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Optimizing of pulsar-cz env for Alphafold #1383

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merged 3 commits into from
Jan 14, 2025
Merged

Optimizing of pulsar-cz env for Alphafold #1383

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46d5e59
Merge pull request #3 from usegalaxy-eu/master
martindemko Jan 9, 2025
36777aa
Update destinations.yml.j2
martindemko Jan 9, 2025
af86eb4
Update destinations.yml.j2
martindemko Jan 14, 2025
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13 changes: 7 additions & 6 deletions files/galaxy/tpv/destinations.yml.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -297,7 +297,7 @@ destinations:
inherits: pulsar_default
runner: pulsar_eu_cz01
max_accepted_cores: 32
max_accepted_mem: 128
max_accepted_mem: 256
min_accepted_gpus: 1
max_accepted_gpus: 1
env:
Expand All @@ -307,15 +307,16 @@ destinations:
TMPDIR: "$SCRATCHDIR"
TMP: "$SCRATCHDIR"
TEMP: "$SCRATCHDIR"
MPLCONFIGDIR: "$SCRATCHDIR"
ALPHAFOLD_DB: "/scratch.ssd/galaxyeu/permanent/alphafold.db"
XDG_CACHE_HOME: "$SCRATCHDIR"
ALPHAFOLD_DB: "/storage/brno11-elixir/projects/alphafold/alphafold.db-2.3.1"
GPU_AVAILABLE: "1"
params:
jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-eu/files/staging"
persistence_directory: "/opt/pulsar/files/persistent"
singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR,/storage/praha5-elixir/home/galaxyeu:/home/galaxyeu,$ALPHAFOLD_DB:/data:ro"
singularity_run_extra_arguments: "--nv --env ALPHAFOLD_USE_GPU=True"
submit_native_specification: "-l select=1:ncpus=1:mem={int(mem)}gb:scratch_local=100gb:ngpus=1:gpu_mem=8gb -l walltime=24:00:00 -q [email protected] -N pulsar_eu_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
singularity_volumes: "$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,/storage/praha5-elixir/home/galaxyeu:/home/galaxyeu,$ALPHAFOLD_DB:/data:ro"
singularity_run_extra_arguments: "--nv --env ALPHAFOLD_USE_GPU=True --env SCRATCHDIR=$SCRATCHDIR --env SCRATCH=$SCRATCHDIR"
submit_native_specification: "-l select=1:ncpus=8:mem={int(mem)}gb:scratch_local=100gb:ngpus=1:gpu_mem=16gb -l walltime=24:00:00 -q [email protected] -N pulsar_eu_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
scheduling:
require:
- cz-pulsar
Expand All @@ -325,7 +326,7 @@ destinations:
ALPHAFOLD_DB: "/storage/brno11-elixir/projects/alphafold/alphafold.db-2.2"
- if: tool.id.startswith("toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold") and helpers.tool_version_gte(tool, "2.3.1+galaxy2")
params:
singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR,/storage/praha5-elixir/home/galaxyeu:/home/galaxyeu,$ALPHAFOLD_DB:/data/2.3:ro"
singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,/storage/praha5-elixir/home/galaxyeu:/home/galaxyeu,$ALPHAFOLD_DB:/data/2.3:ro"


pulsar_egi01_tpv:
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