From f89045d1db0832d54d872376771e547dd731e6d0 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 13:22:46 +0100 Subject: [PATCH 01/77] Create MultiXscale:compile_lammps --- .github/workflows/MultiXscale:compile_lammps | 21 ++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 .github/workflows/MultiXscale:compile_lammps diff --git a/.github/workflows/MultiXscale:compile_lammps b/.github/workflows/MultiXscale:compile_lammps new file mode 100644 index 00000000000..0517ccec9e3 --- /dev/null +++ b/.github/workflows/MultiXscale:compile_lammps @@ -0,0 +1,21 @@ +name: MultiXscale-compile_lammps +run-name: Check new plugins of LAMMPS +on: + push: + paths: + - '.github/**' + - 'src/OBMD/**' + - 'examples/OBMD/**' +jobs: + Get-changed-files: + name: Get changed files + runs-on: ubuntu-latest + steps: + - uses: eessi/github-action-eessi@v3 + - name: set up EasyBuild + run: | + module load EasyBuild/4.9.4 + export EASYBUILD_SOURCEPATH=.github/easybuild/sources + export EASYBUILD_INSTALLPATH=.github/easybuild + export EASYBUILD_TRACE=1 + eb --show-config From 2de4707259e4b5b5155be63859a2aaccd22cc6d0 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 13:26:11 +0100 Subject: [PATCH 02/77] Update MultiXscale:compile_lammps --- .github/workflows/MultiXscale:compile_lammps | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/MultiXscale:compile_lammps b/.github/workflows/MultiXscale:compile_lammps index 0517ccec9e3..e4687884e2d 100644 --- a/.github/workflows/MultiXscale:compile_lammps +++ b/.github/workflows/MultiXscale:compile_lammps @@ -7,8 +7,7 @@ on: - 'src/OBMD/**' - 'examples/OBMD/**' jobs: - Get-changed-files: - name: Get changed files + build: runs-on: ubuntu-latest steps: - uses: eessi/github-action-eessi@v3 @@ -19,3 +18,4 @@ jobs: export EASYBUILD_INSTALLPATH=.github/easybuild export EASYBUILD_TRACE=1 eb --show-config + shell: bash From 0a1165c90670a07ba90565011cfb4fde8de56673 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 13:27:36 +0100 Subject: [PATCH 03/77] Update MultiXscale:compile_lammps --- .github/workflows/MultiXscale:compile_lammps | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps b/.github/workflows/MultiXscale:compile_lammps index e4687884e2d..5ae34f9aa44 100644 --- a/.github/workflows/MultiXscale:compile_lammps +++ b/.github/workflows/MultiXscale:compile_lammps @@ -1,5 +1,5 @@ name: MultiXscale-compile_lammps -run-name: Check new plugins of LAMMPS +run-name: Compile new Plugin OBMD on: push: paths: From a235b57d86482691e76bc1263de3fb7b826432a6 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 13:28:32 +0100 Subject: [PATCH 04/77] Update MultiXscale:compile_lammps --- .github/workflows/MultiXscale:compile_lammps | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/MultiXscale:compile_lammps b/.github/workflows/MultiXscale:compile_lammps index 5ae34f9aa44..fc6086b693d 100644 --- a/.github/workflows/MultiXscale:compile_lammps +++ b/.github/workflows/MultiXscale:compile_lammps @@ -10,12 +10,12 @@ jobs: build: runs-on: ubuntu-latest steps: - - uses: eessi/github-action-eessi@v3 - - name: set up EasyBuild - run: | - module load EasyBuild/4.9.4 - export EASYBUILD_SOURCEPATH=.github/easybuild/sources - export EASYBUILD_INSTALLPATH=.github/easybuild - export EASYBUILD_TRACE=1 - eb --show-config - shell: bash + - uses: eessi/github-action-eessi@v3 + - name: set up EasyBuild + run: | + module load EasyBuild/4.9.4 + export EASYBUILD_SOURCEPATH=.github/easybuild/sources + export EASYBUILD_INSTALLPATH=.github/easybuild + export EASYBUILD_TRACE=1 + eb --show-config + shell: bash From 678a954a4311723462b1dd60aa45c847aadd1116 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 13:29:47 +0100 Subject: [PATCH 05/77] Create MultiXscale:compile_lammps.yml --- .../workflows/MultiXscale:compile_lammps.yml | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 .github/workflows/MultiXscale:compile_lammps.yml diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml new file mode 100644 index 00000000000..fc6086b693d --- /dev/null +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -0,0 +1,21 @@ +name: MultiXscale-compile_lammps +run-name: Compile new Plugin OBMD +on: + push: + paths: + - '.github/**' + - 'src/OBMD/**' + - 'examples/OBMD/**' +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: eessi/github-action-eessi@v3 + - name: set up EasyBuild + run: | + module load EasyBuild/4.9.4 + export EASYBUILD_SOURCEPATH=.github/easybuild/sources + export EASYBUILD_INSTALLPATH=.github/easybuild + export EASYBUILD_TRACE=1 + eb --show-config + shell: bash From dc20da767aebad161a1338163c36a8b017466a58 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 13:36:34 +0100 Subject: [PATCH 06/77] Delete .github/workflows/MultiXscale:compile_lammps --- .github/workflows/MultiXscale:compile_lammps | 21 -------------------- 1 file changed, 21 deletions(-) delete mode 100644 .github/workflows/MultiXscale:compile_lammps diff --git a/.github/workflows/MultiXscale:compile_lammps b/.github/workflows/MultiXscale:compile_lammps deleted file mode 100644 index fc6086b693d..00000000000 --- a/.github/workflows/MultiXscale:compile_lammps +++ /dev/null @@ -1,21 +0,0 @@ -name: MultiXscale-compile_lammps -run-name: Compile new Plugin OBMD -on: - push: - paths: - - '.github/**' - - 'src/OBMD/**' - - 'examples/OBMD/**' -jobs: - build: - runs-on: ubuntu-latest - steps: - - uses: eessi/github-action-eessi@v3 - - name: set up EasyBuild - run: | - module load EasyBuild/4.9.4 - export EASYBUILD_SOURCEPATH=.github/easybuild/sources - export EASYBUILD_INSTALLPATH=.github/easybuild - export EASYBUILD_TRACE=1 - eb --show-config - shell: bash From 059bb0b0760a9b4aa2a2aa37de170533aa5d1baf Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 13:38:54 +0100 Subject: [PATCH 07/77] Add lammps config file --- .../LAMMPS_OBMD-foss-2023a-software-commit.eb | 113 ++++++++++++++++++ 1 file changed, 113 insertions(+) create mode 100644 .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb diff --git a/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb b/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb new file mode 100644 index 00000000000..bfd6bd4e4d0 --- /dev/null +++ b/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb @@ -0,0 +1,113 @@ +name = 'LAMMPS' +version = '%(software_commit)s' +versionsuffix = '-kokkos-dev_OBMD' + +homepage = 'https://www.lammps.org' +description = """LAMMPS is a classical molecular dynamics code, and an acronym +for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has +potentials for solid-state materials (metals, semiconductors) and soft matter +(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be +used to model atoms or, more generically, as a parallel particle simulator at +the atomic, meso, or continuum scale. LAMMPS runs on single processors or in +parallel using message-passing techniques and a spatial-decomposition of the +simulation domain. The code is designed to be easy to modify or extend with new +functionality. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True} + +# 'https://github.com/lammps/lammps/archive/' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = [ + 'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch', + 'LAMMPS-2Aug2023_lammps_obmd_package.patch', +] +checksums = [ +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('archspec', '0.2.1'), +] +dependencies = [ + ('Python', '3.11.3'), + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('netCDF', '4.9.2'), + ('GSL', '2.7'), + ('zlib', '1.2.13'), + ('gzip', '1.12'), + ('cURL', '8.0.1'), + ('HDF5', '1.14.0'), + ('PCRE', '8.45'), + ('libxml2', '2.11.4'), + ('FFmpeg', '6.0'), + ('Voro++', '0.4.6'), + ('kim-api', '2.3.0'), + ('Eigen', '3.4.0'), + ('PLUMED', '2.9.0'), + ('SciPy-bundle', '2023.07'), + # VTK package is auto-disabled if this dep is not available + ('VTK', '9.3.0'), + # We use a custom build of MDI + ('MDI', '1.4.26'), +] +if ARCH == 'x86_64': + # TBB and ScaFaCos are an optional dependency when building on Intel arch + dependencies += [ + ('tbb', '2021.11.0'), + ('ScaFaCoS', '1.0.4'), + ] + +# To use additional custom configuration options, use the 'configopts' easyconfig parameter +# See docs and lammps easyblock for more information. +# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options + +# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, +# which is claimed to be faster in pure MPI calculations +# configopts = "-DKokkos_ENABLE_SERIAL=yes " + + +# packages auto-enabled by easyblock +# 'GPU' - if cuda package is present and kokkos is disabled +# 'KOKKOS' - if kokkos is enabled (by default) +# 'INTEL' - if builing on Intel CPU +# 'OPENMP' - if OpenMP swithed on in 'toolchainopts' + +# include the following extra packages into the build +general_packages = [ + 'DPD-BASIC', + 'MOLECULE', + 'OBMD' +] + +# Excluded packages due to requiring additional (non-trivial) deps +# - ADIOS +# - LATTE +# - MESONT (requires very large files downloaded during build) +# - ML-HDNNP (requires N2P2) +# - ML-QUIP +# - MSCG +# - QMMM (setup seems complex) + +# remove example atm because MANYBODY is not enabled +# remove example colloid because COLLOID package is not enabled +# remove example dipole because DIPOLE package is not enabled +# remove example hugoniostat because EXTRA-PAIR package is not enabled +# removing example msst bacause SHOCK package is not enabled +# removing example pour because GRANULAR package is not enabled +# removing example voronoi beacuse VORONOI package is not enabled +#check_files = [ +# 'balance', 'crack', 'friction', 'indent', +# 'melt', 'min', 'nemd', 'obstacle', +#] + +sanity_check_test_inputs = [ + 'balance', 'crack', 'friction', 'indent', + 'melt', 'min', 'nemd', 'obstacle', +] + +moduleclass = 'chem' From fc1ceb8b97c1ae96a5c5cee8ebd2c993d71ed16d Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:07:38 +0100 Subject: [PATCH 08/77] Update LAMMPS_OBMD-foss-2023a-software-commit.eb --- .