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--- stampede2 [2017/12/21 14:57] – created admin
+++ stampede2 [2020/07/07 17:05] (current) – admin
@@ Line 1: / Line 1: @@
-test
+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.\\
+Also, you can type ''cdw''  to go to your work directory. To setup your directory for group readability please do the following:
+<code commend>
+cdw
+setfacl -d -m u:jklauda:rw .
+</code>
+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:\\
+. ''dyn.csh''\\
+. ''dyn.scr''\\
+. ''dyn-1.inp''\\
+. ''dyn-2.inp''\\
+. ''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 tedious to change every file.