stampede2
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stampede2 [2017/12/21 19:32] – edit | stampede2 [2020/07/07 17:05] (current) – admin | ||
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- | The instructions here assume you know the basics of running NAMD and have done it on a cluster like DT already. The details specific to Stampede2 are presented here. | + | The instructions here assume you know the basics of running NAMD and have done it on a cluster like DT already. The details specific to Stampede2 are presented here. Stampede2 has 1T of space for each user, so clear out your data once in a while. |
- | Your working directory should look similar to this | + | Your working directory should look similar to this\\ |
+ | / | ||
+ | Note that you need the stampede2 directory.\\ | ||
+ | Also, you can type '' | ||
- | /work/ | + | <code commend> |
+ | cdw | ||
+ | setfacl -d -m u: | ||
+ | </code> | ||
- | Note that you need the stampede2 directory which was introduced during the Stampede-Stampede2 transition. | ||
- | Also, you can type '' | + | Equilibrate your system on DT and get your restart files '' |
+ | |||
+ | In your namd directory, you need 5 more files to start production: | ||
+ | 1. '' | ||
+ | 2. '' | ||
+ | 3. '' | ||
+ | 4. '' | ||
+ | 5. '' | ||
+ | |||
+ | Example files using the KNL nodes. Use 1 node per job!\\ | ||
+ | {{ : | ||
+ | |||
+ | Only dyn.csh changes if you're using the SKX nodes. For 30k atoms, 2 nodes is optimal. For 70k atoms, 3 nodes is ok but 4 is not ok. 4 tasks per node is recommended\\ | ||
+ | {{ :dyn.csh.gz |}} | ||
+ | |||
+ | An important note: in '' |
stampede2.1513902762.txt.gz · Last modified: 2017/12/21 19:32 by edit