From 55a41a77262cbd8785d6059d51bd4ddeeff0f6d7 Mon Sep 17 00:00:00 2001 From: "jusong.yu" Date: Mon, 18 Oct 2021 09:36:22 +0200 Subject: [PATCH] pre-commit for yaml file check added by yamllint The yamllint configuration is set in the file .yamllint. In pre-commit, the strict mode is open to list all the warnings. Therefore all the start yaml document warnings are catched and fixed with adding `---` in front of yaml files. --- .../PULL_REQUEST_TEMPLATE/new_configuration.md | 4 ++-- .github/workflows/deploy.yml | 11 +++++++++++ .github/workflows/pre-commit.yml | 15 +++++++++++++++ .make_ghpages/generate_json.py | 8 ++++---- .pre-commit-config.yaml | 18 ++++++++++++++++++ .yamllint | 5 +++++ README.md | 6 +++--- daint.cscs.ch/codes/cp2k-6.1-hybrid.yaml | 1 + daint.cscs.ch/codes/cp2k-6.1-multicore.yaml | 1 + daint.cscs.ch/codes/cp2k-7.1-hybrid.yaml | 1 + daint.cscs.ch/codes/cp2k-7.1-multicore.yaml | 1 + daint.cscs.ch/codes/cp2k-8.1-hybrid.yaml | 1 + daint.cscs.ch/codes/cp2k-8.1-multicore.yaml | 1 + daint.cscs.ch/codes/pp-6.5-multicore.yaml | 1 + daint.cscs.ch/codes/projwfc-6.5-multicore.yaml | 1 + daint.cscs.ch/codes/pw-6.5-multicore.yaml | 1 + .../hybrid-s1005/computer-configure.yaml | 1 + daint.cscs.ch/hybrid-s1005/computer-setup.yaml | 1 + daint.cscs.ch/hybrid-s1005/cp2k-7.1.yaml | 11 +++++++++++ daint.cscs.ch/hybrid-s1005/cp2k-8.1.yaml | 11 +++++++++++ daint.cscs.ch/hybrid-s1005/pp-6.5.yaml | 11 +++++++++++ daint.cscs.ch/hybrid-s1005/projwfc-6.5.yaml | 11 +++++++++++ daint.cscs.ch/hybrid-s1005/pw-6.5.yaml | 11 +++++++++++ .../hybrid-s904/computer-configure.yaml | 1 + daint.cscs.ch/hybrid-s904/computer-setup.yaml | 1 + daint.cscs.ch/hybrid/computer-configure.yaml | 1 + daint.cscs.ch/hybrid/computer-setup.yaml | 1 + .../multicore/computer-configure.yaml | 1 + daint.cscs.ch/multicore/computer-setup.yaml | 1 + eiger.cscs.ch/codes/pw-6.7-multicore.yaml | 1 + .../computer-configure.yaml | 1 + .../multicore-mr0-debug/computer-setup.yaml | 1 + eiger.cscs.ch/multicore-mr0-debug/pw-6.7.yaml | 11 +++++++++++ .../multicore-mr0/computer-configure.yaml | 1 + .../multicore-mr0/computer-setup.yaml | 1 + fidis.epfl.ch/codes/cp2k-5.1.yaml | 1 + fidis.epfl.ch/codes/ddec-09_26_2017.yaml | 1 + fidis.epfl.ch/codes/raspa-4467e14.yaml | 1 + fidis.epfl.ch/codes/zeopp-46ce745.yaml | 1 + .../fidis-ch-315/computer-configure.yaml | 1 + fidis.epfl.ch/fidis-ch-315/computer-setup.yaml | 2 +- fidis.epfl.ch/fidis-ch-315/cp2k-5.1.yaml | 14 ++++++++++++++ .../fidis-ch-315/ddec-09_26_2017.yaml | 9 +++++++++ .../fidis-serial/computer-configure.yaml | 1 + fidis.epfl.ch/fidis-serial/computer-setup.yaml | 1 + fidis.epfl.ch/fidis-serial/raspa-4467e14.yaml | 12 ++++++++++++ fidis.epfl.ch/fidis-serial/zeopp-46ce745.yaml | 9 +++++++++ fidis.epfl.ch/fidis/computer-configure.yaml | 1 + fidis.epfl.ch/fidis/computer-setup.yaml | 2 +- paratera/tianhe-2/README | 2 +- paratera/tianhe-2/computer-configure.yaml | 8 ++++---- paratera/tianhe-2/computer-setup.yaml | 1 - 52 files changed, 205 insertions(+), 17 deletions(-) create mode 100644 .github/workflows/pre-commit.yml create mode 100644 .pre-commit-config.yaml create mode 100644 .yamllint create mode 100644 daint.cscs.ch/hybrid-s1005/cp2k-7.1.yaml create mode 100644 daint.cscs.ch/hybrid-s1005/cp2k-8.1.yaml create mode 100644 daint.cscs.ch/hybrid-s1005/pp-6.5.yaml create mode 100644 daint.cscs.ch/hybrid-s1005/projwfc-6.5.yaml create mode 100644 daint.cscs.ch/hybrid-s1005/pw-6.5.yaml