- Ensure CI tests fail when a subtask fails

- Clean up stderr redirect - Attempt to fix openmp / openblas pinning - Since conda build is in base environment, override package build and staging location to be in the current environment - Remove --use-local (which points to base) and instead use explicit channel location in current env
simonsobs · Feb 13, 2024 · cdbf1c2 · cdbf1c2
1 parent c4b9e9d
commit cdbf1c2
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Showing 11 changed files with 137 additions and 107 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -43,34 +43,34 @@ jobs:
 
       - name: Check Conda Config
         run: |
-          source ~/conda/etc/profile.d/conda.sh
-          conda activate base
-          conda info
-          conda list
-          conda config --show-sources
+          source ~/conda/etc/profile.d/conda.sh &&
+          conda activate base &&
+          conda info &&
+          conda list &&
+          conda config --show-sources &&
           conda config --show
 
       - name: Install
         run: |
-          source ~/conda/etc/profile.d/conda.sh
-          conda activate base
-          pyver=${{ matrix.python }}
-          sed -i -e "s/python=3\.10/python=${pyver}/" ./config/default/packages_conda.txt
-          cat ./config/default/packages_conda.txt
+          source ~/conda/etc/profile.d/conda.sh &&
+          conda activate base &&
+          pyver=${{ matrix.python }} &&
+          sed -i -e "s/python=3\.*/python=${pyver}/" ./config/default/packages_conda.txt &&
+          cat ./config/default/packages_conda.txt &&
           ./soconda.sh -e soconda -v CI
 
       - name: Run Tests
         run: |
-          source ~/conda/etc/profile.d/conda.sh
-          conda activate "soconda_CI"
-          export OMP_NUM_THREADS=2
-          export MPI_DISABLE=1
-          export CI=1
-          python3 -c 'import scipy; import toast'
-          python3 -c 'import toast.tests; toast.tests.run()'
-          git clone --depth=1 --single-branch --branch=master https://github.com/simonsobs/sotodlib.git
-          pushd sotodlib
-          python3 -m unittest
-          popd
-          unset MPI_DISABLE
+          source ~/conda/etc/profile.d/conda.sh &&
+          conda activate "soconda_CI" &&
+          export OMP_NUM_THREADS=2 &&
+          export MPI_DISABLE=1 &&
+          export CI=1 &&
+          python3 -c 'import scipy; import toast; print(toast.__version__)' &&
+          python3 -c 'import toast.tests; toast.tests.run()' &&
+          git clone --depth=1 --single-branch --branch=master https://github.com/simonsobs/sotodlib.git &&
+          pushd sotodlib &&
+          python3 -m unittest &&
+          popd &&
+          unset MPI_DISABLE &&
           unset OMP_NUM_THREADS
diff --git a/deploy/install_nersc_tag.sh b/deploy/install_nersc_tag.sh
@@ -39,13 +39,13 @@ fi
 # always created.
 
 # Update the persistent git checkout and find the most recent tag
-pushd "${git_dir}" 2>&1 >/dev/null
+pushd "${git_dir}" >/dev/null 2>&1
 git checkout main
 git fetch --tags
 git rebase origin/main
 git remote prune origin
 latest=$(git describe --tags $(git rev-list --tags --max-count=1))
-popd 2>&1 >/dev/null
+popd >/dev/null 2>&1
 
 # See if we already have this tag installed
 found=no
@@ -74,7 +74,7 @@ today=$(date +%Y%m%d)
 log_file="${log_dir}/check_tags_${host}_${now}"
 
