Merge pull request #226 from pontus/master

UPPMAX: Allow jobs needing more memory than thin nodes, pick up cluster info through slurm

conf/uppmax.config

@@ -12,25 +12,58 @@ singularity {
   enabled = true
 }
 
+def hostname = "r1"
+try {
+    hostname = "sinfo --local -N -h | grep -F -v CLUSTER: | head -1 | cut -f1 -d' ' ".execute().text.trim()
+} catch (java.io.IOException e) {
+    System.err.println("WARNING: Could not run sinfo to determine current cluster, defaulting to rackham")
+}
+
+// closure to create a suitable clusterOptions
+def clusterOptionsCreator = { m ->
+    String base = "-A $params.project ${params.clusterOptions ?: ''}"
+    // Do not use -p node on irma or if a thin node/core is enough
+    if (m < 125.GB || hostname ==~ "i.*") {
+        return base
+    }
+
+    if (m < 250.GB) {
+        return base + " -p node -C mem256GB "
+    }
+
+
+    // Use mem1TB for remaining cases on rackham (no 512 Gbyte nodes)
+    if (hostname ==~ "r.*") {
+        return base + " -p node -C mem1TB "
+    }
+
+    if (m > 500.GB) {
+       // Special case for snowy very fat node (only remaining case that's above 500 GB)
+       return base + " -p veryfat "
+    }
+
+    // Should only be cases for mem512GB left (snowy and bianca)
+    return base + " -p node -C mem512GB "
+}
+
 process {
   executor = 'slurm'
-  clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" }
+  clusterOptions = { clusterOptionsCreator(task.memory) }
 }
 
 params {
   save_reference = true
 
-  max_memory = 125.GB
+  max_memory = 500.GB
   max_cpus = 16
   max_time = 240.h
   // illumina iGenomes reference file paths on UPPMAX
-  igenomes_base = '/sw/data/uppnex/igenomes/'
+  igenomes_base = '/sw/data/igenomes/'
 }
 
-def hostname = "hostname".execute().text.trim()
+if (hostname ==~ "s[0-9][0-9]*") {
-
+  params.max_time = 700.h
-if (hostname ==~ "b.*" || hostname ==~ "s.*") {
+  params.max_memory = 3880.GB
-  params.max_memory = 109.GB
 }
 
 if (hostname ==~ "i.*") {
@@ -39,6 +72,7 @@ if (hostname ==~ "i.*") {
 
 if (hostname ==~ "r.*") {
   params.max_cpus = 20
+  params.max_memory = 970.GB
 }
 
 profiles {