objects=len(stored), downloaded_bytes=sum(p.stat().st_size for p in stored), + pull_exit_code=pull, fsck_exit_code=fsck, sealed_source_files_checked=source_count, + wall_seconds=time.perf_counter()-start, scientific_experiments_run=0, training_resumed=False, + complete_training_restore=False, historical_scientific_gate_reexecuted=False, + transport='Previously audited LAN-pinned HTTPS adapter, verified TLS and SSH short-lived authorization', + scope='Remote Git commit, two actual LFS downloads, complete public archive contents and 22 sealed code files; not all external scientific dependencies') + archives.save(receipt, report) + print(json.dumps(report, indent=2)) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('--expected-commit', required=True) + parser.add_argument('--receipt', type=Path, required=True) + args = parser.parse_args() + run(args.expected_commit, args.receipt) diff --git a/tools/lfs-publication/lan_lfs_transfer.py b/tools/lfs-publication/lan_lfs_transfer.py new file mode 100644 index 0000000..ad35eeb --- /dev/null +++ b/tools/lfs-publication/lan_lfs_transfer.py @@ -0,0 +1,336 @@ +"""Repository-local, LAN-pinned Git LFS standalone transfer agent. + +Protocol: https://github.com/git-lfs/git-lfs/blob/main/docs/custom-transfers.md +Only fixed-origin SSH authentication and HTTPS basic transfers are supported. +No config/network changes, retries, redirects, credential files, or cache-based +download substitution. Credentials are passed to curl exclusively on stdin. +""" +from __future__ import annotations + +import hashlib +import json +import os +from pathlib import Path +import re +import stat +import subprocess +import sys +import tempfile +from urllib.parse import urlsplit + +ORIGIN = "ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git" +HOST = "git.lain.asia" +IP = "192.168.10.31" +PREFIX = "/qishizhe/digital-drosophila.git/info/lfs" +SOURCE = Path("/data/digital-drosophila") +OID = re.compile(r"^[0-9a-f]{64}$") +HEADER = re.compile(r"^[!#$%&'*+.^_`|~0-9A-Za-z-]+$") +MAX_JSON = 2 * 1024 * 1024 +BLOCK = 1024 * 1024 + + +class TransferError(Exception): + """Only fixed, non-secret messages may be passed to this class.""" + + +def require(ok, code): + if not ok: + raise TransferError(code) + + +def decode_json(data): + def unique(pairs): + result = {} + for key, value in pairs: + require(key not in result, "duplicate-json-key") + result[key] = value + return result + require(len(data) <= MAX_JSON, "json-response-too-large") + try: + return json.loads(data, object_pairs_hook=unique) + except (UnicodeError, ValueError): + raise TransferError("invalid-json") from None + + +def safe_path(value): + require(isinstance(value, (str, Path)), "invalid-file-path") + p = Path(value) + require(p.is_absolute() and ".." not in p.parts, "absolute-safe-path-required") + for component in (p, *p.parents): + if component.exists() or component.is_symlink(): + s = component.lstat() + require(not stat.S_ISLNK(s.st_mode) and not + (getattr(s, "st_file_attributes", 0) & getattr(stat, "FILE_ATTRIBUTE_REPARSE_POINT", 0)), + "symlink-or-reparse-refused") + return p + + +def safe_url(value): + require(isinstance(value, str) and len(value) <= 16384 and + not any(ord(c) <= 32 or ord(c) == 127 for c in value), "invalid-action-url") + try: + p = urlsplit(value) + valid = (p.scheme == "https" and p.netloc in (HOST, HOST + ":443") and + p.hostname == HOST and p.port in (None, 443) and + p.username is None and p.password is None and not p.fragment) + except ValueError: + raise TransferError("url-authority-refused") from None + require(valid, "url-authority-refused") + require(p.path == PREFIX or p.path.startswith(PREFIX + "/"), "url-repository-prefix-refused") + require("%" not in p.path and "\\" not in p.path and + all(x not in ("", ".", "..") for x in p.path.split("/")[1:]), "url-path-refused") + return value + + +def safe_headers(value, *, allow_upload_chunked=False): + require(isinstance(value, dict) and len(value) <= 32, "invalid-action-headers") + result, seen = {}, set() + denied = {"host", "connection", "content-length", "transfer-encoding", "te", + "trailer", "upgrade", "proxy-authorization", "proxy-connection", "range"} + for key, item in value.items(): + upload_chunked = (allow_upload_chunked is True and isinstance(key, str) and + key.lower() == "transfer-encoding" and item == "chunked") + require(isinstance(key, str) and HEADER.fullmatch(key) is not None and + key.lower() not in seen and (key.lower() not in denied or upload_chunked), + "header-name-refused") + require(isinstance(item, str) and len(item) <= 16384 and + not any(ord(c) < 32 or ord(c) == 127 for c in item), "header-value-refused") + seen.add(key.lower()) + result[key] = item + return result + + +def quote(value): + require(isinstance(value, str) and not any(ord(c) < 32 or ord(c) == 127 for c in value), + "curl-config-value-refused") + return '"' + value.replace("\\", "\\\\").replace('"', '\\"') + '"' + + +def fingerprint(s): + return (s.st_dev, s.st_ino, s.st_mode, s.st_size, s.st_mtime_ns, s.st_ctime_ns) + + +def verify_file(path, oid, size): + path = safe_path(path) + before = fingerprint(path.lstat()) + require(stat.S_ISREG(before[2]) and before[3] == size, "object-file-type-or-size-mismatch") + digest, count = hashlib.sha256(), 0 + with path.open("rb") as handle: + opened = fingerprint(os.fstat(handle.fileno())) + # Windows path stat and fstat can expose different ctime definitions. + require(opened[:-1] == before[:-1] if os.name == "nt" else opened == before, + "object-changed-at-open") + while data := handle.read(BLOCK): + digest.update(data) + count += len(data) + require(fingerprint(os.fstat(handle.fileno())) == opened, "object-changed-during-read") + require(fingerprint(path.lstat()) == before and count == size and digest.hexdigest() == oid, + "object-sha-or-stability-mismatch") + return before + + +def git_output(cwd, *args): + try: + result = subprocess.run(["git", "-C", str(cwd), *args], capture_output=True, + timeout=15, check=False) + require(result.returncode == 0, "git-inspection-failed") + return result.stdout.decode("utf-8").strip() + except (OSError, UnicodeError, subprocess.TimeoutExpired): + raise TransferError("git-inspection-failed") from None + + +class Agent: + def __init__(self, message, emit, cwd=None): + require(message.get("event") == "init" and message.get("operation") in ("upload", "download"), + "invalid-init") + require(message.get("remote") in ("origin", ORIGIN), "remote-refused") + concurrency = message.get("concurrenttransfers") + require(type(concurrency) is int and 1 <= concurrency <= 2 and + type(message.get("concurrent")) is bool, "concurrency-must-be-at-most-two") + cwd = safe_path(Path.cwd() if cwd is None else cwd) + require(cwd != SOURCE and SOURCE not in cwd.parents, "scientific-source-cwd-refused") + self.root = safe_path(git_output(cwd, "rev-parse", "--show-toplevel")) + require(self.root != SOURCE and SOURCE not in self.root.parents, "scientific-source-repository-refused") + require(git_output(cwd, "config", "--get", "remote.origin.url") == ORIGIN, "origin-refused") + self.git_dir = safe_path(git_output(cwd, "rev-parse", "--absolute-git-dir")) + require(self.git_dir == self.root / ".git" and self.git_dir.is_dir(), "ordinary-isolated-clone-required") + self.operation, self.emit = message["operation"], emit + + def authenticate(self): + command = ["ssh", "-o", "BatchMode=yes", "-o", "StrictHostKeyChecking=yes", + "-o", "ConnectTimeout=15", "-o", "ConnectionAttempts=1", + "-o", "ServerAliveInterval=10", "-o", "ServerAliveCountMax=2", + "-p", "2222", "git@192.168.10.31", "git-lfs-authenticate", + "qishizhe/digital-drosophila.git", self.operation] + try: + result = subprocess.run(command, capture_output=True, timeout=45, check=False) + require(result.returncode == 0, "ssh-authentication-failed") + auth = decode_json(result.stdout) + except (OSError, subprocess.TimeoutExpired): + raise TransferError("ssh-authentication-failed") from None + require(isinstance(auth, dict), "invalid-ssh-authentication-response") + href = safe_url(auth.get("href")) + parsed = urlsplit(href) + require(parsed.path == PREFIX and not parsed.query, "authentication-base-url-refused") + return href, safe_headers(auth.get("header", {})) + + def curl(self, method, url, headers, *, body=None, upload=None, download=None, size=None): + safe_url(url) + headers = safe_headers(headers, allow_upload_chunked=(self.operation == "upload" and + method == "PUT" and upload is not None and body is None and download is None)) + require(method in ("GET", "POST", "PUT"), "unsupported-http-method") + present = {name.lower() for name in headers} + if "accept" not in present: + headers["Accept"] = "application/vnd.git-lfs+json" + if method == "PUT" and "content-type" not in present: + headers["Content-Type"] = "application/octet-stream" + if body is not None and "content-type" not in present: + headers["Content-Type"] = "application/vnd.git-lfs+json" + lines = ["url = " + quote(url), "request = " + quote(method), + 'noproxy = "*"', 'resolve = "' + HOST + ':443:' + IP + '"', + 'proto = "=https"', 'proto-redir = "=https"', "max-redirs = 0", + "connect-timeout = 15", "max-time = 1800", "fail", "silent", "show-error", + 'write-out = "\\n%{http_code}"'] + for name, value in headers.items(): + lines.append("header = " + quote(name + ": " + value)) + if body is not None: + encoded = json.dumps(body, separators=(",", ":"), allow_nan=False) + lines.append("data-binary = " + quote(encoded)) + if upload is not None: + lines.append("upload-file = " + quote(str(safe_path(upload)))) + if download is not None: + lines.append("output = " + quote(str(safe_path(download)))) + require(type(size) is int and size >= 0, "invalid-download-limit") + # A zero-byte object still needs a full HTTP fetch, not a cache hit. + lines.append("max-filesize = " + str(max(size, 1))) + else: + lines.append("max-filesize = " + str(MAX_JSON)) + config = ("\n".join(lines) + "\n").encode("utf-8") + try: + result = subprocess.run(["curl", "-q", "--config", "-"], input=config, + capture_output=True, timeout=1830, check=False) + except (OSError, subprocess.TimeoutExpired): + raise TransferError("curl-execution-failed") from None + # Never print stderr, response data, URLs, configuration, or headers. + require(result.returncode == 0, "curl-request-failed") + require(len(result.stdout) <= MAX_JSON + 32, "http-response-too-large") + content, separator, status = result.stdout.rpartition(b"\n") + require(separator and len(status) == 3 and status.isdigit() and 200 <= int(status) < 300, + "non-success-http-status") + return content + + def batch(self, oid, size): + href, headers = self.authenticate() + headers = {k: v for k, v in headers.items() if k.lower() not in ("content-type", "accept")} + headers.update({"Content-Type": "application/vnd.git-lfs+json", "Accept": "application/vnd.git-lfs+json"}) + response = decode_json(self.curl("POST", href + "/objects/batch", headers, + body={"operation": self.operation, "transfers": ["basic"], + "objects": [{"oid": oid, "size": size}]})) + require(isinstance(response, dict) and response.get("transfer", "basic") == "basic", + "non-basic-batch-response") + objects = response.get("objects") + require(isinstance(objects, list) and len(objects) == 1 