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb b/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb index bfd6bd4e4d0..4aff77e6a2c 100644 --- a/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb +++ b/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb @@ -18,11 +18,10 @@ toolchain = {'name': 'foss', 'version': '2023a'} toolchainopts = {'openmp': True, 'usempi': True} # 'https://github.com/lammps/lammps/archive/' -source_urls = [GITHUB_LOWER_SOURCE] +source_urls = ['https://github.com/laraPPr/lammps/archive'] sources = ['%(version)s.tar.gz'] patches = [ 'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch', - 'LAMMPS-2Aug2023_lammps_obmd_package.patch', ] checksums = [ ] From d051c2a2c36dbf4c3225ecfbac09cec0f948ffbe Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:09:12 +0100 Subject: [PATCH 09/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index fc6086b693d..4af3fae2f76 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -18,4 +18,5 @@ jobs: export EASYBUILD_INSTALLPATH=.github/easybuild export EASYBUILD_TRACE=1 eb --show-config + eb ./github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --commit 059bb0b0760a9b4aa2a2aa37de170533aa5d1baf -x shell: bash From 3378bf7363ce408f72d131dbd9e2bed383f18e29 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:13:55 +0100 Subject: [PATCH 10/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 4af3fae2f76..4aa03c3634d 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -18,5 +18,5 @@ jobs: export EASYBUILD_INSTALLPATH=.github/easybuild export EASYBUILD_TRACE=1 eb --show-config - eb ./github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --commit 059bb0b0760a9b4aa2a2aa37de170533aa5d1baf -x + eb ./github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${git_hash} -x shell: bash From 2c3b325aac6a2501f502380da7d86e79049ceccc Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:16:42 +0100 Subject: [PATCH 11/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 4aa03c3634d..d4af4578bee 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -18,5 +18,5 @@ jobs: export EASYBUILD_INSTALLPATH=.github/easybuild export EASYBUILD_TRACE=1 eb --show-config - eb ./github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${git_hash} -x + eb ./github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} -x shell: bash From 2f38dd089dd68f8ad71c967d128ca3a230349713 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:18:35 +0100 Subject: [PATCH 12/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index d4af4578bee..500618b407f 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -18,5 +18,5 @@ jobs: export EASYBUILD_INSTALLPATH=.github/easybuild export EASYBUILD_TRACE=1 eb --show-config - eb ./github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} -x + eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} -x shell: bash From 20552403c60953dc76689eab49d1c2bd385c81f2 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:21:51 +0100 Subject: [PATCH 13/77] Update MultiXscale:compile_lammps.yml From cb9f33ee05689736f287ddcc5882ab4ecb5b39b4 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:25:32 +0100 Subject: [PATCH 14/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 500618b407f..0d5c40764ef 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -18,5 +18,8 @@ jobs: export EASYBUILD_INSTALLPATH=.github/easybuild export EASYBUILD_TRACE=1 eb --show-config + - name: get easyconfig + echo $PWD + ls .github/workflows eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} -x shell: bash From a56a4aa1f72fb5abe72a348242efa4d960d4d81c Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:26:35 +0100 Subject: [PATCH 15/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 0d5c40764ef..589c15adfae 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -18,7 +18,9 @@ jobs: export EASYBUILD_INSTALLPATH=.github/easybuild export EASYBUILD_TRACE=1 eb --show-config - - name: get easyconfig + shell: bash + - name: | + get easyconfig echo $PWD ls .github/workflows eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} -x From d7262a8fe238b2ff178aaa717b7da01d9abbcf83 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:27:13 +0100 Subject: [PATCH 16/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 589c15adfae..ee78a025151 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -18,9 +18,6 @@ jobs: export EASYBUILD_INSTALLPATH=.github/easybuild export EASYBUILD_TRACE=1 eb --show-config - shell: bash - - name: | - get easyconfig echo $PWD ls .github/workflows eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} -x From f6476e5d0ca6b4b4b36f6f9fb2bdf15c191a2b56 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:30:29 +0100 Subject: [PATCH 17/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index ee78a025151..de0b6b6a1f2 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -18,7 +18,8 @@ jobs: export EASYBUILD_INSTALLPATH=.github/easybuild export EASYBUILD_TRACE=1 eb --show-config + - name: Get EasyConfig + run: | echo $PWD - ls .github/workflows + ls /home/runner/work/lammps/lammps/.github/workflows eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} -x - shell: bash From 2a1a3086a10e5d0ccffc838b5f71c4ae5bc17c9d Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:33:37 +0100 Subject: [PATCH 18/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index de0b6b6a1f2..0bad98cb831 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -21,5 +21,5 @@ jobs: - name: Get EasyConfig run: | echo $PWD - ls /home/runner/work/lammps/lammps/.github/workflows + ls -a /home/runner/work/lammps/lammps/ eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} -x From d1dbff9e94264ad467e101b29876ab4abd7cfc4f Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:38:23 +0100 Subject: [PATCH 19/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 0bad98cb831..532a1da3c34 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -14,12 +14,12 @@ jobs: - name: set up EasyBuild run: | module load EasyBuild/4.9.4 - export EASYBUILD_SOURCEPATH=.github/easybuild/sources - export EASYBUILD_INSTALLPATH=.github/easybuild + module load EESSI-extend/2023.06-easybuild export EASYBUILD_TRACE=1 eb --show-config - name: Get EasyConfig run: | echo $PWD - ls -a /home/runner/work/lammps/lammps/ - eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} -x + wget https://raw.githubusercontent.com/EESSI/dev.eessi.io-example/refs/heads/main/easyconfigs/LAMMPS_OBMD-foss-2023a-software-commit.eb + ls + eb LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} -x From 9f0fe5d0198fbc66a847935f446ce0ce33091718 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:42:48 +0100 Subject: [PATCH 20/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 532a1da3c34..e104b0443e5 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -17,9 +17,6 @@ jobs: module load EESSI-extend/2023.06-easybuild export EASYBUILD_TRACE=1 eb --show-config - - name: Get EasyConfig - run: | - echo $PWD + echo "Get EasyConfig" wget https://raw.githubusercontent.com/EESSI/dev.eessi.io-example/refs/heads/main/easyconfigs/LAMMPS_OBMD-foss-2023a-software-commit.eb - ls eb LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} -x From cdf07bdfd966525acf1fb8676ed300420e1348e0 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:47:01 +0100 Subject: [PATCH 21/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index e104b0443e5..37aa8acbb4d 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -19,4 +19,4 @@ jobs: eb --show-config echo "Get EasyConfig" wget https://raw.githubusercontent.com/EESSI/dev.eessi.io-example/refs/heads/main/easyconfigs/LAMMPS_OBMD-foss-2023a-software-commit.eb - eb LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} -x + eb LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 -x From b4cf939f21dc2fd764eb61c862c0045c4feef6e3 