From a490e4685ba41fd15bf7c31ae54017be8335c29d Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Fri, 19 Jun 2026 23:55:06 +0800 Subject: [PATCH 1/3] SOF-7933: update currently available software modules --- lang/en/docs/cli/modules.md | 105 +++++++++++++++--------------------- 1 file changed, 42 insertions(+), 63 deletions(-) diff --git a/lang/en/docs/cli/modules.md b/lang/en/docs/cli/modules.md index 1dda8c3dd..60be700de 100644 --- a/lang/en/docs/cli/modules.md +++ b/lang/en/docs/cli/modules.md @@ -30,7 +30,7 @@ A list of compiler and library abbreviations can be found in the following tabl | Intel MPI | impi | Closed-Source implementation of the Message Passing Interface standard from Intel | For example, Quantum Espresso version 5.2.1 built with GCC 4.8.5 and OpenMPI 1.10.0 would be labeled as -`espresso/5.2.1-g-4.8.5-ompi-1.10.0`. +`espresso/5.2.1-g-4.8.5-ompi-1.10.0`. Finally, several package names carry additional metadata about their build configuration at the end of the name string. These abbreviations are specific to the application being built, and a table can be found below which lists @@ -56,83 +56,62 @@ Henkelman group's transition state tools. Several of the older packages on our system adopt a legacy naming convention. It is similar to the above notation, except that in order to shorten the name, periods in the version numbers were removed. To protect compatibility with existing user-made scripts, we have preserved this naming convention. For example, the -`espresso/5.2.1-g-4.8.5-ompi-1.10.0` package has a duplicate listing as `espresso/521-g-485-ompi-110`. We plan for +`espresso/5.2.1-g-4.8.5-ompi-1.10.0` package has a duplicate listing as `espresso/521-g-485-ompi-110`. We plan for these packages to be hidden from the output of the `module avail` command in the future. We discourage the use of modules with this legacy naming convention in any newly-created job submission scripts. Instead, please use the full, current naming convention for modules. ## List Available Modules -The command `module avail` provides a complete list of the **modules made available on our platform**. The common stem for the module installation paths is displayed on top of each section listed in the output, whereas the rest of the path name is specified under each listed entry. +The command `module avail` provides a complete list of the +**modules made available on our platform**. The common stem for the module +installation paths is displayed on top of each section listed in the output, +whereas the rest of the path name is specified under each listed entry. -We have reproduced the output of this command below listing all currently available modules, for reference purposes. The reader is referred to the [software directory overview]({{ reference_url }}/software-directory/overview/) for an introduction to the codes, libraries and software packages listed here. +We have reproduced the output of this command below listing all currently +available modules, for reference purposes. The reader is referred to the +[software directory overview]({{ reference_url }}/software-directory/overview/) +for an introduction to the codes, libraries and software packages listed here. ```text ----------------------------------------------------------------------------- /export/compute/modulefiles/system ----------------------------------------------------------------------------- -emacs/24.5 - -------------------------------------------------------------------------- /export/compute/modulefiles/applications -------------------------------------------------------------------------- -cp2k/4.1-i-14.0.3.174-impi-5.0.2.044 gromacs/2021.5-g-11.2.0-ompi-4.1.1-openblas-0.3.18-gms vasp/5.3.5-g-4.8.5-ompi-1.10.0 -cp2k/41-i-174-impi-044 gromacs/2021.5-g-11.2.0-ompi-4.1.1-openblas-0.3.18-md vasp/5.3.5-g-4.8.5-ompi-1.10.0-nc -espresso/521-g-485-ompi-110 gromacs/2021.5-g-11.2.0-ompi-4.1.1-openblas-0.3.18-ms vasp/5.3.5-g-4.8.5-ompi-1.10.0-vtst -espresso/5.2.1-g-4.8.5-ompi-1.10.0 gromacs/20215-g-11-ompi-411-openblas-0318-gms vasp/535-g-485-ompi-110-nc -espresso/5.2.1-i-14.0.3.174-impi-5.0.2.044 gromacs/20215-g-11-ompi-411-openblas-0318-md vasp/535-g-485-ompi-110-vtst -espresso/521-i-174-impi-044 gromacs/20215-g-11-ompi-411-openblas-0318-ms vasp/5.3.5-i-14.0.3.174-impi-5.0.2.044 -espresso/540-g-485-ompi-110 gromacs/5.1.4-g-4.8.5-ompi-1.10.0-md vasp/5.3.5-i-14.0.3.174-impi-5.0.2.044-nc -espresso/5.4.0-g-4.8.5-ompi-1.10.0 gromacs/5.1.4-g-4.8.5-ompi-1.10.0-ms vasp/5.3.5-i-14.0.3.174-impi-5.0.2.044-vtst -espresso/5.4.0-i-14.0.3.174-impi-5.0.2.044 gromacs/514-g-485-ompi-110-md vasp/535-i-174-impi-044(default) -espresso/540-i-174-impi-044(default) gromacs/514-g-485-ompi-110-ms vasp/535-i-174-impi-044-nc -espresso/600-g-485-ompi-110 gromacs/5.1.4-i-14.0.3.174-impi-5.0.2.044-md vasp/535-i-174-impi-044-vtst -espresso/6.0.0-g-4.8.5-ompi-1.10.0 gromacs/5.1.4-i-14.0.3.174-impi-5.0.2.044-ms vasp/5.4.4-i-14.0.3.174-impi-5.0.2.044 -espresso/6.0.0-i-14.0.3.174-impi-5.0.2.044 gromacs/514-i-174-impi-044-md vasp/5.4.4-i-14.0.3.174-impi-5.0.2.044-gamma -espresso/600-i-174-impi-044 gromacs/514-i-174-impi-044-ms vasp/5.4.4-i-14.0.3.174-impi-5.0.2.044-gpu -espresso/63-g-485-ompi-110 lammps/1116-g-485-ompi-110 vasp/5.4.4-i-14.0.3.174-impi-5.0.2.044-nc -espresso/6.3-g-4.8.5-ompi-1.10.0 lammps/1116-i-174-impi-044 vasp/5.4.4-i-14.0.3.174-impi-5.0.2.044-vtst -espresso/6.3-i-14.0.3.174-impi-5.0.2.044 lammps/1218-i-174-impi-044 vasp/5.4.4-i-14.0.3.174-impi-5.0.2.044-vtst-gamma -espresso/63-i-174-impi-044 lammps/12Dec2018-i-14.0.3.174-impi-5.0.2.044 vasp/5.4.4-i-14.0.3.174-impi-5.0.2.044-vtst-nc -espresso/6.4.1-g-11.2.0-ompi-4.1.1 lammps/2022.01.07-g-11.2.0-ompi-4.1.1-cuda-11.5 vasp/544-i-174-impi-044 -espresso/641-g-1120-ompi-411 lammps/5Nov16-g-4.8.5-ompi-1.10.0 vasp/544-i-174-impi-044-gamma -espresso/6.5.0-g-11.2.0-ompi-4.1.1 lammps/5Nov16-i-14.0.3.174-impi-5.0.2.044 vasp/544-i-174-impi-044-gpu -espresso/650-g-1120-ompi-411 lammps/7Jan2022-g-1120-ompi-411-cuda-115 vasp/544-i-174-impi-044-nc -espresso/6.6.0-g-11.2.0-ompi-4.1.1 nwchem/6.6-i-14.0.3.174-impi-5.0.2.044 vasp/544-i-174-impi-044-vtst -espresso/660-g-1120-ompi-411 nwchem/66-i-174-impi-044 vasp/544-i-174-impi-044-vtst-gamma -espresso/6.7.0-g-11.2.0-ompi-4.1.1 nwchem/702-g-485-ompi-110 vasp/544-i-174-impi-044-vtst-nc -espresso/670-g-1120-ompi-411 nwchem/7.0.2-g-4.8.5-ompi-1.10.0 vesta/3.3.8 -espresso/6.8.0-g-11.2.0-ompi-4.1.1 nwchem/7.0.2-i-14.0.3.174-impi-5.0.2.044 vmd/1.9.3 -espresso/680-g-1120-ompi-411 