From 638758423a10a30b127e6526f620f9eb15e73512 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 21 Dec 2019 20:55:54 +0100 Subject: [PATCH 1/3] Restricts MALT re-tries and hardcodes resources so cannot go above SDAG max --- conf/pipeline/eager/shh.config | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/conf/pipeline/eager/shh.config b/conf/pipeline/eager/shh.config index 824185e..a34f0e2 100644 --- a/conf/pipeline/eager/shh.config +++ b/conf/pipeline/eager/shh.config @@ -10,8 +10,9 @@ params { // Specific nf-core/eager process configuration process { withName: malt { - memory = { 725.GB * task.attempt } - cpus = { 64 * task.attempt } + maxRetries = 1 + memory = { task.attempt > 1 ? 1900.GB : 725.GB } + cpus = { task.attempt > 1 ? 112 : 64 } time = 1440.h queue = { task.memory > 756.GB ? 'supercruncher' : 'long' } } From 435a5892eaed65bd237ff949136c4c610c097691 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 21 Dec 2019 20:59:25 +0100 Subject: [PATCH 2/3] Updated docs corresponding to https://github.com/jfy133/configs/commit/638758423a10a30b127e6526f620f9eb15e73512 --- docs/pipeline/eager/shh.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/pipeline/eager/shh.md b/docs/pipeline/eager/shh.md index 8921a54..07cb159 100644 --- a/docs/pipeline/eager/shh.md +++ b/docs/pipeline/eager/shh.md @@ -14,4 +14,4 @@ Example: `nextflow run nf-core/eager -profile shh` Specific configurations for shh has been made for eager. -* Running with the MALT module turned on, will by default be sent either to long or supercruncher queues with a minimum of 756GB and 64 cores. +* If running with the MALT module turned on, the MALT process by default will be sent either to the long queues with a resource requirement minimum of 725GB and 64 cores. If this fails, the process will be tried once more only and sent to the supercruncher queue. The module will not retry after this, and pipeline will fail. From 799f2d57884e5538038aed887ca5975255561331 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 21 Dec 2019 20:59:48 +0100 Subject: [PATCH 3/3] Grammar tweak --- docs/pipeline/eager/shh.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/pipeline/eager/shh.md b/docs/pipeline/eager/shh.md index 07cb159..a0dc092 100644 --- a/docs/pipeline/eager/shh.md +++ b/docs/pipeline/eager/shh.md @@ -14,4 +14,4 @@ Example: `nextflow run nf-core/eager -profile shh` Specific configurations for shh has been made for eager. -* If running with the MALT module turned on, the MALT process by default will be sent either to the long queues with a resource requirement minimum of 725GB and 64 cores. If this fails, the process will be tried once more only and sent to the supercruncher queue. The module will not retry after this, and pipeline will fail. +* If running with the MALT module turned on, the MALT process by default will be sent to the long queue with a resource requirement minimum of 725GB and 64 cores. If this fails, the process will be tried once more only and sent to the supercruncher queue. The module will not retry after this, and pipeline will fail.