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:49:56 +0100 Subject: [PATCH 22/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 37aa8acbb4d..adea92918e8 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -19,4 +19,4 @@ jobs: eb --show-config echo "Get EasyConfig" wget https://raw.githubusercontent.com/EESSI/dev.eessi.io-example/refs/heads/main/easyconfigs/LAMMPS_OBMD-foss-2023a-software-commit.eb - eb LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 -x + eb LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 From 569ad4501f678b51efc8dad7295ecec75882dc78 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:58:01 +0100 Subject: [PATCH 23/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index adea92918e8..4a90912d8c2 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -18,5 +18,5 @@ jobs: export EASYBUILD_TRACE=1 eb --show-config echo "Get EasyConfig" - wget https://raw.githubusercontent.com/EESSI/dev.eessi.io-example/refs/heads/main/easyconfigs/LAMMPS_OBMD-foss-2023a-software-commit.eb + wget https://raw.githubusercontent.com/laraPPr/lammps/refs/heads/OBMD_compile_in_CI/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb eb LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 From 99b30ef59325b8d6acb0be8b709bf8c71f5c8bde Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 15:35:51 +0100 Subject: [PATCH 24/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 4a90912d8c2..33a84bd4a73 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -20,3 +20,6 @@ jobs: echo "Get EasyConfig" wget https://raw.githubusercontent.com/laraPPr/lammps/refs/heads/OBMD_compile_in_CI/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb eb LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 + module avail LAMMPS + module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD + lmp -in /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/example/OBMD/in.OBMD From f7a0c073860da7b5a44aaa544f8ed2a6185b49fe Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 15:51:00 +0100 Subject: [PATCH 25/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 33a84bd4a73..4687d6c3def 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -22,4 +22,5 @@ jobs: eb LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD - lmp -in /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/example/OBMD/in.OBMD + ls /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS + lmp -in /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/*/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/example/OBMD/in.OBMD From c5e8808479b06b78a601c5e83770fd40df929a5a Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 16:15:18 +0100 Subject: [PATCH 26/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 4687d6c3def..7e27edffdd6 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -22,5 +22,5 @@ jobs: eb LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD - ls /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS + ls /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD lmp -in /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/*/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/example/OBMD/in.OBMD From 284e25f84fe24dac7a53fe9be4a04daf521479f0 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 16:26:31 +0100 Subject: [PATCH 27/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 7e27edffdd6..2a80460e03d 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -23,4 +23,4 @@ jobs: module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD ls /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD - lmp -in /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/*/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/example/OBMD/in.OBMD + lmp -in /home/runner/eessi/versions/2023.06/software/linux/x86_64/amdzen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/examples/OBMD/in.OBMD From 3a1b572dafcdf828a64d38b6369651d9d7a213a4 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 27 Jan 2025 16:38:13 +0100 Subject: [PATCH 28/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 2a80460e03d..6373ec4f7fa 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -23,4 +23,4 @@ jobs: module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD ls /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD - lmp -in /home/runner/eessi/versions/2023.06/software/linux/x86_64/amdzen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/examples/OBMD/in.OBMD + lmp -in /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/examples/OBMD/in.OBMD From 7ba78cc297b9d5108052c606044811e1d5877e46 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Wed, 29 Jan 2025 13:40:31 +0100 Subject: [PATCH 29/77] Update .github/workflows/MultiXscale:compile_lammps.yml Co-authored-by: ocaisa --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 6373ec4f7fa..91e1d995fe7 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -23,4 +23,4 @@ jobs: module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD ls /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD - lmp -in /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/examples/OBMD/in.OBMD + mpiexec -n 4 lmp -in /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/examples/OBMD/in.OBMD From 9fa88fee9448e39788580cf44858807aebf4be37 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Wed, 29 Jan 2025 13:57:25 +0100 Subject: [PATCH 30/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 91e1d995fe7..6806a1de4ae 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -23,4 +23,4 @@ jobs: module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD ls /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD - mpiexec -n 4 lmp -in /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/examples/OBMD/in.OBMD + mpirun -np 4 lmp -in /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/examples/OBMD/in.OBMD From d3883ce1cabdb2f9439cfb1cb5067fbee52913da Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Wed, 29 Jan 2025 14:17:11 +0100 Subject: [PATCH 31/77] source repo and oversubscribe --- .github/workflows/MultiXscale:compile_lammps.yml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 6806a1de4ae..432c2ec6708 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -8,19 +8,22 @@ on: - 'examples/OBMD/**' jobs: build: - runs-on: ubuntu-latest + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: + - ubuntu-24.04-arm + - ubuntu-24.04 steps: + - uses: actions/checkout@v4 - uses: eessi/github-action-eessi@v3 - name: set up EasyBuild run: | - module load EasyBuild/4.9.4 module load EESSI-extend/2023.06-easybuild - export EASYBUILD_TRACE=1 eb --show-config echo "Get EasyConfig" - wget https://raw.githubusercontent.com/laraPPr/lammps/refs/heads/OBMD_compile_in_CI/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb - eb LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 + eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD ls /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD - mpirun -np 4 lmp -in /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/examples/OBMD/in.OBMD + mpirun -np 4 --oversubscribe lmp -in /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/examples/OBMD/in.OBMD From ccd6dca372a40208c78d8c033478403e8da2f8f6 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Thu, 30 Jan 2025 13:40:01 +0100 Subject: [PATCH 32/77] make the easybuild log more verbose in stdout --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 432c2ec6708..add8bc4c7b2 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -22,7 +22,7 @@ jobs: module load EESSI-extend/2023.06-easybuild eb --show-config echo "Get EasyConfig" - eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 + eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 -d -l module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD ls /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD From 02a0e815aedc3b34973fbe15edc74d55abd86286 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Thu, 30 Jan 2025 15:13:12 +0100 Subject: [PATCH 33/77] use artifacts --- .github/workflows/MultiXscale:compile_lammps.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index add8bc4c7b2..fb25f069b9e 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -17,12 +17,13 @@ jobs: steps: - uses: actions/checkout@v4 - uses: eessi/github-action-eessi@v3 + - uses: actions/upload-artifact@v4 - name: set up EasyBuild run: | module load EESSI-extend/2023.06-easybuild eb --show-config echo "Get EasyConfig" - eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 -d -l + eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD ls /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD From 6d9351c6fb25b6cdcd21fc83305567458e7da427 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Thu, 30 Jan 2025 15:18:43 +0100 Subject: [PATCH 34/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index fb25f069b9e..65a18ec9a83 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -17,7 +17,7 @@ jobs: steps: - uses: actions/checkout@v4 - uses: eessi/github-action-eessi@v3 - - uses: actions/upload-artifact@v4 + - uses: actions/download-artifact@v4 - name: set up EasyBuild run: | module load EESSI-extend/2023.06-easybuild From 45b6b5d5e0bebc1a6deb0066f0e7364059e9ec11 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Thu, 30 Jan 2025 15:22:33 +0100 Subject: [PATCH 35/77] try to use download artifacts --- .github/workflows/MultiXscale:compile_lammps.