create mode 100644 eiger.cscs.ch/multicore-mr0-debug/pw-6.7.yaml create mode 100644 fidis.epfl.ch/fidis-ch-315/cp2k-5.1.yaml create mode 100644 fidis.epfl.ch/fidis-ch-315/ddec-09_26_2017.yaml create mode 100644 fidis.epfl.ch/fidis-serial/raspa-4467e14.yaml create mode 100644 fidis.epfl.ch/fidis-serial/zeopp-46ce745.yaml diff --git a/.github/PULL_REQUEST_TEMPLATE/new_configuration.md b/.github/PULL_REQUEST_TEMPLATE/new_configuration.md index f620c65..ec7fce9 100644 --- a/.github/PULL_REQUEST_TEMPLATE/new_configuration.md +++ b/.github/PULL_REQUEST_TEMPLATE/new_configuration.md @@ -1,5 +1,5 @@ --- -name: New configuration +name: New configuration about: Add a new computer/code configuration title: 'New configuration for' labels: new configuration @@ -21,7 +21,7 @@ Please provide below the output of `verdi computer test ` for each ### New codes added Checks: - - The codes are maintained + - The codes are maintained - [ ] by the admins of the HPC center - [ ] by me - [ ] I have verified that the paths to the executables are correct diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index ba10eaa..df50b1a 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -7,7 +7,18 @@ on: jobs: + pre-commit: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - name: Set up Python 3.8 + uses: actions/setup-python@v2 + with: + python-version: 3.8 + - uses: pre-commit/action@v2.0.0 + deploy-gh-pages: + needs: pre-commit runs-on: ubuntu-latest steps: diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml new file mode 100644 index 0000000..20846aa --- /dev/null +++ b/.github/workflows/pre-commit.yml @@ -0,0 +1,15 @@ +name: continuous-integration + +on: [push, pull_request] + +jobs: + + pre-commit: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - name: Set up Python 3.8 + uses: actions/setup-python@v2 + with: + python-version: 3.8 + - uses: pre-commit/action@v2.0.0 \ No newline at end of file diff --git a/.make_ghpages/generate_json.py b/.make_ghpages/generate_json.py index a2135da..5b8c1dc 100755 --- a/.make_ghpages/generate_json.py +++ b/.make_ghpages/generate_json.py @@ -8,7 +8,7 @@ folder_path = Path(__file__).parent.absolute() library_path = folder_path.parent -# Extract all the data. +# Extract all the data. YAML_SUFFIX = '.yaml' @@ -25,17 +25,17 @@ def parse_yaml_files_in_folder(folder_path, exclude=None): file_list = [ fname for fname in os.listdir(folder_path) if fname not in exclude ] else: file_list = os.listdir(folder_path) - + for fname in file_list: with open(folder_path/fname) as yaml_file: if fname.endswith(YAML_SUFFIX): fname = fname[:-len(YAML_SUFFIX)] else: raise ValueError(f"The file {fname} has unsupported extension. Please use '{YAML_SUFFIX}'") - + result[fname] = yaml.load(yaml_file, Loader=yaml.FullLoader) - return result + return result # Loop over the available domains and extract the computes available under them. diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..d5d540e --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,18 @@ +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.0.1 # Use the ref you want to point at + hooks: + - id: trailing-whitespace + - id: check-yaml + + - repo: https://github.com/adrienverge/yamllint.git + rev: v1.17.0 + hooks: + - id: yamllint + args: [-c=.yamllint, -s] + # only check yaml files for codes and computers setting + exclude: > + (?x)^( + .github/.