Merge branch 'eve-guix' into 'master'

[ci] Deploy guix container to eve

See merge request ogs/ogs!4722

CMakeLists.txt

@@ -208,11 +208,6 @@ include(packaging/Pack)
 
 # ---- Subdirectories ----
 include_directories(${PROJECT_SOURCE_DIR})
-# xdmfdiff
-if(OGS_BUILD_TESTING)
-    add_subdirectory(Tests/xdmfdiff)
-endif()
-
 include(scripts/cmake/CheckHeaderCompilation.cmake)
 
 add_subdirectory(Applications)
@@ -233,6 +228,7 @@ if(OGS_BUILD_CLI OR OGS_BUILD_UTILS OR OGS_BUILD_TESTING)
     add_subdirectory(ParameterLib)
     add_subdirectory(MaterialLib)
     add_subdirectory(ProcessLib)
+    add_subdirectory(Tests/xdmfdiff)
 endif()
 if(OGS_BUILD_TESTING AND NOT _IS_SUBPROJECT)
     add_subdirectory(Tests)

scripts/ci/jobs/build-guix.yml

@@ -1,14 +1,56 @@
+variables:
+  GUIX_PETSC_CONTAINER: /data/ogs/apptainer/guix/ogs-petsc-ssd_head.squashfs
+  GUIX_COMMIT: v1.4.0
+
 build guix:
   stage: build
   tags: [guix]
   needs: []
   variables:
     GIT_SUBMODULE_STRATEGY: recursive
+    GUIX_COMMIT: v1.4.0
   rules:
     - if: '$CI_COMMIT_BRANCH == "master"'
       allow_failure: true
     - when: manual
       allow_failure: true
   script:
-    - guix time-machine --commit=v1.4.0 -- build -L $PWD/.guix/modules ogs-ssd
-    - guix time-machine --commit=v1.4.0 -- build -L $PWD/.guix/modules ogs-petsc-ssd
+    # SteadyStateDiffusion only!
+    - guix time-machine --commit=${GUIX_COMMIT} -- build -L $PWD/.guix/modules ogs-ssd
+    - guix time-machine --commit=${GUIX_COMMIT} -- build -L $PWD/.guix/modules ogs-petsc-ssd
+
+deploy guix container eve:
+  stage: build
+  tags: [guix]
+  needs: []
+  variables:
+    GIT_SUBMODULE_STRATEGY: recursive
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "master"'
+  script:
+    # All processes.
+    - image=$( guix time-machine --commit=${GUIX_COMMIT} -- pack --no-substitutes -L $PWD/.guix/modules -S /bin=bin -RR --format=squashfs bash ogs-petsc | tee | tail -1 )
+    - echo "Image $image"
+    - ssh [email protected] rm -f ${GUIX_PETSC_CONTAINER}
+    - scp $image [email protected]:${GUIX_PETSC_CONTAINER}
+
+test guix container eve:
+  stage: build
+  tags: [frontend2]
+  needs: ["deploy guix container eve"]
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "master"'
+  script:
+    - export work_dir=/work/$USER/builds/$CI_JOB_ID
+    - echo "Working directory is ${work_dir}"
+    - mkdir -p $work_dir
+    - cp -r ${CI_PROJECT_DIR}/Tests/Data/EllipticPETSc $work_dir/
+    - export prj_file=${work_dir}/EllipticPETSc/cube_1e3_XDMF_np3.prj
+    - jid=$(sbatch --chdir=${work_dir} --job-name=test-guix-container --mem-per-cpu=1G --ntasks=3 --output=/work/%u/%x_%j.out --parsable --time=1 --partition=rocky-9 --wrap="srun apptainer exec ${GUIX_PETSC_CONTAINER} ogs ${prj_file}")
+    # - touch /work/$USER/ci_log_$jid.out # required on frontend1, tail -F does not recognize file created
+    - while true; do grep "$jid" < <(squeue -hj "$jid") || break; sleep 10; done &> /dev/null & tail -F /work/$USER/test-guix-container_$jid.out --pid="$!" || true
+    - exit_code=$(sacct -j $jid.0 --format=ExitCode --noheader | cut -d':' -f1)
+    - cd $work_dir
+    - apptainer exec ${GUIX_PETSC_CONTAINER} xdmfdiff -a pressure -b pressure --rel 1e-3 --abs 1e-3 EllipticPETSc/cube_1e3_np3.xdmf cube_1e3_np3_cube_1x1x1_hex_1e3.xdmf
+    - apptainer exec ${GUIX_PETSC_CONTAINER} xdmfdiff -a v -b v --rel 1e-3 --abs 1e-3 EllipticPETSc/cube_1e3_np3.xdmf cube_1e3_np3_cube_1x1x1_hex_1e3.xdmf
+    - exit ${exit_code}

scripts/cmake/Dependencies.cmake

@@ -315,7 +315,7 @@ if(OGS_USE_PETSC)
     endif()
 endif()
 
-if(OGS_BUILD_TESTING)
+if(OGS_BUILD_TESTING OR OGS_BUILD_CLI OR OGS_BUILD_UTILS)
     set(XDMF_LIBNAME OgsXdmf CACHE STRING "")
     CPMAddPackage(
         NAME xdmf

web/content/docs/devguide/environments/working-on-eve/index.md

@@ -15,25 +15,9 @@ aliases = ["/docs/devguide/advanced/working-on-eve"]
 
 Members of the Department Environmental Informatics of the Helmholtz Centre for Environmental Research - UFZ can use the `frontend1`- and `frontend2`-machines from the Eve cluster system.
 
-<div class='note'>
-You need to opt-in to use the [EasyBuild modules](https://wiki.ufz.de/eve/index.php/EasyBuild)! To do so follow these steps:
-
-- Login to `frontend1` or `frontend2`
-- Run `touch ~/.easybuild-yes`
-- `exit` and re-login
-
-Also on eve the installed git module (2.10) is over 2 years old and we recommend using a newer module:
-
-```bash
-ml use /global/apps/modulefiles
-ml git/2.20.1
-```
-
-</div>
-
 ## Run OGS within a container
 
-Eve has [Singularity](https://www.sylabs.io/singularity) container runtime installed so you can simply download a prebuilt container and run OGS inside it. See the [user guide]({{< ref "container" >}}) for more information.
+Eve has the [Apptainer/Singularity](https://apptainer.org) container runtime installed so you can simply download a prebuilt container and run OGS inside it. See the [user guide]({{< ref "container" >}}) for more information.
 
 ## Build OGS-6
 
@@ -44,30 +28,3 @@ source scripts/env/eve/cli.sh
 ```
 
 Then do the [build configuration]({{< ref "build-configuration.md" >}}) and [build]({{< ref "/docs/devguide/getting-started/build.md" >}}) the project.
-
-## Optional steps
-
-### Install and use Conan
-
-Follow the instructions on using Python's `virtualenv` [on the Eve-wiki](https://wiki.ufz.de/eve/index.php/Python#virtualenv) for setting up a local Python environment. Then you can `pip install conan` and use Conan.
-
-### Additional Features
-
-Generating Doxygen documentation:
-
-```bash
-module load Doxygen/1.8.14
-```
-
-You can build with Ninja:
-
-```bash
-module load ninja/1.9.0
-```
-
-## Build OGS-5
-
-```bash
-module load CMake/3.11.4
-module load GCC/6.4.0-2.28
-```

web/content/docs/userguide/basics/container/index.md

@@ -27,6 +27,10 @@ To **build** OGS with the help of a container go to the [Developer Guide]({{< re
 
 ### Get a container image
 
+#### Recommended option on EVE: use prebuilt images
+
+On the EVE cluster system (UFZ) you can use prebuilt images which can be used for [PETSc-based cluster jobs]({{< ref "parallel_computing_mpi.md#2a-use-a-container-to-launch-mpi-ogs" >}}).
+
 #### Option: Download a release image (preferred)
 
 Simply download an image from the [releases]({{< ref "/releases" >}}) page.

web/content/docs/userguide/features/parallel_computing_mpi.md

@@ -159,19 +159,17 @@ Here is an example of a job script for the SLURM system on EVE:
 #SBATCH [email protected]
 #SBATCH --mail-type=BEGIN,END
 
-###source /etc/profile.d/000-modules.sh
 export MODULEPATH="/software/easybuild-broadwell/modules/all/Core:/software/modulefiles"
 module load  foss/2020b   petsc-bilke/3.16.5_foss2020b
 module load  OpenMPI/4.0.5  HDF5/1.10.7  GMP/6.2.0
 
 APP="/home/wwang/code/ogs6/exe_petsc/bin/ogs"
+PRJ_FILE="/home/wwang/data_D/project/AREHS/HM_3D/simHM_glaciation.prj"
 /bin/echo In directory: `pwd`
 /bin/echo Number of CPUs: $SLURM_CPUS_PER_TASK
 /bin/echo File name: $1
 
-##load $APP
-
-srun -n "$SLURM_NTASKS"  $APP /home/wwang/data_D/project/AREHS/HM_3D/simHM_glaciation.prj -o /home/wwang/data_D/project/AREHS/HM_3D/output
+srun $APP $PRJ_FILE -o /home/wwang/data_D/project/AREHS/HM_3D/output
 ```
 
 In the job script for EVE, `module load  foss/2020b` must be presented, and
@@ -190,6 +188,21 @@ Once the job script is ready, you can
 For the detailed syntax of job script of SLURM for EVE, please visit <https://wiki.ufz.de/eve/>
 (user login required).
 
+### 2a. Use a container to launch MPI OGS
+
+A prebuilt container with `ogs` (current master) is available at:
+
+* `/data/ogs/apptainer/guix/ogs-petsc-ssd_head.squashfs`
+
+You need to modify your submit script, e.g.:
+
+```bash
+...
+#SBATCH ...
+
+srun apptainer exec /data/ogs/apptainer/guix/ogs-petsc-ssd_head.squashfs ogs $PRJ_FILE
+```
+
 ### 3. Check results
 
 There are two output types available, VTK and XDMF.