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 65a18ec9a83..f7042fcfdd1 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -17,7 +17,6 @@ jobs: steps: - uses: actions/checkout@v4 - uses: eessi/github-action-eessi@v3 - - uses: actions/download-artifact@v4 - name: set up EasyBuild run: | module load EESSI-extend/2023.06-easybuild @@ -28,3 +27,5 @@ jobs: module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD ls /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD mpirun -np 4 --oversubscribe lmp -in /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/examples/OBMD/in.OBMD + - name: download artifact + uses: actions/download-artifact@v4 From e6c1655298f5ea88fc6701ec829b062d46692bdb Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Thu, 30 Jan 2025 15:55:17 +0100 Subject: [PATCH 36/77] add timestep patch to banlance example --- .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb b/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb index 4aff77e6a2c..82f4fcc2325 100644 --- a/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb +++ b/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb @@ -22,6 +22,7 @@ source_urls = ['https://github.com/laraPPr/lammps/archive'] sources = ['%(version)s.tar.gz'] patches = [ 'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch', + 'LAMMPS-2Aug2023_fix-timestep-balance-example.patch', ] checksums = [ ] From 8b967856296a764307dc27ac5efbb06e1526e3e2 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Thu, 30 Jan 2025 16:10:39 +0100 Subject: [PATCH 37/77] use $EESSI_SOFTWARE_SUBDIR --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index f7042fcfdd1..38896462097 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -26,6 +26,6 @@ jobs: module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD ls /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD - mpirun -np 4 --oversubscribe lmp -in /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/examples/OBMD/in.OBMD + mpirun -np 4 --oversubscribe lmp -in /home/runner/eessi/versions/2023.06/software/linux/$EESSI_SOFTWARE_SUBDIR/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/examples/OBMD/in.OBMD - name: download artifact uses: actions/download-artifact@v4 From fa6ebf51b866d4e13ac27c04ff0b6dae6d6f5329 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Thu, 30 Jan 2025 16:15:49 +0100 Subject: [PATCH 38/77] use $EBROOTLAMMPS --- .github/workflows/MultiXscale:compile_lammps.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 38896462097..f3d43940c23 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -25,7 +25,7 @@ jobs: eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD - ls /home/runner/eessi/versions/2023.06/software/linux/x86_64/amd/zen3/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD - mpirun -np 4 --oversubscribe lmp -in /home/runner/eessi/versions/2023.06/software/linux/$EESSI_SOFTWARE_SUBDIR/software/LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD/examples/OBMD/in.OBMD + ls $EBROOTLAMMPS + mpirun -np 4 --oversubscribe lmp -in $EBROOTLAMMPS/examples/OBMD/in.OBMD - name: download artifact uses: actions/download-artifact@v4 From a6c54eca38f840ac010e9232385128122a640def Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Thu, 30 Jan 2025 16:35:12 +0100 Subject: [PATCH 39/77] remove downloading artefacts because is skipped when the run fails Wanted to see if it was possible to get the easibuild logs when it fail but artefacts does not seem to be the tool to use in this case. --- .github/workflows/MultiXscale:compile_lammps.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index f3d43940c23..e9511926b61 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -27,5 +27,3 @@ jobs: module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD ls $EBROOTLAMMPS mpirun -np 4 --oversubscribe lmp -in $EBROOTLAMMPS/examples/OBMD/in.OBMD - - name: download artifact - uses: actions/download-artifact@v4 From 8114130665557fc0bc0ef7f6a951252c80b235fb Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Thu, 30 Jan 2025 16:47:45 +0100 Subject: [PATCH 40/77] Update .github/workflows/MultiXscale:compile_lammps.yml Co-authored-by: ocaisa --- .github/workflows/MultiXscale:compile_lammps.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index e9511926b61..4c5312c1c8b 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -25,5 +25,6 @@ jobs: eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD + echo $EBROOTLAMMPS ls $EBROOTLAMMPS mpirun -np 4 --oversubscribe lmp -in $EBROOTLAMMPS/examples/OBMD/in.OBMD From 02ade008796806ce9f7f22072a77f77c9b794dd7 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Thu, 30 Jan 2025 21:10:09 +0100 Subject: [PATCH 41/77] use new commit of easyblock --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 4c5312c1c8b..9723bd47129 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -22,7 +22,7 @@ jobs: module load EESSI-extend/2023.06-easybuild eb --show-config echo "Get EasyConfig" - eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 + eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 55dc794b03f5d75a9ab31bc41b960abe1605134a module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD echo $EBROOTLAMMPS From 0c66e85c3768a67ee9d1d0e8fb457ebe4b1865d0 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Thu, 30 Jan 2025 21:19:28 +0100 Subject: [PATCH 42/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 9723bd47129..0e0cfc2818d 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -22,7 +22,7 @@ jobs: module load EESSI-extend/2023.06-easybuild eb --show-config echo "Get EasyConfig" - eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 55dc794b03f5d75a9ab31bc41b960abe1605134a + eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 55dc794b03f5d75a9ab31bc41b960abe1605134a --include-easyblocks lammps.py module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD echo $EBROOTLAMMPS From 91139830c3638b1628edf204e36b755d7403b249 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Thu, 30 Jan 2025 21:22:15 +0100 Subject: [PATCH 43/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 0e0cfc2818d..ec231d73d31 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -22,7 +22,7 @@ jobs: module load EESSI-extend/2023.06-easybuild eb --show-config echo "Get EasyConfig" - eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 55dc794b03f5d75a9ab31bc41b960abe1605134a --include-easyblocks lammps.py + eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-pr 3485 module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD echo $EBROOTLAMMPS From 3005c84c547ba3788aae9b234ba33316f9f6a60b Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Thu, 30 Jan 2025 21:26:16 +0100 Subject: [PATCH 44/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index ec231d73d31..4c5312c1c8b 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -22,7 +22,7 @@ jobs: module load EESSI-extend/2023.06-easybuild eb --show-config echo "Get EasyConfig" - eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-pr 3485 + eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD echo $EBROOTLAMMPS From c547cfd5cd5ed686eb371649e773d2f4a867e4d3 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Fri, 31 Jan 2025 18:38:41 +0100 Subject: [PATCH 45/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 4c5312c1c8b..ce951c58268 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -22,7 +22,7 @@ jobs: module load EESSI-extend/2023.06-easybuild eb --show-config echo "Get EasyConfig" - eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3d295a926318468e3e8fdd99fdcfea02cd796403 + eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit ac72ee8cd3c98f1ddf470f8820279660f4845664 module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD echo $EBROOTLAMMPS From e0c3a2bf1df937855a329749050589502fa560b7 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 12:07:33 +0100 Subject: [PATCH 46/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index ce951c58268..ec3f133fd92 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -22,7 +22,7 @@ jobs: module load EESSI-extend/2023.06-easybuild eb --show-config echo "Get EasyConfig" - eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit ac72ee8cd3c98f1ddf470f8820279660f4845664 + eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3725813434972232adde2d84c882801fae629ddf module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD echo $EBROOTLAMMPS From c504cd90374ac0dc68ce65c048e537e3161aee0d Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 14:53:40 +0100 Subject: [PATCH 47/77] Create MultiXscale:generate_patch_file.yml --- .../MultiXscale:generate_patch_file.yml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 .github/workflows/MultiXscale:generate_patch_file.yml diff --git a/.github/workflows/MultiXscale:generate_patch_file.yml b/.github/workflows/MultiXscale:generate_patch_file.yml new file mode 100644 index 00000000000..22021e209a0 --- /dev/null +++ b/.github/workflows/MultiXscale:generate_patch_file.yml @@ -0,0 +1,18 @@ +name: MultiXscale-generate_lammps_patch +run-name: Generate a patch for the OBMD plugin +on: + push: + paths: + - '.github/**' + - 'src/OBMD/**' + - 'examples/OBMD/**' +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Generate patch file + run: | + pwd + git remote -v + ls src/OBMD From 22c0d4261301f0da9d1ba55e635679f80f6455ff Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 15:03:19 +0100 Subject: [PATCH 48/77] Update MultiXscale:generate_patch_file.yml --- .github/workflows/MultiXscale:generate_patch_file.