From e84a524a9483544f3c1dff6a2777e279c1f8fadf Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 2 Sep 2024 20:50:49 +0000 Subject: [PATCH 01/18] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.2...v0.6.3) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ead5764..1d000a9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.2 + rev: v0.6.3 hooks: - id: ruff name: ruff lint From 8c27366e9166796da9abe9104d1804e979579f66 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 9 Sep 2024 20:57:20 +0000 Subject: [PATCH 02/18] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.3 → v0.6.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.3...v0.6.4) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 1d000a9..98d5784 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.3 + rev: v0.6.4 hooks: - id: ruff name: ruff lint From cac335180fa45ae4f0cc28d5a2cbda5360bd0661 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 16 Sep 2024 20:54:50 +0000 Subject: [PATCH 03/18] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.4 → v0.6.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.4...v0.6.5) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 98d5784..23157dd 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.4 + rev: v0.6.5 hooks: - id: ruff name: ruff lint From 4e4a56e633adc64cfbe60e3345529bc440615127 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 23 Sep 2024 20:57:23 +0000 Subject: [PATCH 04/18] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.5 → v0.6.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.5...v0.6.7) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 23157dd..5a9400f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.5 + rev: v0.6.7 hooks: - id: ruff name: ruff lint From 52769675fceba88335a0b65b141ee4b71f136d7b Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 30 Sep 2024 21:10:53 +0000 Subject: [PATCH 05/18] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.7 → v0.6.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.7...v0.6.8) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5a9400f..34c7408 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.7 + rev: v0.6.8 hooks: - id: ruff name: ruff lint From fb6f1ad2287769bc6ba7a87bda5c37fa5d9a58c5 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 2 Oct 2024 03:51:39 +0000 Subject: [PATCH 06/18] Bump executorlib from 0.0.2 to 0.0.3 Bumps [executorlib](https://github.com/pyiron/executorlib) from 0.0.2 to 0.0.3. - [Release notes](https://github.com/pyiron/executorlib/releases) - [Commits](https://github.com/pyiron/executorlib/compare/executorlib-0.0.2...executorlib-0.0.3) --- updated-dependencies: - dependency-name: executorlib dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index cc33f41..693d136 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,7 @@ classifiers = [ ] dependencies = [ "mpi4py==4.0.0", - "executorlib==0.0.2", + "executorlib==0.0.3", "numpy==1.26.4", ] dynamic = ["version"] From a72891d7abe7a6f0ad9174db7365da21ee28682a Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 2 Oct 2024 03:51:59 +0000 Subject: [PATCH 07/18] [dependabot skip] Update environment --- .ci_support/environment-mpich.yml | 2 +- .ci_support/environment-openmpi.yml | 2 +- binder/environment.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.ci_support/environment-mpich.yml b/.ci_support/environment-mpich.yml index 8c6cb28..2875f21 100644 --- a/.ci_support/environment-mpich.yml +++ b/.ci_support/environment-mpich.yml @@ -6,6 +6,6 @@ dependencies: - mpich =4.2.2 - numpy =1.26.4 - mpi4py =4.0.0 -- executorlib =0.0.2 +- executorlib =0.0.3 - ase =3.23.0 - scipy =1.14.1 diff --git a/.ci_support/environment-openmpi.yml b/.ci_support/environment-openmpi.yml index 1925c12..06b4885 100644 --- a/.ci_support/environment-openmpi.yml +++ b/.ci_support/environment-openmpi.yml @@ -6,6 +6,6 @@ dependencies: - openmpi =5.0.5 - numpy =1.26.4 - mpi4py =4.0.0 -- executorlib =0.0.2 +- executorlib =0.0.3 - ase =3.23.0 - scipy =1.14.1 diff --git a/binder/environment.yml b/binder/environment.yml index c5896b5..64b7cf1 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -5,6 +5,6 @@ dependencies: - numpy =1.26.4 - lammps =2024.06.27 - mpi4py =4.0.0 -- executorlib =0.0.2 +- executorlib =0.0.3 - ase =3.23.0 - scipy =1.14.1 From 5ca148c5d3ac4d4083b119b9a7e8e8d0d76131e8 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Wed, 2 Oct 2024 06:06:20 +0200 Subject: [PATCH 08/18] Switch to MPIExecSpawner --- pylammpsmpi/wrapper/concurrent.