From 65d7080921eb37bd7544df601dc4cb3206102131 Mon Sep 17 00:00:00 2001 From: qlr900 Date: Tue, 5 Jul 2022 11:17:49 +0200 Subject: [PATCH 01/25] add conf/ku_sund_dangpu.config --- conf/ku_sund_dangpu.config | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 conf/ku_sund_dangpu.config diff --git a/conf/ku_sund_dangpu.config b/conf/ku_sund_dangpu.config new file mode 100644 index 0000000..3f3ab5d --- /dev/null +++ b/conf/ku_sund_dangpu.config @@ -0,0 +1,36 @@ +# change ${abc123} to your KU ID before using this config + +params { + config_profile_contact = ‘Adrija Kalvisa ’ + config_profile_description = ‘dangpufl01 configuration’ + config_profile_url = ‘’ + + // General cpus/memory/time requirements + max_cpus = 30 + max_memory = 200.GB + max_time = 72.h +} + +process { + # should we change to a newer java env? + beforeScript = ‘module load jdk/1.8.0_291 singularity/3.8.0’ + executor = ‘slurm’ + + # uncomment specifically for running mnaseseq pipeline: + # withName: TrimGalore { + # cpus = 1 + # } + +} + +executor { + queueSize = 10 +} + +singularity { + enabled = true + autoMounts = true + # set up the cache directory outside the $HOME directory + cacheDir = ‘/projects/dan1/people/${abc123}/cache/singularity-images’ + runOptions = ‘--bind /projects:/projects’ +} \ No newline at end of file From 8ba35f721c496b081192cd38f3b2c2e4936f259e Mon Sep 17 00:00:00 2001 From: qlr900 Date: Tue, 5 Jul 2022 12:05:10 +0200 Subject: [PATCH 02/25] add ku_sund_dangpu.md --- docs/ku_sund_dangpu.md | 58 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 docs/ku_sund_dangpu.md diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md new file mode 100644 index 0000000..c2b9454 --- /dev/null +++ b/docs/ku_sund_dangpu.md @@ -0,0 +1,58 @@ +# nf-core/configs: PROFILE Configuration + +All nf-core pipelines have been successfully configured for use on the dangpu PROFILE CLUSTER at the +Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and the Novo Nordisk Foundation Center for Protein Research (CPR) at the University of Copenhagen. + +To use, run the pipeline with `-profile ku_sund_dangpu`. This will download and launch the [`ku_sund_dangpu.config`](../conf/ku_sund_dangpu.config) which has been pre-configured with a setup suitable for the PROFILE CLUSTER. + +## Modules + +Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on PROFILE CLUSTER. You can do this by issuing the commands below: + +```bash +## Load Nextflow and Singularity environment modules +module purge +module load openjdk/11.0.0 nextflow/22.04.3 singularity/3.8.0 +``` + +## How to use the nf-core pipelines on PROFILE CLUSTER + +###1. set up .bash_profile +Add memory restrictions to `.bash_profile`. Use `vim` text editor to edit `.bash_profile` file (or create one if it does not exist in your home directory: + +``` +vi ~/.bash_profile +``` + +paste the following text within the file: +``` +# personalising the profile: change the value of the variable $abc123 to your own user id +abc123=def456 + +# In some cases, the Nextflow Java virtual machines can start to request a large amount of memory. We recommend adding the following line to your environment to limit this +export NXF_OPTS='-Xms1g -Xmx4g' + +# Don't fill up your home directory with cache files +export NXF_HOME=/projects/dan1/people/${abc123}/cache/nxf-home +export NXF_TEMP=${SNIC_TMP:-$HOME/glob/nxftmp} + +# Nextflow singularity image cachedir export +NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${abc123}/cache/singularity-images +``` + +then save the changes and exit the editor. Now you need to activate the `.bash_profile` by logging out and in again to PROFILE CLUSTER or by typing: +``` +source .bash_profile +``` + +The `$HOME` directory at dangpu has restricted space and should not be used to store cache files. Create those designated cache spaces for nextflow and singularity outside your `$HOME`: +``` +mkdir $NXF_SINGULARITY_CACHEDIR +mkdir $NXF_HOME +``` + +### 3. choose a nf-core pipeline and test it with your preferred settings +``` +nextflow run nf-core/rnaseq -profile test -c +``` + From 941a34406aac86bf92c5523a48cea120590ac4e7 Mon Sep 17 00:00:00 2001 From: qlr900 Date: Tue, 5 Jul 2022 12:06:19 +0200 Subject: [PATCH 03/25] update ku_sund_dangpu.md --- docs/ku_sund_dangpu.