Merge devel into master#2871
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wanghan-iapcm merged 64 commits intodeepmodeling:masterfrom Sep 27, 2023
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Fix deepmodeling#1262. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…re not installed (deepmodeling#2777) See https://github.com/search?q=repo%3Alammps%2Flammps+%22Must+install%22&type=code. Just use the same logic as LAMMPS. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Fix deepmodeling#2724. Fix deepmodeling#2780. Add the linear energy model, where the energy is the linear combination of several sub-energy models. Add the frozen model to load the external DP model into the graph. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Previously, the header line does not have columns for atomic model deviation. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Fix deepmodeling#2513. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.286 → v0.0.287](astral-sh/ruff-pre-commit@v0.0.286...v0.0.287) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…ling#2790) The input of the model should be Angstron so that the unit style can only be metal or real. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Fix deepmodeling#2721. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…ing#2776) When `pair_coeff` has set LAMMPS `type_map` (e.g. `pair_coeff * * O H`), `fix_dplr` uses the same LAMMPS `type_map` (i.e. `O H` in this case) to map from LAMMPS types to the DP model types, considering LAMMPS types should always be the same among different commands. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
It's the same as deepmodeling#2782, but one line was missing in that PR. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
This PR migrates the Python build backend from scikit-build to [scikit-build-core](https://github.com/scikit-build/scikit-build-core), which is being actively developed. There are no breaking changes to users; all tests should be passed without modification. The behavior for editable installation (`pip install -e .`) is changed. Before, the compiled binary libraries (e.g. `libdeepmd_op.sp`) are installed into the source directory. In this PR, the library files are installed into `site-packages` separately, while the Python files are still in the source code and can be modified for development. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
```
DeprecationWarning: loadtxt(): Parsing an integer via a float is deprecated. To avoid this warning, you can:
* make sure the original data is stored as integers.
* use the `converters=` keyword argument. If you only use
NumPy 1.23 or later, `converters=float` will normally work.
* Use `np.loadtxt(...).astype(np.int64)` parsing the file as
floating point and then convert it. (On all NumPy versions.)
(Deprecated NumPy 1.23)
return np.loadtxt(str(self.path), **kwargs)
```
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Fix deepmodeling#2017. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Fix deepmodeling#2432. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
This PR fixes an error for the example in the `examples` directory.
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.1.1 to 4.2.1. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/docker/build-push-action/releases">docker/build-push-action's releases</a>.</em></p> <blockquote> <h2>v4.2.1</h2> <blockquote> <p><strong>Note</strong></p> <p>Buildx v0.10 enables support for a minimal <a href="https://slsa.dev/provenance/">SLSA Provenance</a> attestation, which requires support for <a href="https://github.com/opencontainers/image-spec">OCI-compliant</a> multi-platform images. This may introduce issues with registry and runtime support (e.g. <a href="https://redirect.github.com/docker/buildx/issues/1533">Google Cloud Run and AWS Lambda</a>). You can optionally disable the default provenance attestation functionality using <code>provenance: false</code>.</p> </blockquote> <ul> <li>warn if docker config can't be parsed by <a href="https://github.com/crazy-max"><code>@crazy-max</code></a> in <a href="https://redirect.github.com/docker/build-push-action/pull/957">docker/build-push-action#957</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/docker/build-push-action/compare/v4.2.0...v4.2.1">https://github.com/docker/build-push-action/compare/v4.2.0...v4.2.1</a></p> <h2>v4.2.0</h2> <blockquote> <p><strong>Note</strong></p> <p>Buildx v0.10 enables support for a minimal <a href="https://slsa.dev/provenance/">SLSA Provenance</a> attestation, which requires support for <a href="https://github.com/opencontainers/image-spec">OCI-compliant</a> multi-platform images. This may introduce issues with registry and runtime support (e.g. <a href="https://redirect.github.com/docker/buildx/issues/1533">Google Cloud Run and AWS Lambda</a>). You can optionally disable the default provenance attestation functionality using <code>provenance: false</code>.