From 123f199b68ff287afacb2e6a3d3fb3078c3ae81f Mon Sep 17 00:00:00 2001 From: phue Date: Sun, 27 Oct 2019 20:44:08 +0100 Subject: [PATCH 1/3] cbe: dynamic qos logic --- conf/cbe.config | 22 ++++++---------------- 1 file changed, 6 insertions(+), 16 deletions(-) diff --git a/conf/cbe.config b/conf/cbe.config index c303f92..aed9866 100755 --- a/conf/cbe.config +++ b/conf/cbe.config @@ -8,25 +8,15 @@ params { process { executor = 'slurm' module = 'singularity/3.2.1' - queue = 'c' + queue = { task.memory <= 170.GB ? 'c' : 'm' } + clusterOptions = { task.time <= 8.h ? '--qos short': task.time <= 48.h ? '--qos medium' : '--qos long' } } singularity.enabled = true params { - target_qos = 'medium' - params.max_cpus = 36 - params.max_memory = 170.GB - igenomesIgnore = true -} - -if (params.target_qos == 'short') { - params.max_time = 8.h - process.clusterOptions = '--qos short' -} else if (params.target_qos == 'medium') { - params.max_time = 2.d - process.clusterOptions = '--qos medium' -} else { params.max_time = 14.d - process.clusterOptions = '--qos long' -} + params.max_cpus = 36 + params.max_memory = 4.TB + igenomesIgnore = true +} \ No newline at end of file From 18ed48f39839d42e839566f379a1b9e6680b3d3b Mon Sep 17 00:00:00 2001 From: phue Date: Mon, 28 Oct 2019 11:38:24 +0100 Subject: [PATCH 2/3] deprecate igenomesIgnore in favor of igenomes_ignore keep both for now until all the pipelines have been synced --- conf/cbe.config | 3 ++- conf/czbiohub_aws.config | 3 ++- conf/genouest.config | 3 ++- conf/hebbe.config | 3 ++- conf/mendel.config | 3 ++- conf/pasteur.config | 3 ++- 6 files changed, 12 insertions(+), 6 deletions(-) diff --git a/conf/cbe.config b/conf/cbe.config index aed9866..6e47361 100755 --- a/conf/cbe.config +++ b/conf/cbe.config @@ -18,5 +18,6 @@ params { params.max_time = 14.d params.max_cpus = 36 params.max_memory = 4.TB - igenomesIgnore = true + igenomes_ignore = true + igenomesIgnore = true //deprecated } \ No newline at end of file diff --git a/conf/czbiohub_aws.config b/conf/czbiohub_aws.config index 1dd8da2..98aebe8 100644 --- a/conf/czbiohub_aws.config +++ b/conf/czbiohub_aws.config @@ -55,7 +55,8 @@ params { awsregion = "us-west-2" awsqueue = "nextflow" - igenomesIgnore = true + igenomes_ignore = true + igenomesIgnore = true //deprecated fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' diff --git a/conf/genouest.config b/conf/genouest.config index 68d82a6..801b9fb 100644 --- a/conf/genouest.config +++ b/conf/genouest.config @@ -16,7 +16,8 @@ process { } params { - igenomesIgnore = true + igenomes_ignore = true + igenomesIgnore = true //deprecated max_memory = 750.GB max_cpus = 80 max_time = 336.h diff --git a/conf/hebbe.config b/conf/hebbe.config index 500ec31..26296d5 100644 --- a/conf/hebbe.config +++ b/conf/hebbe.config @@ -18,7 +18,8 @@ process { } params { - igenomesIgnore = true + igenomes_ignore = true + igenomesIgnore = true //deprecated saveReference = true max_memory = 64.GB max_cpus = 20 diff --git a/conf/mendel.config b/conf/mendel.config index e658c87..0fb7e81 100644 --- a/conf/mendel.config +++ b/conf/mendel.config @@ -19,5 +19,6 @@ params { max_cpus = 32 max_memory = 128.GB max_time = 192.h - igenomesIgnore = true + igenomes_ignore = true + igenomesIgnore = true //deprecated } diff --git a/conf/pasteur.config b/conf/pasteur.config index 1d95131..01d5227 100644 --- a/conf/pasteur.config +++ b/conf/pasteur.config @@ -16,7 +16,8 @@ process { } params { - igenomesIgnore = true + igenomes_ignore = true + igenomesIgnore = true //deprecated max_memory = 256.GB max_cpus = 28 max_time = 24.h From 5348b8c609bac0b13003cc464f86ff6973ec1b95 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 28 Oct 2019 13:12:31 +0100 Subject: [PATCH 3/3] Revert "BINAC SMP / Short / Long Updates" --- conf/binac.config | 5 ++--- docs/pasteur.md | 34 ++++++++++++++++------------------ 2 files changed, 18 insertions(+), 21 deletions(-) diff --git a/conf/binac.config b/conf/binac.config index e2bce86..9447ca4 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -13,14 +13,13 @@ process { beforeScript = 'module load devel/singularity/3.0.3' executor = 'pbs' queue = 'short' - process.queue = { task.memory > 128.GB ? 'smp': task.time <= 20m ? 'tiny' : task.time <= 48.h ? 'short' : task.time <= 168.h ? 'long'} } params { igenomes_base = '/nfsmounts/igenomes' - max_memory = 1024.GB + max_memory = 128.GB max_cpus = 28 - max_time = 168.h + max_time = 48.h } weblog{ diff --git a/docs/pasteur.md b/docs/pasteur.md index 6e2d825..554761b 100644 --- a/docs/pasteur.md +++ b/docs/pasteur.md @@ -4,38 +4,36 @@ All nf-core pipelines have been successfully configured for use on the tars clus To use, run the pipeline with `-profile pasteur`. This will download and launch the [`pasteur.config`](../conf/pasteur.config) which has been pre-configured with a setup suitable for the Pasteur cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. + + ## Running the workflow on the Pasteur cluster Nextflow is not installed by default on the Pasteur cluster. - - Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#) + Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command. Nextflow shouldn't run directly on the submission node but on a compute node. The compute nodes don't have access to internet so you need to run it offline. To do that: - 1. Create a virtualenv to install nf-core - - ```bash - module purge - module load Python/3.6.0 - module load java - module load singularity - cd /path/to/nf-core/workflows - virtualenv .venv -p python3 - . .venv/bin/activate - ``` - +```bash +module purge +module load Python/3.6.0 +module load java +module load singularity +cd /path/to/nf-core/workflows +virtualenv .venv -p python3 +. .venv/bin/activate +``` 2. Install nf-core: [here](https://nf-co.re/tools#installation) 3. Get nf-core pipeline and container: [here](https://nf-co.re/tools#downloading-pipelines-for-offline-use) -4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/configs#offline-usage) -5. Run nextflow on a compute node: - +4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/rnaseq/blob/master/docs/usage.md#--custom_config_base) +5. Run nextflow on a compute node: ```bash # create a terminal -tmux +tmux # Get a compute node salloc @@ -48,7 +46,7 @@ module load singularity # Run nextflow workflow nextflow run \\ /path/to/pipeline-dir/from/step/3/workflow \\ --resume +-resume -profile pasteur \\ -with-singularity /path/to/pipeline-dir/from/step/3/singularity-images/singularity.img \\ --email my-email@pasteur.fr \\