From e1bc2fc4b5b29845dc61a0438cb7dd4145013ea1 Mon Sep 17 00:00:00 2001 From: cat-bro Date: Tue, 3 Dec 2024 13:22:23 +1100 Subject: [PATCH] disable HDF5 file locking --- .../production/total_perspective_vortex/default_tool.yml.j2 | 3 ++- group_vars/galaxyservers.yml | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) 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 index 57566af0..a08e42f9 100644 --- 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 index 9a351ca1..6e62e6c4 100644 --- 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)