</p> </blockquote> <ul> <li>display proxy configuration by <a href="https://github.com/crazy-max"><code>@crazy-max</code></a> in <a href="https://redirect.github.com/docker/build-push-action/pull/872">docker/build-push-action#872</a></li> <li>chore(deps): Bump <code>@docker/actions-toolkit</code> from 0.6.0 to 0.8.0 in <a href="https://redirect.github.com/docker/build-push-action/pull/930">docker/build-push-action#930</a></li> <li>chore(deps): Bump word-wrap from 1.2.3 to 1.2.5 in <a href="https://redirect.github.com/docker/build-push-action/pull/925">docker/build-push-action#925</a></li> <li>chore(deps): Bump semver from 6.3.0 to 6.3.1 in <a href="https://redirect.github.com/docker/build-push-action/pull/902">docker/build-push-action#902</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/docker/build-push-action/compare/v4.1.1...v4.2.0">https://github.com/docker/build-push-action/compare/v4.1.1...v4.2.0</a></p> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/docker/build-push-action/commit/0a97817b6ade9f46837855d676c4cca3a2471fc9"><code>0a97817</code></a> Merge pull request <a href="https://redirect.github.com/docker/build-push-action/issues/957">#957</a> from crazy-max/warn-docker-config</li> <li><a href="https://github.com/docker/build-push-action/commit/ec39ef320c442d2af669fd8555e7f3b7ad7026bd"><code>ec39ef3</code></a> chore: update generated content</li> <li><a href="https://github.com/docker/build-push-action/commit/f46044b799d766d2bb3e644bd48da06b6c30a978"><code>f46044b</code></a> warn if docker config can't be parsed</li> <li><a href="https://github.com/docker/build-push-action/commit/4e4ee680f69700760d5620a94c020aef883043aa"><code>4e4ee68</code></a> Merge pull request <a href="https://redirect.github.com/docker/build-push-action/issues/951">#951</a> from crazy-max/ci-concurrency</li> <li><a href="https://github.com/docker/build-push-action/commit/e86cf554b69aa5dfd1179937926b6d0cf6550be7"><code>e86cf55</code></a> ci: missing concurrency checks</li> <li><a href="https://github.com/docker/build-push-action/commit/daa0106f78eed71cdc2a900489ce515acedeef64"><code>daa0106</code></a> Merge pull request <a href="https://redirect.github.com/docker/build-push-action/issues/949">#949</a> from docker/dependabot/github_actions/actions/checkout-4</li> <li><a href="https://github.com/docker/build-push-action/commit/ce51e905a661fc760fece3d76496f92e48beb8df"><code>ce51e90</code></a> chore(deps): Bump actions/checkout from 3 to 4</li> <li><a href="https://github.com/docker/build-push-action/commit/1fde16337d494a70a6a0d6c3f24486b201a6a873"><code>1fde163</code></a> Merge pull request <a href="https://redirect.github.com/docker/build-push-action/issues/950">#950</a> from crazy-max/fix-ci</li> <li><a href="https://github.com/docker/build-push-action/commit/ae311c520f6e620595e7fcb93d4f61d6a5573b5e"><code>ae311c5</code></a> ci: fix workflow</li> <li><a href="https://github.com/docker/build-push-action/commit/9311bf5263ae5b36f3ec67aff768790c6e2344ad"><code>9311bf5</code></a> Merge pull request <a href="https://redirect.github.com/docker/build-push-action/issues/932">#932</a> from crazy-max/form-templates</li> <li>Additional commits viewable in <a href="https://github.com/docker/build-push-action/compare/2eb1c1961a95fc15694676618e422e8ba1d63825...0a97817b6ade9f46837855d676c4cca3a2471fc9">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/psf/black: 23.7.0 → 23.9.1](psf/black@23.7.0...23.9.1) - [github.com/astral-sh/ruff-pre-commit: v0.0.287 → v0.0.288](astral-sh/ruff-pre-commit@v0.0.287...v0.0.288) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/actions/checkout/releases">actions/checkout's releases</a>.</em></p> <blockquote> <h2>v4.0.0</h2> <h2>What's Changed</h2> <ul> <li>Update default runtime to node20 by <a href="https://github.com/takost"><code>@takost</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1436">actions/checkout#1436</a></li> <li>Support fetching without the --progress option by <a href="https://github.com/simonbaird"><code>@simonbaird</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1067">actions/checkout#1067</a></li> <li>Release 4.0.0 by <a href="https://github.com/takost"><code>@takost</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1447">actions/checkout#1447</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/takost"><code>@takost</code></a> made their first contribution in <a href="https://redirect.github.com/actions/checkout/pull/1436">actions/checkout#1436</a></li> <li><a href="https://github.com/simonbaird"><code>@simonbaird</code></a> made their first contribution in <a