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index c2b9454..9dafaa0 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -53,6 +53,6 @@ mkdir $NXF_HOME ### 3. choose a nf-core pipeline and test it with your preferred settings ``` -nextflow run nf-core/rnaseq -profile test -c +nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu ``` From 7d59eabd91635879edab05ef9ec8f007b37e5bf4 Mon Sep 17 00:00:00 2001 From: qlr900 Date: Wed, 6 Jul 2022 09:52:06 +0200 Subject: [PATCH 04/25] simplify guideline --- docs/ku_sund_dangpu.md | 43 ++++++++---------------------------------- 1 file changed, 8 insertions(+), 35 deletions(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 9dafaa0..6121c87 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -1,58 +1,31 @@ # nf-core/configs: PROFILE Configuration -All nf-core pipelines have been successfully configured for use on the dangpu PROFILE CLUSTER at the +All nf-core pipelines have been successfully configured for use on the DANGPU at the Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and the Novo Nordisk Foundation Center for Protein Research (CPR) at the University of Copenhagen. -To use, run the pipeline with `-profile ku_sund_dangpu`. This will download and launch the [`ku_sund_dangpu.config`](../conf/ku_sund_dangpu.config) which has been pre-configured with a setup suitable for the PROFILE CLUSTER. +To use, run the pipeline with `-profile ku_sund_dangpu`. This will download and launch the [`ku_sund_dangpu.config`](../conf/ku_sund_dangpu.config) which has been pre-configured with a setup suitable for the DANGPU. ## Modules -Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on PROFILE CLUSTER. You can do this by issuing the commands below: +Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on DANGPU. You can do this by issuing the commands below: ```bash ## Load Nextflow and Singularity environment modules module purge module load openjdk/11.0.0 nextflow/22.04.3 singularity/3.8.0 -``` - -## How to use the nf-core pipelines on PROFILE CLUSTER - -###1. set up .bash_profile -Add memory restrictions to `.bash_profile`. Use `vim` text editor to edit `.bash_profile` file (or create one if it does not exist in your home directory: - -``` -vi ~/.bash_profile -``` - -paste the following text within the file: -``` -# personalising the profile: change the value of the variable $abc123 to your own user id -abc123=def456 - -# In some cases, the Nextflow Java virtual machines can start to request a large amount of memory. We recommend adding the following line to your environment to limit this export NXF_OPTS='-Xms1g -Xmx4g' - -# Don't fill up your home directory with cache files -export NXF_HOME=/projects/dan1/people/${abc123}/cache/nxf-home -export NXF_TEMP=${SNIC_TMP:-$HOME/glob/nxftmp} - -# Nextflow singularity image cachedir export -NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${abc123}/cache/singularity-images +export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home +export NXF_TEMP=/scratch/tmp +NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images ``` -then save the changes and exit the editor. Now you need to activate the `.bash_profile` by logging out and in again to PROFILE CLUSTER or by typing: -``` -source .bash_profile -``` - -The `$HOME` directory at dangpu has