 # Create the log file
-echo "Starting at ${now}" 2>&1 > "${log_file}"
+echo "Starting at ${now}" > "${log_file}"
 
 # Get the module file version that will be installed
 mod_ver="${today}_${latest}"
@@ -83,26 +83,26 @@ send_log=no
 annoy="${git_dir}/.already_annoyed"
 remain=$(get_common_free_gb)
 if (( remain < typical )); then
-    echo "Only ${remain} GB are available in /global/common/software/sobs" 2>&1 >> "${log_file}"
-    echo "Installing latest tag requires approximately ${typical} GB" 2>&1 >> "${log_file}"
-    echo "SKIPPING until disk space is cleared." 2>&1 >> "${log_file}"
+    echo "Only ${remain} GB are available in /global/common/software/sobs" >> "${log_file}"
+    echo "Installing latest tag requires approximately ${typical} GB" >> "${log_file}"
+    echo "SKIPPING until disk space is cleared." >> "${log_file}"
     if [ ! -e "${annoy}" ]; then
         send_log=yes
         touch "${annoy}"
     fi
 else
     send_log=yes
     rm -f "${git_dir}/.already_annoyed"
-    echo "Latest tag '${latest}' not found, installing..." 2>&1 >> "${log_file}"
-    echo "Note: ${remain} GB are available in /global/common/software/sobs" 2>&1 >> "${log_file}"
-    echo "Installing latest tag requires approximately ${typical} GB" 2>&1 >> "${log_file}"
+    echo "Latest tag '${latest}' not found, installing..." >> "${log_file}"
+    echo "Note: ${remain} GB are available in /global/common/software/sobs" >> "${log_file}"
+    echo "Installing latest tag requires approximately ${typical} GB" >> "${log_file}"
     install_log=$(eval "${git_dir}/deploy/install_${host}.sh" "${latest}")
     if [ -f "${install_log}" ]; then
         # There were no errors, and the log file was returned
-        cat "${install_log}" 2>&1 >> "${log_file}"
+        cat "${install_log}" >> "${log_file}"
     else
         # The script must have printed out some errors
-        echo "${install_log}" 2>&1 >> "${log_file}"
+        echo "${install_log}" >> "${log_file}"
     fi
 fi
 
@@ -114,7 +114,7 @@ if [ -e "${mod_latest}" ]; then
     rm -f "${mod_dir}/stable.lua" \
     && ln -s "${mod_latest}" "${mod_dir}/stable.lua"
 else
-    echo "ERROR:  module file ${mod_latest} was not created- leaving stable symlink" 2>&1 >> "${log_file}"
+    echo "ERROR:  module file ${mod_latest} was not created- leaving stable symlink" >> "${log_file}" 
 fi
 
 echo "Finished installing tag '${latest}' on host ${NERSC_HOST} at $(date +%Y%m%d-%H%M%S)" >> "${log_file}"
@@ -124,14 +124,14 @@ if [ "${send_log}" = "yes" ]; then
     slack_web_hook=${SLACKBOT_SOCONDA}
 
     if [ "x${slack_web_hook}" = "x" ]; then
-        echo "Environment variable SLACKBOT_SOCONDA not set- skipping notifications" 2>&1 >> "${log_file}"
+        echo "Environment variable SLACKBOT_SOCONDA not set- skipping notifications" >> "${log_file}"
     else
         # Create the JSON payload.
         slackjson="${log_file}_slack.json"
         headtail=12
         echo -e "{\"text\":\"soconda install tag (log at \`${log_file}\`):\n\`\`\`$(head -n ${headtail} ${log_file} | sed -e "s|'|\\\'|g")\`\`\`\n(Snip)\n\`\`\`$(tail -n ${headtail} ${log_file} | sed -e "s|'|\\\'|g")\`\`\`\"}" > "${slackjson}"
         # Post it.
         slackerror=$(curl -X POST -H 'Content-type: application/json' --data "$(cat ${slackjson})" ${slack_web_hook})
-        echo "Slack API post  ${slackerror}" 2>&1 >> "${log_file}"
+        echo "Slack API post  ${slackerror}" >> "${log_file}"
     fi
 fi
diff --git a/deploy/install_perlmutter.sh b/deploy/install_perlmutter.sh
@@ -49,34 +49,34 @@ if [ -d "${clone_dir}" ]; then
     rm -rf "${clone_dir}"
 fi
 
-git clone --depth=1 --single-branch --branch=${version} https://github.com/simonsobs/soconda.git "${clone_dir}" 2>&1 >> "${logfile}"
+git clone --depth=1 --single-branch --branch=${version} https://github.com/simonsobs/soconda.git "${clone_dir}" >> "${logfile}" 2>&1
 
