This is an old revision of the document!
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
/work/04431/ewang125/stampede2
Note that you need the stampede2 directory which was introduced during the Stampede-Stampede2 transition.
Also, you can type cdw to go to your work directory
Equilibrate your system on DT and get your restart files dyn.xsc, dyn.coor, dyn.vel
In your namd directory, you need 5 more files to start production:
1. dyn.csh
2. dyn.scr
3. dyn-1.inp
4. dyn-2.inp
5. last.seqno
Example files using the KNL nodes. Use 1 node per job!
prod.tar.gz
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 dyn.scr, you need to cd directly to the working directory. If you have a lot of jobs, you may find it to be tedious to change every file and you may hate your life. This is normal.