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--- software:namd:caviness [2024-03-19 09:45] – [Batch job] anita
+++ software:namd:caviness [2024-05-12 15:25] (current) – [Scaling] bkang
@@ Line 20: / Line 20: @@
 </code>
-The ''*'' version is loaded by default when using ''vpkg_require namd''. Make sure you select a GPU variant of the ''namd'' package if you plan to use GPUs, i.e. ''vpkg_require named/2.13:gpu'' and provide the correct options to ''namd'' in the job script
+The ''*'' version is loaded by default when using ''vpkg_require namd''. Make sure you select a GPU variant of the ''namd'' package if you plan to use GPUs, i.e. ''vpkg_require namd:gpu'' and provide the correct options to ''namd'' in the job script
 <code bash>
@@ Line 30: / Line 30: @@
 <note tip>It is always a good idea to periodically check if the templates in ''/opt/shared/templates/slurm'' have changed especially as we learn more about what works well on a particular cluster.</note>
+===== Scaling =====
+Using ApoA1 as an example, the scaling results are presented. The performance improved with increasing CPU and GPU numbers.
+<code bash>
+vpkg_require namd/3.0b3
+charmrun namd3  +p$SLURM_NTASKS  apoa1.namd > apoa1.log
+</code>
+{{:software:namd:scaling_namd_cpu.jpg?400|}}
+<code bash>
+vpkg_require namd/3.0b3:cuda-12.1.1
+charmrun namd3 +idlepoll +p$SLURM_CPUS_PER_TASK +devices $CUDA_VISIBLE_DEVICES apoa1.namd > apoa1.log
+</code>
+{{:software:namd:scaling_namd_gpu.jpg?400|}}
+{{:software:namd:scaling_namd_cpu_gpu.jpg?400|}}