nwchem/702-i-174-impi-044 vnl-atk/2016.2 -gromacs/2018.2-i-14.0.3.174-impi-5.0.2.044-gms p4vasp/0.3.30 wien2k/17.1-i-14.0.3.174-impi-5.0.2.044 -gromacs/20182-i-174-impi-044-gms sisso/sisso-1.0-g-11.2.0-ompi-4.1.1-openblas-0.3.18 wien2k/171-i-174-impi-044(default) -gromacs/2018.3-i-14.0.3.174-impi-5.0.2.044-gms turbomole/v7.0 xcrysden/1.5.60 -gromacs/20183-i-174-impi-044-gms vasp/535-g-485-ompi-110 - ---------------------------------------------------------------------------- /export/compute/modulefiles/compilers --------------------------------------------------------------------------- -gcc/11.2.0(default) gcc/5.4.0 intel/14.0.3.174 intel/i-174(default) - ---------------------------------------------------------------------------- /export/compute/modulefiles/libraries --------------------------------------------------------------------------- -cuda/11.5(default) mkl/i-11.1.3.174 mpi/impi-044(default) mpi/ompi-110 mpi/ompi-4.1.1 openblas/0.3.18-g-11.2.0 -cuda/9.2 mkl/i-174(default) mpi/impi-5.0.2.044 mpi/ompi-1.10 openblas/0.2.18-g-5.4.0 openblas/218-g-540 - ---------------------------------------------------------------------------- /export/compute/modulefiles/languages --------------------------------------------------------------------------- -python/2.7.5 python/3.6.12 python/3.7.9 python/3.8.6(default) python/3.9.1 python/anaconda3-5.2.0 +mat3ra@master-production-20250821-cluster-001:~$ module avail +--------------------------- /export/compute/modulefiles/applications --------------------------- +deepmd/3.1.2-cpu espresso/7.5-host-intel-2023.1-libxc-7.0 nwchem/7.0.2-gnu +espresso/6.3-gnu lammps/2025.07.22.2-gnu vasp/5.4.4-gnu +espresso/7.5-cuda-12.8 lammps/2025.07.22.2-intel-2023.1 +espresso/7.5-gnu lammps/2025.07.22.2-intel-2023.1-cuda-12.8 + +---------------------------- /export/compute/modulefiles/libraries ----------------------------- +cuda/12.4-cudnn-9.6 intel/oneapi-2023.1.0 mpi/ompi-4.1.1 nvhpc/25.3-cuda-12.8 + +---------------------------- /export/compute/modulefiles/compilers ----------------------------- +gcc/11.2.0 + +---------------------------- /export/compute/modulefiles/languages ----------------------------- +python/3.10.13 + +Key: +modulepath default-version ``` -Through the `module avail` command, the user can also **search** for available modules, by partially inserting the module's name. This functionality is demonstrated in the example below. - -```bash -[steve@login.mat3ra.com:~]$ module avail espresso -------------------------------------------------------------------------- /export/compute/modulefiles/applications -------------------------------------------------------------------------- -espresso/521-g-485-ompi-110 espresso/540-i-174-impi-044(default) espresso/6.3-i-14.0.3.174-impi-5.0.2.044 espresso/660-g-1120-ompi-411 -espresso/5.2.1-g-4.8.5-ompi-1.10.0 espresso/600-g-485-ompi-110 espresso/63-i-174-impi-044 espresso/6.7.0-g-11.2.0-ompi-4.1.1 -espresso/5.2.1-i-14.0.3.174-impi-5.0.2.044 espresso/6.0.0-g-4.8.5-ompi-1.10.0 espresso/6.4.1-g-11.2.0-ompi-4.1.1 espresso/670-g-1120-ompi-411 -espresso/521-i-174-impi-044 espresso/6.0.0-i-14.0.3.174-impi-5.0.2.044 espresso/641-g-1120-ompi-411 espresso/6.8.0-g-11.2.0-ompi-4.1.1 -espresso/540-g-485-ompi-110 espresso/600-i-174-impi-044 