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doku:lammps [2014/10/29 13:38] – sh | doku:lammps [2014/11/04 09:46] (current) – sh | ||
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cp ./ | cp ./ | ||
</ | </ | ||
+ | |||
+ | NOTE: To get information about included packages | ||
+ | < | ||
+ | make package-status | ||
+ | </ | ||
+ | |||
===== LAMMPS on GPUs ====== | ===== LAMMPS on GPUs ====== | ||
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make clean-vsc1 | make clean-vsc1 | ||
make vsc1 | make vsc1 | ||
- | cp ./ | + | cp ./ |
</ | </ | ||
| | ||
- | NOTE: for the fermi nodes use '' | + | NOTE: for the fermi nodes use '' |
- | + | ||
- | NOTE2: To get information about packages that will be used | + | |
< | < | ||
- | make package-status | + | cd .../ |
+ | cp Makefile.fermi Makefile.kepler | ||
+ | vi Makefile.kepler | ||
+ | make -f Makefile.kepler clean | ||
+ | | ||
+ | cd ../../src | ||
+ | ... continue with the above block to build lmp_vsc1 | ||
</ | </ | ||
+ | |||
+ | |||
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=== For example / | === For example / | ||
- | 1. Change into some temporary directory and prepare the submit script for SGE; | + | 1. Change into some temporary directory and prepare the submit script for SGE. |
vi ./ | vi ./ | ||
< | < | ||
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</ | </ | ||
- | 2. Submit it and compare the results | + | 2. Submit it and compare the results - log.lammps - to the reference |
< | < | ||
qsub ./ | qsub ./ | ||
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+ | ==== GPU fermi ==== | ||
+ | |||
+ | === For example / | ||
+ | |||
+ | 1. Change into some temporary directory and prepare the submit script for SGE (fermi queue). Two consecutive short test runs will employ 1 GPU and 2 GPUs per node. | ||
+ | |||
+ | vi ./ | ||
+ | < | ||
+ | #$ -N lammps_kokkos | ||
+ | #$ -S /bin/bash | ||
+ | #$ -cwd | ||
+ | #$ -pe smp 12 | ||
+ | #$ -V | ||
+ | #$ -q fermi | ||
+ | #$ -P fermi | ||
+ | |||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export I_MPI_FABRICS=shm: | ||
+ | |||
+ | # single GPU | ||
+ | / | ||
+ | mv ./ | ||
+ | |||
+ | # 2 x GPU | ||
+ | mpirun -np 2 / | ||
+ | mv ./ | ||
+ | </ | ||
+ | |||
+ | |||
+ | 2. Change into the fermi group and submit it to the appropriate queue. | ||
+ | < | ||
+ | sg fermi | ||
+ | qsub.py ./ | ||
+ | </ | ||
+ | |||
+ | 3. Compare the results - ./ | ||
+ | |||
+ | |||
+ | ==== GPU kepler ==== | ||
+ | |||
+ | === For example / | ||
+ | |||
+ | 1. Change into some temporary directory and prepare the submit script for SGE (kepler queue). The test is analogous to the one for fermi, hence two consecutive short runs employing 1 GPU or 2 GPUs per node. | ||
+ | |||
+ | vi ./ | ||
+ | < | ||
+ | #$ -N lammps_kokkos | ||
+ | #$ -S /bin/bash | ||
+ | #$ -cwd | ||
+ | #$ -pe smp 12 | ||
+ | #$ -V | ||
+ | #$ -q kepler | ||
+ | #$ -P fermi | ||
+ | |||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export I_MPI_FABRICS=shm: | ||
+ | |||
+ | # single GPU | ||
+ | / | ||
+ | mv ./ | ||
+ | |||
+ | # 2 x GPU | ||
+ | mpirun -np 2 / | ||
+ | mv ./ | ||
+ | </ | ||
+ | |||
+ | |||
+ | 2. Change into the fermi group and submit it to the appropriate --- kepler --- queue. | ||
+ | < | ||
+ | sg fermi | ||
+ | qsub.py ./ | ||
+ | </ | ||
+ | |||
+ | 3. Compare the results - ./ |