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/.github/workflows/MultiXscale:generate_patch_file.yml b/.github/workflows/MultiXscale:generate_patch_file.yml index 22021e209a0..358c6e4a404 100644 --- a/.github/workflows/MultiXscale:generate_patch_file.yml +++ b/.github/workflows/MultiXscale:generate_patch_file.yml @@ -14,5 +14,15 @@ jobs: - name: Generate patch file run: | pwd + git remote add lammps git@github.com:lammps/lammps.git git remote -v + git branch ls src/OBMD + # This commit needs to be updated when developping on top of another commit of lammps! + git checkout 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 # upstream commit of lammps 2Aug2023_update2 + git branch + ls src/OBMD + git checkout ${{ github.sha }} # commit of this pr + ls src/OBMD + echo $HOME + From fe06b15066182682e05badd057fc6cd8943610c1 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 15:14:36 +0100 Subject: [PATCH 49/77] Update MultiXscale:generate_patch_file.yml --- .github/workflows/MultiXscale:generate_patch_file.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/MultiXscale:generate_patch_file.yml b/.github/workflows/MultiXscale:generate_patch_file.yml index 358c6e4a404..ef8de4830b1 100644 --- a/.github/workflows/MultiXscale:generate_patch_file.yml +++ b/.github/workflows/MultiXscale:generate_patch_file.yml @@ -19,10 +19,12 @@ jobs: git branch ls src/OBMD # This commit needs to be updated when developping on top of another commit of lammps! - git checkout 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 # upstream commit of lammps 2Aug2023_update2 + git checkout 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 + # upstream commit of lammps 2Aug2023_update2 + git checkout -b upstream_lammps git branch ls src/OBMD - git checkout ${{ github.sha }} # commit of this pr + git checkout ${{ github.ref_name }} ls src/OBMD echo $HOME From f00e8d0fb488877f2039656f7934787199442725 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 15:19:02 +0100 Subject: [PATCH 50/77] Update MultiXscale:generate_patch_file.yml --- .github/workflows/MultiXscale:generate_patch_file.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/MultiXscale:generate_patch_file.yml b/.github/workflows/MultiXscale:generate_patch_file.yml index ef8de4830b1..13229d8efdd 100644 --- a/.github/workflows/MultiXscale:generate_patch_file.yml +++ b/.github/workflows/MultiXscale:generate_patch_file.yml @@ -14,15 +14,14 @@ jobs: - name: Generate patch file run: | pwd - git remote add lammps git@github.com:lammps/lammps.git + git remote add lammps https://github.com/laraPPr/lammps.git git remote -v git branch ls src/OBMD # This commit needs to be updated when developping on top of another commit of lammps! - git checkout 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 - # upstream commit of lammps 2Aug2023_update2 + git checkout 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 # upstream commit of lammps 2Aug2023_update2 git checkout -b upstream_lammps - git branch + git -a branch ls src/OBMD git checkout ${{ github.ref_name }} ls src/OBMD From ff5af13a88b3da225d9bbf8ff768ee6af38bfb48 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 15:23:07 +0100 Subject: [PATCH 51/77] Update MultiXscale:generate_patch_file.yml --- .github/workflows/MultiXscale:generate_patch_file.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:generate_patch_file.yml b/.github/workflows/MultiXscale:generate_patch_file.yml index 13229d8efdd..6c4d80cdfa4 100644 --- a/.github/workflows/MultiXscale:generate_patch_file.yml +++ b/.github/workflows/MultiXscale:generate_patch_file.yml @@ -14,7 +14,7 @@ jobs: - name: Generate patch file run: | pwd - git remote add lammps https://github.com/laraPPr/lammps.git + git remote add lammps https://github.com/laraPPr/lammps git remote -v git branch ls src/OBMD From 5696e391edc8bbcb896febe70150eda3296193ab Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 15:34:44 +0100 Subject: [PATCH 52/77] Update MultiXscale:generate_patch_file.yml --- .github/workflows/MultiXscale:generate_patch_file.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:generate_patch_file.yml b/.github/workflows/MultiXscale:generate_patch_file.yml index 6c4d80cdfa4..e3a25ae02c2 100644 --- a/.github/workflows/MultiXscale:generate_patch_file.yml +++ b/.github/workflows/MultiXscale:generate_patch_file.yml @@ -10,11 +10,14 @@ jobs: build: runs-on: ubuntu-latest steps: + - uses: actions/checkout@v4 + with: + repository: lammps/lammps - uses: actions/checkout@v4 - name: Generate patch file run: | pwd - git remote add lammps https://github.com/laraPPr/lammps + git remote add lammps https://github.com/laraPPr/lammps.git git remote -v git branch ls src/OBMD From c640edf0f316e22cab6f9378afd5fc0a3ea007b8 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 15:35:00 +0100 Subject: [PATCH 53/77] Update MultiXscale:generate_patch_file.yml --- .github/workflows/MultiXscale:generate_patch_file.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/MultiXscale:generate_patch_file.yml b/.github/workflows/MultiXscale:generate_patch_file.yml index e3a25ae02c2..e09424cd342 100644 --- a/.github/workflows/MultiXscale:generate_patch_file.yml +++ b/.github/workflows/MultiXscale:generate_patch_file.yml @@ -17,7 +17,6 @@ jobs: - name: Generate patch file run: | pwd - git remote add lammps https://github.com/laraPPr/lammps.git git remote -v git branch ls src/OBMD From 1833cccf2b8dcf64a2d741c399f2c41bb3fa39d7 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 15:38:21 +0100 Subject: [PATCH 54/77] Update MultiXscale:generate_patch_file.yml --- .../MultiXscale:generate_patch_file.yml | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/.github/workflows/MultiXscale:generate_patch_file.yml b/.github/workflows/MultiXscale:generate_patch_file.yml index e09424cd342..361701eb3fb 100644 --- a/.github/workflows/MultiXscale:generate_patch_file.yml +++ b/.github/workflows/MultiXscale:generate_patch_file.yml @@ -13,6 +13,12 @@ jobs: - uses: actions/checkout@v4 with: repository: lammps/lammps + - name: get remote branch + run: | + pwd + git branch + echo $HOME + ls $HOME - uses: actions/checkout@v4 - name: Generate patch file run: | @@ -21,11 +27,12 @@ jobs: git branch ls src/OBMD # This commit needs to be updated when developping on top of another commit of lammps! - git checkout 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 # upstream commit of lammps 2Aug2023_update2 - git checkout -b upstream_lammps - git -a branch - ls src/OBMD - git checkout ${{ github.ref_name }} - ls src/OBMD + #git checkout 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 # upstream commit of lammps 2Aug2023_update2 + #git checkout -b upstream_lammps + #git -a branch + #ls src/OBMD + #git checkout ${{ github.ref_name }} + #ls src/OBMD echo $HOME + ls $HOME From ebaa2aad2610654b17b12ff530876e3da52ec0e2 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 15:42:18 +0100 Subject: [PATCH 55/77] Update MultiXscale:generate_patch_file.yml --- .github/workflows/MultiXscale:generate_patch_file.yml | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/.github/workflows/MultiXscale:generate_patch_file.yml b/.github/workflows/MultiXscale:generate_patch_file.yml index 361701eb3fb..b271ba62200 100644 --- a/.github/workflows/MultiXscale:generate_patch_file.yml +++ b/.github/workflows/MultiXscale:generate_patch_file.yml @@ -13,18 +13,12 @@ jobs: - uses: actions/checkout@v4 with: repository: lammps/lammps - - name: get remote branch - run: | - pwd - git branch - echo $HOME - ls $HOME + path: lammps_upstream - uses: actions/checkout@v4 - name: Generate patch file run: | pwd - git remote -v - git branch + ls $HOME/work ls src/OBMD # This commit needs to be updated when developping on top of another commit of lammps! #git checkout 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 # upstream commit of lammps 2Aug2023_update2 @@ -34,5 +28,4 @@ jobs: #git checkout ${{ github.ref_name }} #ls src/OBMD echo $HOME - ls $HOME From 1f97b40caa558201df34d4dccd79cf86f66f7344 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 15:44:19 +0100 Subject: [PATCH 56/77] Update MultiXscale:generate_patch_file.yml --- .github/workflows/MultiXscale:generate_patch_file.