production_run
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production_run [2018/04/18 13:32] – admin | production_run [2022/09/28 17:23] (current) – admin | ||
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[[bilayer_simulations]] | [[bilayer_simulations]] | ||
- | ==== Production run instructions for DT1/ | + | ==== Production run instructions for Zaratan |
- | Listed below are some instructions for the production run simulation on DT1/DT2 (slight differences for MARCC). As we discussed, this will automatically run your simulation in chunks with each being a certain length. | + | Listed below are some instructions for the production run simulation on Zaratan. As we discussed, this will automatically run your simulation in chunks with each being a certain length. |
- | for DT2, **/homes/ | + | **/home/ |
There are key things to change in the dyn.csh file: | There are key things to change in the dyn.csh file: | ||
- | - # number of tasks and nodes to run your job (talk to Dr. Klauda) | + | - # number of nodes to run your job (talk to Dr. Klauda) |
- You should adjust the job name to something for your system. | - You should adjust the job name to something for your system. | ||
- | - mpirun -np command with the same number of tasks | + | - Adjust the SBATCH and namd run lines per the number of nodes (see examples in the the following directory: ~jbklauda/ |
- Also there is a line with set simt = 1000000. This is to run 1 Million steps of 2ns per block (with 2fs timesteps). | - Also there is a line with set simt = 1000000. This is to run 1 Million steps of 2ns per block (with 2fs timesteps). | ||
- | You then will need to adjust dyn-1.inp and dyn-2.inp to match with what step7_production.inp has. This file will be combined into a dyn.inp file with the firsttimestep defined (see dyn.csh file). | + | You then will need to adjust dyn-1.inp and dyn-2.inp to match with what step7_production.inp has. These files will be combined into a dyn.inp file with the firsttimestep defined (see dyn.csh file). |
Note: dyn-1.inp inputname should stay as dyn | Note: dyn-1.inp inputname should stay as dyn |
production_run.1524072730.txt.gz · Last modified: 2018/04/18 13:32 by admin