Differences

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--- namd2023 [2024/02/28 21:16] – root
+++ namd2023 [2025/10/15 19:51] (current) – external edit 127.0.0.1
@@ Line 84: / Line 84: @@
 ==GPU==
-Here using the number of cores available on the node (24/32/64) and one GPU (two or more GPUs ``devices 0,1,2,3`` scale poorly, not recommended or approved for AHPCC public use partitions).
+Here we are using the number of CPU cores available on the node (24/32/64) and one GPU (two or more GPUs ``devices 0,1,2,3`` scale poorly, not recommended or approved for AHPCC public use partitions). This benchmark simulation scaled significantly with the CPU cores used up to the number of cores present.  A different test simulation didn't really scale at all and ``+p4`` was best.  It's not apparent to us from the input files why there is a difference. Test runs would be useful if you are going to do a lot of them.
-On the ``gpu72`` partitions with Intel 6130 and single NVidia V100, it's about 5 times faster than the best CPU version.  On ``agpu72`` partitions with AMD7543 and single A100, it's only about 10% faster than V100, so that's not a good use case for the more expensive AMD/A100 nodes.
+On the ``gpu72`` nodes with Intel 6130 and single NVidia V100, it's about 5 times faster than the best CPU version, so are a good use case.  On ``agpu72`` nodes with AMD7543 and single A100, it's only about 10% faster than 6130/V100, so that's not a good use case for the more expensive AMD/A100 nodes, unless gpu memory requires the newer GPU.  The even more expensive multi-gpu ``qgpu72`` nodes also don't scale well over single-gpu and are not a good use case.
 <code>
+#gpu72/v100:
 module load namd/3.0a7
 namd3 +p32 +setcpuaffinity +isomalloc_sync +devices 0 step7.2_production_colvar.inp
 Info: Benchmark time: 32 CPUs 0.0393942 s/step 0.227976 days/ns 0 MB memory
+#agpu72/a100: not recommended unless memory requires
-namd3 +p64 +setcpuaffinity +isomalloc_sync step7.24_production.inp
+namd3 +p64 +setcpuaffinity +isomalloc_sync _devices 0 step7.24_production.inp
 Info: Benchmark time: 64 CPUs 0.0344332 s/step 0.199266 days/ns 0 MB memory
 </code>