and isinstance(objects[0], dict), + "invalid-batch-object-count") + item = objects[0] + require(item.get("oid") == oid and type(item.get("size")) is int and item["size"] == size, + "batch-object-identity-mismatch") + require("error" not in item, "batch-object-rejected") + actions = item.get("actions", {}) + require(isinstance(actions, dict), "invalid-batch-actions") + allowed = {"upload", "verify"} if self.operation == "upload" else {"download"} + require(set(actions) <= allowed, "unexpected-batch-action") + for name, action in actions.items(): + require(isinstance(action, dict), "invalid-batch-action") + safe_url(action.get("href")) + safe_headers(action.get("header", {}), allow_upload_chunked=(self.operation == "upload" and name == "upload")) + return actions + + def progress(self, oid, size, previous=0): + self.emit({"event": "progress", "oid": oid, "bytesSoFar": size, "bytesSinceLast": size - previous}) + + def transfer(self, message): + require(message.get("event") == self.operation and message.get("action") is None, + "standalone-operation-required") + oid, size = message.get("oid"), message.get("size") + require(isinstance(oid, str) and OID.fullmatch(oid) is not None and + type(size) is int and 0 <= size <= 2**63 - 1, "invalid-object-identity") + source, before = None, None + if self.operation == "upload": + source = safe_path(message.get("path")) + require(source == self.git_dir / "lfs" / "objects" / oid[:2] / oid[2:4] / oid, + "upload-outside-current-lfs-object-store") + before = verify_file(source, oid, size) + actions = self.batch(oid, size) + self.progress(oid, 0) + if self.operation == "upload": + if "upload" in actions: + action = actions["upload"] + self.curl("PUT", action["href"], action.get("header", {}), upload=source) + require(fingerprint(source.lstat()) == before, "upload-source-changed") + if "verify" in actions: + action = actions["verify"] + headers = {k: v for k, v in action.get("header", {}).items() if k.lower() != "content-type"} + headers["Content-Type"] = "application/vnd.git-lfs+json" + self.curl("POST", action["href"], headers, body={"oid": oid, "size": size}) + else: + require(not actions, "verify-without-upload-refused") + require(fingerprint(source.lstat()) == before, "upload-source-changed") + self.progress(oid, size) + return {"event": "complete", "oid": oid} + require("download" in actions, "download-action-missing") + directory = safe_path(self.git_dir / "lfs" / "lan-transfer-tmp") + directory.mkdir(parents=True, exist_ok=True) + safe_path(directory) + fd, name = tempfile.mkstemp(prefix=oid + ".", suffix=".partial", dir=directory) + os.close(fd) + target = Path(name) + action = actions["download"] + # On failure the uniquely created partial remains for investigation; + # it is never used as a fallback/cache input on a later transfer. + self.curl("GET", action["href"], action.get("header", {}), download=target, size=size) + verify_file(target, oid, size) + self.progress(oid, size) + return {"event": "complete", "oid": oid, "path": str(target)} + + +def emit(value): + sys.stdout.write(json.dumps(value, separators=(",", ":"), allow_nan=False) + "\n") + sys.stdout.flush() + + +def serve(inp=None, send=None, factory=Agent): + inp, send = sys.stdin if inp is None else inp, emit if send is None else send + agent = None + while True: + line = inp.readline(MAX_JSON + 1) + if not line: + return 0 + try: + message = decode_json(line) + require(isinstance(message, dict), "protocol-object-required") + if agent is None: + agent = factory(message, send) + send({}) + elif message.get("event") == "terminate": + return 0 + else: + oid = message.get("oid") + safe_oid = oid if isinstance(oid, str) and OID.fullmatch(oid) else "" + try: + send(agent.transfer(message)) + except Exception