Merge pull request #2314 from cat-bro/disable_HDF5_file_locking

disable HDF5 file locking
usegalaxy-au · Dec 8, 2024 · 8063d75 · 8063d75
2 parents 6e66162 + e1bc2fc
commit 8063d75
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diff --git a/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/default_tool.yml.j2 b/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/default_tool.yml.j2
@@ -5,7 +5,8 @@ tools:
   default:
     cores: 1
     mem: cores * 3.8
-    env: {}
+    env: 
+      HDF5_USE_FILE_LOCKING: "FALSE"
     context:
       partition: main
       test_cores: 1  # TODO: test_mem?

diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml
@@ -147,6 +147,7 @@ galaxy_process_env:  # environment variables for gunicorn and handlers processes
   DRMAA_LIBRARY_PATH: "/usr/lib/slurm-drmaa/lib/libdrmaa.so.1"
   SINGULARITY_CACHEDIR: "{{ galaxy_user_singularity_cachedir }}"
   SINGULARITY_TMPDIR: "{{ galaxy_user_singularity_tmpdir }}"
+  HDF5_USE_FILE_LOCKING: "FALSE"
 
 #########################################
 # group_galaxy_config contains variables for galaxy_config that can be overridden by variables in host_galaxy_config (defined in host_vars)