href="https://redirect.github.com/actions/checkout/pull/1067">actions/checkout#1067</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/checkout/compare/v3...v4.0.0">https://github.com/actions/checkout/compare/v3...v4.0.0</a></p> <h2>v3.6.0</h2> <h2>What's Changed</h2> <ul> <li>Mark test scripts with Bash'isms to be run via Bash by <a href="https://github.com/dscho"><code>@dscho</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1377">actions/checkout#1377</a></li> <li>Add option to fetch tags even if fetch-depth > 0 by <a href="https://github.com/RobertWieczoreck"><code>@RobertWieczoreck</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/579">actions/checkout#579</a></li> <li>Release 3.6.0 by <a href="https://github.com/luketomlinson"><code>@luketomlinson</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1437">actions/checkout#1437</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/RobertWieczoreck"><code>@RobertWieczoreck</code></a> made their first contribution in <a href="https://redirect.github.com/actions/checkout/pull/579">actions/checkout#579</a></li> <li><a href="https://github.com/luketomlinson"><code>@luketomlinson</code></a> made their first contribution in <a href="https://redirect.github.com/actions/checkout/pull/1437">actions/checkout#1437</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/checkout/compare/v3.5.3...v3.6.0">https://github.com/actions/checkout/compare/v3.5.3...v3.6.0</a></p> <h2>v3.5.3</h2> <h2>What's Changed</h2> <ul> <li>Fix: Checkout Issue in self hosted runner due to faulty submodule check-ins by <a href="https://github.com/megamanics"><code>@megamanics</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1196">actions/checkout#1196</a></li> <li>Fix typos found by codespell by <a href="https://github.com/DimitriPapadopoulos"><code>@DimitriPapadopoulos</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1287">actions/checkout#1287</a></li> <li>Add support for sparse checkouts by <a href="https://github.com/dscho"><code>@dscho</code></a> and <a href="https://github.com/dfdez"><code>@dfdez</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1369">actions/checkout#1369</a></li> <li>Release v3.5.3 by <a href="https://github.com/TingluoHuang"><code>@TingluoHuang</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1376">actions/checkout#1376</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/megamanics"><code>@megamanics</code></a> made their first contribution in <a href="https://redirect.github.com/actions/checkout/pull/1196">actions/checkout#1196</a></li> <li><a href="https://github.com/DimitriPapadopoulos"><code>@DimitriPapadopoulos</code></a> made their first contribution in <a href="https://redirect.github.com/actions/checkout/pull/1287">actions/checkout#1287</a></li> <li><a href="https://github.com/dfdez"><code>@dfdez</code></a> made their first contribution in <a href="https://redirect.github.com/actions/checkout/pull/1369">actions/checkout#1369</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/checkout/compare/v3...v3.5.3">https://github.com/actions/checkout/compare/v3...v3.5.3</a></p> <h2>v3.5.2</h2> <h2>What's Changed</h2> <ul> <li>Fix: Use correct API url / endpoint in GHES by <a href="https://github.com/fhammerl"><code>@fhammerl</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1289">actions/checkout#1289</a> based on <a href="https://redirect.github.com/actions/checkout/issues/1286">#1286</a> by <a href="https://github.com/1newsr"><code>@1newsr</code></a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/checkout/compare/v3.5.1...v3.5.2">https://github.com/actions/checkout/compare/v3.5.1...v3.5.2</a></p> <h2>v3.5.1</h2> <h2>What's Changed</h2> <ul> <li>Improve checkout performance on Windows runners by upgrading <code>@actions/github</code> dependency by <a href="https://github.com/BrettDong"><code>@BrettDong</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1246">actions/checkout#1246</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/BrettDong"><code>@BrettDong</code></a> made their first contribution in <a href="https://redirect.github.com/actions/checkout/pull/1246">actions/checkout#1246</a></li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/actions/checkout/blob/main/CHANGELOG.md">actions/checkout's changelog</a>.