include beforescript logic to accomodate new module load logic

nf-core · Jan 9, 2025 · 1240bbb · 1240bbb
1 parent 6d07e08
commit 1240bbb
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diff --git a/conf/vsc_kul_uhasselt.config b/conf/vsc_kul_uhasselt.config
@@ -115,9 +115,10 @@ def determineGeniusGpuQueue = { task ->
         return task.time >= TIME_THRESHOLD ? 'gpu_v100_long' : 'gpu_v100'
     }
     if (task.time >= TIME_THRESHOLD) {
-        return AVAILABLE_QUEUES.contains('dedicated_rega_gpu') ? 'dedicated_rega_gpu' : 'gpu_p100_long,amd_long'
+        return AVAILABLE_QUEUES.contains('dedicated_rega_gpu') ? 'dedicated_rega_gpu' :
+        AVAILABLE_QUEUES.contains('amd') ? 'amd_long' : 'gpu_p100_long'
     }
-    return 'gpu_p100,amd'
+    return AVAILABLE_QUEUES.contains('amd') ? 'amd' : 'gpu_p100'
 }
 
 /*
@@ -183,7 +184,7 @@ profiles {
         process {
             // 768 - 65 so 65GB for overhead, max is 720000MB
             resourceLimits = [ memory: 703.GB, cpus: 36, time: 168.h ]
-            beforeScript   = 'module load cluster/genius'
+            beforeScript   = { 'module load cluster/genius/' + determineGeniusQueue(task).toString().split(',')[0] }
             queue          = { determineGeniusQueue(task) }
             clusterOptions = {
                 determineGeniusQueue(task) =~ /dedicated/ ?
@@ -193,6 +194,7 @@ profiles {
 
             withLabel: '.*gpu.*'{
                 resourceLimits         = [ memory: 703.GB, cpus: 36 , time: 168.h ]
+                beforeScript           = { 'module load cluster/genius/' + determineGeniusGpuQueue(task).toString().split(',')[0] }
                 apptainer.runOptions   = '--containall --cleanenv --nv'
                 singularity.runOptions = '--containall --cleanenv --nv'
                 queue                  = { determineGeniusGpuQueue(task) }
@@ -212,8 +214,8 @@ profiles {
         process {
             // 768 - 65 so 65GB for overhead, max is 720000MB
             resourceLimits = [ memory: 703.GB, cpus: 36, time: 168.h]
-            beforeScript   = 'module load cluster/genius'
-            queue         = { determineGeniusGpuQueue(task) }
+            beforeScript   = { 'module load cluster/genius/' + determineGeniusGpuQueue(task).toString().split(',')[0] }
+            queue          = { determineGeniusGpuQueue(task) }
             clusterOptions = {
                 def gpus = task.accelerator?.request ?: Math.max(1, Math.floor((task.cpus ?:1)/9) as int)
                 "--gres=gpu:${gpus} --clusters=genius --account=$TIER2_PROJECT"
@@ -227,7 +229,7 @@ profiles {
         process {
             // max is 2016000
             resourceLimits = [ memory: 1968.GB, cpus: 72, time: 168.h ]
-            beforeScript   = 'module load cluster/wice'
+            beforeScript   = { 'module load cluster/wice/' + determineWiceQueue(task).toString().split(',')[0] }
             queue          = { determineWiceQueue(task) }
             clusterOptions = {
                 determineWiceQueue(task) =~ /dedicated/ ?
@@ -239,6 +241,7 @@ profiles {
                 resourceLimits         = [ memory: 703.GB, cpus: 64, time: 168.h ]
                 apptainer.runOptions   = '--containall --cleanenv --nv'
                 singularity.runOptions = '--containall --cleanenv --nv'
+                beforeScript           = { 'module load cluster/wice/' + determineWiceGpuQueue(task).toString().split(',')[0] }
                 queue                  = { determineWiceGpuQueue(task) }
                 clusterOptions         = {
                     def gpus = task.accelerator?.request ?: Math.max(1, Math.floor((task.cpus ?:1)/16) as int)
@@ -258,10 +261,10 @@ profiles {
 
         process {
             // 768 - 65 so 65GB for overhead, max is 720000MB
-            beforeScript           = 'module load cluster/wice'
-            resourceLimits         = [ memory: 703.GB, cpus: 64, time: 168.h ]
-            queue                  = { determineWiceGpuQueue(task) }
-            clusterOptions         = {
+            beforeScript   = { 'module load cluster/wice/' + determineWiceGpuQueue(task).toString().split(',')[0] }
+            resourceLimits = [ memory: 703.GB, cpus: 64, time: 168.h ]
+            queue          = { determineWiceGpuQueue(task) }
+            clusterOptions = {
                 def gpus = task.accelerator?.request ?: Math.max(1, Math.floor((task.cpus ?:1)/16) as int)
                 def queueValue = determineWiceGpuQueue(task)
                 queueValue =~ /dedicated_big_gpu_h100/ ? "--clusters=wice --account=lp_big_wice_gpu_h100 --gres=gpu:${gpus}" :

diff --git a/docs/vsc_kul_uhasselt.md b/docs/vsc_kul_uhasselt.md
@@ -15,7 +15,7 @@ A nextflow module is available that can be loaded `module load Nextflow` but it
 2. Set up the environment variables in `~/.bashrc` or `~/.bash_profile`:
 
 :::note
-If you have access to dedicated nodes, you can export these as a command separated list. These queues will only be used if specified task requirements are not available in the normal partitions but they are available in dedicated partitions.
+If you have access to dedicated nodes, you can export these as a command separated list. These queues will only be used if specified task requirements are not available in the normal partitions but they are available in dedicated partitions. AMD is considered a dedicated partition.
 :::
 
 ```bash
-Original file line number
+Diff line change
@@ Expand Up @@
 . Set up the environment variables in `~/.bashrc` or `~/.bash_profile`:
     :::note
-    If you have access to dedicated nodes, you can export these as a command separated list. These queues will only be used if specified task requirements are not available in the normal partitions but they are available in dedicated partitions.
+    If you have access to dedicated nodes, you can export these as a command separated list. These queues will only be used if specified task requirements are not available in the normal partitions but they are available in dedicated partitions. AMD is considered a dedicated partition.
     :::
     ```bash
@@ Expand Down @@