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/MultiXscale:generate_patch_file.yml b/.github/workflows/MultiXscale:generate_patch_file.yml index b271ba62200..9373562e65b 100644 --- a/.github/workflows/MultiXscale:generate_patch_file.yml +++ b/.github/workflows/MultiXscale:generate_patch_file.yml @@ -18,12 +18,11 @@ jobs: - name: Generate patch file run: | pwd - ls $HOME/work ls src/OBMD # This commit needs to be updated when developping on top of another commit of lammps! #git checkout 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 # upstream commit of lammps 2Aug2023_update2 #git checkout -b upstream_lammps - #git -a branch + git -a branch #ls src/OBMD #git checkout ${{ github.ref_name }} #ls src/OBMD From 68430570d0086dace52ae1ab0a2741b87cca4df3 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 15:45:15 +0100 Subject: [PATCH 57/77] Update MultiXscale:generate_patch_file.yml --- .github/workflows/MultiXscale:generate_patch_file.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:generate_patch_file.yml b/.github/workflows/MultiXscale:generate_patch_file.yml index 9373562e65b..b991eaff9b5 100644 --- a/.github/workflows/MultiXscale:generate_patch_file.yml +++ b/.github/workflows/MultiXscale:generate_patch_file.yml @@ -22,7 +22,7 @@ jobs: # This commit needs to be updated when developping on top of another commit of lammps! #git checkout 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 # upstream commit of lammps 2Aug2023_update2 #git checkout -b upstream_lammps - git -a branch + git branch #ls src/OBMD #git checkout ${{ github.ref_name }} #ls src/OBMD From 700a830f31b9f33770bcd6b302446ebfcf2777bd Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 15:48:23 +0100 Subject: [PATCH 58/77] Update MultiXscale:generate_patch_file.yml --- .github/workflows/MultiXscale:generate_patch_file.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:generate_patch_file.yml b/.github/workflows/MultiXscale:generate_patch_file.yml index b991eaff9b5..e6f6d8da482 100644 --- a/.github/workflows/MultiXscale:generate_patch_file.yml +++ b/.github/workflows/MultiXscale:generate_patch_file.yml @@ -14,6 +14,7 @@ jobs: with: repository: lammps/lammps path: lammps_upstream + ref: 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 - uses: actions/checkout@v4 - name: Generate patch file run: | @@ -26,5 +27,5 @@ jobs: #ls src/OBMD #git checkout ${{ github.ref_name }} #ls src/OBMD - echo $HOME + echo $HOME/work From 7a7e54457bfba13855b2353d12b8c2feb5d498a1 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 15:49:33 +0100 Subject: [PATCH 59/77] Update MultiXscale:generate_patch_file.yml --- .github/workflows/MultiXscale:generate_patch_file.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/MultiXscale:generate_patch_file.yml b/.github/workflows/MultiXscale:generate_patch_file.yml index e6f6d8da482..5ca0ed75e2e 100644 --- a/.github/workflows/MultiXscale:generate_patch_file.yml +++ b/.github/workflows/MultiXscale:generate_patch_file.yml @@ -28,4 +28,5 @@ jobs: #git checkout ${{ github.ref_name }} #ls src/OBMD echo $HOME/work + ls $HOME/work From c5d5454e047786bad70681a2749192905a31c7a1 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 15:53:31 +0100 Subject: [PATCH 60/77] Update MultiXscale:generate_patch_file.yml --- .github/workflows/MultiXscale:generate_patch_file.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:generate_patch_file.yml b/.github/workflows/MultiXscale:generate_patch_file.yml index 5ca0ed75e2e..2cef330d9ef 100644 --- a/.github/workflows/MultiXscale:generate_patch_file.yml +++ b/.github/workflows/MultiXscale:generate_patch_file.yml @@ -11,6 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 + path: new_lammps with: repository: lammps/lammps path: lammps_upstream @@ -28,5 +29,7 @@ jobs: #git checkout ${{ github.ref_name }} #ls src/OBMD echo $HOME/work - ls $HOME/work + ls $HOME/work/lammps/lammps/upstream + ls $HOME/work/lammps/lammps/new_lammps + cat $HOME/work/lammps/lammps/upstream/scr/version.h From 9160d44b2cc15538689cf870d98e003562fcbe87 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 16:01:50 +0100 Subject: [PATCH 61/77] Update MultiXscale:generate_patch_file.yml --- .github/workflows/MultiXscale:generate_patch_file.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/MultiXscale:generate_patch_file.yml b/.github/workflows/MultiXscale:generate_patch_file.yml index 2cef330d9ef..9565d390c23 100644 --- a/.github/workflows/MultiXscale:generate_patch_file.yml +++ b/.github/workflows/MultiXscale:generate_patch_file.yml @@ -15,7 +15,6 @@ jobs: with: repository: lammps/lammps path: lammps_upstream - ref: 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 - uses: actions/checkout@v4 - name: Generate patch file run: | From a479281b214c252c389a1efe5de13ab2ffc7796b Mon Sep 17 00:00:00 2001 From: lara Date: Mon, 3 Feb 2025 20:27:47 +0100 Subject: [PATCH 62/77] add patch file workflow to compile workflow and get easyconfig from multixscale/dev.eessi.io-lammps-plugin-obmd --- .../LAMMPS_OBMD-foss-2023a-software-commit.eb | 113 ------------------ .../workflows/MultiXscale:compile_lammps.yml | 24 +++- .../MultiXscale:generate_patch_file.yml | 34 ------ 3 files changed, 23 insertions(+), 148 deletions(-) delete mode 100644 .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb delete mode 100644 .github/workflows/MultiXscale:generate_patch_file.yml diff --git a/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb b/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb deleted file mode 100644 index 82f4fcc2325..00000000000 --- a/.github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb +++ /dev/null @@ -1,113 +0,0 @@ -name = 'LAMMPS' -version = '%(software_commit)s' -versionsuffix = '-kokkos-dev_OBMD' - -homepage = 'https://www.lammps.org' -description = """LAMMPS is a classical molecular dynamics code, and an acronym -for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has -potentials for solid-state materials (metals, semiconductors) and soft matter -(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be -used to model atoms or, more generically, as a parallel particle simulator at -the atomic, meso, or continuum scale. LAMMPS runs on single processors or in -parallel using message-passing techniques and a spatial-decomposition of the -simulation domain. The code is designed to be easy to modify or extend with new -functionality. -""" - -toolchain = {'name': 'foss', 'version': '2023a'} -toolchainopts = {'openmp': True, 'usempi': True} - -# 'https://github.com/lammps/lammps/archive/' -source_urls = ['https://github.com/laraPPr/lammps/archive'] -sources = ['%(version)s.tar.gz'] -patches = [ - 'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch', - 'LAMMPS-2Aug2023_fix-timestep-balance-example.patch', -] -checksums = [ -] - -builddependencies = [ - ('CMake', '3.26.3'), - ('pkgconf', '1.9.5'), - ('archspec', '0.2.1'), -] -dependencies = [ - ('Python', '3.11.3'), - ('libpng', '1.6.39'), - ('libjpeg-turbo', '2.1.5.1'), - ('netCDF', '4.9.2'), - ('GSL', '2.7'), - ('zlib', '1.2.13'), - ('gzip', '1.12'), - ('cURL', '8.0.1'), - ('HDF5', '1.14.0'), - ('PCRE', '8.45'), - ('libxml2', '2.11.4'), - ('FFmpeg', '6.0'), - ('Voro++', '0.4.6'), - ('kim-api', '2.3.0'), - ('Eigen', '3.4.0'), - ('PLUMED', '2.9.0'), - ('SciPy-bundle', '2023.07'), - # VTK package is auto-disabled if this dep is not available - ('VTK', '9.3.0'), - # We use a custom build of MDI - ('MDI', '1.4.26'), -] -if ARCH == 'x86_64': - # TBB and ScaFaCos are an optional dependency when building on Intel arch - dependencies += [ - ('tbb', '2021.11.0'), - ('ScaFaCoS', '1.0.4'), - ] - -# To use additional custom configuration options, use the 'configopts' easyconfig parameter -# See docs and lammps easyblock for more information. -# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options - -# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, -# which is claimed to be faster in pure MPI calculations -# configopts = "-DKokkos_ENABLE_SERIAL=yes " - - -# packages auto-enabled by easyblock -# 'GPU' - if cuda package is present and kokkos is disabled -# 'KOKKOS' - if kokkos is enabled (by default) -# 'INTEL' - if builing on Intel CPU -# 'OPENMP' - if OpenMP swithed on in 'toolchainopts' - -# include the following extra packages into the build -general_packages = [ - 'DPD-BASIC', - 'MOLECULE', - 'OBMD' -] - -# Excluded packages due to requiring additional (non-trivial) deps -# - ADIOS -# - LATTE -# - MESONT (requires very large files downloaded during build) -# - ML-HDNNP (requires N2P2) -# - ML-QUIP -# - MSCG -# - QMMM (setup seems complex) - -# remove example atm because MANYBODY is not enabled -# remove example colloid because COLLOID package is not enabled -# remove example dipole because DIPOLE package is not enabled -# remove example hugoniostat because EXTRA-PAIR package is not enabled -# removing example msst bacause SHOCK package is not enabled -# removing example pour because GRANULAR package is not enabled -# removing example voronoi beacuse VORONOI package is not enabled -#check_files = [ -# 'balance', 'crack', 'friction', 'indent', -# 'melt', 'min', 'nemd', 'obstacle', -#] - -sanity_check_test_inputs = [ - 'balance', 'crack', 'friction', 'indent', - 'melt', 'min', 'nemd', 'obstacle', -] - -moduleclass = 'chem' diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index ec3f133fd92..575dc84d98d 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -16,13 +16,35 @@ jobs: - ubuntu-24.04 steps: - uses: actions/checkout@v4 + with: + repository: lammps/lammps + path: lammps_upstream + # This commit needs to be updated when developping on top of another commit of lammps! + ref: 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 + - uses: actions/checkout@v4 + with: + path: lammps_dev + - name: Generate patch file + continue-on-error: true + run: | + # make patch file + diff -ruN --exclude .* lammps_upstream lammps_dev > LAMMPS-2Aug2023_lammps_obmd_package.patch + - name: Check if patch file was generated + run: | + ls LAMMPS-2Aug2023_lammps_obmd_package.patch + cat LAMMPS-2Aug2023_lammps_obmd_package.patch + - uses: actions/checkout@v4 + with: + repository: multixscale/dev.eessi.io-lammps-plugin-obmd + path: multixscale_dev - uses: eessi/github-action-eessi@v3 - name: set up EasyBuild run: | module load EESSI-extend/2023.06-easybuild eb --show-config + echo ${{ github.sha }} echo "Get EasyConfig" - eb .github/workflows/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3725813434972232adde2d84c882801fae629ddf + eb multixscale_dev/easyconfigs/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3725813434972232adde2d84c882801fae629ddf module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD echo $EBROOTLAMMPS diff --git a/.github/workflows/MultiXscale:generate_patch_file.yml b/.github/workflows/MultiXscale:generate_patch_file.yml deleted file mode 100644 index 9565d390c23..00000000000 --- a/.github/workflows/MultiXscale:generate_patch_file.yml +++ /dev/null @@ -1,34 +0,0 @@ -name: MultiXscale-generate_lammps_patch -run-name: Generate a patch for the OBMD plugin -on: - push: - paths: - - '.github/**' - - 'src/OBMD/**' - - 'examples/OBMD/**' -jobs: - build: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - path: new_lammps - with: - repository: lammps/lammps - path: lammps_upstream - - uses: actions/checkout@v4 - - name: Generate patch file - run: | - pwd - ls src/OBMD - # This commit needs to be updated when developping on top of another commit of lammps! - #git checkout 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 # upstream commit of lammps 2Aug2023_update2 - #git checkout -b upstream_lammps - git branch - #ls src/OBMD - #git checkout ${{ github.ref_name }} - #ls src/OBMD - echo $HOME/work - ls $HOME/work/lammps/lammps/upstream - ls $HOME/work/lammps/lammps/new_lammps - cat $HOME/work/lammps/lammps/upstream/scr/version.h - From 3baf875d83523ec2efdc182706ae2b8e27589aa6 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 20:36:16 +0100 Subject: [PATCH 63/77] copy patch file to directory where easybuild will find it --- .github/workflows/MultiXscale:compile_lammps.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 575dc84d98d..3e017ee278b 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -32,6 +32,7 @@ jobs: - name: Check if patch file was generated run: | ls LAMMPS-2Aug2023_lammps_obmd_package.patch + cp LAMMPS-2Aug2023_lammps_obmd_package.patch multixscale_dev/easyconfigs/l/LAMMPS/. cat LAMMPS-2Aug2023_lammps_obmd_package.patch - uses: actions/checkout@v4 with: From 5d845f34c66d626bb3f9f99343851a01541faf59 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 20:38:34 +0100 Subject: [PATCH 64/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 3e017ee278b..78e891534c4 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -32,7 +32,6 @@ jobs: - name: Check if patch file was generated run: | ls LAMMPS-2Aug2023_lammps_obmd_package.patch - cp LAMMPS-2Aug2023_lammps_obmd_package.patch multixscale_dev/easyconfigs/l/LAMMPS/. cat LAMMPS-2Aug2023_lammps_obmd_package.patch - uses: actions/checkout@v4 with: @@ -41,6 +40,8 @@ jobs: - uses: eessi/github-action-eessi@v3 - name: set up EasyBuild run: | + pwd + cp LAMMPS-2Aug2023_lammps_obmd_package.patch multixscale_dev/easyconfigs/l/LAMMPS/. module load EESSI-extend/2023.06-easybuild eb --show-config echo ${{ github.sha }} From f56037c56b12b135049587caebe62efbec0f054a Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 20:45:12 +0100 Subject: [PATCH 65/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 78e891534c4..f6b6465bbe5 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -41,7 +41,7 @@ jobs: - name: set up EasyBuild run: | pwd - cp LAMMPS-2Aug2023_lammps_obmd_package.patch multixscale_dev/easyconfigs/l/LAMMPS/. + cp LAMMPS-2Aug2023_lammps_obmd_package.patch multixscale_dev/. module load EESSI-extend/2023.06-easybuild eb --show-config echo ${{ github.sha }} From e82532017f648bc326d377e9f01eac69265c44d2 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 20:52:16 +0100 Subject: [PATCH 66/77] update path to patch --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index f6b6465bbe5..2518283249e 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -41,7 +41,7 @@ jobs: - name: set up EasyBuild run: | pwd - cp LAMMPS-2Aug2023_lammps_obmd_package.patch multixscale_dev/. + mkdir -p multixscale_dev/easyconfigs/l/LAMMPS && cp LAMMPS-2Aug2023_lammps_obmd_package.patch multixscale_dev/easyconfigs/l/LAMMPS/. module load EESSI-extend/2023.06-easybuild eb --show-config echo ${{ github.sha }} From 4abdd3d64db7ffd3df2b9df18eb714086bc0f791 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 21:00:56 +0100 Subject: [PATCH 67/77] Use commit used in dev.eessi.io-example --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 2518283249e..30e4eb21000 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -20,7 +20,7 @@ jobs: repository: lammps/lammps path: lammps_upstream # This commit needs to be updated when developping on top of another commit of lammps! - ref: 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 + ref: 3d295a926318468e3e8fdd99fdcfea02cd796403 - uses: actions/checkout@v4 with: path: lammps_dev From 327ea2d49604c05ea8a00e3d221d44ba41e84e0a Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Mon, 3 Feb 2025 21:02:47 +0100 Subject: [PATCH 68/77] Use the commit used in eessi.dev.io-example --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 30e4eb21000..7e8bb1002dd 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -20,7 +20,7 @@ jobs: repository: lammps/lammps path: lammps_upstream # This commit needs to be updated when developping on top of another commit of lammps! - ref: 3d295a926318468e3e8fdd99fdcfea02cd796403 + ref: 0cb72423b8ed2fdf138831c145a3bfb6ea42394e - uses: actions/checkout@v4 with: path: lammps_dev From dfddef6c92c27e69c160b61f9df76c7aaafd8948 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 4 Feb 2025 10:08:07 +0100 Subject: [PATCH 69/77] Use other lammps commit --- .github/workflows/MultiXscale:compile_lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 7e8bb1002dd..2518283249e 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -20,7 +20,7 @@ jobs: repository: lammps/lammps path: lammps_upstream # This commit needs to be updated when developping on top of another commit of lammps! - ref: 0cb72423b8ed2fdf138831c145a3bfb6ea42394e + ref: 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 - uses: actions/checkout@v4 with: path: lammps_dev From 164e36f7365e0f09cfc31a4b26b169b0434eef9a Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 4 Feb 2025 10:19:21 +0100 Subject: [PATCH 70/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 2518283249e..7a119cc79dc 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -20,7 +20,7 @@ jobs: repository: lammps/lammps path: lammps_upstream # This commit needs to be updated when developping on top of another commit of lammps! - ref: 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 + ref: ${{ LAMMPS_COMMIT }} - uses: actions/checkout@v4 with: path: lammps_dev @@ -46,7 +46,7 @@ jobs: eb --show-config echo ${{ github.sha }} echo "Get EasyConfig" - eb multixscale_dev/easyconfigs/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ github.sha }} --include-easyblocks-from-commit 3725813434972232adde2d84c882801fae629ddf + eb multixscale_dev/easyconfigs/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ LAMMPS_COMMIT }} --include-easyblocks-from-commit 3725813434972232adde2d84c882801fae629ddf module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD echo $EBROOTLAMMPS From b8a22ca1e3976941bb23a7f7ed155d5738ebe80c Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 4 Feb 2025 10:20:25 +0100 Subject: [PATCH 71/77] Update MultiXscale:compile_lammps.yml --- .github/workflows/MultiXscale:compile_lammps.