From 51d057564f9fc43248f718a2aff0f710ff3ee8e3 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 15 Jun 2022 15:40:42 +0200 Subject: [PATCH 01/12] Fix python related seg faults mag@eva --- conf/pipeline/mag/eva.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/conf/pipeline/mag/eva.config b/conf/pipeline/mag/eva.config index 81d8d0c..37a531d 100644 --- a/conf/pipeline/mag/eva.config +++ b/conf/pipeline/mag/eva.config @@ -4,6 +4,11 @@ params { config_profile_description = 'nf-core/mag EVA profile provided by nf-core/configs' } +env { + OPENBLAS_NUM_THREADS=1 + OMP_NUM_THREADS=1 +} + process { withName: FASTQC { From c479780d8f2e0e802b56c12ff836d11aa223397f Mon Sep 17 00:00:00 2001 From: Cedric Arisdakessian Date: Mon, 3 Oct 2022 03:38:20 +0000 Subject: [PATCH 02/12] create mana config --- conf/mana.config | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 conf/mana.config diff --git a/conf/mana.config b/conf/mana.config new file mode 100644 index 0000000..47f1992 --- /dev/null +++ b/conf/mana.config @@ -0,0 +1,20 @@ +params { + config_profile_description = 'University of Hawaii at Manoa' + config_profile_url = 'http://www.hawaii.edu/its/ci/' + config_profile_contact = 'Cedric Arisdakessian' + + max_memory = 400.GB + max_cpus = 96 + max_time = 72.h +} + +process { + executor = 'slurm' + queue = 'shared,exclusive,kill-shared,kill-exclusive' + module = 'tools/Singularity' +} + +singularity { + enabled = true + cacheDir = "$HOME/.singularity_images_cache" +} From 32cdea4b59788dedee89fd88e0e4f799fb91cc20 Mon Sep 17 00:00:00 2001 From: Cedric Arisdakessian Date: Mon, 3 Oct 2022 03:38:48 +0000 Subject: [PATCH 03/12] documentation for mana config --- docs/mana.md | 46 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 docs/mana.md diff --git a/docs/mana.md b/docs/mana.md new file mode 100644 index 0000000..030749c --- /dev/null +++ b/docs/mana.md @@ -0,0 +1,46 @@ +# nf-core/configs Mana (at University of Hawaii at Manoa) Configuration + +To use, run the pipeline with `-profile mana`. It will use the following parameters for Mana (UHM HPCC): + +- Load singularity and use it as default container technology +- Setup a container cache directory in your home (~/.singularity_images_cache) +- Select appropriate queues (currently: `shared,exclusive,kill-shared,kill-exclusive`) +- Set the maximum available resources (available in 09/02/2022): + - CPUs: 96 + - Memory: 400.GB + - Time: 72.h + + +## Pre-requisites + +In order to run a nf-core pipeline on Mana, you will need to setup nextflow in your environment. +At the moment, nextflow is not available as a module (but might be in the future). + +### Install nextflow in a conda environment + +Before we start, we will need to work on an interactive node (currently, mana doesn't let you execute any program in the login node): + +```bash +# Request an interactive sandbox node for 30 min +srun --pty -t 30 -p sandbox /bin/bash +``` + +To setup nextflow on your account, follow these steps. + +```bash +# Load the latest anaconda3 module +module load lang/Anaconda3 + +# Initialize environment +. /opt/apps/software/lang/Anaconda3/5.1.0/etc/profile.d/conda.sh + +# Install nextflow (here in base environment, but you can create a new one if you'd like) +conda install -c bioconda nextflow +``` + +If you want these settings to be persistent, you can add the first 2 commands in your .bash_profile file like this: + +```bash +echo "module load lang/Anaconda3" >> ~/.bash_profile +echo ". /opt/apps/software/lang/Anaconda3/5.1.0/etc/profile.d/conda.sh >> ~/.bash_profile" +``` \ No newline at end of file From 9b710a07f54be03cb161fcda83b31c5a407d8d25 Mon Sep 17 00:00:00 2001 From: Cedric Arisdakessian Date: Mon, 3 Oct 2022 03:41:23 +0000 Subject: [PATCH 04/12] add mana config --- nfcore_custom.