as exc: + code = str(exc) if isinstance(exc, TransferError) else "transfer-internal-failure" + send({"event": "complete", "oid": safe_oid, + "error": {"code": 2, "message": code}}) + except Exception as exc: + code = str(exc) if isinstance(exc, TransferError) else "agent-initialization-or-protocol-failure" + if agent is None: + send({"error": {"code": 32, "message": code}}) + else: + # No attacker-supplied raw line or exception text is printed. + sys.stderr.write("lan-lfs: invalid protocol; stopping\n") + return 1 + + +if __name__ == "__main__": + raise SystemExit(serve()) diff --git a/tools/lfs-publication/test_lan_lfs_transfer.py b/tools/lfs-publication/test_lan_lfs_transfer.py new file mode 100644 index 0000000..48fcbc2 --- /dev/null +++ b/tools/lfs-publication/test_lan_lfs_transfer.py @@ -0,0 +1,286 @@ +"""Pure temporary/mocked protocol tests: never SSH, curl, GPU, or real Git.""" +import contextlib +import hashlib +import io +import json +from pathlib import Path +import subprocess +import tempfile +import unittest +from unittest.mock import patch + +import lan_lfs_transfer as M + +BASE = "https://" + M.HOST + M.PREFIX +TOKEN = "synthetic-fixture-" + "credential-value" + + +class AdapterTests(unittest.TestCase): + def setUp(self): + self.temp = tempfile.TemporaryDirectory() + self.addCleanup(self.temp.cleanup) + self.root = Path(self.temp.name) / "clone" + self.git = self.root / ".git" + self.git.mkdir(parents=True) + self.data = b"synthetic content\x00\xff\n" + self.oid = hashlib.sha256(self.data).hexdigest() + self.size = len(self.data) + self.events = [] + self.agent = object.__new__(M.Agent) + self.agent.root, self.agent.git_dir = self.root, self.git + self.agent.operation, self.agent.emit = "upload", self.events.append + self.source = self.git / "lfs" / "objects" / self.oid[:2] / self.oid[2:4] / self.oid + self.source.parent.mkdir(parents=True) + self.source.write_bytes(self.data) + + def request(self, operation="upload", **extra): + value = {"event": operation, "oid": self.oid, "size": self.size, "action": None} + if operation == "upload": + value["path"] = str(self.source) + value.update(extra) + return value + + def init_message(self, **extra): + return dict(event="init", operation="upload", remote="origin", concurrent=True, + concurrenttransfers=2, **extra) + + def action(self, suffix="objects/" ): + return {"href": BASE + "/" + suffix + self.oid, + "header": {"Authorization": "Bearer " + TOKEN}} + + def test_strict_url_policy(self): + self.assertEqual(M.safe_url(BASE + "/objects/" + self.oid + "?signed=opaque"), + BASE + "/objects/" + self.oid + "?signed=opaque") + invalid = [BASE.replace("https:", "http:"), BASE.replace(M.HOST, M.IP), + BASE.replace(M.HOST, "other.example"), BASE.replace(M.HOST, M.HOST + ":444"), + BASE.replace(M.HOST, "user:opaque@" + M.HOST), BASE + "-other/objects/x", + BASE + "/../other", BASE + "/%2e%2e/other", BASE + "/objects/x#fragment", + BASE + "//objects/x", BASE + "/objects\\x", BASE + "\n"] + for url in invalid: + with self.subTest(url=url), self.assertRaises(M.TransferError): + M.safe_url(url) + + def test_headers_reject_injection_and_routing_overrides(self): + for headers in ({"Authorization": "x\r\nHost: bad"}, {"Host": "bad"}, + {"Authorization": "a", "authorization": "b"}, + {"Range": "bytes=1-"}, {"bad\nkey": "x"}, {"X": "\x00"}): + with self.subTest(headers=headers), self.assertRaises(M.TransferError): + M.safe_headers(headers) + + def test_init_checks_origin_and_isolated_git_directory(self): + values = [str(self.root), M.ORIGIN, str(self.git)] + with patch.object(M, "git_output", side_effect=values): + actual = M.Agent(self.init_message(), self.events.append, cwd=self.root) + self.assertEqual(actual.git_dir, self.git) + with