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pylammpsmpi/wrapper/concurrent.py b/pylammpsmpi/wrapper/concurrent.py index 405ed81..08bb3ce 100644 --- a/pylammpsmpi/wrapper/concurrent.py +++ b/pylammpsmpi/wrapper/concurrent.py @@ -9,7 +9,7 @@ from typing import Any, List, Optional from executorlib.shared import ( - MpiExecInterface, + MpiExecSpawner, RaisingThread, cancel_items_in_queue, interface_bootup, @@ -55,7 +55,7 @@ def execute_async( cmds.extend(cmdargs) interface = interface_bootup( command_lst=cmds, - connections=MpiExecInterface( + connections=MpiExecSpawner( cwd=cwd, cores=cores, oversubscribe=oversubscribe, From 0d2d248fc874eb282b869d5d5ca268da22053016 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Wed, 2 Oct 2024 06:06:59 +0200 Subject: [PATCH 09/18] update old environment --- .ci_support/environment-old.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-old.yml b/.ci_support/environment-old.yml index f2f6145..11ab944 100644 --- a/.ci_support/environment-old.yml +++ b/.ci_support/environment-old.yml @@ -5,6 +5,6 @@ dependencies: - openmpi - numpy =1.23.5 - mpi4py =3.1.4 -- executorlib =0.0.1 +- executorlib =0.0.3 - ase =3.23.0 - scipy =1.9.3 From 19034d32bc919d6d0d6cb09bad137259113e186e Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Wed, 2 Oct 2024 06:21:54 +0200 Subject: [PATCH 10/18] fix --- pylammpsmpi/wrapper/concurrent.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pylammpsmpi/wrapper/concurrent.py b/pylammpsmpi/wrapper/concurrent.py index 08bb3ce..7cecb2e 100644 --- a/pylammpsmpi/wrapper/concurrent.py +++ b/pylammpsmpi/wrapper/concurrent.py @@ -58,7 +58,7 @@ def execute_async( connections=MpiExecSpawner( cwd=cwd, cores=cores, - oversubscribe=oversubscribe, + openmpi_oversubscribe=oversubscribe, ), ) while True: From 363c581de52a31406c2636ef8d284ec0538daf65 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 7 Oct 2024 22:16:16 +0000 Subject: [PATCH 11/18] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.8 → v0.6.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.8...v0.6.9) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 34c7408..697edb3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.8 + rev: v0.6.9 hooks: - id: ruff name: ruff lint From e9ffb245d9f3b1db3783a65af48efb593fcd581b Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 14 Oct 2024 06:42:15 +0200 Subject: [PATCH 12/18] Update environment-mpich.yml --- .ci_support/environment-mpich.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-mpich.yml b/.ci_support/environment-mpich.yml index 2875f21..7d1897b 100644 --- a/.ci_support/environment-mpich.yml +++ b/.ci_support/environment-mpich.yml @@ -3,7 +3,7 @@ channels: dependencies: - coverage - lammps =2024.06.27=*_mpi_mpich_* -- mpich =4.2.2 +- mpich =4.2.3 - numpy =1.26.4 - mpi4py =4.0.0 - executorlib =0.0.3 From 4eb18197a0aefe34d19fa5351f4e63769a5263e7 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 14 Oct 2024 04:46:35 +0000 Subject: [PATCH 13/18] Bump mpi4py from 4.0.0 to 4.0.1 Bumps [mpi4py](https://github.com/mpi4py/mpi4py) from 4.0.0 to 4.0.1. - [Release notes](https://github.com/mpi4py/mpi4py/releases) - [Changelog](https://github.com/mpi4py/mpi4py/blob/master/CHANGES.rst) - [Commits](https://github.com/mpi4py/mpi4py/compare/4.0.0...4.0.1) --- updated-dependencies: - dependency-name: mpi4py dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 693d136..f1ffdd9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,7 +24,7 @@ classifiers = [ "Programming Language :: Python :: 3.12", ] dependencies = [ - "mpi4py==4.0.0", + "mpi4py==4.0.1", "executorlib==0.0.3", "numpy==1.26.4", ] From 0fa5a7c19047c2b940d95773ed5b94f72059a05d Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 14 Oct 2024 04:46:48 +0000 Subject: [PATCH 14/18] [dependabot skip] Update environment --- .ci_support/environment-mpich.yml | 2 +- .ci_support/environment-openmpi.yml | 2 +- binder/environment.