restricted space and should not be used to store cache files. Create those designated cache spaces for nextflow and singularity outside your `$HOME`: +create nextflow directories if they dont exist: ``` mkdir $NXF_SINGULARITY_CACHEDIR mkdir $NXF_HOME ``` -### 3. choose a nf-core pipeline and test it with your preferred settings +finally download and test the pipeline of choice using the `-profile ku_sund_dangpu` ``` nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu ``` - From 56026c5ac4fec88f85eb1e0a44b2ea4e3d053853 Mon Sep 17 00:00:00 2001 From: qlr900 Date: Wed, 6 Jul 2022 09:52:51 +0200 Subject: [PATCH 05/25] remove beforeScript --- conf/ku_sund_dangpu.config | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/conf/ku_sund_dangpu.config b/conf/ku_sund_dangpu.config index 3f3ab5d..442b8af 100644 --- a/conf/ku_sund_dangpu.config +++ b/conf/ku_sund_dangpu.config @@ -12,8 +12,7 @@ params { } process { - # should we change to a newer java env? - beforeScript = ‘module load jdk/1.8.0_291 singularity/3.8.0’ + executor = ‘slurm’ # uncomment specifically for running mnaseseq pipeline: From 49e756d1bc94d3070c08232233ffc374bcdf5536 Mon Sep 17 00:00:00 2001 From: qlr900 Date: Wed, 6 Jul 2022 12:39:55 +0200 Subject: [PATCH 06/25] fix typos --- conf/ku_sund_dangpu.config | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/conf/ku_sund_dangpu.config b/conf/ku_sund_dangpu.config index 442b8af..7712376 100644 --- a/conf/ku_sund_dangpu.config +++ b/conf/ku_sund_dangpu.config @@ -1,9 +1,7 @@ -# change ${abc123} to your KU ID before using this config - params { - config_profile_contact = ‘Adrija Kalvisa ’ - config_profile_description = ‘dangpufl01 configuration’ - config_profile_url = ‘’ + config_profile_contact = 'Adrija Kalvisa ' + config_profile_description = 'dangpufl01 configuration' + config_profile_url = '' // General cpus/memory/time requirements max_cpus = 30 @@ -13,7 +11,7 @@ params { process { - executor = ‘slurm’ + executor = 'slurm' # uncomment specifically for running mnaseseq pipeline: # withName: TrimGalore { @@ -30,6 +28,6 @@ singularity { enabled = true autoMounts = true # set up the cache directory outside the $HOME directory - cacheDir = ‘/projects/dan1/people/${abc123}/cache/singularity-images’ - runOptions = ‘--bind /projects:/projects’ + cacheDir = '/projects/dan1/people/$USER/cache/singularity-images' + runOptions = '--bind /projects:/projects' } \ No newline at end of file From 7ac08a101577c04283b7592d6583d6ab17551d42 Mon Sep 17 00:00:00 2001 From: qlr900 Date: Wed, 6 Jul 2022 12:42:14 +0200 Subject: [PATCH 07/25] add alternative module load --- docs/ku_sund_dangpu.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 6121c87..92e73b5 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -13,6 +13,7 @@ Before running the pipeline you will need to load Nextflow and Singularity using ## Load Nextflow and Singularity environment modules module purge module load openjdk/11.0.0 nextflow/22.04.3 singularity/3.8.0 +# alternative module load jdk/1.8.0_291 nextflow/22.04.3 singularity/3.8.0 export NXF_OPTS='-Xms1g -Xmx4g' export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home export NXF_TEMP=/scratch/tmp From 8a781b6bb2267cca0b1d4ec87da2a7c577e69906 Mon Sep 17 00:00:00 2001 From: qlr900 Date: Wed, 6 Jul 2022 12:54:07 +0200 Subject: [PATCH 08/25] modify alternative module load --- docs/ku_sund_dangpu.