also bwrap module installpath

.github/workflows/end2end_bwrap.yml

@@ -54,6 +54,123 @@ jobs:
               bash -lc "source /tmp/eb_env; $cmd"
           done
 
+      - name: Define bwrap validation helper
+        shell: bash
+        run: |
+          cat > /tmp/check_bwrap_install.sh <<'EOF'
+          #!/usr/bin/env bash
+
+          check_no_glob_matches() {
+              local label="$1"
+              local pattern="$2"
+
+              echo ">>> CHECK: $label"
+              echo "    glob: $pattern"
+
+              if compgen -G "$pattern" > /dev/null; then
+                  echo "FAIL: files/directories matched"
+                  compgen -G "$pattern" | sort
+                  return 1
+              fi
+
+              echo "PASS: no files/directories matched"
+              echo
+          }
+
+          check_path_exists() {
+              local label="$1"
+              local path="$2"
+
+              echo ">>> CHECK: $label"
+              echo "    path: $path"
+
+              if [[ -e "$path" ]]; then
+                  echo "PASS: path exists"
+                  ls -ld "$path"
+                  echo
+                  return 0
+              fi
+
+              echo "FAIL: path does not exist"
+              echo "Parent contents:"
+              ls -la "$(dirname "$path")" || true
+              echo
+              return 1
+          }
+
+          check_glob_exists() {
+              local label="$1"
+              local pattern="$2"
+
+              echo ">>> CHECK: $label"
+              echo "    glob: $pattern"
+
+              if compgen -G "$pattern" > /dev/null; then
+                  echo "PASS: matches found"
+                  compgen -G "$pattern" | sort | xargs -r ls -l
+                  echo
+                  return 0
+              fi
+
+              echo "FAIL: no matches found"
+              echo
+              return 1
+          }
+
+          main() {
+              local failures=0
+
+              echo "=== Host-side EasyBuild path state ==="
+              find "$HOME/.local/easybuild" -maxdepth 5 -print || true
+              echo
+
+              echo "=== bwrap install path state ==="
+              find /tmp/bwrap-installpath -maxdepth 5 -print || true
+              echo
+
+              check_no_glob_matches "no host UnZip modules" \
+                  "$HOME/.local/easybuild/modules/all/UnZip/*" || failures=$((failures + 1))
+
+              check_no_glob_matches "no host bzip2 modules" \
+                  "$HOME/.local/easybuild/modules/all/bzip2/*" || failures=$((failures + 1))
+
+              check_no_glob_matches "no host UnZip software files" \
+                  "$HOME/.local/easybuild/software/UnZip/6.0/*" || failures=$((failures + 1))
+
+              check_no_glob_matches "no host bzip2 software files" \
+                  "$HOME/.local/easybuild/software/bzip2/1.0.8/*" || failures=$((failures + 1))
+
+              check_path_exists "bwrap bzip2 module file exists" \
+                  "/tmp/bwrap-installpath/modules/all/bzip2/1.0.8.lua" || failures=$((failures + 1))
+
+              check_path_exists "bwrap UnZip module file exists" \
+                  "/tmp/bwrap-installpath/modules/all/UnZip/6.0.lua" || failures=$((failures + 1))
+
+              check_glob_exists "bwrap UnZip installed binaries exist" \
+                  "/tmp/bwrap-installpath/software/UnZip/*/bin/*" || failures=$((failures + 1))
+
+              check_glob_exists "bwrap bzip2 installed binaries exist" \
+                  "/tmp/bwrap-installpath/software/bzip2/*/bin/*" || failures=$((failures + 1))
+
+              check_glob_exists "bwrap UnZip EasyBuild logs exist" \
+                  "/tmp/bwrap-installpath/software/UnZip/*/easybuild/*log*" || failures=$((failures + 1))
+
+              check_glob_exists "bwrap bzip2 EasyBuild logs exist" \
+                  "/tmp/bwrap-installpath/software/bzip2/*/easybuild/*log*" || failures=$((failures + 1))
+
+              if [[ "$failures" -ne 0 ]]; then
+                  echo "ERROR: $failures bwrap validation check(s) failed"
+                  return 1
+              fi
+
+              echo "All bwrap validation checks passed"
+          }
+
+          main "$@"
+          EOF
+
+          chmod +x /tmp/check_bwrap_install.sh
+
       - name: End-to-end test of installing UnZip with EasyBuild in bwrap namespace
         shell: bash
         run: |
@@ -66,16 +183,8 @@ jobs:
             # test installation of UnZip + bzip2 dependency
             eb UnZip-6.0.eb --trace --robot --experimental --bwrap --bwrap-installpath /tmp/bwrap-installpath --filter-deps=binutils
 