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.ci_support/environment-mpich.yml b/.ci_support/environment-mpich.yml index 7d1897b..b9d36a6 100644 --- a/.ci_support/environment-mpich.yml +++ b/.ci_support/environment-mpich.yml @@ -5,7 +5,7 @@ dependencies: - lammps =2024.06.27=*_mpi_mpich_* - mpich =4.2.3 - numpy =1.26.4 -- mpi4py =4.0.0 +- mpi4py =4.0.1 - executorlib =0.0.3 - ase =3.23.0 - scipy =1.14.1 diff --git a/.ci_support/environment-openmpi.yml b/.ci_support/environment-openmpi.yml index 06b4885..abca03f 100644 --- a/.ci_support/environment-openmpi.yml +++ b/.ci_support/environment-openmpi.yml @@ -5,7 +5,7 @@ dependencies: - lammps =2024.06.27=*_mpi_openmpi_* - openmpi =5.0.5 - numpy =1.26.4 -- mpi4py =4.0.0 +- mpi4py =4.0.1 - executorlib =0.0.3 - ase =3.23.0 - scipy =1.14.1 diff --git a/binder/environment.yml b/binder/environment.yml index 64b7cf1..262a7cd 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -4,7 +4,7 @@ dependencies: - openmpi - numpy =1.26.4 - lammps =2024.06.27 -- mpi4py =4.0.0 +- mpi4py =4.0.1 - executorlib =0.0.3 - ase =3.23.0 - scipy =1.14.1 From 4a53b92df028dd9536be480527d08efb97675407 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 15 Oct 2024 03:17:59 +0000 Subject: [PATCH 15/18] Bump executorlib from 0.0.3 to 0.0.4 Bumps [executorlib](https://github.com/pyiron/executorlib) from 0.0.3 to 0.0.4. - [Release notes](https://github.com/pyiron/executorlib/releases) - [Commits](https://github.com/pyiron/executorlib/compare/executorlib-0.0.3...executorlib-0.0.4) --- updated-dependencies: - dependency-name: executorlib dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index f1ffdd9..5c4f6ba 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,7 @@ classifiers = [ ] dependencies = [ "mpi4py==4.0.1", - "executorlib==0.0.3", + "executorlib==0.0.4", "numpy==1.26.4", ] dynamic = ["version"] From e1b49f2d64348f6a796680553ce585f8b4e5c620 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 15 Oct 2024 03:18:13 +0000 Subject: [PATCH 16/18] [dependabot skip] Update environment --- .ci_support/environment-mpich.yml | 2 +- .ci_support/environment-openmpi.yml | 2 +- binder/environment.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.ci_support/environment-mpich.yml b/.ci_support/environment-mpich.yml index b9d36a6..e8c61cb 100644 --- a/.ci_support/environment-mpich.yml +++ b/.ci_support/environment-mpich.yml @@ -6,6 +6,6 @@ dependencies: - mpich =4.2.3 - numpy =1.26.4 - mpi4py =4.0.1 -- executorlib =0.0.3 +- executorlib =0.0.4 - ase =3.23.0 - scipy =1.14.1 diff --git a/.ci_support/environment-openmpi.yml b/.ci_support/environment-openmpi.yml index abca03f..ef1990e 100644 --- a/.ci_support/environment-openmpi.yml +++ b/.ci_support/environment-openmpi.yml @@ -6,6 +6,6 @@ dependencies: - openmpi =5.0.5 - numpy =1.26.4 - mpi4py =4.0.1 -- executorlib =0.0.3 +- executorlib =0.0.4 - ase =3.23.0 - scipy =1.14.1 diff --git a/binder/environment.yml b/binder/environment.yml index 262a7cd..ae1984c 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -5,6 +5,6 @@ dependencies: - numpy =1.26.4 - lammps =2024.06.27 - mpi4py =4.0.1 -- executorlib =0.0.3 +- executorlib =0.0.4 - ase =3.23.0 - scipy =1.14.1 From 1aa6a61ef188c958189c6ec48db5e23b434da609 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 21 Oct 2024 21:14:28 +0000 Subject: [PATCH 17/18] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.9 → v0.7.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.9...v0.7.0) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 697edb3..d7bc337 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.9 + rev: v0.7.0 hooks: - id: ruff name: ruff lint From 774f6932b810fc2a082391c9f16b569627656bf7 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 28 Oct 2024 21:31:27 +0000 Subject: [PATCH 18/18] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.7.0 → v0.7.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.7.0...v0.7.1) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d7bc337..f8d8dbf 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.7.0 + rev: v0.7.1 hooks: - id: ruff name: ruff lint