cluster:213
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cluster:213 [2022/05/12 09:11] hmeij07 |
cluster:213 [2022/07/25 14:52] hmeij07 [Amber22] |
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| Line 266: | Line 266: | ||
| < | < | ||
| + | |||
| + | # First **all the necessary packages ** (yum install...) | ||
| | | ||
| Line 275: | Line 277: | ||
| # Assume this is Linux: | # Assume this is Linux: | ||
| - | # serial, do on heasd node, pull down miniconda, compile, install | + | # serial, do on head node, with miniconda |
| cmake $AMBER_PREFIX/ | cmake $AMBER_PREFIX/ | ||
| -DCMAKE_INSTALL_PREFIX=/ | -DCMAKE_INSTALL_PREFIX=/ | ||
| Line 333: | Line 335: | ||
| </ | </ | ||
| + | |||
| + | ==== Amber22 ==== | ||
| + | |||
| + | OpenHPC | ||
| + | |||
| + | < | ||
| + | |||
| + | # First **all the necessary packages ** (yum install...) | ||
| + | |||
| + | | ||
| + | 989 tar xvfj ../ | ||
| + | 993 cd amber20_src/ | ||
| + | 994 cd build/ | ||
| + | 996 vi run_cmake | ||
| + | |||
| + | # Assume this is Linux: | ||
| + | |||
| + | # serial, do on head node, with miniconda true, compile, install | ||
| + | cmake $AMBER_PREFIX/ | ||
| + | -DCMAKE_INSTALL_PREFIX=/ | ||
| + | -DCOMPILER=GNU | ||
| + | -DMPI=FALSE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \ | ||
| + | -DDOWNLOAD_MINICONDA=TRUE \ | ||
| + | 2>&1 | tee cmake.log | ||
| + | ./run_cmake | ||
| + | make install | ||
| + | |||
| + | |||
| + | # Note !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! | ||
| + | The OpenMPI and MPICH system installations provided by CentOS | ||
| + | (i.e., through yum install) | ||
| + | are known to be somehow incompatible with Amber22. | ||
| + | # OUCH !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! | ||
| + | |||
| + | |||
| + | # GO TO node n100 | ||
| + | |||
| + | # copy head node's amber22_src/ | ||
| + | |||
| + | |||
| + | source / | ||
| + | echo $AMBERHOME | ||
| + | |||
| + | # install latest openmpi version | ||
| + | cd amber_src/ | ||
| + | tar xvfj ../ | ||
| + | |||
| + | ./ | ||
| + | |||
| + | |||
| + | # on n100 now, parallel, set | ||
| + | -MPI=TRUE | ||
| + | -DDOWNLOAD_MINICONDA=FALSE | ||
| + | ./run_cmake | ||
| + | make install | ||
| + | |||
| + | # on n100 just change cuda flag | ||
| + | |||
| + | [hmeij@n100 build]$ module load cuda/11.6 | ||
| + | [hmeij@n100 build]$ which gcc mpicc nvcc | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | [hmeij@n100 ~]$ echo $CUDA_HOME | ||
| + | / | ||
| + | |||
| + | -MPI=TRUE | ||
| + | -CUDA=TRUE | ||
| + | -DDOWNLOAD_MINICONDA=FALSE | ||
| + | ./run_cmake | ||
| + | make install | ||
| + | |||
| + | |||
| + | [hmeij@n100 ~]$ which nvcc mpicc gcc | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | |||
| + | #tests | ||
| + | cd $AMBERHOME | ||
| + | make test.serial | ||
| + | export DO_PARALLEL=" | ||
| + | make test.parallel | ||
| + | export CUDA_VISIBLE_DEVICES=0 | ||
| + | make test.cuda.serial | ||
| + | make test.cuda.parallel | ||
| + | |||
| + | </ | ||
| + | |||
| **[[cluster: | **[[cluster: | ||
cluster/213.txt ยท Last modified: 2024/01/12 10:09 by hmeij07
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