Merge pull request #1053 from sguizard/master

Update roslin.config

Author: jfy133

conf/roslin.config

@@ -11,17 +11,20 @@ executor {
 
 process {
     stageInMode = 'symlink'
-    scratch     = 'false'
+    // Will use a local tmp dir instead of /tmp.
+    // Set TMPDIR when true
+    // https://www.wiki.ed.ac.uk/spaces/ResearchServices/pages/478073369/Bioinformatics#Bioinformatics-TMPDIR
+    scratch     = true
     penv        = { task.cpus > 1 ? "sharedmem" : null }
 
     // This will override all jobs clusterOptions
     clusterOptions = {
         def memoryPerCpu = task.memory.toMega() / task.cpus
-        def nodeExclusion = System.getenv('NFX_NODE_EXCLUSION') ?
-            "-l h=!(${System.getenv('NFX_NODE_EXCLUSION')})" :
+        def nodeExclusion = System.getenv('NXF_NODE_EXCLUSION') ?
+            "-l h=!(${System.getenv('NXF_NODE_EXCLUSION')})" :
             ""
-        def projectCode = System.getenv('NFX_SGE_PROJECT') ?
-            "${System.getenv('NFX_SGE_PROJECT')}" :
+        def projectCode = System.getenv('NXF_SGE_PROJECT') ?
+            "${System.getenv('NXF_SGE_PROJECT')}" :
             "uoe_baseline"
 
         "-l h_rss=${memoryPerCpu}M -P ${projectCode} ${nodeExclusion}"
@@ -37,23 +40,24 @@ process {
     """
     . /etc/profile.d/modules.sh
     module load igmm/apps/apptainer/1.3.4
-    export SINGULARITY_TMPDIR="\$TMPDIR"
+    export APPTAINER_TMPDIR="\$TMPDIR"
     """
 }
 
 env {
     MALLOC_ARENA_MAX=1
 }
 
-singularity {
-    envWhitelist = "SINGULARITY_TMPDIR,TMPDIR"
-    runOptions   = '-p -B "$TMPDIR"'
+apptainer {
+    envWhitelist = "APPTAINER_TMPDIR,TMPDIR"
+    // --scratch /dev/shm allows to use local tmp dir within container
+    runOptions   = '-p --scratch /dev/shm -B "$TMPDIR"'
     enabled      = true
     autoMounts   = true
     // Define the singularity cache directory depending on the presence of the NFX_SGE_PROJECT variable
     // User without compute project can't access to the shared cache directory.
     // So, they need to store singularity images into the work directory.
-    cacheDir     = System.getenv('NFX_SGE_PROJECT') ?
+    cacheDir     = System.getenv('NXF_SGE_PROJECT') ?
         "/exports/cmvm/eddie/eb/groups/alaw3_eb_singularity_cache" :
         null
 }

docs/roslin.md

@@ -45,16 +45,20 @@ Apptainer/Singularity will by default create a directory `.singularity` in your
 
 ```bash
 cd $HOME
+
+mkdir /exports/eddie/path/to/my/area/.apptainer
+ln -s /exports/eddie/path/to/my/area/.apptainer .apptainer
+
 mkdir /exports/eddie/path/to/my/area/.singularity
 ln -s /exports/eddie/path/to/my/area/.singularity .singularity
 ```
 
 ## SGE project set up
 
-By default, users’ jobs are started with the `uoe_baseline` project that gives access to free nodes. If you have a project code that gives you access to paid nodes. It can be used by jobs submitted by Nextflow. To do so, you need to set up an environment variable called `NFX_SGE_PROJECT`:
+By default, users’ jobs are started with the `uoe_baseline` project that gives access to free nodes. If you have a project code that gives you access to paid nodes. It can be used by jobs submitted by Nextflow. To do so, you need to set up an environment variable called `NXF_SGE_PROJECT`:
 
 ```bash
-export NFX_SGE_PROJECT="<PROJECT_NAME_HERE>"
+export NXF_SGE_PROJECT="<PROJECT_NAME_HERE>"
 ```
 
 If you wish, you place this variable declaration in your `.bashrc` file located in your home directory to automatically set it up each time you log on Eddie.
@@ -73,10 +77,10 @@ Finding those nodes can be done by extracting the job ids from the execution tra
 The script take as input an execution trace file via the `--file` option. It reads it, find the failed jobs, extract job ids, request info to scheduler, extract the execution nodes and format the names before printing.
 `get_fail_jobs_nodes.sh --file execution_trace_2026-01-20_09-32-27.txt`.
 
-Then, you can set up an environment variable called `NFX_NODE_EXCLUSION` and copy/paste the printed node list.
+Then, you can set up an environment variable called `NXF_NODE_EXCLUSION` and copy/paste the printed node list.
 
 ```bash
-export NFX_NODE_EXCLUSION="<FORMATED_LIST_OF_NODES_TO_EXCLUDE>"
+export NXF_NODE_EXCLUSION="<FORMATED_LIST_OF_NODES_TO_EXCLUDE>"
 ```
 
 ## Running Nextflow