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--- cluster:116 [2013/08/05 15:44]
hmeij
+++ cluster:116 [2013/08/21 10:48]
hmeij [Clashes]
@@ Line 78: / Line 78: @@
 In both cases you do not need to target any specific core, the operating system will handle that part of the scheduling.
+==== NOTE ====
+----
+Instructions below are obsolete, resources are now available via the scheduler.
+Please read [[cluster:119|Submitting GPU Jobs]]
+ --- //[[hmeij@wesleyan.edu|Meij, Henk]] 2013/08/21 10:46//
+----
@@ Line 242: / Line 255: @@
 Note: ran out of time to get an example running but it should follow the LAMMPS approach of above pretty closely.  The binary is in /cm/share/apps/amber/amber12/bin/pmemd.cuda.MPI
+Here is quick Amber example
+<code>
+[hmeij@sharptail nucleosome]$ export AMBER_HOME=/cm/shared/apps/amber/amber12
+# find a GPU ID with gpu-info then expose that GPU to pmemd
+[hmeij@sharptail nucleosome]$ export CUDA_VISIBLE_DEVICES=1
+# you only need one cpu core
+[hmeij@sharptail nucleosome]$ mpirun_rsh -ssh -hostfile ~/sharptail/hostfile -np 1 \
+/cm/shared/apps/amber/amber12/bin/pmemd.cuda.MPI -O -o mdout.1K10 -inf mdinfo.1K10 -x mdcrd.1K10 -r restrt.1K10 -ref inpcrd &
+</code>

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