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 92e73b5..f63aa0c 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -13,7 +13,7 @@ Before running the pipeline you will need to load Nextflow and Singularity using ## Load Nextflow and Singularity environment modules module purge module load openjdk/11.0.0 nextflow/22.04.3 singularity/3.8.0 -# alternative module load jdk/1.8.0_291 nextflow/22.04.3 singularity/3.8.0 +# alternative module load jdk/1.8.0_291 nextflow/21.04.1.5556 singularity/3.8.0 export NXF_OPTS='-Xms1g -Xmx4g' export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home export NXF_TEMP=/scratch/tmp @@ -26,7 +26,9 @@ mkdir $NXF_SINGULARITY_CACHEDIR mkdir $NXF_HOME ``` -finally download and test the pipeline of choice using the `-profile ku_sund_dangpu` +Finally, download and test the pipeline of choice using the `-profile ku_sund_dangpu`. Note that normally you would run resource-intensive commands with slurm, but in case of nf-core pipelines you do not have to do this: we have pre-configured slurm as resource manager within the ku_sund_dangpu profile. Just make sure that the pipeline is run within a tmux session. + ``` nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu ``` + From f45b8645f63a5c25a16d66626546bc1d96ea86b5 Mon Sep 17 00:00:00 2001 From: qlr900 Date: Wed, 6 Jul 2022 13:05:13 +0200 Subject: [PATCH 09/25] update wording --- docs/ku_sund_dangpu.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index f63aa0c..5515b87 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -26,7 +26,7 @@ mkdir $NXF_SINGULARITY_CACHEDIR mkdir $NXF_HOME ``` -Finally, download and test the pipeline of choice using the `-profile ku_sund_dangpu`. Note that normally you would run resource-intensive commands with slurm, but in case of nf-core pipelines you do not have to do this: we have pre-configured slurm as resource manager within the ku_sund_dangpu profile. Just make sure that the pipeline is run within a tmux session. +Finally, download and test the pipeline of choice using the `-profile ku_sund_dangpu`. Note that normally you would run resource-intensive commands with slurm, but in case of nf-core pipelines you do not have to do this: we have pre-configured slurm as resource manager within the `ku_sund_dangpu profile`. Just make sure that the pipeline is run within a tmux session. ``` nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu From 6939c6f0033e0bc419ff44747d0fd9a2fa1dae99 Mon Sep 17 00:00:00 2001 From: qlr900 Date: Wed, 6 Jul 2022 13:34:18 +0200 Subject: [PATCH 10/25] lower queueSize to 5 --- conf/ku_sund_dangpu.config | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/conf/ku_sund_dangpu.config b/conf/ku_sund_dangpu.config index 7712376..bb70515 100644 --- a/conf/ku_sund_dangpu.config +++ b/conf/ku_sund_dangpu.config @@ -21,13 +21,11 @@ process { } executor { - queueSize = 10 + queueSize = 5 } singularity { enabled = true autoMounts = true - # set up the cache directory outside the $HOME directory - cacheDir = '/projects/dan1/people/$USER/cache/singularity-images' runOptions = '--bind /projects:/projects' } \ No newline at end of file From 4f98876429cb5ba81ed7f4564670a90d0e4d40b7 Mon Sep 17 00:00:00 2001 From: qlr900 Date: Wed, 6 Jul 2022 13:35:10 +0200 Subject: [PATCH 11/25] add export to NXF_SINGULARITY_CACHEDIR --- docs/ku_sund_dangpu.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 5515b87..96bff9f 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -1,4 +1,4 @@ -# nf-core/configs: PROFILE Configuration +# nf-core/configs: ku_sund_dangpu configuration All nf-core pipelines have been successfully configured for use on the DANGPU at the Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and the Novo Nordisk Foundation Center for Protein Research (CPR) at the University of Copenhagen. @@ -13,11 +13,12 @@ Before running the pipeline you will need to load Nextflow and Singularity using ## Load Nextflow and Singularity environment modules module purge module load openjdk/11.0.0 nextflow/22.04.3 singularity/3.8.0 -# alternative module load jdk/1.8.0_291 nextflow/21.04.1.5556 singularity/3.8.0 +# alternative +# module load jdk/1.8.0_291 nextflow/21.04.1.5556 singularity/3.8.0 export