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Optimize czech pulsar configuration #1213

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merged 4 commits into from
May 27, 2024
Merged

Optimize czech pulsar configuration #1213

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88e9823
Update destinations.yml.j2
martindemko May 26, 2024
1f4075b
Update job_conf.yml
martindemko May 27, 2024
646241e
Merge branch 'usegalaxy-eu:master' into master
martindemko May 27, 2024
cb5db16
Merge pull request #2 from martindemko/patch-3
martindemko May 27, 2024
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10 changes: 7 additions & 3 deletions files/galaxy/tpv/destinations.yml.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -244,12 +244,13 @@ destinations:
inherits: pulsar_default
runner: pulsar_eu_cz01
max_accepted_cores: 32
max_accepted_mem: 128
max_accepted_mem: 256
min_accepted_gpus: 0
max_accepted_gpus: 0
env:
LC_ALL: C
SINGULARITY_CACHEDIR: "/storage/praha5-elixir/home/galaxyeu/singularity"
#SINGULARITY_CACHEDIR: "/storage/praha5-elixir/home/galaxyeu/singularity"
SINGULARITY_CACHEDIR: "/cvmfs/singularity.galaxyproject.org/all/"
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SINGULARITY_TMPDIR: "$SCRATCHDIR"
TMPDIR: "$SCRATCHDIR"
TMP: "$SCRATCHDIR"
Expand All @@ -260,6 +261,7 @@ destinations:
persistence_directory: "/opt/pulsar/files/persistent"
singularity_volumes: "$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,/cvmfs/data.galaxyproject.org/managed/:/data/db/data_managers/:ro"
singularity_run_extra_arguments: --env "_JAVA_OPTIONS=\"-Djava.io.tmpdir=$SCRATCHDIR\""
submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local=100gb -l walltime=24:00:00 -q [email protected] -N pulsar_eu_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
scheduling:
require:
- cz-pulsar
Expand All @@ -273,7 +275,8 @@ destinations:
max_accepted_gpus: 1
env:
LC_ALL: C
SINGULARITY_CACHEDIR: "/storage/praha5-elixir/home/galaxyeu/singularity"
#SINGULARITY_CACHEDIR: "/storage/praha5-elixir/home/galaxyeu/singularity"
SINGULARITY_CACHEDIR: "/cvmfs/singularity.galaxyproject.org/all/"
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SINGULARITY_TMPDIR: "$SCRATCHDIR"
TMPDIR: "$SCRATCHDIR"
TMP: "$SCRATCHDIR"
Expand All @@ -286,6 +289,7 @@ destinations:
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={int(cores)}: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'}"
scheduling:
require:
- cz-pulsar
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12 changes: 0 additions & 12 deletions templates/galaxy/config/job_conf.yml
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Expand Up @@ -169,18 +169,6 @@ galaxy_jobconf:
params:
amqp_url: "pyamqp://galaxy_cz01:{{ rabbitmq_password_galaxy_cz01 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_cz01?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: production
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amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
amqp_publish_retry: "true"
amqp_publish_retry_max_retries: 60
- id: pulsar_eu_cz02
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_cz01:{{ rabbitmq_password_galaxy_cz01 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_cz01?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: gpu
amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
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