From 4570718b12ef8b5b1e781a94bd3a270167d3d004 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Sun, 21 Mar 2021 21:45:39 -0500 Subject: [PATCH 1/3] fix(ganymede): Add TMPDIR and SINGULARITY_CACHEDIR env variables --- conf/utd_ganymede.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/conf/utd_ganymede.config b/conf/utd_ganymede.config index 409dc0a..f701a3c 100644 --- a/conf/utd_ganymede.config +++ b/conf/utd_ganymede.config @@ -5,6 +5,11 @@ params { config_profile_url = 'http://docs.oithpc.utdallas.edu/' } +env { + TMPDIR = '/home/$USER/scratch/tmp' + SINGULARITY_CACHEDIR = '/home/$USER/scratch/tmp' +} + singularity { enabled = true envWhitelist='SINGULARITY_BINDPATH' From 34ccce9531351fd8133c3dc3a77dab20398a5735 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Sun, 21 Mar 2021 21:46:25 -0500 Subject: [PATCH 2/3] fix(ganymede): Add process resources Trimgalore though it can be a bottom neck, doesn't require the 1 big memory node we have and can be run on the genomics queue. --- conf/utd_ganymede.config | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/conf/utd_ganymede.config b/conf/utd_ganymede.config index f701a3c..c64e673 100644 --- a/conf/utd_ganymede.config +++ b/conf/utd_ganymede.config @@ -20,6 +20,28 @@ process { beforeScript = 'module load singularity/3.2.1' executor = 'slurm' queue = { task.memory >= 32.GB && task.cpu <= 12 ? 'Kim': task.memory <= 24.GB && task.cpu <= 8 ? 'smallmem' : 'genomics' } + + withName:TRIMGALORE { + memory = 31.GB + } + + withLabel:process_low { + cpus = { check_max( 2 * task.attempt, 'cpus' ) } + memory = { check_max( 12.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } + + withLabel:process_medium { + cpus = { check_max( 16 * task.attempt, 'cpus' ) } + memory = { check_max( 31.GB * task.attempt, 'memory' ) } + time = { check_max( 8.h * task.attempt, 'time' ) } + } + + withLabel:process_large { + cpus = { check_max( 12 * task.attempt, 'cpus' ) } + memory = { check_max( 1.GB * task.attempt, 'memory' ) } + time = { check_max( 16.h * task.attempt, 'time' ) } + } } params { From a6975cdd4ef05a552aaa6de492d88a525974a313 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 22 Mar 2021 12:42:56 -0500 Subject: [PATCH 3/3] fix(ganymede): large => high Co-authored-by: drpatelh --- conf/utd_ganymede.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/utd_ganymede.config b/conf/utd_ganymede.config index c64e673..01bb10b 100644 --- a/conf/utd_ganymede.config +++ b/conf/utd_ganymede.config @@ -37,9 +37,9 @@ process { time = { check_max( 8.h * task.attempt, 'time' ) } } - withLabel:process_large { + withLabel:process_high { cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 1.GB * task.attempt, 'memory' ) } + memory = { check_max( 120.GB * task.attempt, 'memory' ) } time = { check_max( 16.h * task.attempt, 'time' ) } } }