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cluster:182 [2019/08/12 16:28] hmeij07 [Scripts] |
cluster:182 [2019/08/13 12:38] hmeij07 [Scripts] |
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==== Lammps ==== | ==== Lammps ==== | ||
+ | Precision for GPU calculations | ||
+ | * [DD] -D_DOUBLE_DOUBLE | ||
+ | * [SD] -D_SINGLE_DOUBLE | ||
+ | * [SS] -D_SINGLE_SINGLE | ||
+ | |||
+ | |||
+ | ^ tau/ | ||
+ | | DD | 856, | ||
+ | | SD | 981, | ||
+ | | SS | 1, | ||
+ | |||
+ | Forgot run run the 4 GPU P100 scenarios, deh. | ||
+ | |||
+ | As with Amber, it is best to run one job per GPU to achieve max node performance. Depending on problem set performance can be boosted by requesting more MPI threads. In previous tests the P100 in double_double precision mode achieved 2.7 million tau/day, so these results are surprising. The RTX 6000 does a decent job of keeping up with the P100. | ||
+ | |||
+ | But the T4 shines in this application. The mixed or single precision modes compete well given the T4's price and wattage consumption. | ||
+ | |||
+ | ==== Gromacs ==== | ||
+ | |||
+ | Gromacs was build on each of the nodes locally letting it select the optimal CPU (AVX, SSE) and GPU accelerators. The '' | ||
^ ns/ | ^ ns/ | ||
- | | | + | | |
- | | | + | | |
- | | | + | | |
+ | | Mixed | | | | | 733| gpu=4, 01-16 | | ||
+ | |||
+ | The T4 is P100's equal in mixed precision performance. Add the wattage factor and you have a favorite. | ||
==== Scripts ==== | ==== Scripts ==== | ||
Line 139: | Line 163: | ||
</ | </ | ||
+ | |||
+ | * Gromacs | ||
+ | |||
+ | < | ||
+ | |||
+ | #!/bin/bash | ||
+ | #SBATCH --nodes=1 | ||
+ | #SBATCH --nodelist=node9 | ||
+ | #SBATCH --job-name=" | ||
+ | #SBATCH --ntasks-per-node=32 | ||
+ | #SBATCH --gres=gpu: | ||
+ | #SBATCH --exclusive | ||
+ | |||
+ | export PATH=$HOME/ | ||
+ | export LD_LIBRARY_PATH=$HOME/ | ||
+ | . $HOME/ | ||
+ | rm -f gpu/??/c* gpu/??/e* gpu/??/s* gpu/??/ | ||
+ | cd gpu | ||
+ | |||
+ | # T4 | ||
+ | #export CUDA_VISIBLE_DEVICES=0123 | ||
+ | |||
+ | mpirun -np 8 gmx_mpi mdrun -maxh 1 -gpu_id 0123 \ | ||
+ | -nsteps 1000000 -multidir 05 06 07 08 \ | ||
+ | -ntmpi 0 -npme 0 -s topol.tpr -ntomp 0 -pin on -nb gpu | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | |||
\\ | \\ | ||
**[[cluster: | **[[cluster: |