-            # no module files should be created in configured install path (default: $HOME/.local/easybuild),
-            # not for UnZip, nor for bzip2 dependency
-            (test -d $HOME/.local/easybuild/modules/all/UnZip || echo 'no UnZip module dir found: OK') > /tmp/out-UnZip-mod
-            (test -d $HOME/.local/easybuild/modules/all/bzip2 || echo 'no bzip2 module dir found: OK') > /tmp/out-bzip2-mod
+            /tmp/check_bwrap_install.sh
 
-            # software subdirectories in configured install path should be empty
-            (test -e $HOME/.local/easybuild/software/UnZip/6.0/* || echo 'UnZip software dir in $HOME/.local/easybuild is empty: OK') > /tmp/out-UnZip-sw-dir
-            (test -e $HOME/.local/easybuild/software/bzip2/1.0.8/* || echo 'bzip2 software dir in $HOME/.local/easybuild is empty: OK') > /tmp/out-bzip2-sw-dir
-
-            grep 'no UnZip module dir found: OK' /tmp/out-UnZip-mod && grep 'no bzip2 module dir found: OK' /tmp/out-bzip2-mod && grep 'UnZip software dir in .* is empty' /tmp/out-UnZip-sw-dir && grep 'bzip2 software dir in .* is empty' /tmp/out-bzip2-sw-dir && ls -l /tmp/bwrap-installpath/modules/all/{bzip2/1.0.8.lua,UnZip/6.0.lua} && ls -l /tmp/bwrap-installpath/software/{UnZip,bzip2}/*/bin/* && ls -l /tmp/bwrap-installpath/software/{UnZip,bzip2}/*/easybuild/*log*
           EOF
 
       - name: End-to-end test of installing UnZip with EasyBuild in bwrap namespace with overlay
@@ -89,22 +198,14 @@ jobs:
             source /tmp/eb_env
 
             # remove previously created install directories
-            rm -r $HOME/.local/easybuild/software/* /tmp/bwrap-installpath
+            rm -r $HOME/.local/easybuild/{software,modules}/* /tmp/bwrap-installpath
 
             # make install directory read-only to force using overlay
-            chmod -w $HOME/.local/easybuild/software
+            chmod -w $HOME/.local/easybuild/{software,modules}
 
             # test installation of UnZip + bzip2 dependency
             eb UnZip-6.0.eb --trace --robot --experimental --bwrap --bwrap-installpath /tmp/bwrap-installpath --filter-deps=binutils
 
-            # no module files should be created in configured install path (default: $HOME/.local/easybuild),
-            # not for UnZip, nor for bzip2 dependency
-            (test -d $HOME/.local/easybuild/modules/all/UnZip || echo 'no UnZip module dir found: OK') > /tmp/out-UnZip-mod
-            (test -d $HOME/.local/easybuild/modules/all/bzip2 || echo 'no bzip2 module dir found: OK') > /tmp/out-bzip2-mod
-
-            # software subdirectories in configured install path should be empty
-            (test -e $HOME/.local/easybuild/software/UnZip/6.0/* || echo 'UnZip software dir in $HOME/.local/easybuild is empty: OK') > /tmp/out-UnZip-sw-dir
-            (test -e $HOME/.local/easybuild/software/bzip2/1.0.8/* || echo 'bzip2 software dir in $HOME/.local/easybuild is empty: OK') > /tmp/out-bzip2-sw-dir
+            /tmp/check_bwrap_install.sh
 
-            grep 'no UnZip module dir found: OK' /tmp/out-UnZip-mod && grep 'no bzip2 module dir found: OK' /tmp/out-bzip2-mod && grep 'UnZip software dir in .* is empty' /tmp/out-UnZip-sw-dir && grep 'bzip2 software dir in .* is empty' /tmp/out-bzip2-sw-dir && ls -l /tmp/bwrap-installpath/modules/all/{bzip2/1.0.8.lua,UnZip/6.0.lua} && ls -l /tmp/bwrap-installpath/software/{UnZip,bzip2}/*/bin/* && ls -l /tmp/bwrap-installpath/software/{UnZip,bzip2}/*/easybuild/*log*
           EOF

easybuild/tools/bwrap.py

@@ -36,7 +36,7 @@
 from easybuild.base import fancylogger
 from easybuild.tools.build_log import EasyBuildError, print_msg
 from easybuild.tools.config import install_path, ConfigurationVariables
-from easybuild.tools.filetools import mkdir, write_file
+from easybuild.tools.filetools import copy_dir, mkdir, write_file
 from easybuild.tools.utilities import trace_msg
 
 
@@ -104,10 +104,11 @@ def prepare_bwrap(bwrap_installpath):
 
     set_bwrap_info('bwrap_installpath', bwrap_installpath)
 
-    installpath_software = install_path(typ='software')
+    installpath_software = os.path.realpath(install_path(typ='software'))
     set_bwrap_info('installpath_software', installpath_software)
 