</em></p> <blockquote> <h1>Changelog</h1> <h2>v4.0.0</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1067">Support fetching without the --progress option</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1436">Update to node20</a></li> </ul> <h2>v3.6.0</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1377">Fix: Mark test scripts with Bash'isms to be run via Bash</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/579">Add option to fetch tags even if fetch-depth > 0</a></li> </ul> <h2>v3.5.3</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1196">Fix: Checkout fail in self-hosted runners when faulty submodule are checked-in</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1287">Fix typos found by codespell</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1369">Add support for sparse checkouts</a></li> </ul> <h2>v3.5.2</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1289">Fix api endpoint for GHES</a></li> </ul> <h2>v3.5.1</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1246">Fix slow checkout on Windows</a></li> </ul> <h2>v3.5.0</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1237">Add new public key for known_hosts</a></li> </ul> <h2>v3.4.0</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1209">Upgrade codeql actions to v2</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1210">Upgrade dependencies</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1225">Upgrade <code>@actions/io</code></a></li> </ul> <h2>v3.3.0</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1045">Implement branch list using callbacks from exec function</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1050">Add in explicit reference to private checkout options</a></li> <li>[Fix comment typos (that got added in <a href="https://redirect.github.com/actions/checkout/issues/770">#770</a>)](<a href="https://redirect.github.com/actions/checkout/pull/1057">actions/checkout#1057</a>)</li> </ul> <h2>v3.2.0</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/942">Add GitHub Action to perform release</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/967">Fix status badge</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1002">Replace datadog/squid with ubuntu/squid Docker image</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/964">Wrap pipeline commands for submoduleForeach in quotes</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1029">Update <code>@actions/io</code> to 1.1.2</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1039">Upgrading version to 3.2.0</a></li> </ul> <h2>v3.1.0</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/939">Use <code>@actions/core</code> <code>saveState</code> and <code>getState</code></a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/922">Add <code>github-server-url</code> input</a></li> </ul> <h2>v3.0.2</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/770">Add input <code>set-safe-directory</code></a></li> </ul> <h2>v3.0.1</h2> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/actions/checkout/commit/3df4ab11eba7bda6032a0b82a6bb43b11571feac"><code>3df4ab1</code></a> Release 4.0.0 (<a href="https://redirect.github.com/actions/checkout/issues/1447">#1447</a>)</li> <li><a href="https://github.com/actions/checkout/commit/8b5e8b768746b50394015010d25e690bfab9dfbc"><code>8b5e8b7</code></a> Support fetching without the --progress option (<a href="https://redirect.github.com/actions/checkout/issues/1067">#1067</a>)</li> <li><a href="https://github.com/actions/checkout/commit/97a652b80035363df47baee5031ec8670b8878ac"><code>97a652b</code></a> Update default runtime to node20 (<a href="https://redirect.github.com/actions/checkout/issues/1436">#1436</a>)</li> <li>See full diff in <a href="https://github.com/actions/checkout/compare/v3...v4">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. 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`tostring` has been deprecated. See https://numpy.org/devdocs/reference/generated/numpy.ndarray.tostring.html Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
`tf.accumulate_n` has been deprecated, and from the source code, I see that `tf.accumulate_n` is just a wrapper of `tf.add_n` since TF 2.1 (tensorflow/tensorflow@292d309). See: https://www.tensorflow.org/api_docs/python/tf/math/accumulate_n https://www.tensorflow.org/api_docs/python/tf/math/add_n Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
…eepmodeling#2816) `tf.test.TestCase.test_session` is deprecated in TF 1.11. We used it when we still tested TF 1.8, and now it is ok to replace it.
One should set the variable do_compute in pair_deepmd.cpp false by default, so that fparam can be used correctly. The current version will trigger the error https://github.com/deepmodeling/deepmd-kit/blob/7da9aaf075e8dea1eca9a08f99f3917235b55e3b/source/lmp/pair_deepmd.cpp#L1044-L1046 unexpectedly.
This PR speeds up multiple GitHub Actions in the following way: - only install `cuda-nvcc` and `cuda-cudart-dev` instead of the whole cudatoolkit - skip installing clang as it's already shipped with the GitHub Action image - enable cache for all `setup-python` - use Ninja instead of Make as the CMake generator --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Fix grammatical errors in the document.