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nfcore_custom.config b/nfcore_custom.config index aba5349..aec233f 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -52,6 +52,7 @@ profiles { ku_sund_dangpu {includeConfig "${params.custom_config_base}/conf/ku_sund_dangpu.config"} lugh { includeConfig "${params.custom_config_base}/conf/lugh.config" } maestro { includeConfig "${params.custom_config_base}/conf/maestro.config" } + mana { includeConfig "${params.custom_config_base}/conf/mana.config" } marvin { includeConfig "${params.custom_config_base}/conf/marvin.config" } medair { includeConfig "${params.custom_config_base}/conf/medair.config" } mjolnir_globe { includeConfig "${params.custom_config_base}/conf/mjolnir_globe.config" } From 7b1e360a3588627de30c76431d7a561d39b792da Mon Sep 17 00:00:00 2001 From: Cedric Arisdakessian Date: Mon, 3 Oct 2022 03:42:07 +0000 Subject: [PATCH 05/12] added mana --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 838d288..e432ec7 100644 --- a/README.md +++ b/README.md @@ -125,6 +125,7 @@ Currently documentation is available for the following systems: - [KU SUND DANGPU](docs/ku_sund_dangpu.md) - [LUGH](docs/lugh.md) - [MAESTRO](docs/maestro.md) +- [MANA](docs/mana.md) - [MARVIN](docs/marvin.md) - [MEDAIR](docs/medair.md) - [MJOLNIR_GLOBE](docs/mjolnir_globe.md) From 9cc679c811bda824f581cacbcdc764ee63b48642 Mon Sep 17 00:00:00 2001 From: Cedric Arisdakessian Date: Mon, 3 Oct 2022 03:43:51 +0000 Subject: [PATCH 06/12] fix mana name --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e432ec7..c476905 100644 --- a/README.md +++ b/README.md @@ -125,7 +125,7 @@ Currently documentation is available for the following systems: - [KU SUND DANGPU](docs/ku_sund_dangpu.md) - [LUGH](docs/lugh.md) - [MAESTRO](docs/maestro.md) -- [MANA](docs/mana.md) +- [Mana](docs/mana.md) - [MARVIN](docs/marvin.md) - [MEDAIR](docs/medair.md) - [MJOLNIR_GLOBE](docs/mjolnir_globe.md) From 3b8b1702030e6e85e1ff147b0b7355de4b7b17f2 Mon Sep 17 00:00:00 2001 From: Cedric Arisdakessian Date: Mon, 3 Oct 2022 03:47:03 +0000 Subject: [PATCH 07/12] added mana in gh actions --- .github/workflows/main.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e4d68ca..16453da 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -69,6 +69,7 @@ jobs: - "jax" - "ku_sund_dangpu" - "lugh" + - "mana" - "marvin" - "medair" - "mjolnir_globe" From e89cb7bd5e6257a8918bbfe427396cab8758c74d Mon Sep 17 00:00:00 2001 From: Cedric Arisdakessian Date: Mon, 3 Oct 2022 03:49:04 +0000 Subject: [PATCH 08/12] fix indentation --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 16453da..c057f2b 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -69,7 +69,7 @@ jobs: - "jax" - "ku_sund_dangpu" - "lugh" - - "mana" + - "mana" - "marvin" - "medair" - "mjolnir_globe" From d429a59a0d76207dbff6be8c98984df4138372be Mon Sep 17 00:00:00 2001 From: Cedric Date: Sun, 2 Oct 2022 18:44:22 -1000 Subject: [PATCH 09/12] add automounts for singularity --- conf/mana.