-    set_bwrap_info('installpath_modules', install_path(typ='modules'))
+    installpath_modules = os.path.realpath(install_path(typ='modules'))
+    set_bwrap_info('installpath_modules', installpath_modules)
 
     variables = ConfigurationVariables()
     bwrap_installpath_software = os.path.join(bwrap_installpath, variables['subdir_software'])
@@ -117,34 +118,64 @@ def prepare_bwrap(bwrap_installpath):
 
     bwrap_cmd = ['bwrap', '--dev-bind', '/', '/']
 
+    mkdir(bwrap_installpath_modules, parents=True)
+
+    bwrap_workdir = os.path.join(bwrap_installpath, 'workdir')
+
+    try:
+        mkdir(installpath_modules, parents=True)
+        # copy installpath_modules to bwrap_installpath_modules to ensure all installed modules are available
+        # required for building multiple unrelated easyconfigs (e.g. easystacks)
+        if os.path.exists(installpath_modules):
+            copy_dir(installpath_modules, bwrap_installpath_modules, dirs_exist_ok=True)
+        # bind mount the modules installpath
+        bwrap_cmd.extend([
+            '--bind', bwrap_installpath_modules, installpath_modules])
+
+    except EasyBuildError:
+        # if we can't create the external modules directory, try to use overlayfs
+        mkdir(bwrap_workdir, parents=True)
+        bwrap_cmd.extend([
+            '--overlay-src', installpath_modules,
+            '--overlay', bwrap_installpath_modules, bwrap_workdir, installpath_modules])
+
+    # store bwrap options in a set to avoid duplicate binds
+    bwrap_opts = set()
+
     # bind mount all software directories
     for mod in sorted(get_bwrap_info('modules_to_install')):
         installdir = os.path.join(os.path.realpath(installpath_software), mod)
         bwrap_installdir = os.path.join(bwrap_installpath_software, mod)
+        mkdir(bwrap_installdir, parents=True)
+
         use_overlayfs = False
         try:
             mkdir(installdir, parents=True)
         except EasyBuildError:
             # if we can't create the external installation directory, try to use overlayfs
             use_overlayfs = True
-        mkdir(bwrap_installdir, parents=True)
+
         if use_overlayfs:
-            bwrap_workdir = os.path.join(bwrap_installpath, 'workdir', mod)
-            mkdir(bwrap_workdir, parents=True)
             # go up the tree until we find a directory that exists
             while not os.path.exists(installdir):
                 installdir = os.path.dirname(installdir)
                 bwrap_installdir = os.path.dirname(bwrap_installdir)
-            opts = ['--overlay-src', installdir, '--overlay', bwrap_installdir, bwrap_workdir, installdir]
+            mkdir(bwrap_workdir, parents=True)
+            bwrap_opts.add((
+                '--overlay-src', installdir,
+                '--overlay', bwrap_installdir, bwrap_workdir, installdir))
         else:
-            opts = ['--bind', bwrap_installdir, installdir]
-        bwrap_cmd.extend(opts)
+            bwrap_opts.add((
+                '--bind', bwrap_installdir, installdir))
+
+    for x in bwrap_opts:
+        bwrap_cmd.extend(x)
 
     set_bwrap_info('bwrap_cmd', bwrap_cmd)
     bwrap_cmd_str = ' '.join(bwrap_cmd)
 
     # disable `--bwrap` to prepare for a real installation (in bwrap namespace)
-    bwrap_eb_options = ['--disable-bwrap', f'--installpath-modules={bwrap_installpath_modules}']
+    bwrap_eb_options = ['--disable-bwrap']
     set_bwrap_info('bwrap_eb_options', bwrap_eb_options)
 
     _log.info(f'Info needed for bwrap: {_bwrap_info}')

easybuild/tools/modules.py

@@ -877,13 +877,16 @@ def check_module_path(self):
             self.set_mod_paths()
             self.log.debug("self.mod_paths set based on $MODULEPATH: %s" % self.mod_paths)
 
-            # determine module path for EasyBuild install path to be included in $MODULEPATH
-            eb_modpath = os.path.join(install_path(typ='modules'), build_option('suffix_modules_path'))
-
-            # make sure EasyBuild module path is in 1st place
-            mkdir(eb_modpath, parents=True)
-            self.prepend_module_path(eb_modpath)
-            self.log.info("Prepended list of module paths with path used by EasyBuild: %s" % eb_modpath)
+            # avoid creating the module path when in --bwrap mode (before actually running with bwrap),
+            # in case the user does not have the necessary write permissions
+            if not build_option('bwrap'):
+                # determine module path for EasyBuild install path to be included in $MODULEPATH
+                eb_modpath = os.path.join(install_path(typ='modules'), build_option('suffix_modules_path'))
+
+                # make sure EasyBuild module path is in 1st place
+                mkdir(eb_modpath, parents=True)
+                self.prepend_module_path(eb_modpath)
+                self.log.info("Prepended list of module paths with path used by EasyBuild: %s" % eb_modpath)
 
         # set the module path environment accordingly
         curr_mod_paths = curr_module_paths()