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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -131,7 +131,7 @@ destinations: | |
| outputs_to_working_directory: "false" | ||
| dependency_resolution: "none" | ||
| submit_request_cpus: "{cores}" | ||
| submit_request_memory: "{mem}G" | ||
| docker_volumes: "$job_directory:rw, | ||
| $tool_directory:ro, | ||
| $job_directory/outputs:rw, | ||
|
|
@@ -183,7 +183,7 @@ destinations: | |
| inherits: pulsar_default | ||
| runner: pulsar_eu_sk01 | ||
| max_accepted_cores: 8 | ||
| max_accepted_mem: 31 | ||
| min_accepted_gpus: 0 | ||
| max_accepted_gpus: 0 | ||
| scheduling: | ||
|
|
@@ -244,46 +244,52 @@ destinations: | |
| inherits: pulsar_default | ||
| runner: pulsar_eu_cz01 | ||
| max_accepted_cores: 32 | ||
| max_accepted_mem: 256 | ||
| min_accepted_gpus: 0 | ||
| max_accepted_gpus: 0 | ||
| env: | ||
| LC_ALL: C | ||
| #SINGULARITY_CACHEDIR: "/storage/praha5-elixir/home/galaxyeu/singularity" | ||
| SINGULARITY_CACHEDIR: "/cvmfs/singularity.galaxyproject.org/all/" | ||
| SINGULARITY_TMPDIR: "$SCRATCHDIR" | ||
| TMPDIR: "$SCRATCHDIR" | ||
| TMP: "$SCRATCHDIR" | ||
| TEMP: "$SCRATCHDIR" | ||
| XDG_CACHE_HOME: "$SCRATCHDIR" | ||
| 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,$SCRATCHDIR,/storage/praha5-elixir/home/galaxyeu:/home/galaxyeu,/cvmfs/data.galaxyproject.org/managed/:/data/db/data_managers/:ro" | ||
| singularity_run_extra_arguments: --env "_JAVA_OPTIONS=\"-Djava.io.tmpdir=$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 | ||
|
|
||
| pulsar_cz02_tpv: | ||
| inherits: pulsar_default | ||
| runner: pulsar_eu_cz01 | ||
| max_accepted_cores: 32 | ||
| max_accepted_mem: 128 | ||
| min_accepted_gpus: 1 | ||
| max_accepted_gpus: 1 | ||
| env: | ||
| LC_ALL: C | ||
| #SINGULARITY_CACHEDIR: "/storage/praha5-elixir/home/galaxyeu/singularity" | ||
| SINGULARITY_CACHEDIR: "/cvmfs/singularity.galaxyproject.org/all/" | ||
| SINGULARITY_TMPDIR: "$SCRATCHDIR" | ||
| TMPDIR: "$SCRATCHDIR" | ||
| TMP: "$SCRATCHDIR" | ||
| TEMP: "$SCRATCHDIR" | ||
| 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'}" | ||
| scheduling: | ||
| require: | ||
| - cz-pulsar | ||
|
|
@@ -347,6 +353,10 @@ destinations: | |
| max_accepted_mem: 30 | ||
| min_accepted_gpus: 0 | ||
| max_accepted_gpus: 0 | ||
| env: | ||
| TMP: $_GALAXY_JOB_TMP_DIR | ||
| TEMP: $_GALAXY_JOB_TMP_DIR | ||
| TMPDIR: $_GALAXY_JOB_TMP_DIR | ||
| scheduling: | ||
| require: | ||
| - hcmr-gr-pulsar | ||
|
|
||
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