This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
cluster:119 [2013/09/20 19:16] hmeij [gromacs.sub] |
cluster:119 [2013/09/26 13:01] hmeij [Articles] |
||
---|---|---|---|
Line 2: | Line 2: | ||
**[[cluster: | **[[cluster: | ||
- | Jobs need to be submitted to the scheduler on host sharptail itself for now and will be dispatched to nodes n33-n37 in queue mwgpu. | + | Please plenty of time between multiple GPU job submissions. Like minutes. |
- | --- // | + | |
+ | Jobs need to be submitted to the scheduler on host sharptail itself for now and will be dispatched to nodes n33-n37 in queue mwgpu. They can also be submitted from host greentail but remember any output will be in shraptail' | ||
+ | --- // | ||
+ | |||
+ | ==== Articles ==== | ||
+ | |||
+ | * [[http:// | ||
+ | * [[http:// | ||
==== Submitting GPU Jobs ==== | ==== Submitting GPU Jobs ==== | ||
Line 121: | Line 127: | ||
#BSUB -q mwgpu | #BSUB -q mwgpu | ||
#BSUB -J test | #BSUB -J test | ||
+ | |||
+ | # from greentail we need to set up the module env | ||
+ | export PATH=/ | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | # signal that this is charmrun/ | ||
## leave sufficient time between job submissions (30-60 secs) | ## leave sufficient time between job submissions (30-60 secs) | ||
Line 158: | Line 180: | ||
# NAMD | # NAMD | ||
- | # signal that this is charmrun/ | + | # from greentail we need to recreate module env |
export CHARMRUN=1 | export CHARMRUN=1 | ||
# stage the data | # stage the data | ||
Line 215: | Line 237: | ||
##BSUB -q mwgpu | ##BSUB -q mwgpu | ||
##BSUB -n 1 | ##BSUB -n 1 | ||
- | ##BSUB -R " | + | ##BSUB -R " |
## signal GMXRC is a gpu run with: 1=thread_mpi | ## signal GMXRC is a gpu run with: 1=thread_mpi | ||
#export GMXRC=1 | #export GMXRC=1 | ||
Line 226: | Line 248: | ||
#BSUB -q mwgpu | #BSUB -q mwgpu | ||
#BSUB -n 1 | #BSUB -n 1 | ||
- | #BSUB -R " | + | #BSUB -R " |
# signal GMXRC is a gpu run with: 2=mvapich2 | # signal GMXRC is a gpu run with: 2=mvapich2 | ||
export GMXRC=2 | export GMXRC=2 | ||
Line 236: | Line 258: | ||
</ | </ | ||
+ | |||
+ | ==== matlab.sub ==== | ||
+ | |||
+ | < | ||
+ | |||
+ | #!/bin/bash | ||
+ | |||
+ | rm -rf out err *.out | ||
+ | |||
+ | # from greentail we need to recreate module env | ||
+ | export PATH=/ | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | |||
+ | #BSUB -o out | ||
+ | #BSUB -e err | ||
+ | #BSUB -N | ||
+ | #BSUB -J test | ||
+ | |||
+ | # GPU RUN: (1-4), queue mwgpu, n (1-4, matches gpu count), must run on one node | ||
+ | #BSUB -q mwgpu | ||
+ | #BSUB -n 1 | ||
+ | #BSUB -R " | ||
+ | # signal MATGPU is a gpu run | ||
+ | export MATGPU=1 | ||
+ | lava.mvapich2.wrapper matlab -nodisplay | ||
+ | |||
+ | |||
+ | </ | ||
+ | |||
==== lava.mvampich2.wrapper ==== | ==== lava.mvampich2.wrapper ==== | ||
Line 362: | Line 425: | ||
fi | fi | ||
+ | elif [ -n " | ||
+ | echo " | ||
+ | ${MYARGS} | ||
elif [ -n " | elif [ -n " | ||
cat ${MACHFILE}.lst | tr '\/ ' ' | cat ${MACHFILE}.lst | tr '\/ ' ' |