From 0826ac09cb981c8ee06c3ce1ab861fa163f4bedb Mon Sep 17 00:00:00 2001 From: davidecarlson Date: Tue, 7 Mar 2023 16:10:17 -0500 Subject: [PATCH 1/4] minor config changes --- conf/seawulf.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/seawulf.config b/conf/seawulf.config index 98a5439a9..363422023 100644 --- a/conf/seawulf.config +++ b/conf/seawulf.config @@ -5,7 +5,7 @@ singularity { } profiles { - 40core { + 40core { process { execute = 'slurm' max_memory = 175.GB From f52cd4a5af514699544a1d4e9aad612812299c39 Mon Sep 17 00:00:00 2001 From: davidecarlson Date: Tue, 7 Mar 2023 16:15:31 -0500 Subject: [PATCH 2/4] added seawulf to github actions yaml file --- .github/workflows/main.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index c99bd953e..2383b1a28 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -93,6 +93,7 @@ jobs: - "sanger" - "sbc_sharc" - "scw" + - "seawulf" - "seg_globe" - "tigem" - "ucl_myriad" From 3bff2fe18fa2a49c8d8e988f4d3b18ada59cb419 Mon Sep 17 00:00:00 2001 From: davidecarlson Date: Mon, 16 Sep 2024 10:54:52 -0400 Subject: [PATCH 3/4] update to using shared partitions for nf-core jobs --- conf/seawulf.config | 50 +++++++++++++++++---------------------------- 1 file changed, 19 insertions(+), 31 deletions(-) diff --git a/conf/seawulf.config b/conf/seawulf.config index 363422023..8ce527e18 100644 --- a/conf/seawulf.config +++ b/conf/seawulf.config @@ -4,35 +4,23 @@ singularity { autoMounts = true } -profiles { - 40core { - process { - execute = 'slurm' - max_memory = 175.GB - max_cpus = 40 - max_time = 168.h - maxRetries = 2 - queue = { task.time <= 4.h ? 'short-40core' : task.time <= 48.h ? 'long-40core': task.time <= 168.h ? 'extended-40core' } - } - params { - config_profile_description = 'Stony Brook University's SeaWulf cluster '24core' cluster profile profile provided by nf-core/configs.' - config_profile_contact = 'David Carlson (@davidecarlson)' - config_profile_url = 'https://it.stonybrook.edu/services/high-performance-computing' - } - } - - 96core { - process { - max_memory = 240.GB - max_cpus = 96 - max_time = 168.h - maxRetries = 2 - queue = { task.time <= 4.h ? 'short-96core' : task.time <= 48.h ? 'long-96core': task.time <= 168.h ? 'extended-96core' } - } - params { - config_profile_description = 'Stony Brook University's SeaWulf cluster '96core' cluster profile profile provided by nf-core/configs.' - config_profile_contact = 'David Carlson (@davidecarlson)' - config_profile_url = 'https://it.stonybrook.edu/services/high-performance-computing' - } - } +process { + executor = 'slurm' + maxRetries = 12 + queue = { task.time <= 4.h ? 'short-40core-shared' : task.memory >= 150.GB ? ' long-96core-shared' : task.cpus > 10 ? 'long-96core-shared' : 'long-40core-shared' } +} + +params { + config_profile_contact = 'David Carlson (@davidecarlson)' + config_profile_url = 'https://it.stonybrook.edu/services/high-performance-computing' + config_profile_description = 'Stony Brook Universitys seaWulf cluster profile provided by nf-core/configs.' + max_time = 24.h + max_memory = 251.GB + max_cpus = 96 + +} + +executor { + queueSize = 99 + submitRateLimit = '5 sec' } From 02714724a8293b5fb22aae444201d45e62032f63 Mon Sep 17 00:00:00 2001 From: davidecarlson Date: Mon, 16 Sep 2024 11:44:06 -0400 Subject: [PATCH 4/4] fix linting --- conf/seawulf.config | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/conf/seawulf.config b/conf/seawulf.config index f296e8bb1..0bc87119b 100644 --- a/conf/seawulf.config +++ b/conf/seawulf.config @@ -4,23 +4,23 @@ singularity { } process { - executor = 'slurm' - maxRetries = 12 - queue = { task.time <= 4.h ? 'short-40core-shared' : task.memory >= 150.GB ? ' long-96core-shared' : task.cpus > 10 ? 'long-96core-shared' : 'long-40core-shared' } + executor = 'slurm' + maxRetries = 12 + queue = { task.time <= 4.h ? 'short-40core-shared' : task.memory >= 150.GB ? ' long-96core-shared' : task.cpus > 10 ? 'long-96core-shared' : 'long-40core-shared' } } params { - config_profile_contact = 'David Carlson (@davidecarlson)' - config_profile_url = 'https://it.stonybrook.edu/services/high-performance-computing' - config_profile_description = 'Stony Brook Universitys seaWulf cluster profile provided by nf-core/configs.' - max_time = 24.h - max_memory = 251.GB - max_cpus = 96 + config_profile_contact = 'David Carlson (@davidecarlson)' + config_profile_url = 'https://it.stonybrook.edu/services/high-performance-computing' + config_profile_description = 'Stony Brook Universitys seaWulf cluster profile provided by nf-core/configs.' + max_time = 24.h + max_memory = 251.GB + max_cpus = 96 } executor { - queueSize = 99 - submitRateLimit = '5 sec' + queueSize = 99 + submitRateLimit = '5 sec' -} \ No newline at end of file +}