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/mana.config b/conf/mana.config index 47f1992..93d674c 100644 --- a/conf/mana.config +++ b/conf/mana.config @@ -17,4 +17,5 @@ process { singularity { enabled = true cacheDir = "$HOME/.singularity_images_cache" + autoMounts = true } From 2825f33ded98415fbd5bac31c6c74a3618b999a9 Mon Sep 17 00:00:00 2001 From: Cedric Date: Sun, 2 Oct 2022 19:15:59 -1000 Subject: [PATCH 10/12] conda env setup improvement --- docs/mana.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/mana.md b/docs/mana.md index 030749c..d3c3230 100644 --- a/docs/mana.md +++ b/docs/mana.md @@ -29,10 +29,10 @@ To setup nextflow on your account, follow these steps. ```bash # Load the latest anaconda3 module -module load lang/Anaconda3 +module load lang/Anaconda3/2022.05 # Initialize environment -. /opt/apps/software/lang/Anaconda3/5.1.0/etc/profile.d/conda.sh +. $(conda info --base)/etc/profile.d/conda.sh # Install nextflow (here in base environment, but you can create a new one if you'd like) conda install -c bioconda nextflow @@ -41,6 +41,6 @@ conda install -c bioconda nextflow If you want these settings to be persistent, you can add the first 2 commands in your .bash_profile file like this: ```bash -echo "module load lang/Anaconda3" >> ~/.bash_profile -echo ". /opt/apps/software/lang/Anaconda3/5.1.0/etc/profile.d/conda.sh >> ~/.bash_profile" -``` \ No newline at end of file +echo "module load lang/Anaconda3/2022.05" >> ~/.bash_profile +echo "$(conda info --base)/etc/profile.d/conda.sh" >> ~/.bash_profile +``` From e5b798e21f157dec8d6cc51a7b705cdc940c1022 Mon Sep 17 00:00:00 2001 From: Marc Hoeppner Date: Tue, 4 Oct 2022 14:07:44 +0200 Subject: [PATCH 11/12] Updating CCGA med to use the new Beegfs file system --- conf/ccga_med.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/ccga_med.config b/conf/ccga_med.config index d55fde2..c9b7b44 100644 --- a/conf/ccga_med.config +++ b/conf/ccga_med.config @@ -13,8 +13,8 @@ params { singularity { enabled = true - runOptions = "-B /work_ifs -B /scratch" - cacheDir = "/work_ifs/ikmb_repository/singularity_cache/" + runOptions = "-B /work_ifs -B /scratch -B /work_beegfs" + cacheDir = "/work_beegfs/ikmb_repository/singularity_cache/" } executor { @@ -31,7 +31,7 @@ process { params { // illumina iGenomes reference file paths on RZCluster - igenomes_base = '/work_ifs/ikmb_repository/references/iGenomes/references/' + igenomes_base = '/work_beegfs/ikmb_repository/references/iGenomes/references/' saveReference = true max_memory = 250.GB max_cpus = 24 From cade84aacd7d533f34c9e52d2abc39c54a290084 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 4 Oct 2022 19:50:51 +0000 Subject: [PATCH 12/12] [automated] Fix linting with Prettier --- docs/mana.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/mana.md b/docs/mana.md index d3c3230..4d0be0d 100644 --- a/docs/mana.md +++ b/docs/mana.md @@ -1,6 +1,6 @@ # nf-core/configs Mana (at University of Hawaii at Manoa) Configuration -To use, run the pipeline with `-profile mana`. It will use the following parameters for Mana (UHM HPCC): +To use, run the pipeline with `-profile mana`. It will use the following parameters for Mana (UHM HPCC): - Load singularity and use it as default container technology - Setup a container cache directory in your home (~/.singularity_images_cache) @@ -10,7 +10,6 @@ To use, run the pipeline with `-profile mana`. It will use the following paramet - Memory: 400.GB - Time: 72.h - ## Pre-requisites In order to run a nf-core pipeline on Mana, you will need to setup nextflow in your environment.