diff --git a/files/galaxy/tpv/destinations.yml.j2 b/files/galaxy/tpv/destinations.yml.j2 index fa12c2554..a19ee5e6b 100644 --- a/files/galaxy/tpv/destinations.yml.j2 +++ b/files/galaxy/tpv/destinations.yml.j2 @@ -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/" SINGULARITY_TMPDIR: "$SCRATCHDIR" TMPDIR: "$SCRATCHDIR" TMP: "$SCRATCHDIR" @@ -260,6 +261,7 @@ destinations: persistence_directory: "/opt/pulsar/files/persistent" singularity_volumes: "$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=$SCRATCHDIR\"" + submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local=100gb -l walltime=24:00:00 -q galaxyeu@pbs-m1.metacentrum.cz -N pulsar_eu_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" scheduling: require: - cz-pulsar @@ -273,7 +275,8 @@ destinations: max_accepted_gpus: 1 env: LC_ALL: C - SINGULARITY_CACHEDIR: "/storage/praha5-elixir/home/galaxyeu/singularity" + #SINGULARITY_CACHEDIR: "/storage/praha5-elixir/home/galaxyeu/singularity" + SINGULARITY_CACHEDIR: "/cvmfs/singularity.galaxyproject.org/all/" SINGULARITY_TMPDIR: "$SCRATCHDIR" TMPDIR: "$SCRATCHDIR" TMP: "$SCRATCHDIR" @@ -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 gpu@pbs-m1.metacentrum.cz -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 diff --git a/templates/galaxy/config/job_conf.yml b/templates/galaxy/config/job_conf.yml index 037f95d6b..f2d08ce94 100644 --- a/templates/galaxy/config/job_conf.yml +++ b/templates/galaxy/config/job_conf.yml @@ -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 - 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