NXF_OPTS='-Xms1g -Xmx4g' export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home export NXF_TEMP=/scratch/tmp -NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images +export NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images ``` create nextflow directories if they dont exist: From d2b6b07de81be19c081fd610c20eccaf6389abce Mon Sep 17 00:00:00 2001 From: qlr900 Date: Wed, 6 Jul 2022 14:18:31 +0200 Subject: [PATCH 12/25] remove comments for mnaseseq --- conf/ku_sund_dangpu.config | 6 ------ 1 file changed, 6 deletions(-) diff --git a/conf/ku_sund_dangpu.config b/conf/ku_sund_dangpu.config index bb70515..51ca462 100644 --- a/conf/ku_sund_dangpu.config +++ b/conf/ku_sund_dangpu.config @@ -10,14 +10,8 @@ params { } process { - executor = 'slurm' - # uncomment specifically for running mnaseseq pipeline: - # withName: TrimGalore { - # cpus = 1 - # } - } executor { From d19d6c0ae0e545202ad8983accf2c83e1e040ca1 Mon Sep 17 00:00:00 2001 From: qlr900 Date: Wed, 6 Jul 2022 16:19:16 +0200 Subject: [PATCH 13/25] update wording --- docs/ku_sund_dangpu.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 96bff9f..5c6fc4e 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -21,13 +21,13 @@ export NXF_TEMP=/scratch/tmp export NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images ``` -create nextflow directories if they dont exist: +Create the user-specific nextflow directories if they don't exist yet: ``` mkdir $NXF_SINGULARITY_CACHEDIR mkdir $NXF_HOME ``` -Finally, download and test the pipeline of choice using the `-profile ku_sund_dangpu`. Note that normally you would run resource-intensive commands with slurm, but in case of nf-core pipelines you do not have to do this: we have pre-configured slurm as resource manager within the `ku_sund_dangpu profile`. Just make sure that the pipeline is run within a tmux session. +Finally, download and test the pipeline of choice using the `-profile ku_sund_dangpu`. Note that normally you would run resource-intensive commands with slurm, but in case of nf-core pipelines you do not have to do this: we have pre-configured slurm to be the resource manager within the `ku_sund_dangpu profile`. Just make sure that the pipeline is run within a tmux session. ``` nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu From ff55ec67b4672376e3754b898f21be2c2d112cbd Mon Sep 17 00:00:00 2001 From: qlr900 Date: Thu, 7 Jul 2022 14:30:48 +0200 Subject: [PATCH 14/25] update to current java+nextflow module combination --- docs/ku_sund_dangpu.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 5c6fc4e..aea1b40 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -12,8 +12,8 @@ Before running the pipeline you will need to load Nextflow and Singularity using ```bash ## Load Nextflow and Singularity environment modules module purge -module load openjdk/11.0.0 nextflow/22.04.3 singularity/3.8.0 -# alternative +module load java/11.0.15 nextflow/22.04.4 singularity/3.8.0 +# alternative modules for older nextflow version (v.21) that works with java 8: # module load jdk/1.8.0_291 nextflow/21.04.1.5556 singularity/3.8.0 export NXF_OPTS='-Xms1g -Xmx4g' export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home From 8448bb9a1edb7aaf4103077f4d36e3a971e5ad7c Mon Sep 17 00:00:00 2001 From: Lara Ianov <61988230+lianov@users.noreply.github.com> Date: Thu, 1 Sep 2022 10:12:07 -0500 Subject: [PATCH 15/25] re-define TMPDIR --- conf/cheaha.