 # Activate the base environment and keep it up to date.
 source "${base_dir}/etc/profile.d/conda.sh"
-conda activate base 2>&1 >> "${logfile}"
-conda update --yes -n base conda conda-build 2>&1 >> "${logfile}"
-conda update --yes --all -n base 2>&1 >> "${logfile}"
+conda activate base >> "${logfile}" 2>&1
+conda update --yes -n base conda conda-build >> "${logfile}" 2>&1
+conda update --yes --all -n base >> "${logfile}" 2>&1
 
 # Build things from the temp directory
 
-pushd "${clone_dir}" 2>&1 >/dev/null
+pushd "${clone_dir}" >/dev/null 2>&1
 mkdir -p "build"
-pushd "build" 2>&1 >/dev/null
+pushd "build" >/dev/null 2>&1
 
 export MPICC="cc"
 
 eval "${clone_dir}/soconda.sh" \
     -c "perlmutter" \
     -e "${env_name}" \
     -v "${env_version}" \
-    -m "${module_dir}" 2>&1 >> "${logfile}"
+    -m "${module_dir}" >> "${logfile}" 2>&1
 
-popd 2>&1 >/dev/null
-popd 2>&1 >/dev/null
+popd >/dev/null 2>&1
+popd >/dev/null 2>&1
 
 # Update permissions
-chmod -R g-w,g+rX "${env_name}_${env_version}" 2>&1 >> "${logfile}"
-chmod -R g-w,g+rX "${module_dir}/soconda" 2>&1 >> "${logfile}"
+chmod -R g-w,g+rX "${env_name}_${env_version}" >> "${logfile}" 2>&1
+chmod -R g-w,g+rX "${module_dir}/soconda" >> "${logfile}" 2>&1
 
 # Return name of log file
 echo "${logfile}"
diff --git a/pkgs/libactpol/meta.yaml b/pkgs/libactpol/meta.yaml
@@ -20,12 +20,12 @@ build:
 requirements:
   build:
     - {{ compiler('c') }}
-    - llvm-openmp # [osx or linux]
+    - llvm-openmp
+    - _openmp_mutex * *_llvm
   host:
-    - llvm-openmp # [osx or linux]
+    - llvm-openmp
+    - _openmp_mutex * *_llvm
     - openblas * openmp_*
-    - libopenblas * openmp_*
-    - libblas * *openblas
     - liblapack * *openblas
     - automake
     - autoconf
@@ -42,11 +42,12 @@ requirements:
     # https://github.com/conda-forge/perl-feedstock/issues/56
     - libxcrypt1   # [linux]
   run:
-    - llvm-openmp # [osx or linux]
+    - llvm-openmp
+    - _openmp_mutex * *_llvm
     - openblas * openmp_*
-    - libopenblas * openmp_*
-    - libblas * *openblas
     - liblapack * *openblas
+    - {{ pin_compatible('openblas') }}
+    - {{ pin_compatible('liblapack') }}
     - {{ pin_compatible('libactpol_deps') }}
     - {{ pin_compatible('cfitsio') }}
     - {{ pin_compatible('wcslib') }}

diff --git a/pkgs/libactpol_deps/meta.yaml b/pkgs/libactpol_deps/meta.yaml
@@ -21,12 +21,12 @@ requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('fortran') }}
-    - llvm-openmp # [osx or linux]
+    - llvm-openmp
+    - _openmp_mutex * *_llvm
   host:
-    - llvm-openmp # [osx or linux]
+    - llvm-openmp
+    - _openmp_mutex * *_llvm
     - openblas * openmp_*
-    - libopenblas * openmp_*
-    - libblas * *openblas
     - liblapack * *openblas
     - automake
     - autoconf
@@ -35,11 +35,12 @@ requirements:
     - make
     - zziplib
   run:
-    - llvm-openmp # [osx or linux]
+    - llvm-openmp
+    - _openmp_mutex * *_llvm
     - openblas * openmp_*
-    - libopenblas * openmp_*
-    - libblas * *openblas
     - liblapack * *openblas
+    - {{ pin_compatible('openblas') }}
+    - {{ pin_compatible('liblapack') }}
     - {{ pin_compatible('zziplib') }}
 
