membrane_simulation
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membrane_simulation [2022/09/18 16:53] – admin | membrane_simulation [2023/08/17 16:08] (current) – admin | ||
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These are based off running on Zaratan. If running on another resource see sample inputs from Dr. Klauda or others. | These are based off running on Zaratan. If running on another resource see sample inputs from Dr. Klauda or others. | ||
- | Once you've built the bilayer in CHARMM-GUI per Dr. Klauda' | + | Once you've built the bilayer in CHARMM-GUI per Dr. Klauda' |
- | After approval of the setup, you will need to do is look at some files in the following directory | + | After approval of the setup, you will need to do is copy all the files in the following directory on Zaratan |
// | // | ||
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Changes in // | Changes in // | ||
- | You will need to change the job-name to something relevant to you. On Zaratan, | + | You will need to change the job-name to something relevant to you. On Zaratan, |
- | <code commend> charmrun namd2 +p 128 +ppn 128 +setcpuaffinity </ | + | <code commend> charmrun namd2 +p 48 +ppn 48 +setcpuaffinity </ |
- | To changing | + | 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, this depends on the resource. Zaratan with its AMD EPYC 7763 chips works best when you put 8 processes on a node with its 8 CCDs. Each CCD has 16 threads so you would want to list -n in the mpirun equal to the (# of processes) * (# of nodes). Plus change |
- | <code commend> mpirun -n 2 namd2 +auto-provision | + | <code commend> mpirun |
So the charmrun is removed and other and you only change '-n #' with # being the # of nodes. | So the charmrun is removed and other and you only change '-n #' with # being the # of nodes. |
membrane_simulation.1663534393.txt.gz · Last modified: 2022/09/18 16:53 by admin