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--- calcoloscientifico:userguide:fsl [28/01/2026 14:34] – creata fabio.spataro
+++ calcoloscientifico:userguide:fsl [28/01/2026 16:14] (versione attuale) – fabio.spataro
@@ Linea 3: / Linea 3: @@
 [[https://fsl.fmrib.ox.ac.uk/fsl|FSL]]
-FSL is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data. Most of the tools can be run both from the command line and as GUIs ("point-and-click" graphical user interfaces).
+FSL is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data. Most of the tools can be run both from the command line and as GUIs (''point-and-click'' graphical user interfaces).
+=== Job FSL 6.0.7.19 (single node, multitasks) for CPU ===
 Example script ''slurm-fsl.sh'' to run ''fslmath'' on 1 node of the ''cpu'' partition using 4 cores and at most 8 GB of memory:
@@ Linea 31: / Linea 33: @@
 apptainer exec "$FSL_CONTAINER" /bin/bash -lc '. "$FSLDIR/etc/fslconf/fsl.sh" && fslmaths -h'
 </code>
+Submission example:
+<code>
+sbatch slurm-fsl.sh
+</code>
+=== Interactive FSL 6.0.7.19 session ===
+To run an interactive work session, you need to connect to the ''[[gui|gui.hpc.unipr.it]]'' server via RDP (Remote Desktop Protocol), change your keyboard layout (if necessary), open a terminal window. The following commands must be run in the terminal window.
+To work in ''Group'' mode, run the newgrp command.
+Example:
+<code>
+[foo@ui03 ~]$ groups
+Person G_BAR
+[foo@ui03 ~]$ newgrp G_BAR
+</code>
+In case you want to work in the ''$GROUP'' directory:
+<code>
+(G_BAR)[foo@ui03 ~]$ echo $GROUP
+/hpc/group/G_BAR
+(G_BAR)[foo@ui03 ~]$ cd $GROUP
+(G_BAR)[foo@ui03 G_BAR]$ ...
+</code>
+In case you want to work in the ''$ARCHIVE'' directory:
+<code>
+(G_BAR)[foo@ui03 ~]$ echo $ARCHIVE
+/hpc/archive/G_BAR
+(G_BAR)[foo@ui03 ~]$ cd $ARCHIVE
+(G_BAR)[foo@ui03 G_BAR]$ ...
+</code>
+== Interactive FSL 6.0.7.19 session (single node, multitasks) for CPU ==
+Command to run ''fsl'' on 1 node of the ''cpu'' partition using 4 cores and at most 16 GB of memory:
+<code>
+srun \
+    --job-name=fsl \
+    --nodes=1 \
+    --ntasks-per-node=1 \
+    --cpus-per-task=4 \
+    --mem=16G \
+    --partition=cpu \
+    --qos=cpu \
+    --time=0-06:00:00 \
+    --x11 \
+    --pty \
+    bash
+</code>
+Once you have access to the compute node, run these commands:
+<code>
+module load apptainer fsl
+fsl.sh
+fsleyes
+</code>
+Example:
+<code>
+[foo@wn82 ~]$ module load apptainer fsl
+[foo@wn82 ~]$ fsl.sh
+(fsl-6.0.7.19.sif)[foo@wn82 ~]$ fsleyes
+</code>
+To close your work session, run the ''exit'' command twice. The first command exits the ''[[calcoloscientifico:userguide:apptainer|Apptainer]]'' container, while the second exits the remote node.
+== Interactive FSL 6.0.7.19 session (single node, multitasks) for GPU ==
+Command to run ''fsl'' on 1 node of the ''gpu'' partition using 4 cores, at most 16 GB of memory and 1 ''NVIDIA P100'' GPU:
+<code>
+srun \
+    --job-name=fsl \
+    --nodes=1 \
+    --ntasks-per-node=1 \
+    --cpus-per-task=4 \
+    --mem=16G \
+    --partition=gpu \
+    --qos=gpu \
+    --gres=gpu:p100:1 \
+    --time=0-06:00:00 \
+    --pty \
+    --x11 \
+    bash
+</code>
+Once you have access to the compute node, run these commands:
+<code>
+module load apptainer fsl
+fsl.sh
+fsleyes
+</code>
+Example:
+<code>
+[foo@wn41 ~]$ module load apptainer fsl
+[foo@wn41 ~]$ fsl.sh
+(fsl-6.0.7.19.sif)[foo@wn41 ~]$ fsleyes
+</code>
+To close your work session, run the ''exit'' command twice. The first command exits the ''[[calcoloscientifico:userguide:apptainer|Apptainer]]'' container, while the second exits the remote node.