From c5070f3eba267bbf58862c489c6748045e837d31 Mon Sep 17 00:00:00 2001
From: Pontus Freyhult <pontus_github@soua.net>
Date: Wed, 7 Apr 2021 17:07:49 +0200
Subject: [PATCH] Use node queue when more memory than thin nodes have

---
 conf/uppmax.config | 33 ++++++++++++++++++++++++++++-----
 1 file changed, 28 insertions(+), 5 deletions(-)

diff --git a/conf/uppmax.config b/conf/uppmax.config
index bc3d8c4..da25dfc 100644
--- a/conf/uppmax.config
+++ b/conf/uppmax.config
@@ -9,25 +9,48 @@ singularity {
   enabled = true
 }
 
+def hostname = "hostname".execute().text.trim()
+
 process {
+  // 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 "
+			    }
+			    // Remaining cases use the largest available node (1 Tbyte for rackham, 512 Gbyte for others)
+			    if (hostname ==~ "r.*") {
+			      return base + " -p node -C mem1TB "
+			    }
+			    return base + " -p node -C mem512GB "
+			  }
+
+
   executor = 'slurm'
-  clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" }
+  clusterOptions = { clusterOptionsCreator(task.memory) }
 }
 
 params {
   save_reference = true
 
-  max_memory = 125.GB
+  max_memory = 970.GB
   max_cpus = 16
   max_time = 240.h
   // illumina iGenomes reference file paths on UPPMAX
   igenomes_base = '/sw/data/uppnex/igenomes/'
 }
 
-def hostname = "hostname".execute().text.trim()
+if (hostname ==~ "b.*") {
+  params.max_memory = 500.GB
+}
 
-if (hostname ==~ "b.*" || hostname ==~ "s.*") {
-  params.max_memory = 109.GB
+if (hostname ==~ "s.*") {
+  params.max_memory = 500.GB
+  params.max_time = 700.h
 }
 
 if (hostname ==~ "i.*") {