From ca6ddcadb07d44725c12c81af27f86f326753eed Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 26 Nov 2019 15:25:35 +0100 Subject: [PATCH 1/4] Matching max CPUs to SDAG (supercruncher8) --- conf/shh.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/shh.config b/conf/shh.config index 14da627..8a7f812 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -23,8 +23,8 @@ executor { params { max_memory = 2.TB - max_cpus = 32 + max_cpus = 128 max_time = 720.h //Illumina iGenomes reference file path igenomes_base = "/projects1/public_data/igenomes/" -} \ No newline at end of file +} From c3d27099ca02436fc3462504dfddfbfd4ceb3961 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 26 Nov 2019 15:26:05 +0100 Subject: [PATCH 2/4] Updated authors --- conf/shh.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/shh.config b/conf/shh.config index 8a7f812..424a0ee 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -1,7 +1,7 @@ //Profile config names for nf-core/configs params { config_profile_description = 'MPI SHH cluster profile provided by nf-core/configs.' - config_profile_contact = 'James Fellows Yates (@jfy133)' + config_profile_contact = 'James Fellows Yates (@jfy133), Maxime Borry (@Maxibor)' config_profile_url = 'https://shh.mpg.de' } From 12ec22838c5a23f74940b2912aa98bd3e3a78419 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 26 Nov 2019 15:29:03 +0100 Subject: [PATCH 3/4] Specified max sources currently at SDAG limits (exceeds cdag) --- docs/shh.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/shh.md b/docs/shh.md index 78abed0..ec268b5 100644 --- a/docs/shh.md +++ b/docs/shh.md @@ -11,7 +11,11 @@ To use, run the pipeline with `-profile shh`. This will download and launch the however this will likely change to a read-only directory in the future that will be managed by IT. This configuration will automatically choose the correct SLURM queue (`short`,`medium`,`long`,`supercruncher`) depending on the time and memory required by each process. + Please note that there is no `supercruncher` queue on CDAG. >NB: You will need an account and VPN access to use the cluster at MPI-SHH in order to run the pipeline. If in doubt contact IT. + >NB: Nextflow will need to submit the jobs via SLURM to the clusters and as such the commands above will have to be executed on one of the head nodes. If in doubt contact IT. + +>NB: The maximum CPUs/Mem are currently adapted for SDAG resource maximums - i.e. will exceed CDAG. Be careful when running larges jobs that error-retries may exceed limits and get 'stuck' in SLURM. From 89506a653cbe6edbbab5459febfae40ffe9f9cff Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 26 Nov 2019 15:34:25 +0100 Subject: [PATCH 4/4] Remove empty lines in block quotes for linting --- docs/shh.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/shh.md b/docs/shh.md index ec268b5..c89d550 100644 --- a/docs/shh.md +++ b/docs/shh.md @@ -15,7 +15,5 @@ This configuration will automatically choose the correct SLURM queue (`short`,`m Please note that there is no `supercruncher` queue on CDAG. >NB: You will need an account and VPN access to use the cluster at MPI-SHH in order to run the pipeline. If in doubt contact IT. - >NB: Nextflow will need to submit the jobs via SLURM to the clusters and as such the commands above will have to be executed on one of the head nodes. If in doubt contact IT. - >NB: The maximum CPUs/Mem are currently adapted for SDAG resource maximums - i.e. will exceed CDAG. Be careful when running larges jobs that error-retries may exceed limits and get 'stuck' in SLURM.