1. use `black-pre-commit-mirror` instead of `black` which is faster; 2. first ruff and then black; 3. remove `tool.ruff.target-version` which can be detected automatically; 4. add `RUF` and `NPY` rules to `tool.ruff.select`; 5. set `tool.ruff.pydocstyle.convention` to `numpy`, which can automatically add several rules to `ignore`. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Merge `source/lib/src/cuda` and `source/lib/src/rocm` into `source/lib/src/gpu`. - Define macros `gpuGetLastError`, `gpuDeviceSynchronize`, `gpuMemcpy`, `gpuMemcpyDeviceToHost`, `gpuMemcpyHostToDevice`, and `gpuMemset` to make them available for both CUDA and ROCm. - Use `<<< >>> syntax` for both CUDA and ROCm. Per ROCm/hip@cf78d85, it has been supported in HIP since 2018. - Fix several int const numbers that should be double or float. - For tabulate: - Fix `WARP_SIZE` for ROCm. Per pytorch/pytorch#64302, WARP_SIZE can be 32 or 64, so it should not be hardcoded to 64. - Add `GpuShuffleSync`. Per ROCm/hip#1491, `__shfl_sync` is not supported by HIP. - After merging the code, deepmodeling#1274 should also work for ROCm. - Use the same `ii` for deepmodeling#830 and deepmodeling#2357. Although both of them work, `ii` has different meanings in these two PRs, but now it should be the same. - However, `ii` in `tabulate_fusion_se_a_fifth_order_polynomial` (rocm) added by deepmodeling#2532 is wrong. After merging the codes, it should be corrected. - Optimization in deepmodeling#830 was not applied to ROCm. - `__syncwarp` is not supported by ROCm. - After merging the code, deepmodeling#2661 will be applied to ROCm. Although TF ROCm stream is still blocking (https://github.com/tensorflow/tensorflow/blob/9d1262082e761cd85d6726bcbdfdef331d6d72c6/tensorflow/compiler/xla/stream_executor/rocm/rocm_driver.cc#L566), we don't know whether it will change to non-blocking. - There are several other differences between CUDA and ROCm. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Fix deepmodeling#2852. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Update this section to reflect the latest state. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
When setting the `INSTALL_TENSORFLOW` variable, previously CMake calls conda to install tensorflow. Now we use pip to install it. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Use modern `HIP` language instead of `hip_add_library`. Use modern `find_package` to find `hip` and `hipcub` instead of `FindROCM.cmake` (which is removed in this PR). --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Fix deepmodeling#2472. The previous implementation tried to allocate a (N, N) array and the RMSE result was actually MAE instead. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Signed-off-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com> Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…oad only once (deepmodeling#2864) fix deepmodeling#2862 Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.15 to 2.16. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/releases">pypa/cibuildwheel's releases</a>.</em></p> <blockquote> <h2>v2.16.0</h2> <ul> <li>✨ Add the ability to pass additional flags to a build frontend through the <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#build-frontend">CIBW_BUILD_FRONTEND</a> option (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1588">#1588</a>).</li> <li>✨ The environment variable SOURCE_DATE_EPOCH is now automatically passed through to container Linux builds (useful for <a href="https://reproducible-builds.org/docs/source-date-epoch/">reproducible builds</a>!) (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1589">#1589</a>)</li> <li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0rc2 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1604">#1604</a>)</li> <li>🐛 Fix <code>requires_python</code> auto-detection from setup.py when the call to <code>setup()</code> is within an <code>if __name__ == "__main__"</code> block (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1613">#1613</a>)</li> <li>🐛 Fix a bug that prevented building Linux wheels in Docker on a Windows host (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1573">#1573</a>)</li> <li>🐛 <code>--only</code> can now select prerelease-pythons (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1564">#1564</a>)</li> <li>📚 Docs & examples updates (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1582">#1582</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1593">#1593</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1598">#1598</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1615">#1615</a>)</li> </ul> </blockquote> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md">pypa/cibuildwheel's changelog</a>.</em></p> <blockquote> <hr /> <h2>title: Changelog</h2> <h1>Changelog</h1> <h3>v2.16.0</h3> <p><em>18 September 2023</em></p> <ul> <li>✨ Add the ability to pass additional flags to a build frontend through the <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#build-frontend">CIBW_BUILD_FRONTEND</a> option (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1588">#1588</a>).