docs:trillian
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| ====== Channelflow on trillian ====== | ====== Channelflow on trillian ====== | ||
| - | Here are some extra instructions for installing and using channelflow on | + | Some extra instructions for installing and using channelflow on |
| [[http://trillian-use.sr.unh.edu/index.php/Main_Page|trillian]], | [[http://trillian-use.sr.unh.edu/index.php/Main_Page|trillian]], | ||
| UNH's CRAY XE6m-200 supercomputer. | UNH's CRAY XE6m-200 supercomputer. | ||
| Line 31: | Line 31: | ||
| mkdir ~/channelflow/build | mkdir ~/channelflow/build | ||
| cd ~/channelflow/build | cd ~/channelflow/build | ||
| - | cmake -DCMAKE_CXX_COMPILER=/opt/gcc/4.7.2/bin/g++ -DWITH_FFTW=/opt/fftw/3.3.0.2/x86_64/lib -DWITH_HDF5=~gibson/packages/hdf5-1.8.15/lib -DWITH_EIGEN3=~gibson/packages/eigen-3.2.4 -DCMAKE_INSTALL_PREFIX=~/channelflow ~/svnrepos/channelflow/trunk/ | + | cmake -DCMAKE_C_COMPILER=/opt/gcc/4.7.2/bin/gcc -DCMAKE_CXX_COMPILER=/opt/gcc/4.7.2/bin/g++ -DWITH_FFTW=/opt/fftw/3.3.0.2/x86_64/lib -DWITH_HDF5=~gibson/packages/hdf5-1.8.15/lib -DWITH_EIGEN3=~gibson/packages/eigen-3.2.4 -DCMAKE_INSTALL_PREFIX=~/channelflow ~/svnrepos/channelflow/trunk/ |
| make | make | ||
| make test | make test | ||
| Line 45: | Line 45: | ||
| </code> | </code> | ||
| + | Note: Sometimes CMake can get confused if changes in the build system conflict with cached values of build system variables. If the above sequence doesn't work for you, try removing ''CMakeCache.txt'' and ''CMakeFiles/'' from your build directory and rerunning the ''cmake ...'' command above. | ||
| ===== Submitting jobs ===== | ===== Submitting jobs ===== | ||
| - | If you start a computation by just typing in a command at the command prompt, it'll execute on trillian's login node. That's a no-no! (except for software builds and quick tests). Instead, you should run any long computation but submitting it to the [[https://hpcc.usc.edu/support/documentation/running-a-job-on-the-hpcc-cluster-using-pbs/PBS|PBS]] job control system. PBS will then farm the job out to one of the compute nodes. | + | If you start a computation by just typing in a command at the command prompt, it'll execute on trillian's login node. That's a no-no! (except for software builds and quick tests). Instead, you should run any long computation but submitting it to the [[https://hpcc.usc.edu/support/documentation/running-a-job-on-the-hpcc-cluster-using-pbs/PBS|PBS]] (Portable Batch System) job control system. PBS will then farm the job out to one of the compute nodes. |
| + | |||
| + | There are three main PBS commands: | ||
| + | * **qsub** submit a job to the PBS queue | ||
| + | * **qstat** list jobs running in the queue | ||
| + | * **qdel** delete a job from the queue | ||
| + | |||
| + | ''qsub'' can be a bit tedious and complicated, so I wrote a some bash code for a simplified interface. Place the following in your ''~/.bashrc'' file (and then run ''source ~/.bashrc'') to make your current shell process and load this code). | ||
| + | |||
| + | <code> | ||
| + | PATH=$PATH:~/channelflow/bin | ||
| + | module unload cray-hdf5-parallel | ||
| + | module unload cce | ||
| + | module unload xt-asyncpe | ||
| + | module load gcc | ||
| + | module load fftw | ||
| + | module load cmake | ||
| + | module load pbs | ||
| + | |||
| + | function qsubmit() { | ||
| + | tag=$1 | ||
| + | shift | ||
| + | echo "#PBS -N $tag" > tmp.pbs | ||
| + | echo "#PBS -l nodes=1:ppn=1,walltime=48:00:00" >> tmp.pbs | ||
| + | echo "#PBS -j oe" >> tmp.pbs | ||
| + | echo "#PBS -m ae" >> tmp.pbs | ||
| + | echo "cd $(pwd)" >> tmp.pbs | ||
| + | echo aprun $* >> tmp.pbs | ||
| + | qsub tmp.pbs | ||
| + | } | ||
| + | </code> | ||
| + | This bit of code tells bash where your channelflow programs are, configures the Cray programming environment correctly, and then defines a ''qsubmit'' function, which can be used as follows | ||
| + | |||
| + | <code> | ||
| + | cd ~/simulations/test-qsubmit | ||
| + | qsubmit qtest couette -R 500 u0.h5 | ||
| + | </code> | ||
| + | |||
| + | This will submit the command ''couette -R 500 u0.h5'' to the PBS queue with jobname "qtest", in working directory ''~/simulations/test-qsubmit''. | ||
docs/trillian.1434389622.txt.gz · Last modified: 2015/06/15 10:33 by gibson
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