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 7a119cc79dc..5799d81370a 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -19,7 +19,8 @@ jobs: with: repository: lammps/lammps path: lammps_upstream - # This commit needs to be updated when developping on top of another commit of lammps! + # This commit needs to be updated when developping on top of another commit of lammps! + # by setting a new value here https://github.com/laraPPr/lammps/settings/variables/actions. ref: ${{ LAMMPS_COMMIT }} - uses: actions/checkout@v4 with: From 28b76c172a23faa5fc861444f858133fb93b9753 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 4 Feb 2025 10:32:13 +0100 Subject: [PATCH 72/77] Use LAMMPS_COMMIT set variable in actions --- .github/workflows/MultiXscale:compile_lammps.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 5799d81370a..2f77b665bab 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -21,7 +21,7 @@ jobs: path: lammps_upstream # This commit needs to be updated when developping on top of another commit of lammps! # by setting a new value here https://github.com/laraPPr/lammps/settings/variables/actions. - ref: ${{ LAMMPS_COMMIT }} + ref: ${{ env.LAMMPS_COMMIT }} - uses: actions/checkout@v4 with: path: lammps_dev @@ -47,7 +47,7 @@ jobs: eb --show-config echo ${{ github.sha }} echo "Get EasyConfig" - eb multixscale_dev/easyconfigs/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ LAMMPS_COMMIT }} --include-easyblocks-from-commit 3725813434972232adde2d84c882801fae629ddf + eb multixscale_dev/easyconfigs/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ env.LAMMPS_COMMIT }} --include-easyblocks-from-commit 3725813434972232adde2d84c882801fae629ddf module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD echo $EBROOTLAMMPS From 626fe59d8f2a3a85da2d5034d07bdc2ef1c03c47 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 4 Feb 2025 10:37:44 +0100 Subject: [PATCH 73/77] use two different variable for LAMMPS_COMMIT --- .github/workflows/MultiXscale:compile_lammps.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 2f77b665bab..ae90c0a98c2 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -19,9 +19,8 @@ jobs: with: repository: lammps/lammps path: lammps_upstream - # This commit needs to be updated when developping on top of another commit of lammps! - # by setting a new value here https://github.com/laraPPr/lammps/settings/variables/actions. - ref: ${{ env.LAMMPS_COMMIT }} + # Can change the LAMMPS commit which will be build by updating LAMMPS_COMMIT_PATCH https://github.com/laraPPr/lammps/settings/variables/actions + ref: ${{ env.LAMMPS_COMMIT_PATCH }} - uses: actions/checkout@v4 with: path: lammps_dev @@ -47,7 +46,8 @@ jobs: eb --show-config echo ${{ github.sha }} echo "Get EasyConfig" - eb multixscale_dev/easyconfigs/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ env.LAMMPS_COMMIT }} --include-easyblocks-from-commit 3725813434972232adde2d84c882801fae629ddf + # Can change the LAMMPS commit which will be build by updating LAMMPS_COMMIT_BUILD https://github.com/laraPPr/lammps/settings/variables/actions + eb multixscale_dev/easyconfigs/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ env.LAMMPS_COMMIT_BUILD }} --include-easyblocks-from-commit 3725813434972232adde2d84c882801fae629ddf module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD echo $EBROOTLAMMPS From 1ea50196816451cf1b389b27e430d0e2c12d0a1d Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 4 Feb 2025 10:44:41 +0100 Subject: [PATCH 74/77] Check env.LAMMPS_COMMIT_... --- .github/workflows/MultiXscale:compile_lammps.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index ae90c0a98c2..4fdf159373d 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -20,7 +20,7 @@ jobs: repository: lammps/lammps path: lammps_upstream # Can change the LAMMPS commit which will be build by updating LAMMPS_COMMIT_PATCH https://github.com/laraPPr/lammps/settings/variables/actions - ref: ${{ env.LAMMPS_COMMIT_PATCH }} + ref: 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 - uses: actions/checkout@v4 with: path: lammps_dev @@ -31,6 +31,8 @@ jobs: diff -ruN --exclude .* lammps_upstream lammps_dev > LAMMPS-2Aug2023_lammps_obmd_package.patch - name: Check if patch file was generated run: | + echo ${{ env.LAMMPS_COMMIT_BUILD }} + echo ${{ env.LAMMPS_COMMIT_PATCH }} ls LAMMPS-2Aug2023_lammps_obmd_package.patch cat LAMMPS-2Aug2023_lammps_obmd_package.patch - uses: actions/checkout@v4 From 140cd4f11561c952cf0c918ae671d212effc2549 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 4 Feb 2025 10:50:55 +0100 Subject: [PATCH 75/77] Find where the variable are stored --- .github/workflows/MultiXscale:compile_lammps.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index 4fdf159373d..f5aade41132 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -31,8 +31,8 @@ jobs: diff -ruN --exclude .* lammps_upstream lammps_dev > LAMMPS-2Aug2023_lammps_obmd_package.patch - name: Check if patch file was generated run: | - echo ${{ env.LAMMPS_COMMIT_BUILD }} - echo ${{ env.LAMMPS_COMMIT_PATCH }} + echo ${{ vars.LAMMPS_COMMIT_BUILD }} + echo ${{ vars.LAMMPS_COMMIT_PATCH }} ls LAMMPS-2Aug2023_lammps_obmd_package.patch cat LAMMPS-2Aug2023_lammps_obmd_package.patch - uses: actions/checkout@v4 From b1239546e0ba08b702882e3aa3828ee16f8a7d1d Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 4 Feb 2025 10:53:47 +0100 Subject: [PATCH 76/77] Test environment variables --- .github/workflows/MultiXscale:compile_lammps.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index f5aade41132..ceab9bbd52d 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -20,7 +20,7 @@ jobs: repository: lammps/lammps path: lammps_upstream # Can change the LAMMPS commit which will be build by updating LAMMPS_COMMIT_PATCH https://github.com/laraPPr/lammps/settings/variables/actions - ref: 27e8d0f19cfd60ff513828af74d07d2c8f3c4451 + ref: ${{ vars.LAMMPS_COMMIT_PATCH }} - uses: actions/checkout@v4 with: path: lammps_dev @@ -31,8 +31,6 @@ jobs: diff -ruN --exclude .* lammps_upstream lammps_dev > LAMMPS-2Aug2023_lammps_obmd_package.patch - name: Check if patch file was generated run: | - echo ${{ vars.LAMMPS_COMMIT_BUILD }} - echo ${{ vars.LAMMPS_COMMIT_PATCH }} ls LAMMPS-2Aug2023_lammps_obmd_package.patch cat LAMMPS-2Aug2023_lammps_obmd_package.patch - uses: actions/checkout@v4 @@ -49,7 +47,7 @@ jobs: echo ${{ github.sha }} echo "Get EasyConfig" # Can change the LAMMPS commit which will be build by updating LAMMPS_COMMIT_BUILD https://github.com/laraPPr/lammps/settings/variables/actions - eb multixscale_dev/easyconfigs/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ env.LAMMPS_COMMIT_BUILD }} --include-easyblocks-from-commit 3725813434972232adde2d84c882801fae629ddf + eb multixscale_dev/easyconfigs/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ vars.LAMMPS_COMMIT_BUILD }} --include-easyblocks-from-commit 3725813434972232adde2d84c882801fae629ddf module avail LAMMPS module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD echo $EBROOTLAMMPS From 1ea797f6edd260348a880c03360238c2f84a7a0a Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 4 Feb 2025 11:07:08 +0100 Subject: [PATCH 77/77] Change module name by using variable --- .github/workflows/MultiXscale:compile_lammps.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/MultiXscale:compile_lammps.yml b/.github/workflows/MultiXscale:compile_lammps.yml index ceab9bbd52d..7d924d8d2cc 100644 --- a/.github/workflows/MultiXscale:compile_lammps.yml +++ b/.github/workflows/MultiXscale:compile_lammps.yml @@ -44,12 +44,11 @@ jobs: mkdir -p multixscale_dev/easyconfigs/l/LAMMPS && cp LAMMPS-2Aug2023_lammps_obmd_package.patch multixscale_dev/easyconfigs/l/LAMMPS/. module load EESSI-extend/2023.06-easybuild eb --show-config - echo ${{ github.sha }} echo "Get EasyConfig" # Can change the LAMMPS commit which will be build by updating LAMMPS_COMMIT_BUILD https://github.com/laraPPr/lammps/settings/variables/actions eb multixscale_dev/easyconfigs/LAMMPS_OBMD-foss-2023a-software-commit.eb --software-commit ${{ vars.LAMMPS_COMMIT_BUILD }} --include-easyblocks-from-commit 3725813434972232adde2d84c882801fae629ddf module avail LAMMPS - module load LAMMPS/${{ github.sha }}-foss-2023a-kokkos-dev_OBMD + module load LAMMPS/${{ vars.LAMMPS_COMMIT_BUILD }}-foss-2023a-kokkos-dev_OBMD echo $EBROOTLAMMPS ls $EBROOTLAMMPS mpirun -np 4 --oversubscribe lmp -in $EBROOTLAMMPS/examples/OBMD/in.OBMD