patch.object(M, "git_output", side_effect=[str(self.root), "ssh://other/repo"]): + with self.assertRaisesRegex(M.TransferError, "origin-refused"): + M.Agent(self.init_message(), self.events.append, cwd=self.root) + + def test_original_source_and_excess_concurrency_refused(self): + with patch.object(M, "SOURCE", self.root): + with self.assertRaisesRegex(M.TransferError, "scientific-source-cwd"): + M.Agent(self.init_message(), self.events.append, cwd=self.root) + message = self.init_message() + message["concurrenttransfers"] = 3 + with self.assertRaisesRegex(M.TransferError, "concurrency"): + M.Agent(message, self.events.append, cwd=self.root) + + def test_ssh_authentication_is_strict_and_operation_scoped(self): + response = {"href": BASE, "header": {"Authorization": "Bearer " + TOKEN}} + result = subprocess.CompletedProcess([], 0, stdout=json.dumps(response).encode(), stderr=b"") + with patch.object(M.subprocess, "run", return_value=result) as call: + href, headers = self.agent.authenticate() + args = call.call_args.args[0] + self.assertIn("BatchMode=yes", args) + self.assertIn("StrictHostKeyChecking=yes", args) + self.assertEqual(args[-3:], ["git-lfs-authenticate", "qishizhe/digital-drosophila.git", "upload"]) + self.assertEqual(href, BASE) + self.assertIn(TOKEN, headers["Authorization"]) + self.assertNotIn(TOKEN, json.dumps(args)) + + def test_curl_secrets_only_in_stdin_and_secure_defaults(self): + result = subprocess.CompletedProcess([], 0, stdout=b"{}\n200", stderr=b"") + with patch.object(M.subprocess, "run", return_value=result) as call: + body = self.agent.curl("PUT", BASE + "/objects/" + self.oid + "?signature=" + TOKEN, + {"Authorization": "Bearer " + TOKEN}, upload=self.source) + self.assertEqual(body, b"{}") + self.assertEqual(call.call_args.args[0], ["curl", "-q", "--config", "-"]) + self.assertNotIn(TOKEN, json.dumps(call.call_args.args[0])) + config = call.call_args.kwargs["input"].decode() + for wanted in ('noproxy = "*"', M.HOST + ":443:" + M.IP, 'proto = "=https"', + "max-redirs = 0", "Accept: application/vnd.git-lfs+json", + "Content-Type: application/octet-stream", TOKEN): + self.assertIn(wanted, config) + self.assertNotIn("insecure", config) + self.assertNotIn("location", config) + self.assertNotIn("retry", config) + + def test_redirect_or_curl_error_is_sanitized(self): + for rc, output in ((0, b"redirect body\n302"), (22, b"")): + result = subprocess.CompletedProcess([], rc, stdout=output, stderr=TOKEN.encode()) + with patch.object(M.subprocess, "run", return_value=result): + with self.assertRaises(M.TransferError) as caught: + self.agent.curl("GET", BASE + "/objects/" + self.oid, {}) + self.assertNotIn(TOKEN, str(caught.exception)) + + def test_post_json_sets_both_gitea_headers(self): + result = subprocess.CompletedProcess([], 0, stdout=b"\n204", stderr=b"") + with patch.object(M.subprocess, "run", return_value=result) as call: + self.agent.curl("POST", BASE + "/verify", {}, body={"oid": self.oid, "size": self.size}) + config = call.call_args.kwargs["input"].decode() + self.assertIn("Accept: application/vnd.git-lfs+json", config) + self.assertIn("Content-Type: application/vnd.git-lfs+json", config) + + def test_batch_requests_basic_and_checks_exact_identity(self): + response = {"objects": [{"oid": self.oid, "size": self.size, "actions": {"upload": self.action()}}]} + with patch.object(self.agent, "authenticate", return_value=(BASE, {"Authorization": TOKEN})), \ + patch.object(self.agent, "curl", return_value=json.dumps(response).encode()) as call: + self.assertIn("upload", self.agent.batch(self.oid, self.size)) + args, kwargs = call.call_args + self.assertEqual(args[1], BASE + "/objects/batch") + self.assertEqual(args[2]["Accept"], "application/vnd.git-lfs+json") + self.assertEqual(kwargs["body"]["transfers"], ["basic"]) + response["objects"][0]["size"] += 