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.

.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 <computername>` 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

.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/[email protected]
+
   deploy-gh-pages:
+    needs: pre-commit
     runs-on: ubuntu-latest
 
     steps:

.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/[email protected]

.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.

.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 |
+          )$

.yamllint

@@ -0,0 +1,5 @@
+---
+extends: default
+
+rules:
+    line-length: disable

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.
 

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"

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"

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"

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"

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"

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"

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"

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"

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"

daint.cscs.ch/hybrid-s1005/computer-configure.yaml

@@ -1,2 +1,3 @@
+---
 safe_interval: 60
 proxy_command: "ssh -q -Y [email protected] netcat ela.cscs.ch 22"

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"

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: " "

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: " "

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: " "

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: " "

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: " "

daint.cscs.ch/hybrid-s904/computer-configure.yaml

@@ -1,2 +1,3 @@
+---
 safe_interval: 60
 proxy_command: "ssh -q -Y [email protected] netcat ela.cscs.ch 22"

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"

daint.cscs.ch/hybrid/computer-configure.yaml

@@ -1,2 +1,3 @@
+---
 safe_interval: 60
 proxy_command: "ssh -q -Y [email protected] netcat ela.cscs.ch 22"

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"

daint.cscs.ch/multicore/computer-configure.yaml

@@ -1,2 +1,3 @@
+---
 safe_interval: 60
 proxy_command: "ssh -q -Y [email protected] netcat ela.cscs.ch 22"

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.

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"

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"

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.

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: " "

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"

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.

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"

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"

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"

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"

fidis.epfl.ch/fidis-ch-315/computer-configure.yaml

@@ -1 +1,2 @@
+---
 proxy_command: "ssh -q -Y [email protected] netcat fidis.epfl.ch 22"

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

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: " "

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: " "

fidis.epfl.ch/fidis-serial/computer-configure.yaml

@@ -1 +1,2 @@
+---
 proxy_command: "ssh -q -Y [email protected] netcat fidis.epfl.ch 22"

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

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: " "

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: " "

fidis.epfl.ch/fidis/computer-configure.yaml

@@ -1 +1,2 @@
+---
 proxy_command: "ssh -q -Y [email protected] netcat fidis.epfl.ch 22"