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/cheaha.config b/conf/cheaha.config index 58963b5..ec79f10 100644 --- a/conf/cheaha.config +++ b/conf/cheaha.config @@ -9,7 +9,7 @@ params { } env { - TMPDIR="$USER" + TMPDIR="$scratch_dir" SINGULARITY_TMPDIR="$scratch_dir" } From b20f28a3c9f3e4df21030b179a46ddb2fe151307 Mon Sep 17 00:00:00 2001 From: phue Date: Mon, 5 Sep 2022 11:25:33 +0200 Subject: [PATCH 16/25] biohpc_gen: load charliecloud from lrz software tree and remove conda fallback the biohpc_gen specific software tree is less maintained and outdated --- conf/biohpc_gen.config | 9 ++++----- docs/biohpc_gen.md | 6 ++---- 2 files changed, 6 insertions(+), 9 deletions(-) diff --git a/conf/biohpc_gen.config b/conf/biohpc_gen.config index e3f4069..694a25f 100755 --- a/conf/biohpc_gen.config +++ b/conf/biohpc_gen.config @@ -11,9 +11,8 @@ env { process { executor = 'slurm' - queue = { task.memory <= 1536.GB ? (task.time > 2.d || task.memory > 384.GB ? 'biohpc_gen_production' : 'biohpc_gen_normal') : 'biohpc_gen_highmem' } - beforeScript = 'module use /dss/dsslegfs02/pn73se/pn73se-dss-0000/spack/modules/x86_avx2/linux*' - module = 'charliecloud/0.22:miniconda3' + queue = { task.memory <= 1536.GB ? (task.time > 2.d || task.memory > 384.GB ? 'biohpc_gen_production' : 'biohpc_gen_normal') : 'biohpc_gen_highmem' } + module = 'charliecloud/0.25' } charliecloud { @@ -21,7 +20,7 @@ charliecloud { } params { - params.max_time = 14.d - params.max_cpus = 80 + params.max_time = 14.d + params.max_cpus = 80 params.max_memory = 3.TB } diff --git a/docs/biohpc_gen.md b/docs/biohpc_gen.md index c007cad..660e789 100644 --- a/docs/biohpc_gen.md +++ b/docs/biohpc_gen.md @@ -4,14 +4,12 @@ All nf-core pipelines have been successfully configured for use on the BioHPC Ge To use, run the pipeline with `-profile biohpc_gen`. This will download and launch the [`biohpc_gen.config`](../conf/biohpc_gen.config) which has been pre-configured with a setup suitable for the biohpc_gen cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Charliecloud container before execution of the pipeline. -Before running the pipeline you will need to load Nextflow and Charliecloud using the environment module system on biohpc_gen. You can do this by issuing the commands below: +Before running the pipeline you will need to load Nextflow and Charliecloud using the environment module system on a login node. You can do this by issuing the commands below: ```bash ## Load Nextflow and Charliecloud environment modules -module purge -module load nextflow charliecloud/0.22 +module load nextflow/21.04.3 charliecloud/0.25 ``` -> NB: Charliecloud support requires Nextflow version `21.03.0-edge` or later. > NB: You will need an account to use the LRZ Linux cluster as well as group access to the biohpc_gen cluster in order to run nf-core pipelines. > NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. From c709be3b599d463fcfa82196fd4c9c5fa1e99513 Mon Sep 17 00:00:00 2001 From: ggabernet Date: Sun, 18 Sep 2022 12:06:37 +0200 Subject: [PATCH 17/25] update cfc config maintenance --- conf/cfc.config | 2 +- conf/cfc_dev.config | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/cfc.config b/conf/cfc.config index 1948e14..999e8d6 100644 --- a/conf/cfc.config +++ b/conf/cfc.config @@ -12,7 +12,7 @@ singularity { process { executor = 'slurm' - queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' } + queue = 'qbic' scratch = 'true' } diff --git a/conf/cfc_dev.config b/conf/cfc_dev.config index 1d61baf..87caf66 100644 --- a/conf/cfc_dev.config +++ b/conf/cfc_dev.config @@ -11,7 +11,7 @@ singularity { process { executor = 'slurm' - queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' } + queue = 'qbic' scratch = 'true' } @@ -25,4 +25,4 @@ params { max_memory = 1999.GB max_cpus = 128 max_time = 140.h -} \ No newline at end of file +} From 2e9578498aae79e6fdbdd67ddc59c0b04ef94868 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Thu, 22 Sep 2022 13:20:42 +0200 Subject: [PATCH 18/25] add ku_sund_dangpu.config --- nfcore_custom.