Ceci est une ancienne révision du document !
NAMD vient en 5 versions :
Version | Compilateur | Interconnexion | chemin d'accès | OS |
---|---|---|---|---|
2.11 | N/A | N/A | /applis/PSMN/generic/NAMD/2.11/NAMD_2.11_Linux-x86_64-multicore/ | Debian 7 |
modulefile : NAMD/2.11-multicore | ||||
2.11 | N/A | N/A | /applis/PSMN/generic/NAMD/2.11/NAMD_2.11_Linux-x86_64-multicore-CUDA/ | Debian 7 +GPU |
modulefile : NAMD/2.11-multicore-CUDA | ||||
2.11 | N/A | Infiniband | /applis/PSMN/generic/NAMD/2.11/NAMD_2.11_Linux-x86_64-ibverbs | Debian 7 |
modulefile : NAMD/2.11-ibverbs | ||||
2.11 | N/A | Infiniband | /applis/PSMN/generic/NAMD/2.11/NAMD_2.11_Linux-x86_64-ibverbs-smp | Debian 7 |
modulefile : NAMD/2.11-ibverbs-smp | ||||
2.11 | N/A | Infiniband | /applis/PSMN/generic/NAMD/2.11/NAMD_2.11_Linux-x86_64-ibverbs-smp-CUDA | Debian 7 +GPU |
modulefile : NAMD/2.11-ibverbs-smp-CUDA |
Pour utiliser les modules, consulter Environment Modules
NAMD vient en 5 versions :
Version | Compilateur | Interconnexion | chemin d'accès | OS |
---|---|---|---|---|
2.9 | N/A | N/A | /applis/PSMN/generic/NAMD/2.9/NAMD_2.9_Linux-x86_64-multicore/ | Debian 7 |
modulefile : NAMD/2.9-multicore | ||||
2.9 | N/A | N/A | /applis/PSMN/generic/NAMD/2.9/NAMD_2.9_Linux-x86_64-multicore-CUDA/ | Debian 7 +GPU |
modulefile : NAMD/2.9-multicore-CUDA | ||||
2.9 | N/A | Infiniband | /applis/PSMN/generic/NAMD/2.9/NAMD_2.9_Linux-x86_64-ibverbs | Debian 7 |
modulefile : NAMD/2.9-ibverbs | ||||
2.9 | N/A | Infiniband | /applis/PSMN/generic/NAMD/2.9/NAMD_2.9_Linux-x86_64-ibverbs-smp | Debian 7 |
modulefile : NAMD/2.9-ibverbs-smp | ||||
2.9 | N/A | Infiniband | /applis/PSMN/generic/NAMD/2.9/NAMD_2.9_Linux-x86_64-ibverbs-smp-CUDA | Debian 7 +GPU |
modulefile : NAMD/2.9-ibverbs-smp-CUDA |
Pour utiliser les modules, consulter Environment Modules
mkdir $HOME/test_namd cd $HOME/test_namd
wget http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-files.tar.gz tar -zxvf namd-tutorial-files.tar.gz
cd namd-tutorial-files/1-2-sphere
module load NAMD/2.11-multicore
namd2 ubq_ws_eq.conf > ubq_ws_eq.log
tail -f ubq_ws_eq_sequentiel.log
tail -2 ubq_ws_eq_sequentiel.log WallClock: 89.548943 CPUTime: 89.548943 Memory: 62.207031 MB [Partition 0][Node 0] End of program
namd2 ubq_ws_eq.conf +p4 > ubq_ws_eq_4cores.log
tail -2 ubq_ws_eq_4cores.log WallClock: 24.876143 CPUTime: 24.876143 Memory: 313.214844 MB [Partition 0][Node 0] End of program
module load NAMD/2.11-multicore-CUDA namd2 +p4 +setcpuaffinity +devices 0,1 ubq_ws_eq.conf > ubq_ws_eq_4cores_2GPUs.log
nvidia-smi --loop=1
tail -2 ubq_ws_eq_4cores_2GPUs.log WallClock: 7.821550 CPUTime: 7.821550 Memory: 86.968750 MB [Partition 0][Node 0] End of program