From 7e8a6378207d9d2beecf68d52cfea32f22ed0594 Mon Sep 17 00:00:00 2001 From: Mira Kuntz Date: Wed, 13 Nov 2024 17:23:13 +0100 Subject: [PATCH] move java env options to default tool and reduce xms --- files/galaxy/tpv/tool_defaults.yml | 5 ++- files/galaxy/tpv/tools.yml | 51 ------------------------------ 2 files changed, 4 insertions(+), 52 deletions(-) diff --git a/files/galaxy/tpv/tool_defaults.yml b/files/galaxy/tpv/tool_defaults.yml index 19d3d0b3c..f880736b4 100644 --- a/files/galaxy/tpv/tool_defaults.yml +++ b/files/galaxy/tpv/tool_defaults.yml @@ -8,7 +8,10 @@ tools: mem: cores * 3.8 gpus: 0 env: - GALAXY_MEMORY_MB: "{int(mem * 1024)}" # set 5/2023 might be moved to runner or tool wrappers, related to Galaxy issue 15952 + - name: GALAXY_MEMORY_MB + value: "{int(mem * 1024)}" # set 5/2023 might be moved to runner or tool wrappers, related to Galaxy issue 15952 + - name: _JAVA_OPTIONS + value: -Xmx{round(mem*0.9*1024)}m -Xms256m -Duser.home=/data/2/galaxy_db/tmp -Djava.io.tmpdir=$_GALAXY_JOB_TMP_DIR params: metadata_strategy: "extended" tmp_dir: true diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index b367b1ff6..a28f95ca2 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -930,14 +930,7 @@ tools: scheduling: prefer: - condor-tpv - env: - _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx{int(mem)}G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp rules: - - if: helpers.tool_version_gte(tool, '2.15.1') - # see usegalaxy-eu/issues#473: https://github.com/usegalaxy-eu/issues/issues/473 - env: - _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp - - if: input_size < 0.1 cores: 1 mem: 4 @@ -1019,8 +1012,6 @@ tools: inherits: basic_docker_tool params: docker_run_extra_arguments: --user 999 - env: - _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G toolshed.g2.bx.psu.edu/repos/bgruening/diamond/diamond/.*: cores: 6 @@ -1093,12 +1084,6 @@ tools: inherits: basic_numba_tool toolshed.g2.bx.psu.edu/repos/computational-metabolomics/dimspy_align_samples/dimspy_align_samples/.*: inherits: basic_numba_tool - toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/.*: - env: - _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp - toolshed.g2.bx.psu.edu/repos/iracooke/msgfplus/msgfplus/.*: - env: - _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/.*: rules: - if: helpers.tool_version_gte(tool, '4.1.5') @@ -1109,29 +1094,6 @@ tools: RM_LIB_PATH: "/data/db/databases/dfam/3.4/" - if: helpers.tool_version_gte(tool, '4.1.5') cores: 4 - toolshed.g2.bx.psu.edu/repos/galaxyp/reactome_pathwaymatcher/reactome_pathwaymatcher/.*: - env: - _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx17G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp - - toolshed.g2.bx.psu.edu/repos/iuc/bbtools_callvariants/bbtools_callvariants/.*: - env: - _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx15G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp - - toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/.*: - env: - _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx15G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp - - toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/.*: - env: - _JAVA_OPTIONS: -Xmx4G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp - - toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/.*: - env: - _JAVA_OPTIONS: -XX:MaxPermSize=4G -Xmx120G -Xms4G -Djava.io.tmpdir=/data/2/galaxy_db/tmp - - toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/.*: - env: - _JAVA_OPTIONS: -XX:MaxPermSize=6G -Xmx14G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/.*: inherits: basic_numba_tool @@ -1151,24 +1113,11 @@ tools: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/.*: inherits: basic_numba_tool - toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/.*: - env: - _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx15G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp - - toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/.*: - env: - _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp - - toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/.*: - env: - _JAVA_OPTIONS: -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp - toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/.*: cores: 24 mem: 80 env: TERM: vt100 - _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xmx{int(mem)}G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp scheduling: accept: - pulsar