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--- calcoloscientifico:userguide:amber [30/06/2022 12:52] – ↷ Pagina spostata da calcoloscientifico:userguide:applications:amber a calcoloscientifico:userguide:amber 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 21: / Linea 23: @@
 module load gnu8 openmpi4
-module load apptainer
+module load apptainer/1.0
 container='/hpc/share/applications/amber/20/amber-20-cpu'
@@ 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 49: / Linea 53: @@
 shopt -q login_shell || exit 1
-module load apptainer
+module load apptainer/1.0
 container='/hpc/share/applications/amber/20/amber-20-gpu'
@@ Linea 62: / Linea 66: @@
 pmemd.cuda -i test_amber_MD.in -o test-MD.out -p test.prmtop -c test-min.rst -r test-MD.rst -x test-MD.nc -e test-MD.en -inf test-MD.mdinfo -O
 </code>
+=== pdb4amber ===
+Run the following commands on the login node to open a shell on the compute node:
+<code>
+srun \
+    --nodes=1 \
+    --ntasks-per-node=4 \
+    --time=0-01:00:00 \
+    --mem=16G \
+    --partition=cpu \
+    --qos=cpu \
+    --constraint='broadwell|skylake' \
+    --account=<account> \
+    --pty \
+    bash
+</code>
+As usual the argument to the
+<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
+apptainer shell "$CONTAINER"
+</code>
+Inside the container run ''pdb4amber'':
+<code>
+pdb4amber
+</code>
+To exit the container run ''exit''.
+To exit the shell on the compute node run the ''exit''.