* | + .pre-commit-config.yaml | + )$ \ No newline at end of file diff --git a/.yamllint b/.yamllint new file mode 100644 index 0000000..851816e --- /dev/null +++ b/.yamllint @@ -0,0 +1,5 @@ +--- +extends: default + +rules: + line-length: disable diff --git a/README.md b/README.md index 8940939..9b0c577 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ This repository collects configurations of simulation codes on public compute re In the following we'll take the example of [Piz Daint](https://www.cscs.ch/computers/piz-daint/), a HPC system at the Swiss National Supercomputing Centre. -### `verdi computer setup` +### `verdi computer setup` 1. Navigate to the [`daint.cscs.ch`](./daint.cscs.ch) folder in the GitHub web interface 2. Select the partition you would like to run on, for example [`hybrid`](./daint.cscs.ch/hybrid) @@ -23,7 +23,7 @@ You can overwrite any of the parameters provided in the yaml file by appending t Note: Alternatively, you can first create a local clone of the `aiida-code-registry` and pass the the local file path of the yaml file to the `--config` option. -### `verdi computer configure` +### `verdi computer configure` Some computers require specific configuration options (e.g. to jump over a login node) and provide a dedicated `computer-configure.yaml` file. @@ -38,7 +38,7 @@ At this point, you should be able to successfully run: verdi computer test daint-hybrid ``` -### `verdi code setup` +### `verdi code setup` The [`daint.cscs.ch`](./daint.cscs.ch/) folder contains a [`codes`](./daint.cscs.ch/codes) subfolder with configuration files for individual codes. diff --git a/daint.cscs.ch/codes/cp2k-6.1-hybrid.yaml b/daint.cscs.ch/codes/cp2k-6.1-hybrid.yaml index d8b4737..24ae7c6 100644 --- a/daint.cscs.ch/codes/cp2k-6.1-hybrid.yaml +++ b/daint.cscs.ch/codes/cp2k-6.1-hybrid.yaml @@ -1,3 +1,4 @@ +--- label: "cp2k-6.1" description: "CP2K with CUDA on daint, compiled by CSCS" input_plugin: "cp2k" diff --git a/daint.cscs.ch/codes/cp2k-6.1-multicore.yaml b/daint.cscs.ch/codes/cp2k-6.1-multicore.yaml index 6e92e28..f93be5b 100644 --- a/daint.cscs.ch/codes/cp2k-6.1-multicore.yaml +++ b/daint.cscs.ch/codes/cp2k-6.1-multicore.yaml @@ -1,3 +1,4 @@ +--- label: "cp2k-6.1" description: "CP2K 6.1 compiled by CSCS" input_plugin: "cp2k" diff --git a/daint.cscs.ch/codes/cp2k-7.1-hybrid.yaml b/daint.cscs.ch/codes/cp2k-7.1-hybrid.yaml index f86c814..d33b9f4 100644 --- a/daint.cscs.ch/codes/cp2k-7.1-hybrid.yaml +++ b/daint.cscs.ch/codes/cp2k-7.1-hybrid.yaml @@ -1,3 +1,4 @@ +--- label: "cp2k-7.1" description: "CP2K compiled for daint-gpu" input_plugin: "cp2k" diff --git a/daint.cscs.ch/codes/cp2k-7.1-multicore.yaml b/daint.cscs.ch/codes/cp2k-7.1-multicore.yaml index 2411073..4ec416d 100644 --- a/daint.cscs.ch/codes/cp2k-7.1-multicore.yaml +++ b/daint.cscs.ch/codes/cp2k-7.1-multicore.yaml @@ -1,3 +1,4 @@ +--- label: "cp2k-7.1" description: "CP2K 7.1 compiled by CSCS" input_plugin: "cp2k" diff --git a/daint.cscs.ch/codes/cp2k-8.1-hybrid.yaml b/daint.cscs.ch/codes/cp2k-8.1-hybrid.yaml index 2a70419..d2a7582 100644 --- a/daint.cscs.ch/codes/cp2k-8.1-hybrid.yaml +++ b/daint.cscs.ch/codes/cp2k-8.1-hybrid.yaml @@ -1,3 +1,4 @@ +--- label: "cp2k-8.1" description: "CP2K compiled for daint-gpu" input_plugin: "cp2k" diff --git a/daint.cscs.ch/codes/cp2k-8.1-multicore.yaml b/daint.cscs.ch/codes/cp2k-8.1-multicore.yaml index 0a9657e..9e20189 100644 --- a/daint.cscs.ch/codes/cp2k-8.1-multicore.yaml +++ b/daint.cscs.ch/codes/cp2k-8.1-multicore.yaml @@ -1,3 +1,4 @@ +--- label: "cp2k-8.1" description: "CP2K 8.1 compiled by CSCS" input_plugin: "cp2k" diff --git a/daint.cscs.ch/codes/pp-6.5-multicore.yaml b/daint.cscs.ch/codes/pp-6.5-multicore.yaml index 169404e..9a25c6b 100644 --- a/daint.cscs.ch/codes/pp-6.5-multicore.yaml +++ b/daint.cscs.ch/codes/pp-6.5-multicore.yaml @@ -1,3 +1,4 @@ +--- label: "pp-6.5" description: "PP compiled for daint-mc" input_plugin: "quantumespresso.pp" diff --git a/daint.cscs.ch/codes/projwfc-6.5-multicore.yaml b/daint.cscs.ch/codes/projwfc-6.5-multicore.yaml index 1572998..f416a43 100644 --- a/daint.cscs.ch/codes/projwfc-6.5-multicore.yaml +++ b/daint.cscs.ch/codes/projwfc-6.5-multicore.yaml @@ -1,3 +1,4 @@ +--- label: "projwfc-6.5" description: "PROJWFC compiled for daint-mc" input_plugin: "quantumespresso.projwfc" diff --git a/daint.cscs.ch/codes/pw-6.5-multicore.yaml b/daint.cscs.ch/codes/pw-6.5-multicore.yaml index 80b204a..b161527 100644 --- a/daint.cscs.ch/codes/pw-6.5-multicore.yaml +++ b/daint.cscs.ch/codes/pw-6.5-multicore.yaml @@ -1,3 +1,4 @@ +--- label: "pw-6.5" description: "PW compiled for daint-mc" input_plugin: "quantumespresso.pw" diff --git a/daint.cscs.ch/hybrid-s1005/computer-configure.yaml b/daint.cscs.ch/hybrid-s1005/computer-configure.yaml index f624eba..ae0f602 100644 --- a/daint.cscs.ch/hybrid-s1005/computer-configure.yaml +++ b/daint.cscs.ch/hybrid-s1005/computer-configure.yaml @@ -1,2 +1,3 @@ +--- safe_interval: 60 proxy_command: "ssh -q -Y put_your_username@ela.cscs.ch netcat ela.cscs.ch 22" diff --git a/daint.cscs.ch/hybrid-s1005/computer-setup.yaml b/daint.cscs.ch/hybrid-s1005/computer-setup.yaml index 68540ac..279ddcb 100644 --- a/daint.cscs.ch/hybrid-s1005/computer-setup.yaml +++ b/daint.cscs.ch/hybrid-s1005/computer-setup.yaml @@ -1,3 +1,4 @@ +--- label: "daint-hybrid-s1005" hostname: "daint.cscs.ch" description: "Piz Daint supercomputer at CSCS Lugano, Switzerland, using the hybrid partition. Project s1005" diff --git a/daint.cscs.ch/hybrid-s1005/cp2k-7.1.yaml b/daint.cscs.ch/hybrid-s1005/cp2k-7.1.yaml new file mode 100644 index 0000000..4ab86b5 --- /dev/null +++ b/daint.cscs.ch/hybrid-s1005/cp2k-7.1.yaml @@ -0,0 +1,11 @@ +--- +label: "cp2k-7.1" +description: "CP2K compiled for daint-gpu" +input_plugin: "cp2k" +on_computer: true +remote_abs_path: "/apps/daint/UES/jenkins/7.0.UP02/gpu/easybuild/software/CP2K/7.1-CrayGNU-20.08-cuda/bin/cp2k.psmp" +computer: "daint-hybrid-s1005" +prepend_text: | + module load daint-gpu + module load CP2K/7.1-CrayGNU-20.08-cuda +append_text: " " diff --git a/daint.cscs.ch/hybrid-s1005/cp2k-8.1.yaml b/daint.cscs.ch/hybrid-s1005/cp2k-8.1.yaml new file mode 100644 index 0000000..ee17cbe --- /dev/null +++ b/daint.cscs.ch/hybrid-s1005/cp2k-8.1.yaml @@ -0,0 +1,11 @@ +--- +label: "cp2k-8.1" +description: "CP2K compiled for daint-gpu" +input_plugin: "cp2k" +on_computer: true +remote_abs_path: "/apps/daint/UES/jenkins/7.0.UP02/gpu/easybuild/software/CP2K/8.1-CrayGNU-20.08-cuda/bin/cp2k.psmp" +computer: "daint-hybrid-s1005" +prepend_text: | + module load daint-gpu + module load CP2K/8.1-CrayGNU-20.08-cuda +append_text: " " diff --git a/daint.cscs.ch/hybrid-s1005/pp-6.5.yaml b/daint.cscs.ch/hybrid-s1005/pp-6.5.yaml new file mode 100644 index 0000000..012d64d --- /dev/null +++ b/daint.cscs.ch/hybrid-s1005/pp-6.5.yaml @@ -0,0 +1,11 @@ +--- +label: "pp-6.5" +description: "PP compiled for daint-mc" +input_plugin: "quantumespresso.pp" +on_computer: true +remote_abs_path: "/apps/daint/UES/jenkins/7.0.UP02/mc/easybuild/software/QuantumESPRESSO/6.5-CrayIntel-20.08/bin/pp.x" +computer: "daint-hybrid-s1005" +prepend_text: | + module load daint-mc + module load QuantumESPRESSO/6.5-CrayIntel-20.08 +append_text: " " diff --git a/daint.cscs.ch/hybrid-s1005/projwfc-6.5.yaml b/daint.cscs.ch/hybrid-s1005/projwfc-6.5.yaml new file mode 100644 index 0000000..a766ca6 --- /dev/null +++ b/daint.cscs.ch/hybrid-s1005/projwfc-6.5.yaml @@ -0,0 +1,11 @@ +--- +label: "projwfc-6.5" +description: "PROJWFC compiled for daint-mc" +input_plugin: "quantumespresso.projwfc" +on_computer: true +remote_abs_path: "/apps/daint/UES/jenkins/7.0.UP02/mc/easybuild/software/QuantumESPRESSO/6.5-CrayIntel-20.08/bin/projwfc.x" +computer: "daint-hybrid-s1005" +prepend_text: | + module load daint-mc + module load QuantumESPRESSO/6.5-CrayIntel-20.08 +append_text: " " diff --git a/daint.cscs.ch/hybrid-s1005/pw-6.5.yaml b/daint.cscs.ch/hybrid-s1005/pw-6.5.yaml new file mode 100644 index 0000000..af1e2b3 --- /dev/null +++ b/daint.cscs.ch/hybrid-s1005/pw-6.5.yaml @@ -0,0 +1,11 @@ +--- +label: "pw-6.5" +description: "PW compiled for daint-mc" +input_plugin: "quantumespresso.pw" +on_computer: true +remote_abs_path: "/apps/daint/UES/jenkins/7.0.UP02/mc/easybuild/software/QuantumESPRESSO/6.5-CrayIntel-20.08/bin/pw.x" +computer: "daint-hybrid-s1005" +prepend_text: | + module load daint-mc + module load QuantumESPRESSO/6.5-CrayIntel-20.08 +append_text: " " diff --git a/daint.cscs.ch/hybrid-s904/computer-configure.yaml b/daint.cscs.ch/hybrid-s904/computer-configure.yaml index f624eba..ae0f602 100644 --- a/daint.cscs.ch/hybrid-s904/computer-configure.yaml +++ b/daint.cscs.ch/hybrid-s904/computer-configure.yaml @@ -1,2 +1,3 @@ +--- safe_interval: 60 proxy_command: "ssh -q -Y put_your_username@ela.cscs.ch netcat ela.cscs.ch 22" diff --git a/daint.cscs.ch/hybrid-s904/computer-setup.yaml b/daint.cscs.ch/hybrid-s904/computer-setup.yaml index 2f0231a..9954cdf 100644 --- a/daint.cscs.ch/hybrid-s904/computer-setup.yaml +++ b/daint.cscs.ch/hybrid-s904/computer-setup.yaml @@ -1,3 +1,4 @@ +--- label: "daint-hybrid-s904" hostname: "daint.cscs.ch" description: "Piz Daint supercomputer at CSCS Lugano, Switzerland, using the hybrid partition. Project s904" diff --git a/daint.cscs.ch/hybrid/computer-configure.yaml b/daint.cscs.ch/hybrid/computer-configure.yaml index f624eba..ae0f602 100644 --- a/daint.cscs.ch/hybrid/computer-configure.yaml +++ b/daint.cscs.ch/hybrid/computer-configure.yaml @@ -1,2 +1,3 @@ +--- safe_interval: 60 proxy_command: "ssh -q -Y put_your_username@ela.cscs.ch netcat ela.cscs.ch 22" diff --git a/daint.cscs.ch/hybrid/computer-setup.yaml b/daint.cscs.ch/hybrid/computer-setup.yaml index 6be191b..b315124 100644 --- a/daint.cscs.ch/hybrid/computer-setup.yaml +++ b/daint.cscs.ch/hybrid/computer-setup.yaml @@ -1,3 +1,4 @@ +--- label: "daint-hybrid" hostname: "daint.cscs.ch" description: "Piz Daint supercomputer at CSCS Lugano, Switzerland, using the hybrid partition. HyperThreading is off" diff --git a/daint.cscs.ch/multicore/computer-configure.yaml b/daint.cscs.ch/multicore/computer-configure.yaml index f624eba..ae0f602 100644 --- a/daint.cscs.ch/multicore/computer-configure.yaml +++ b/daint.cscs.ch/multicore/computer-configure.yaml @@ -1,2 +1,3 @@ +--- safe_interval: 60 proxy_command: "ssh -q -Y put_your_username@ela.cscs.ch netcat ela.cscs.ch 22" diff --git a/daint.cscs.ch/multicore/computer-setup.yaml