Merge pull request #3975 from boegel/apptainer

extend (experimental) support for generating container images with Apptainer

.github/workflows/container_tests.yml

@@ -1,5 +1,5 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
-name: Tests for container support
+name: Tests for Singularity container support
 on: [push, pull_request]
 
 permissions:

.github/workflows/container_tests_apptainer.yml

@@ -0,0 +1,96 @@
+# documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
+name: Tests for Apptainer container support
+on: [push, pull_request]
+
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
+concurrency:
+  group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        python: [2.7, 3.7]
+        apptainer: [1.0.0, 1.1.7]
+      fail-fast: false
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{matrix.python}}
+        architecture: x64
+
+    - name: install OS & Python packages
+      run: |
+        # for building CentOS 7 container images
+        sudo apt-get install rpm
+        sudo apt-get install dnf
+        # for modules tool
+        sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev
+        # fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082
+        # needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists
+        if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then
+            sudo ln -s /usr/lib/x86_64-linux-gnu/lua/5.2/posix_c.so /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so
+        fi
+
+    - name: install Lmod
+      run: |
+          # avoid downloading modules tool sources into easybuild-framework dir
+          cd $HOME
+          export INSTALL_DEP=$GITHUB_WORKSPACE/easybuild/scripts/install_eb_dep.sh
+          # install Lmod
+          source $INSTALL_DEP Lmod-8.4.27 $HOME
+          # changes in environment are not passed to other steps, so need to create files...
+          echo $MOD_INIT > mod_init
+          echo $PATH > path
+          if [ ! -z $MODULESHOME ]; then echo $MODULESHOME > moduleshome; fi
+
+    - name: install Apptainer
+      run: |
+        curl -OL https://github.com/apptainer/apptainer/releases/download/v${{matrix.apptainer}}/apptainer_${{matrix.apptainer}}_amd64.deb
+        sudo apt install ./apptainer*.deb
+        # Apptainer provides both apptainer and singularity commands
+        apptainer --version
+        singularity --version
+
+    - name: install sources
+      run: |
+          # install from source distribution tarball, to test release as published on PyPI
+          python setup.py sdist
+          ls dist
+          export PREFIX=/tmp/$USER/$GITHUB_SHA
+          pip install --prefix $PREFIX dist/easybuild-framework*tar.gz
+          pip install --prefix $PREFIX https://github.com/easybuilders/easybuild-easyblocks/archive/develop.tar.gz
+
+    - name: run test
+      run: |
+          # run tests *outside* of checked out easybuild-framework directory,
+          # to ensure we're testing installed version (see previous step)
+          cd $HOME
+          # initialize environment for modules tool
+          if [ -f $HOME/moduleshome ]; then export MODULESHOME=$(cat $HOME/moduleshome); fi
+          source $(cat $HOME/mod_init); type module
+          # make sure 'eb' is available via $PATH, and that $PYTHONPATH is set (some tests expect that);
+          # also pick up changes to $PATH set by sourcing $MOD_INIT
+          export PREFIX=/tmp/$USER/$GITHUB_SHA
+          export PATH=$PREFIX/bin:$(cat $HOME/path)
+          export PYTHONPATH=$PREFIX/lib/python${{matrix.python}}/site-packages:$PYTHONPATH
+          eb --version
+          # create $HOME/.rpmmacros, see also https://github.com/apptainer/singularity/issues/241
+          echo '%_var /var' > $HOME/.rpmmacros
+          echo '%_dbpath %{_var}/lib/rpm' >> $HOME/.rpmmacros
+          # build CentOS 7 container image for bzip2 1.0.8 using EasyBuild;
+          # see https://docs.easybuild.io/en/latest/Containers.html
+          curl -OL https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/develop/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb
+          export EASYBUILD_CONTAINERPATH=$PWD
+          export EASYBUILD_CONTAINER_CONFIG='bootstrap=docker,from=ghcr.io/easybuilders/centos-7.9-python3-amd64'
+          export EASYBUILD_CONTAINER_TYPE='apptainer'
+          eb bzip2-1.0.8.eb --containerize --experimental --container-build-image
+          apptainer exec bzip2-1.0.8.sif command -v bzip2 | grep '/app/software/bzip2/1.0.8/bin/bzip2' || (echo "Path to bzip2 '$which_bzip2' is not correct" && exit 1)
+          apptainer exec bzip2-1.0.8.sif bzip2 --help

easybuild/tools/config.py

@@ -84,9 +84,10 @@
     CONT_IMAGE_FORMAT_SQUASHFS,
 ]
 