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nfcore_custom.config b/nfcore_custom.config index d93e266..f777280 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -49,6 +49,7 @@ profiles { ifb_core { includeConfig "${params.custom_config_base}/conf/ifb_core.config" } imperial { includeConfig "${params.custom_config_base}/conf/imperial.config" } jax { includeConfig "${params.custom_config_base}/conf/jax.config" } + ku_sund_sdangpu {includeConfig "${params.custom_config_base}/conf/ku_sund_dangpu.config"} lugh { includeConfig "${params.custom_config_base}/conf/lugh.config" } maestro { includeConfig "${params.custom_config_base}/conf/maestro.config" } marvin { includeConfig "${params.custom_config_base}/conf/marvin.config" } From ce916bf4b56255174afc3b4bc76182ba4806d61d Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Thu, 22 Sep 2022 13:21:10 +0200 Subject: [PATCH 19/25] fix typo --- nfcore_custom.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nfcore_custom.config b/nfcore_custom.config index f777280..aba5349 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -49,7 +49,7 @@ profiles { ifb_core { includeConfig "${params.custom_config_base}/conf/ifb_core.config" } imperial { includeConfig "${params.custom_config_base}/conf/imperial.config" } jax { includeConfig "${params.custom_config_base}/conf/jax.config" } - ku_sund_sdangpu {includeConfig "${params.custom_config_base}/conf/ku_sund_dangpu.config"} + ku_sund_dangpu {includeConfig "${params.custom_config_base}/conf/ku_sund_dangpu.config"} lugh { includeConfig "${params.custom_config_base}/conf/lugh.config" } maestro { includeConfig "${params.custom_config_base}/conf/maestro.config" } marvin { includeConfig "${params.custom_config_base}/conf/marvin.config" } From 5315ddd92f207528ab512dedac78d0e6b1fb685e Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Thu, 22 Sep 2022 13:22:26 +0200 Subject: [PATCH 20/25] add KU_SUND_DANGPU --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 5264a3c..8eee40a 100644 --- a/README.md +++ b/README.md @@ -122,6 +122,7 @@ Currently documentation is available for the following systems: - [ICR_DAVROS](docs/icr_davros.md) - [IMPERIAL](docs/imperial.md) - [JAX](docs/jax.md) +- KU_SUND_DANGPU (docs/ku_sund_dangpu.md) - [LUGH](docs/lugh.md) - [MAESTRO](docs/maestro.md) - [MARVIN](docs/marvin.md) From 55d7b3fc000c228b90e4da4b4afbbec1fcfb98a4 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Thu, 22 Sep 2022 13:35:08 +0200 Subject: [PATCH 21/25] add KU SUND DANGPU add the profile for Dangpu server hosted by Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW)/ Novo Nordisk Foundation Center for Protein Research (CPR) --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 8eee40a..e3cff9f 100644 --- a/README.md +++ b/README.md @@ -122,7 +122,7 @@ Currently documentation is available for the following systems: - [ICR_DAVROS](docs/icr_davros.md) - [IMPERIAL](docs/imperial.md) - [JAX](docs/jax.md) -- KU_SUND_DANGPU (docs/ku_sund_dangpu.md) +- [KU SUND DANGPU] (docs/ku_sund_dangpu.md) - [LUGH](docs/lugh.md) - [MAESTRO](docs/maestro.md) - [MARVIN](docs/marvin.md) From 339a072884667fbe9dd5cc4784ad3d1356fa2ac0 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Thu, 22 Sep 2022 13:35:42 +0200 Subject: [PATCH 22/25] fix typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e3cff9f..838d288 100644 --- a/README.md +++ b/README.md @@ -122,7 +122,7 @@ Currently documentation is available for the following systems: - [ICR_DAVROS](docs/icr_davros.md) - [IMPERIAL](docs/imperial.md) - [JAX](docs/jax.md) -- [KU SUND DANGPU] (docs/ku_sund_dangpu.md) +- [KU SUND DANGPU](docs/ku_sund_dangpu.md) - [LUGH](docs/lugh.md) - [MAESTRO](docs/maestro.md) - [MARVIN](docs/marvin.md) From 65b6bf7c623643d312c946e011eaf5a39baf25c8 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Thu, 22 Sep 2022 13:37:45 +0200 Subject: [PATCH 23/25] add ku_sund_dangpu --- .github/workflows/main.