b/daint.cscs.ch/multicore/computer-setup.yaml index 36b311b..d344114 100644 --- a/daint.cscs.ch/multicore/computer-setup.yaml +++ b/daint.cscs.ch/multicore/computer-setup.yaml @@ -1,3 +1,4 @@ +--- label: "daint-mc" hostname: "daint.cscs.ch" description: Piz Daint supercomputer at CSCS Lugano, Switzerland, multicore partition. diff --git a/eiger.cscs.ch/codes/pw-6.7-multicore.yaml b/eiger.cscs.ch/codes/pw-6.7-multicore.yaml index 2e07bb6..8b6b0d4 100644 --- a/eiger.cscs.ch/codes/pw-6.7-multicore.yaml +++ b/eiger.cscs.ch/codes/pw-6.7-multicore.yaml @@ -1,3 +1,4 @@ +--- label: "pw-6.7" description: "QuantumESPRESSO 6.7.0 compiled by CSCS" input_plugin: "quantumespresso.pw" diff --git a/eiger.cscs.ch/multicore-mr0-debug/computer-configure.yaml b/eiger.cscs.ch/multicore-mr0-debug/computer-configure.yaml index 5fbf670..f839fc6 100644 --- a/eiger.cscs.ch/multicore-mr0-debug/computer-configure.yaml +++ b/eiger.cscs.ch/multicore-mr0-debug/computer-configure.yaml @@ -1,2 +1,3 @@ +--- safe_interval: 60 proxy_command: "ssh -q -Y {username}@ela.cscs.ch netcat ela.cscs.ch 22" diff --git a/eiger.cscs.ch/multicore-mr0-debug/computer-setup.yaml b/eiger.cscs.ch/multicore-mr0-debug/computer-setup.yaml index 9292a59..366ab6f 100644 --- a/eiger.cscs.ch/multicore-mr0-debug/computer-setup.yaml +++ b/eiger.cscs.ch/multicore-mr0-debug/computer-setup.yaml @@ -1,3 +1,4 @@ +--- label: "eiger-mc-mr0-debug" hostname: "eiger.cscs.ch" description: Eiger is the production partition on Alps, the HPE Cray EX Supercomputer. diff --git a/eiger.cscs.ch/multicore-mr0-debug/pw-6.7.yaml b/eiger.cscs.ch/multicore-mr0-debug/pw-6.7.yaml new file mode 100644 index 0000000..d6a2391 --- /dev/null +++ b/eiger.cscs.ch/multicore-mr0-debug/pw-6.7.yaml @@ -0,0 +1,11 @@ +--- +label: "pw-6.7" +description: "QuantumESPRESSO 6.7.0 compiled by CSCS" +input_plugin: "quantumespresso.pw" +on_computer: true +remote_abs_path: "/apps/eiger/UES/jenkins/1.4.0/software/QuantumESPRESSO/6.7.0-cpeIntel-21.06/bin/pw.x" +computer: "eiger-mc-mr0-debug" +prepend_text: | + module load cpeIntel/21.06 + module load QuantumESPRESSO/6.7.0 +append_text: " " diff --git a/eiger.cscs.ch/multicore-mr0/computer-configure.yaml b/eiger.cscs.ch/multicore-mr0/computer-configure.yaml index 5fbf670..f839fc6 100644 --- a/eiger.cscs.ch/multicore-mr0/computer-configure.yaml +++ b/eiger.cscs.ch/multicore-mr0/computer-configure.yaml @@ -1,2 +1,3 @@ +--- safe_interval: 60 proxy_command: "ssh -q -Y {username}@ela.cscs.ch netcat ela.cscs.ch 22" diff --git a/eiger.cscs.ch/multicore-mr0/computer-setup.yaml b/eiger.cscs.ch/multicore-mr0/computer-setup.yaml index dc14191..1bfee03 100644 --- a/eiger.cscs.ch/multicore-mr0/computer-setup.yaml +++ b/eiger.cscs.ch/multicore-mr0/computer-setup.yaml @@ -1,3 +1,4 @@ +--- label: "eiger-mc-mr0" hostname: "eiger.cscs.ch" description: Eiger is the production partition on Alps, the HPE Cray EX Supercomputer. diff --git a/fidis.epfl.ch/codes/cp2k-5.1.yaml b/fidis.epfl.ch/codes/cp2k-5.1.yaml index 645dece..c0a072c 100644 --- a/fidis.epfl.ch/codes/cp2k-5.1.yaml +++ b/fidis.epfl.ch/codes/cp2k-5.1.yaml @@ -1,3 +1,4 @@ +--- label: "cp2k-5.1" description: "CP2K 5.1 compiled by SCITAS" input_plugin: "cp2k" diff --git a/fidis.epfl.ch/codes/ddec-09_26_2017.yaml b/fidis.epfl.ch/codes/ddec-09_26_2017.yaml index 5b3f7e4..304dba3 100644 --- a/fidis.epfl.ch/codes/ddec-09_26_2017.yaml +++ b/fidis.epfl.ch/codes/ddec-09_26_2017.yaml @@ -1,3 +1,4 @@ +--- label: "ddec-09_26_2017" description: "chargemol_09_26_2017 precompiled linux/parallel binary from https://sourceforge.net/projects/ddec/files/" input_plugin: "ddec" diff --git a/fidis.epfl.ch/codes/raspa-4467e14.yaml b/fidis.epfl.ch/codes/raspa-4467e14.yaml index b184650..6fbbbf1 100644 --- a/fidis.epfl.ch/codes/raspa-4467e14.yaml +++ b/fidis.epfl.ch/codes/raspa-4467e14.yaml @@ -1,3 +1,4 @@ +--- label: "raspa-4467e14" description: "RASPA2 cloned from https://github.com/iRASPA/RASPA2.git" input_plugin: "raspa" diff --git a/fidis.epfl.ch/codes/zeopp-46ce745.yaml b/fidis.epfl.ch/codes/zeopp-46ce745.yaml index c7399b2..d1fff5f 100644 --- a/fidis.epfl.ch/codes/zeopp-46ce745.yaml +++ b/fidis.epfl.ch/codes/zeopp-46ce745.yaml @@ -1,3 +1,4 @@ +--- label: "zeopp-46ce745" description: "Zeo++ cloned from https://github.com/mharanczyk/zeoplusplus" input_plugin: "zeopp.network" diff --git a/fidis.epfl.ch/fidis-ch-315/computer-configure.yaml b/fidis.epfl.ch/fidis-ch-315/computer-configure.yaml index f4c9bb8..5e7267c 100644 --- a/fidis.epfl.ch/fidis-ch-315/computer-configure.yaml +++ b/fidis.epfl.ch/fidis-ch-315/computer-configure.yaml @@ -1 +1,2 @@ +--- proxy_command: "ssh -q -Y put_your_username@lsmosrv1.epfl.ch netcat fidis.epfl.ch 22" diff --git a/fidis.epfl.ch/fidis-ch-315/computer-setup.yaml b/fidis.epfl.ch/fidis-ch-315/computer-setup.yaml index 6afa65b..185a8d3 100644 --- a/fidis.epfl.ch/fidis-ch-315/computer-setup.yaml +++ b/fidis.epfl.ch/fidis-ch-315/computer-setup.yaml @@ -1,4 +1,4 @@ - +--- label: "fidis-ch-315" hostname: "fidis.epfl.ch" description: fidis EPFL computer diff --git a/fidis.epfl.ch/fidis-ch-315/cp2k-5.1.yaml b/fidis.epfl.ch/fidis-ch-315/cp2k-5.1.yaml new file mode 100644 index 0000000..94eeff2 --- /dev/null +++ b/fidis.epfl.ch/fidis-ch-315/cp2k-5.1.yaml @@ -0,0 +1,14 @@ +--- +label: "cp2k-5.1" +description: "CP2K 5.1 compiled by SCITAS" +input_plugin: "cp2k" +on_computer: true +remote_abs_path: "/ssoft/spack/cornalin/v2/opt/spack/linux-rhel7-x86_E5v4_Mellanox/intel-17.0.2/cp2k-5.1-gke4ujsx5qhx6zt7ncfo22hajqhp6n6b/bin/cp2k.popt" +computer: "fidis-ch-315" +prepend_text: | + source /ssoft/spack/bin/slmodules.sh -r deprecated + module load intel + module load intel-mpi intel-mkl + module load cp2k/5.1-mpi + export CP2K_DATA_DIR=/work/lsmo/aiida-lsmo-codes/data/cp2k/data +append_text: " " diff --git a/fidis.epfl.ch/fidis-ch-315/ddec-09_26_2017.yaml b/fidis.epfl.ch/fidis-ch-315/ddec-09_26_2017.yaml new file mode 100644 index 0000000..33f4bc5 --- /dev/null +++ b/fidis.epfl.ch/fidis-ch-315/ddec-09_26_2017.yaml @@ -0,0 +1,9 @@ +--- +label: "ddec-09_26_2017" +description: "chargemol_09_26_2017 precompiled linux/parallel binary from https://sourceforge.net/projects/ddec/files/" +input_plugin: "ddec" +on_computer: true +remote_abs_path: "/work/lsmo/aiida-lsmo-codes/bin/chargemol_09_26_2017_ubu18" +computer: "fidis-ch-315" +prepend_text: " " +append_text: " " diff --git a/fidis.epfl.ch/fidis-serial/computer-configure.yaml b/fidis.epfl.ch/fidis-serial/computer-configure.yaml index f4c9bb8..5e7267c 100644 --- a/fidis.epfl.ch/fidis-serial/computer-configure.yaml +++ b/fidis.epfl.ch/fidis-serial/computer-configure.yaml @@ -1 +1,2 @@ +--- proxy_command: "ssh -q -Y put_your_username@lsmosrv1.epfl.ch netcat fidis.epfl.ch 22" diff --git a/fidis.epfl.ch/fidis-serial/computer-setup.yaml b/fidis.epfl.ch/fidis-serial/computer-setup.yaml index 66c7fa0..9b40b64 100644 --- a/fidis.epfl.ch/fidis-serial/computer-setup.yaml +++ b/fidis.epfl.ch/fidis-serial/computer-setup.yaml @@ -1,3 +1,4 @@ +--- label: "fidis-serial" hostname: "fidis.epfl.ch" description: Fidis EPFL computer using serial partition diff --git a/fidis.epfl.ch/fidis-serial/raspa-4467e14.yaml b/fidis.epfl.ch/fidis-serial/raspa-4467e14.yaml new file mode 100644 index 0000000..193cdb6 --- /dev/null +++ b/fidis.epfl.ch/fidis-serial/raspa-4467e14.yaml @@ -0,0 +1,12 @@ +--- +label: "raspa-4467e14" +description: "RASPA2 cloned from https://github.com/iRASPA/RASPA2.git" +input_plugin: "raspa" +on_computer: true +remote_abs_path: "/work/lsmo/aiida-lsmo-codes/bin/simulate_4467e14_fidis" +computer: "fidis-serial" +prepend_text: | + export RASPA_DIR=/work/lsmo/aiida-lsmo-codes/data/raspa + export DYLD_LIBRARY_PATH=/work/lsmo/aiida-lsmo-codes/lib/raspa_4467e14_fidis + export LD_LIBRARY_PATH=/work/lsmo/aiida-lsmo-codes/lib/raspa_4467e14_fidis +append_text: " " diff --git a/fidis.epfl.ch/fidis-serial/zeopp-46ce745.yaml b/fidis.epfl.ch/fidis-serial/zeopp-46ce745.yaml new file mode 100644 index 0000000..59de5f4 --- /dev/null +++ b/fidis.epfl.ch/fidis-serial/zeopp-46ce745.yaml @@ -0,0 +1,9 @@ +--- +label: "zeopp-46ce745" +description: "Zeo++ cloned from https://github.com/mharanczyk/zeoplusplus" +input_plugin: "zeopp.network" +on_computer: true +remote_abs_path: "/work/lsmo/aiida-lsmo-codes/bin/network_46ce745_ubu18" +computer: "fidis-serial" +prepend_text: " " +append_text: " " diff --git a/fidis.epfl.ch/fidis/computer-configure.yaml b/fidis.epfl.ch/fidis/computer-configure.yaml index f4c9bb8..5e7267c 100644 --- a/fidis.epfl.ch/fidis/computer-configure.yaml +++ b/fidis.epfl.ch/fidis/computer-configure.yaml @@ -1 +1,2 @@ +--- proxy_command: "ssh -q -Y put_your_username@lsmosrv1.epfl.ch netcat fidis.epfl.ch 22" diff --git a/fidis.epfl.ch/fidis/computer-setup.yaml b/fidis.epfl.ch/fidis/computer-setup.yaml index 3337c9d..f313de8 100644 --- a/fidis.epfl.ch/fidis/computer-setup.yaml +++ b/fidis.epfl.ch/fidis/computer-setup.yaml @@ -1,4 +1,4 @@ - +--- label: "fidis" hostname: "fidis.epfl.ch" description: fidis EPFL computer diff --git a/paratera/tianhe-2/README b/paratera/tianhe-2/README index 301e501..fd7c74d 100644 --- a/paratera/tianhe-2/README +++ b/paratera/tianhe-2/README @@ -1,6 +1,6 @@ #### NOTE The hostname of the computer maybe different depend on the proxy host provide by paratera. -If the username is `@` then the user's aiida scratch directory should be setting to `/PARA//aiida`. +If the username is `@` then the user's aiida scratch directory should be setting to `/PARA//aiida`. For example, if the username to login to the server is `pp00@GZ` the user directory after login would be seems like `/PARA/pp00/`. diff --git a/paratera/tianhe-2/computer-configure.yaml b/paratera/tianhe-2/computer-configure.yaml index 532358e..dbfccf8 100644 --- a/paratera/tianhe-2/computer-configure.yaml +++ b/paratera/tianhe-2/computer-configure.yaml @@ -1,5 +1,5 @@ --- -port: 2200 -allow_agent: False -safe_interval: 60.0 -use_login_shell: True +port: 2200 +allow_agent: false +safe_interval: 60.0 +use_login_shell: true diff --git a/paratera/tianhe-2/computer-setup.yaml b/paratera/tianhe-2/computer-setup.yaml index e36c33c..d021c22 100644 --- a/paratera/tianhe-2/computer-setup.yaml +++ b/paratera/tianhe-2/computer-setup.yaml @@ -10,4 +10,3 @@ mpirun_command: 'srun -n {tot_num_mpiprocs}' mpiprocs_per_machine: 24 prepend_text: '' append_text: '' -