Differences

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--- membrane_simulation [2023/03/14 13:28] – admin
+++ membrane_simulation [2023/07/10 10:07] – admin
@@ Line 16: / Line 16: @@
 Changes in //first-dyn.csh//:
-You will need to change the job-name to something relevant to you. On Zaratan, the example runs on a single 128-core node.  You may adjust this and the associated lines from:
+You will need to change the job-name to something relevant to you. On Zaratan, there are 128-core nodes. For small bilayers (<30,000 atoms) the use of the whole node is inefficient. Beyond these small systems, you will need to do some benchmarking with varied number of cores to determine the optimal size (talk with Dr. Klauda on details). However, for small bilayers you should use:
-<code commend> charmrun namd2 +p 128 +ppn 128 +setcpuaffinity </code>
+<code commend> charmrun namd2 +p 48 +ppn 48 +setcpuaffinity </code>
-To changing the -N and -n in #SBATCH to the number of nodes that you are using. So for example if you are using 2 nodes the above part of the code will change:
+If you wanted to use all the cores on the node then you would replace 48 with 128 in the .csh file (#SBATCH --cpus-per-task 128 and in charmmrun). If you need to used more than one node, change the -N and -n in #SBATCH to the number of nodes that you are using. So for example if you are using 2 nodes the above part of the code will change:
 <code commend> mpirun -n 2 namd2 +auto-provision +setcpuaffinity  </code>