Differenze

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--- calcoloscientifico:userguide:amber [20/03/2023 18:26] – fabio.spataro
+++ calcoloscientifico:userguide:amber [20/03/2023 18:50] (versione attuale) – fabio.spataro
@@ Linea 3: / Linea 3: @@
 ==== Amber 20 ====
-Script ''slurm-amber-20-cpu.sh'' to run Amber 20 on 2 nodes (16 tasks per node):
+=== sander ===
+Script ''slurm-amber-20-cpu.sh'' to run ''sander.MPI'' on 2 nodes (16 tasks per node):
 <code bash slurm-amber-20-cpu.sh>
@@ Linea 32: / Linea 34: @@
 </code>
-Script ''slurm-amber-20-gpu.sh'' to run Amber 20 on 1 node with 1 GPU (4 tasks per node):
+=== pmemd.cuda ===
+Script ''slurm-amber-20-gpu.sh'' to run ''pmemd.cuda'' on 1 node with 1 GPU (4 tasks per node):
 <code bash slurm-amber-20-gpu.sh>
@@ Linea 63: / Linea 67: @@
 </code>
-==== pdb4amber ====
+=== pdb4amber ===
 Run the following commands on the login node to open a shell on the compute node:
-<code bash>
+<code>
 srun \
     --nodes=1 \
@@ Linea 76: / Linea 80: @@
     --qos=cpu \
     --constraint='broadwell|skylake' \
-    --account=es_calcolo \
+    --account=<account> \
     --pty \
     bash
 </code>
-On the compute node:
+As usual the argument to the
-<code bash>
+<code>
+--account=<account>
+</code>
+option must be the account you intend to use.
+On the compute node run a shell within the ''amber/20/cpu'' container:
+<code>
 module load apptainer/1.0
 module load amber/20/cpu
@@ Linea 90: / Linea 102: @@
 </code>
-Inside the container:
+Inside the container run ''pdb4amber'':
-<code bash>
+<code>
-Apptainer> pdb4amber
+pdb4amber
 </code>
+To exit the container run ''exit''.
+To exit the shell on the compute node run the ''exit''.