production_run
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- | [[sidebar]] | + | [[bilayer_simulations]] |
- | Here are production | + | ==== Production |
- | Listed below are some instructions for the production run simulation. As we discussed, this will automatically run your simulation in chunks with each being a certain length. | ||
- | for DT1, **/ | + | Listed below are some instructions |
- | 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: |
- | 1. # 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. | ||
+ | - 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). | ||
- | 2. You should | + | You then will need to adjust |
- | 3. mpirun -np command with the same number of tasks | + | Note: dyn-1.inp |
- | + | ||
- | 4. Also there is a line with set simt = 1000000. This is to run 1 Million steps of 2ns per block. | + | |
- | + | ||
- | You then will need to adjust | + | |
Once the changes are made you will also need to copy the step*6.6.xsc/ | Once the changes are made you will also need to copy the step*6.6.xsc/ | ||
- | **./dyn.scr** | + | <code commend> |
Also note that there is an important file (last.seqno). This tells the daisy-chain script when to stop. So if you want to run for a total of 100ns you'll need 50 files so this is the value that should be in the last.seqno file. If you want this to be longer or short just change the number in the file. | Also note that there is an important file (last.seqno). This tells the daisy-chain script when to stop. So if you want to run for a total of 100ns you'll need 50 files so this is the value that should be in the last.seqno file. If you want this to be longer or short just change the number in the file. |
production_run.1472411114.txt.gz · Last modified: 2016/08/28 14:05 (external edit)