+CONT_TYPE_APPTAINER = 'apptainer'
 CONT_TYPE_DOCKER = 'docker'
 CONT_TYPE_SINGULARITY = 'singularity'
-CONT_TYPES = [CONT_TYPE_DOCKER, CONT_TYPE_SINGULARITY]
+CONT_TYPES = [CONT_TYPE_APPTAINER, CONT_TYPE_DOCKER, CONT_TYPE_SINGULARITY]
 DEFAULT_CONT_TYPE = CONT_TYPE_SINGULARITY
 
 DEFAULT_BRANCH = 'develop'

easybuild/tools/containers/apptainer.py

@@ -0,0 +1,112 @@
+# Copyright 2022-2023 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# https://github.com/easybuilders/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+#
+"""
+Support for generating Apptainer container recipes and creating container images
+
+:author: Kenneth Hoste (HPC-UGent)
+"""
+import os
+import re
+
+from easybuild.tools.build_log import EasyBuildError, print_msg
+from easybuild.tools.containers.singularity import SingularityContainer
+from easybuild.tools.config import CONT_IMAGE_FORMAT_EXT3, CONT_IMAGE_FORMAT_SANDBOX
+from easybuild.tools.config import CONT_IMAGE_FORMAT_SIF, CONT_IMAGE_FORMAT_SQUASHFS
+from easybuild.tools.config import build_option, container_path
+from easybuild.tools.filetools import remove_file, which
+from easybuild.tools.run import run_cmd
+
+
+class ApptainerContainer(SingularityContainer):
+
+    TOOLS = {'apptainer': '1.0', 'sudo': None}
+
+    RECIPE_FILE_NAME = 'Apptainer'
+
+    @staticmethod
+    def apptainer_version():
+        """Get Apptainer version."""
+        version_cmd = "apptainer --version"
+        out, ec = run_cmd(version_cmd, simple=False, trace=False, force_in_dry_run=True)
+        if ec:
+            raise EasyBuildError("Error running '%s': %s for tool {1} with output: {2}" % (version_cmd, out))
+
+        res = re.search(r"\d+\.\d+(\.\d+)?", out.strip())
+        if not res:
+            raise EasyBuildError("Error parsing Apptainer version: %s" % out)
+
+        return res.group(0)
+
+    def build_image(self, recipe_path):
+        """Build container image by calling out to 'sudo apptainer build'."""
+
+        cont_path = container_path()
+        def_file = os.path.basename(recipe_path)
+
+        # use --imagename if specified, otherwise derive based on filename of recipe
+        img_name = self.img_name
+        if img_name is None:
+            # definition file Apptainer.<app>-<version, container name <app>-<version>.<img|simg>
+            img_name = def_file.split('.', 1)[1]
+
+        cmd_opts = ''
+
+        image_format = self.image_format
+
+        # singularity image format (default for Apptainer)
+        if image_format in [None, CONT_IMAGE_FORMAT_SQUASHFS, CONT_IMAGE_FORMAT_SIF]:
+            img_path = os.path.join(cont_path, img_name + '.sif')
+
+        # ext3 image format, creating as writable container
+        elif image_format == CONT_IMAGE_FORMAT_EXT3:
+            raise EasyBuildError("ext3 image format is not supported with Apptainer")
+
+        # sandbox image format, creates as a directory but acts like a container
+        elif image_format == CONT_IMAGE_FORMAT_SANDBOX:
+            img_path = os.path.join(cont_path, img_name)
+            cmd_opts = '--sandbox'
+
+        else:
+            raise EasyBuildError("Unknown container image format specified for Apptainer: %s" % image_format)
+
+        if os.path.exists(img_path):
+            if build_option('force'):
+                print_msg("WARNING: overwriting existing container image at %s due to --force" % img_path)
+                remove_file(img_path)
+            else:
+                raise EasyBuildError("Container image already exists at %s, not overwriting it without --force",
+                                     img_path)
+
+        # resolve full path to 'apptainer' binary, since it may not be available via $PATH under sudo...
+        apptainer = which('apptainer')
+        cmd_env = ''
+
+        apptainer_tmpdir = self.tmpdir
+        if apptainer_tmpdir:
+            cmd_env += 'APPTAINER_TMPDIR=%s' % apptainer_tmpdir
+
+        cmd = ' '.join(['sudo', cmd_env, apptainer, 'build', cmd_opts, img_path, recipe_path])
+        print_msg("Running '%s', you may need to enter your 'sudo' password..." % cmd)
+        run_cmd(cmd, stream_output=True)
+        print_msg("Apptainer image created at %s" % img_path, log=self.log)

easybuild/tools/containers/common.py

@@ -34,6 +34,7 @@
 from easybuild.base import fancylogger
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
+from easybuild.tools.containers.apptainer import ApptainerContainer  # noqa
 from easybuild.tools.containers.docker import DockerContainer  # noqa
 from easybuild.tools.containers.singularity import SingularityContainer  # noqa