 test:

diff --git a/pkgs/moby2/meta.yaml b/pkgs/moby2/meta.yaml
@@ -21,35 +21,37 @@ build:
 requirements:
   build:
     - {{ compiler('c') }}
-    - llvm-openmp # [osx or linux]
+    - llvm-openmp
+    - _openmp_mutex * *_llvm
   host:
-    - llvm-openmp # [osx or linux]
+    - llvm-openmp
+    - _openmp_mutex * *_llvm
     - openblas * openmp_*
-    - libopenblas * openmp_*
-    - libblas * *openblas
     - liblapack * *openblas
     - python
     - fftw
     - gsl
     - libactpol
     - future
     - numpy=1.26.*
+    - scipy
     # Although not a dependency, we put numba here to force
     # building with a numba-compatible numpy version
     - numba
   run:
-    - llvm-openmp # [osx or linux]
+    - llvm-openmp
+    - _openmp_mutex * *_llvm
     - openblas * openmp_*
-    - libopenblas * openmp_*
-    - libblas * *openblas
     - liblapack * *openblas
     - python
+    - {{ pin_compatible('openblas') }}
+    - {{ pin_compatible('liblapack') }}
+    - {{ pin_compatible('scipy') }}
+    - {{ pin_compatible('numpy') }}
     - {{ pin_compatible('fftw') }}
     - {{ pin_compatible('gsl') }}
     - {{ pin_compatible('libactpol') }}
-    - {{ pin_compatible('numpy') }}
     - future
-    - scipy
     - matplotlib
     - astropy
     - ephem

diff --git a/pkgs/pixell/meta.yaml b/pkgs/pixell/meta.yaml
@@ -20,12 +20,12 @@ requirements:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - {{ compiler('fortran') }}
-    - llvm-openmp # [osx or linux]
+    - llvm-openmp
+    - _openmp_mutex * *_llvm
   host:
-    - llvm-openmp # [osx or linux]
+    - llvm-openmp
+    - _openmp_mutex * *_llvm
     - openblas * openmp_*
-    - libopenblas * openmp_*
-    - libblas * *openblas
     - liblapack * *openblas
     - automake
     - autoconf
@@ -46,14 +46,15 @@ requirements:
     # https://github.com/conda-forge/perl-feedstock/issues/56
     - libxcrypt1   # [linux]
   run:
-    - llvm-openmp # [osx or linux]
+    - llvm-openmp
+    - _openmp_mutex * *_llvm
     - openblas * openmp_*
-    - libopenblas * openmp_*
-    - libblas * *openblas
     - liblapack * *openblas
     - python
+    - {{ pin_compatible('openblas') }}
+    - {{ pin_compatible('liblapack') }}
+    - {{ pin_compatible('scipy') }}
     - {{ pin_compatible('numpy') }}
-    - scipy
     - astropy
     - healpy
     - matplotlib

diff --git a/pkgs/qpoint/meta.yaml b/pkgs/qpoint/meta.yaml
@@ -20,20 +20,32 @@ build:
 requirements:
   build:
     - {{ compiler('c') }}
-    - llvm-openmp # [osx or linux]
+    - llvm-openmp
+    - _openmp_mutex * *_llvm
   host:
-    - llvm-openmp # [osx or linux]
+    - llvm-openmp
+    - _openmp_mutex * *_llvm
+    - openblas * openmp_*
+    - liblapack * *openblas
     - python
     - setuptools
     - numpy=1.26.*
+    - scipy
     # Although not a dependency, we put numba here to force
     # building with a numba-compatible numpy version
     - numba
     # Adding astropy as a host dependency will download the current
     # IERS data and store it in the package
     - astropy
   run:
+    - llvm-openmp
+    - _openmp_mutex * *_llvm
+    - openblas * openmp_*
+    - liblapack * *openblas
     - python
+    - {{ pin_compatible('openblas') }}
+    - {{ pin_compatible('liblapack') }}
+    - {{ pin_compatible('scipy') }}
     - {{ pin_compatible('numpy') }}
 
 test: