Specify GPU device(s) visible to docker (#19)

NAICNO · Sep 6, 2024 · fff8335 · fff8335
2 parents b1c4594 + 1156614
commit fff8335
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Showing 2 changed files with 34 additions and 4 deletions.
diff --git a/workflows/conf/docker.conf b/workflows/conf/docker.conf
@@ -2,17 +2,33 @@ process {
 
     docker.runOptions = '-u $(id -u):$(id -g)'
 
+    // Parabricks configurations
+    // Specify the GPU devices visible to each process
+    withName:'pbrun_fq2bam' {
+        container = "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1"
+        containerOptions = '--gpus \'"device=0,1,2,3"\'  --rm'
+    }
+    withName:'pbrun_applybqsr' {
+        container = "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1"
+        containerOptions = '--gpus \'"device=0"\' --rm'
+    }
+    withName:'pbrun_haplotypecaller' {
+        container = "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1"
+        containerOptions = '--gpus \'"device=0,1,2,3"\' --rm'
+    }
+    withName:'pbrun_deepvariant' {
+        container = "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1"
+        containerOptions = '--gpus \'"device=0,1,2,3"\' --rm'
+    }
+
+
     withName:'bwa' {
         container = "pubudusaneth/bwa_samtools_amd64:v0.7.17.v1.18"
         // Source: https://github.com/NAICNO/NAIC-Dockerfiles/blob/main/bwa-samtools/Dockerfile
     }
     withName:'gatk_.*' {
         container = "docker.io/broadinstitute/gatk:4.3.0.0"
     }
-    withName:'pbrun_.*' {
-        container = "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1"
-        containerOptions = '--gpus all --rm'
-    }
     withName:"deepvariant" {
         container = "google/deepvariant:1.5.0"
     }

diff --git a/workflows/conf/resource.conf b/workflows/conf/resource.conf
@@ -30,14 +30,28 @@ process {
         cpus='12'
     }
 
+    // Parabricks configurations
+    // Specify resources for each process
+
+    withName:'pbrun_fq2bam' {
+        memory='120 GB'
+        cpus='42'
+        gpu='4'
+    }
     // pbrun_applybqsr is recommended to run on 1 GPU
     withName:'pbrun_applybqsr' {
+        memory='120 GB'
+        cpus='42'
         gpu='1'
     }
     withName:'pbrun_deepvariant' {
+        memory='120 GB'
+        cpus='42'
         gpu='4'
     }
     withName:'pbrun_haplotypecaller' {
+        memory='120 GB'
+        cpus='42'
         gpu='4'
     }