Merge pull request #25 from pneerincx/for_LoR_clusters

Bugfixes and updated EasyBuild
molgenis · Jul 16, 2019 · 567a475 · 567a475
2 parents 9e4b35e + dbfd249
commit 567a475
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Showing 5 changed files with 12 additions and 15 deletions.
diff --git a/group_vars/fender-cluster/vars.yml b/group_vars/fender-cluster/vars.yml
@@ -16,7 +16,7 @@
 #
 lua_version: '5.1.4.9'
 lmod_version: '7.8.8'
-easybuild_version: '3.7.1'
+easybuild_version: '3.9.3'
 extra_easyconfigs_version: '2.8.31'
 #
 # Group folder structures to construct on shared storage systems.

diff --git a/group_vars/gearshift-cluster/vars.yml b/group_vars/gearshift-cluster/vars.yml
@@ -16,7 +16,7 @@
 #
 lua_version: '5.1.4.9'
 lmod_version: '7.8.8'
-easybuild_version: '3.7.1'
+easybuild_version: '3.9.3'
 extra_easyconfigs_version: '2.8.31'
 #
 # Group folder structures to construct on shared storage systems.

diff --git a/group_vars/hyperchicken-cluster/vars.yml b/group_vars/hyperchicken-cluster/vars.yml
@@ -16,7 +16,7 @@
 #
 lua_version: '5.1.4.9'
 lmod_version: '7.8.8'
-easybuild_version: '3.7.1'
+easybuild_version: '3.9.3'
 extra_easyconfigs_version: '2.8.31'
 #
 # Group folder structures to construct on shared storage systems.

diff --git a/roles/install-easybuild/handlers/main.yml b/roles/install-easybuild/handlers/main.yml
@@ -12,17 +12,14 @@
   #
 - name: Install_Lua
   listen: Install_Lua
-  include_tasks:
-    file: tasks/install_lua.yml
+  include_tasks: tasks/install_lua.yml
   #static: no
 - name: Install_Lmod
   listen: Install_Lmod
-  include_tasks:
-    file: tasks/install_lmod.yml
+  include_tasks: tasks/install_lmod.yml
   #static: no
 - name: Install_EasyBuild
   listen: Install_EasyBuild
-  include_tasks:
-    file: tasks/install_easybuild.yml
+  include_tasks: tasks/install_easybuild.yml
   #static: no
 ...
diff --git a/roles/install-easybuild/templates/modules.bashrc b/roles/install-easybuild/templates/modules.bashrc
@@ -10,13 +10,13 @@
 # but in the first case there are no SLURM related environment variables defined.
 #
 # NOTE: when using the --get-user-env=L option for SLURM's sbatch command,
-#       the ${SLURM_JOBID} variable is not yet available when the environment is 
-#       configured and hence when this file is sourced. The only way to make 
-#       --get-user-env=L work reliably without causing problems with other 'dumb'
-#       shells is to make sure the SLURM slurmd daemon is started using a regular 
-#       (pseudo) terminal, so ${TERM} won't be 'dumb'.
+#       various SLURM_* environment variables are not yet available 
+#       when the environment is configured and hence when this file is sourced.
+#       The only way to make --get-user-env=L work reliably without causing problems with other 'dumb'
+#       shells is to check the BASH_EXECUTION_STRING variable which contains the slurm command 
+#       used to parse the environment variables from a simulated login.
 #
-if [ ${TERM} == 'dumb' ] && [ -z ${SLURM_JOBID} ] && [ -z ${SOURCE_HPC_ENV} ]; then
+if [[ "${TERM}" == 'dumb' ]] && [[ ! "${BASH_EXECUTION_STRING}" =~ 'slurm' ]] && [[ -z "${SOURCE_HPC_ENV}" ]]; then
     return
 fi