1 + with patch.object(self.agent, "authenticate", return_value=(BASE, {})), \ + patch.object(self.agent, "curl", return_value=json.dumps(response).encode()): + with self.assertRaisesRegex(M.TransferError, "identity"): + self.agent.batch(self.oid, self.size) + + def test_batch_action_host_rejected(self): + action = self.action() + action["href"] = action["href"].replace(M.HOST, "other.example") + response = {"objects": [{"oid": self.oid, "size": self.size, "actions": {"upload": action}}]} + with patch.object(self.agent, "authenticate", return_value=(BASE, {})), \ + patch.object(self.agent, "curl", return_value=json.dumps(response).encode()): + with self.assertRaisesRegex(M.TransferError, "authority"): + self.agent.batch(self.oid, self.size) + + def test_upload_chunked_exact_value_allowed_in_action_and_put(self): + action = self.action() + action["header"]["Transfer-Encoding"] = "chunked" + response = {"objects": [{"oid": self.oid, "size": self.size, "actions": {"upload": action}}]} + with patch.object(self.agent, "authenticate", return_value=(BASE, {})), \ + patch.object(self.agent, "curl", return_value=json.dumps(response).encode()): + self.assertEqual(self.agent.batch(self.oid, self.size)["upload"]["header"]["Transfer-Encoding"], "chunked") + result = subprocess.CompletedProcess([], 0, stdout=b"\n200", stderr=b"") + with patch.object(M.subprocess, "run", return_value=result) as call: + self.agent.curl("PUT", action["href"], action["header"], upload=self.source) + config = call.call_args.kwargs["input"].decode() + self.assertIn('header = "Transfer-Encoding: chunked"', config) + self.assertIn('request = "PUT"', config) + self.assertIn("upload-file = ", config) + + def test_chunked_forbidden_outside_upload_or_for_other_values(self): + for value in ("gzip", "CHUNKED", "chunked, gzip", "chunked\r\nX: y", " chunked"): + with self.subTest(value=value), self.assertRaises(M.TransferError): + self.agent.curl("PUT", BASE + "/objects/" + self.oid, + {"Transfer-Encoding": value}, upload=self.source) + for method, kwargs in (("GET", {}), ("POST", {"body": {}}), ("PUT", {})): + with self.subTest(method=method, kwargs=kwargs), self.assertRaises(M.TransferError): + self.agent.curl(method, BASE + "/objects/" + self.oid, + {"Transfer-Encoding": "chunked"}, **kwargs) + with self.assertRaises(M.TransferError): + M.safe_headers({"Transfer-Encoding": "chunked"}) + for operation, name in (("upload", "verify"), ("download", "download")): + self.agent.operation = operation + action = self.action() + action["header"]["Transfer-Encoding"] = "chunked" + response = {"objects": [{"oid": self.oid, "size": self.size, "actions": {name: action}}]} + with patch.object(self.agent, "authenticate", return_value=(BASE, {})), \ + patch.object(self.agent, "curl", return_value=json.dumps(response).encode()): + with self.subTest(operation=operation, action=name), self.assertRaises(M.TransferError): + self.agent.batch(self.oid, self.size) + + def test_upload_existing_object_needs_no_put(self): + with patch.object(self.agent, "batch", return_value={}) as batch, patch.object(self.agent, "curl") as curl: + result = self.agent.transfer(self.request()) + self.assertEqual(result, {"event": "complete", "oid": self.oid}) + batch.assert_called_once() + curl.assert_not_called() + self.assertEqual(self.events[-1]["bytesSoFar"], self.size) + + def test_upload_put_then_verification_post(self): + actions = {"upload": self.action(), "verify": self.action("verify/")} + with patch.object(self.agent, "batch", return_value=actions), \ + patch.object(self.agent, "curl", return_value=b"") as curl: + self.agent.transfer(self.request()) + self.assertEqual([c.args[0] for c in curl.call_args_list], ["PUT", "POST"]) + self.assertEqual(curl.call_args_list[1].kwargs["body"], {"oid": self.oid, "size": self.size}) + + def test_upload_wrong_sha_fails_before_network(self): + self.source.write_bytes(b"x" * self.size) + with patch.object(self.agent, "batch") as batch: + with self.assertRaisesRegex(M.TransferError, "sha"): + self.agent.transfer(self.request()) + batch.assert_not_called() + + def test_upload_outside_lfs_store_refused(self): + other = self.root / self.oid + other.write_bytes(self.data) + with self.assertRaisesRegex(M.TransferError, "outside-current-lfs"): + self.agent.transfer(self.request(path=str(other))) + + def test_upload_source_mutation_detected(self): + def change(*args, **kwargs): + self.source.write_bytes(b"changed") + with patch.object(self.agent, "batch", return_value={"upload": self.action()}), \ + patch.object(self.agent, "curl", side_effect=change): + with self.assertRaisesRegex(M.TransferError, "upload-source-changed"): + self.agent.transfer(self.request()) + + def test_download_is_fresh_unique_and_verified(self): + self.agent.operation = "download" + def fetch(*args, **kwargs): + kwargs["download"].write_bytes(self.data) + return b"" + with patch.object(self.agent, "batch", return_value={"download": self.action()}), \ + patch.object(self.agent, "curl", side_effect=fetch) as curl: + first = self.agent.transfer(self.request("download")) + second = self.agent.transfer(self.request("download")) + self.assertNotEqual(first["path"], second["path"]) + self.assertEqual(Path(first["path"]).read_bytes(), self.data) + self.assertEqual(curl.call_count, 2) + self.assertEqual(self.source.read_bytes(), self.data) + + def test_download_hash_failure_retains_partial(self): + self.agent.operation = "download" + def fetch(*args, **kwargs): + kwargs["download"].write_bytes(b"x" * self.size) + with patch.object(self.agent, "batch", return_value={"download": self.action()}), \ + patch.object(self.agent, "curl", side_effect=fetch): + with self.assertRaisesRegex(M.TransferError, "sha"): + self.agent.transfer(self.request("download")) + partials = list((self.git / "lfs" / "lan-transfer-tmp").glob("*.partial")) + self.assertEqual(len(partials), 1) + self.assertEqual(partials[0].read_bytes(), b"x" * self.size) + + def test_protocol_init_progress_completion_terminate(self): + requests = [self.init_message(), self.request(), {"event": "terminate"}] + incoming = io.StringIO("".join(json.dumps(x) + "\n" for x in requests)) + with patch.object(self.agent, "batch", return_value={}): + code = M.serve(incoming, self.events.append, factory=lambda message, send: self.agent) + self.assertEqual(code, 0) + self.assertEqual(self.events[0], {}) + self.assertEqual(self.events[-1], {"event": "complete", "oid": self.oid}) + + def test_transfer_error_continues_and_never_echoes_exception_secret(self): + incoming = io.StringIO("\n".join(json.dumps(x) for x in + [self.init_message(), self.request(), self.request(), {"event": "terminate"}]) + "\n") + with patch.object(self.agent, "transfer", side_effect=[RuntimeError(TOKEN), {"event": "complete", "oid": self.oid}]): + code = M.serve(incoming, self.events.append, factory=lambda message, send: self.agent) + self.assertEqual(code, 0) + self.assertIn("error", self.events[1]) + self.assertNotIn(TOKEN, json.dumps(self.events)) + self.assertNotIn("error", self.events[2]) + + def test_bad_initialization_uses_init_error_schema(self): + incoming = io.StringIO(json.dumps(self.init_message()) + "\n") + with patch.object(M, "git_output", side_effect=RuntimeError(TOKEN)): + code = M.serve(incoming, self.events.append) + self.assertEqual(code, 1) + self.assertEqual(self.events[0]["error"]["code"], 32) + self.assertNotIn(TOKEN, json.dumps(self.events)) + + +if __name__ == "__main__": + unittest.main()