</li> <li>✨ The environment variable SOURCE_DATE_EPOCH is now automatically passed through to container Linux builds (useful for <a href="https://reproducible-builds.org/docs/source-date-epoch/">reproducible builds</a>!) (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1589">#1589</a>)</li> <li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0rc2 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1604">#1604</a>)</li> <li>🐛 Fix <code>requires_python</code> auto-detection from setup.py when the call to <code>setup()</code> is within an `if <strong>name</strong> == "<strong>main</strong>" block (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1613">#1613</a>)</li> <li>🐛 Fix a bug that prevented building Linux wheels in Docker on a Windows host (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1573">#1573</a>)</li> <li>🐛 <code>--only</code> can now select prerelease-pythons (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1564">#1564</a>)</li> <li>📚 Docs & examples updates (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1582">#1582</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1593">#1593</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1598">#1598</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1615">#1615</a>)</li> </ul> <h3>v2.15.0</h3> <p><em>8 August 2023</em></p> <ul> <li>🌟 CPython 3.12 wheels are now built by default - without the CIBW_PRERELEASE_PYTHONS flag. It's time to build and upload these wheels to PyPI! This release includes CPython 3.12.0rc1, which is guaranteed to be ABI compatible with the final release. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1565">#1565</a>)</li> <li>✨ Adds musllinux_1_2 support - this allows packagers to build for musl-based Linux distributions on a more recent Alpine image, and a newer musl libc. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1561">#1561</a>)</li> </ul> <h3>v2.14.1</h3> <p><em>15 July 2023</em></p> <ul> <li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0b4 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1550">#1550</a>)</li> </ul> <h3>v2.14.0</h3> <p><em>10 July 2023</em></p> <ul> <li>✨ Adds support for building PyPy 3.10 wheels. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1525">#1525</a>)</li> <li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0b3.</li> <li>✨ Allow the use of the <code>{wheel}</code> placeholder in CIBW_TEST_COMMAND (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1533">#1533</a>)</li> <li>📚 Docs & examples updates (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1532">#1532</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1416">#1416</a>)</li> <li>⚠️ Removed support for running cibuildwheel in Python 3.7. Python 3.7 is EOL. However, cibuildwheel continues to build Python 3.7 wheels for the moment. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1175">#1175</a>)</li> </ul> <h3>v2.13.1</h3> <p><em>10 June 2023</em></p> <ul> <li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0b2. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1516">#1516</a>)</li> <li>🛠 Adds a moving <code>v<major>.<minor></code> tag for use in GitHub Actions workflow files. If you use this, you'll get the latest patch release within a minor version. Additionally, Dependabot won't send you PRs for patch releases. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1517">#1517</a>)</li> </ul> <h3>v2.13.0</h3> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pypa/cibuildwheel/commit/a873dd9cbf9e3c4c73a1fd11ac31cf835f6eb502"><code>a873dd9</code></a> Bump version: v2.16.0</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/e8ba0d49edd2845a1a46395921609f1b7a194bbf"><code>e8ba0d4</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1615">#1615</a> from pypa/dependabot/github_actions/docker/setup-qem...</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/f0feaffbaabd508d48bb83b5d46b83cac7107181"><code>f0feaff</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1613">#1613</a> from henryiii/henryiii/fix/mainif</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/80a54b0226a8a4cc643bc24a968570871dd84364"><code>80a54b0</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1589">#1589</a> from dalcinl/source_date_epoch</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/76dba0b9ba3b5143ff833d8414b023ecf2ce8a90"><code>76dba0b</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1588">#1588</a> from pypa/frontend-flags</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/0954ffaa6586fffcdc720ab2b788ec1abcdf3481"><code>0954ffa</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1618">#1618</a> from pypa/rtd-update</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/753cbd1ca526543d317f0678fb5bc16018ed5ee9"><code>753cbd1</code></a> Update RtD config to include mandatory build.os option</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/825d89818ab1c7ca0bb9b9781b0b9beb74925b6d"><code>825d898</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1614">#1614</a> from henryiii/henryiii/chore/minor</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/f5e60d647fe700ba6e357c30376e8a48f91e5974"><code>f5e60d6</code></a> fix: include examples too</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/adc991c47b1cb56b6de3bb052686f8081791b21b"><code>adc991c</code></a> [Bot] Update dependencies (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1604">#1604</a>)</li> <li>Additional commits viewable in <a href="https://github.com/pypa/cibuildwheel/compare/v2.15...v2.16">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. 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<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.290 → v0.0.291](astral-sh/ruff-pre-commit@v0.0.290...v0.0.291) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Many people suggest not using `git submodule`. CMake FetchContent might be a better option (which we have used for googletest and lammps). (only take effect for CUDA 10; CUDA 11 contains cub) Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
njzjz
approved these changes
Sep 27, 2023
Codecov ReportAttention:
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Files 242 242
Lines 25641 24424 -1217
Branches 1517 1580 +63
==========================================
- Hits 20193 18404 -1789
- Misses 5058 5089 +31
- Partials 390 931 +541
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