diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml index b23e5df..3bb22af 100644 --- a/group_vars/galaxyservers.yml +++ b/group_vars/galaxyservers.yml @@ -15,7 +15,8 @@ galaxy_user: # galaxy_commit_id: 1ad49865fbeb03551cf7774dc0c12e5cd27ff797 # release_23.0 #galaxy_commit_id: 72070dbd0a6d0f418d0b8f914825ea2b8e6a0a88 #galaxy_commit_id: release_23.2 -galaxy_commit_id: release_24.1 +#galaxy_commit_id: release_24.1 +galaxy_commit_id: 07fa2e32d7bbaec497b49f74355edb2cd252f2b2 galaxy_force_checkout: true miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda" miniconda_version: 'latest' # 23.5.2 # 23.5.0 # 4.12.0 @@ -187,21 +188,7 @@ galaxy_config: - auto_install: false cache_directory: /cvmfs/singularity.galaxyproject.org/all/ type: build_mulled_singularity -# - type: cached_explicit_singularity -# cache_directory: "{{ singularity_local_cache_dir }}" -# - type: explicit_singularity -# cache_directory: "{{ singularity_local_cache_dir }}" -# - type: cached_mulled_singularity -# cache_directory: "{{ singularity_local_cache_dir }}" -# - type: mulled_singularity -# auto_install: False -# cache_directory: "{{ singularity_local_cache_dir }}" -# - type: build_mulled_singularity -# auto_install: False -# cache_directory: "{{ singularity_local_cache_dir }}" - # Data Library Directories library_import_dir: /mnt/sally -# user_library_import_dir: /libraries/user # Celery amqp_internal_connection: "pyamqp://galaxy:{{ vault_rabbitmq_password.galaxy }}@localhost:5671/galaxy_internal?ssl=1" celery_conf: diff --git a/templates/galaxy/config/tpv_rules_local.yml.j2 b/templates/galaxy/config/tpv_rules_local.yml.j2 index 37c3285..8635aed 100644 --- a/templates/galaxy/config/tpv_rules_local.yml.j2 +++ b/templates/galaxy/config/tpv_rules_local.yml.j2 @@ -28,6 +28,9 @@ tools: cores: 1 mem: 10 + .*/ms2deepscore_training/.*: + mem: 16 + .*testing.*: cores: 1 mem: 1 @@ -60,14 +63,20 @@ tools: - pulsar - singularity -#roles: -# training.*: -# max_cores: 2 -# max_mem: max_cores * 4 # TODO check multiplier -# scheduling: -# require: -# - pulsar -# - training + __IMPORT_HISTORY__: + scheduling: + require: + - local + - pulsar + +roles: + training.*: + max_cores: 2 + max_mem: max_cores * 4 # TODO check multiplier + scheduling: + require: + - pulsar + - training destinations: tpv_local: @@ -81,7 +90,6 @@ destinations: require: - local reject: - - pulsar - singularity tpv_singularity: runner: local_runner @@ -104,8 +112,6 @@ destinations: - local prefer: - singularity - reject: - - pulsar tpv_pulsar: runner: pulsar_runner @@ -179,65 +185,16 @@ destinations: - pulsar - singularity -# pulsar_gpu: -# runner: pulsar_gpu_runner -# max_accepted_cores: 128 -# max_accepted_mem: 512 -# max_accepted_gpus: 2 -# max_cores: 16 -# max_mem: 64 -# max_gpus: 1 -# params: -# default_file_action: remote_transfer -# transport: curl -# dependency_resolution: remote -# jobs_directory: "/auto/brno11-elixir/home/galaxyumsa/pulsar-umsa/files/staging" -# persistence_directory: "/opt/pulsar/files/persistent" -# remote_metadata: false -# rewrite_parameters: true -# outputs_to_working_directory: false -# singularity_enabled: true -# singularity_run_extra_arguments: '--nv' -# singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,$ALPHAFOLD_DB:/data/2.3:ro' -# env: -# # The cache directory holds the docker containers that get converted -# - name: SINGULARITY_CACHEDIR -# value: "/storage/praha5-elixir/home/galaxyeu/singularity/cache" -# - name: APPTAINER_CACHEDIR -# value: "/storage/praha5-elixir/home/galaxyeu/singularity/cache" -# # Singularity uses a temporary directory to build the squashfs filesystem -# - name: SINGULARITY_TMPDIR -# value: "/storage/praha5-elixir/home/galaxyeu/singularity/tmp" -# - name: APPTAINER_TMPDIR -# value: "/storage/praha5-elixir/home/galaxyeu/singularity/tmp" -# # Alphafold specific variables -# - name: ALPHAFOLD_DB -# value: "/storage/brno11-elixir/projects/alphafold/alphafold.db-2.3.1" -# # Default variables -# - name: TMPDIR -# value: "$SCRATCHDIR" -# - name: TMP -# value: "$SCRATCHDIR" -# - name: TEMP -# value: "$SCRATCHDIR" -# # Ensuring a consistent collation environment is good for reproducibility. -# - name: LC_ALL -# value: C -# scheduling: -# require: -# - pulsar -# - gpu - -# pulsar-training: -# inherits: pulsar -# runner: pulsar_runner -# max_accepted_cores: 12 -# max_accepted_mem: 120 -# max_cores: 2 # Limit the cores -# max_mem: 8 # Limit the memory -# params: -# native_specification: --nodes=1 --ntasks=1 --mem={round(mem*1024)} --cpus-per-task={cores} --time=00:30:00 -# scheduling: -# require: -# - pulsar -# - training + tpv_pulsar_training: + inherits: tpv_pulsar + runner: pulsar_runner + max_accepted_cores: 12 + max_accepted_mem: 120 + max_cores: 2 # Limit the cores + max_mem: 8 # Limit the memory + params: + native_specification: --nodes=1 --ntasks=1 --mem={round(mem*1024)} --cpus-per-task={cores} --time=00:30:00 + scheduling: + require: + - pulsar + - training