From e9ca6153b38d57479655958af79bbc3b51f27ae3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jos=C3=A9=20Manuel=20Dom=C3=ADnguez?= Date: Thu, 31 Aug 2023 16:48:47 +0200 Subject: [PATCH 1/3] freebayes: Dynamic memory allocation Most freebayes jobs have inputs smaller than 10GB and use less than 15GB of memory, rather than the 90GB that are currently being requested. Since UseGalaxy.eu resubmits jobs up to two times when they run out of memory, tripling the memory request each time, this change should cover about 99% of jobs within two resubmissions (see the graph in PR #881). --- files/galaxy/tpv/tools.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 84b651813..36b079786 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -688,6 +688,9 @@ tools: - if: input_size >= 25 fail: Too much data, please check if the input is correct. + toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/.*: + mem: 9 + input_size * 1 + toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/.*: inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.* From 8fda5f69ba84d00cfaefbe248daacdbf4de96998 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jos=C3=A9=20Manuel=20Dom=C3=ADnguez?= <43052541+kysrpex@users.noreply.github.com> Date: Fri, 1 Sep 2023 13:22:41 +0200 Subject: [PATCH 2/3] freebayes: set cores to 10 Set cores to 10 explicitly in tools.yml. --- files/galaxy/tpv/tools.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 36b079786..f032277df 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -689,6 +689,7 @@ tools: fail: Too much data, please check if the input is correct. toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/.*: + cores: 10 mem: 9 + input_size * 1 toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/.*: From 7cdcfd2966ff16816515b73ecd8fc03d96206cde Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 1 Sep 2023 23:06:47 +1000 Subject: [PATCH 3/3] add comment --- files/galaxy/tpv/tools.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index f032277df..0c19ced42 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -689,6 +689,7 @@ tools: fail: Too much data, please check if the input is correct. toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/.*: + # see https://github.com/usegalaxy-eu/infrastructure-playbook/pull/881 for some numbers cores: 10 mem: 9 + input_size * 1