espresso/6.5.0-g-11.2.0-ompi-4.1.1 espresso/680-g-1120-ompi-411 -espresso/5.4.0-g-4.8.5-ompi-1.10.0 espresso/63-g-485-ompi-110 espresso/650-g-1120-ompi-411 -espresso/5.4.0-i-14.0.3.174-impi-5.0.2.044 espresso/6.3-g-4.8.5-ompi-1.10.0 espresso/6.6.0-g-11.2.0-ompi-4.1.1 +Through the `module avail` command, the user can also **search** for available +modules, by partially inserting the module's name. This functionality is +demonstrated in the example below. + +```text +[mat3ra@master-production-20250821-cluster-001:~]$ $ module avail espresso +--------------------------- /export/compute/modulefiles/applications --------------------------- +espresso/6.3-gnu espresso/7.5-gnu +espresso/7.5-cuda-12.8 espresso/7.5-host-intel-2023.1-libxc-7.0 + +Key: +modulepath default-version ``` ## Actions -See the [module actions documentation](actions/modules-actions.md) for more information on listing, loading, and resetting software modules. +See the [module actions documentation](actions/modules-actions.md) for more +information on listing, loading, and resetting software modules. ## Links From 5a59389f6f7726d2d25cd5448642b93e82307e9b Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Fri, 19 Jun 2026 23:57:55 +0800 Subject: [PATCH 2/3] bump gh actions/checkout --- .github/workflows/build-tests.yml | 6 +++--- .github/workflows/s3-deploy.yml | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build-tests.yml b/.github/workflows/build-tests.yml index 06360ffe6..71b94d883 100644 --- a/.github/workflows/build-tests.yml +++ b/.github/workflows/build-tests.yml @@ -23,7 +23,7 @@ jobs: steps: - name: Checkout repository and submodules - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: fetch-depth: 0 lfs: true @@ -89,12 +89,12 @@ jobs: steps: - name: Checkout this repository - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: lfs: true - name: Checkout actions repository - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: repository: Exabyte-io/actions token: ${{ secrets.BOT_GITHUB_TOKEN }} diff --git a/.github/workflows/s3-deploy.yml b/.github/workflows/s3-deploy.yml index 79d688d48..ccb048d53 100644 --- a/.github/workflows/s3-deploy.yml +++ b/.github/workflows/s3-deploy.yml @@ -18,7 +18,7 @@ jobs: AWS_SECRET_ACCESS_KEY: ${{ secrets.S3_SECRET_KEY }} steps: - name: Checkout - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: fetch-depth: 0 lfs: true From ec24e83ad0d4e4861f2e9f48386a7c76f48e33b5 Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Sat, 20 Jun 2026 00:17:34 +0800 Subject: [PATCH 3/3] chore: minor edit --- lang/en/docs/cli/modules.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lang/en/docs/cli/modules.md b/lang/en/docs/cli/modules.md index 60be700de..b72ac8409 100644 --- a/lang/en/docs/cli/modules.md +++ b/lang/en/docs/cli/modules.md @@ -99,7 +99,7 @@ modules, by partially inserting the module's name. This functionality is demonstrated in the example below. ```text -[mat3ra@master-production-20250821-cluster-001:~]$ $ module avail espresso +[mat3ra@master-production-20250821-cluster-001:~]$ module avail espresso --------------------------- /export/compute/modulefiles/applications --------------------------- espresso/6.3-gnu espresso/7.5-gnu espresso/7.5-cuda-12.8 espresso/7.5-host-intel-2023.1-libxc-7.0