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 56755f1..e4d68ca 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -67,6 +67,7 @@ jobs: - "ifb_core" - "imperial" - "jax" + - "ku_sund_dangpu" - "lugh" - "marvin" - "medair" From 798d845a0dd327b7ae4eb4c091588e463574fbcf Mon Sep 17 00:00:00 2001 From: AdrijaK Date: Thu, 22 Sep 2022 14:21:02 +0200 Subject: [PATCH 24/25] run prettier --- docs/ku_sund_dangpu.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index aea1b40..72baf46 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -1,6 +1,6 @@ # nf-core/configs: ku_sund_dangpu configuration -All nf-core pipelines have been successfully configured for use on the DANGPU at the +All nf-core pipelines have been successfully configured for use on the DANGPU at the Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and the Novo Nordisk Foundation Center for Protein Research (CPR) at the University of Copenhagen. To use, run the pipeline with `-profile ku_sund_dangpu`. This will download and launch the [`ku_sund_dangpu.config`](../conf/ku_sund_dangpu.config) which has been pre-configured with a setup suitable for the DANGPU. @@ -14,22 +14,22 @@ Before running the pipeline you will need to load Nextflow and Singularity using module purge module load java/11.0.15 nextflow/22.04.4 singularity/3.8.0 # alternative modules for older nextflow version (v.21) that works with java 8: -# module load jdk/1.8.0_291 nextflow/21.04.1.5556 singularity/3.8.0 +# module load jdk/1.8.0_291 nextflow/21.04.1.5556 singularity/3.8.0 export NXF_OPTS='-Xms1g -Xmx4g' export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home export NXF_TEMP=/scratch/tmp -export NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images +export NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images ``` Create the user-specific nextflow directories if they don't exist yet: + ``` mkdir $NXF_SINGULARITY_CACHEDIR mkdir $NXF_HOME ``` -Finally, download and test the pipeline of choice using the `-profile ku_sund_dangpu`. Note that normally you would run resource-intensive commands with slurm, but in case of nf-core pipelines you do not have to do this: we have pre-configured slurm to be the resource manager within the `ku_sund_dangpu profile`. Just make sure that the pipeline is run within a tmux session. +Finally, download and test the pipeline of choice using the `-profile ku_sund_dangpu`. Note that normally you would run resource-intensive commands with slurm, but in case of nf-core pipelines you do not have to do this: we have pre-configured slurm to be the resource manager within the `ku_sund_dangpu profile`. Just make sure that the pipeline is run within a tmux session. ``` nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu ``` - From 17c3767fef85f129eee9632ee6202822ad550ba8 Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Fri, 23 Sep 2022 12:53:54 +0100 Subject: [PATCH 25/25] Update crukmi.config Fix the singularity cache dir and add process_single. --- conf/crukmi.config | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/conf/crukmi.config b/conf/crukmi.config index 4823585..778935b 100644 --- a/conf/crukmi.config +++ b/conf/crukmi.config @@ -5,11 +5,8 @@ params { config_profile_url = 'http://scicom.picr.man.ac.uk/projects/user-support/wiki' } -env { - SINGULARITY_CACHEDIR = '/lmod/nextflow_software' -} - singularity { + cacheDir = '/lmod/nextflow_software' enabled = true autoMounts = true } @@ -22,6 +19,11 @@ process { maxErrors = '-1' maxRetries = 3 + withLabel:process_single { + cpus = { check_max( 1 * task.attempt, 'cpus' ) } + memory = { check_max( 5.GB * task.attempt, 'memory' ) } + } + withLabel:process_low { cpus = { check_max( 1 * task.attempt, 'cpus' ) } memory = { check_max( 5.GB * task.attempt, 'memory' ) }