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cluster:172 [2018/08/22 15:05] hmeij07 [Amber] |
cluster:172 [2018/08/23 18:17] hmeij07 [mapd] |
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* unmount NFS mounts while installing nvidia as root | * unmount NFS mounts while installing nvidia as root | ||
* install other software as regular user | * install other software as regular user | ||
+ | * | ||
==== Nvidia ==== | ==== Nvidia ==== | ||
Line 86: | Line 87: | ||
* export PATH=/ | * export PATH=/ | ||
* export LD_LIBRARY_PATH=/ | * export LD_LIBRARY_PATH=/ | ||
+ | * export CUDA_HOME=/ | ||
**Verification** | **Verification** | ||
Line 223: | Line 225: | ||
export PATH=/ | export PATH=/ | ||
export LD_LIBRARY_PATH=/ | export LD_LIBRARY_PATH=/ | ||
- | $AMBERHOME/ | + | # $AMBERHOME/ |
+ | # edit and bypass cuda test for 9.0 -> 9.2 version | ||
+ | # please be sure to verify any results against known outcomes | ||
export CUDA_HOME=/ | export CUDA_HOME=/ | ||
+ | |||
./configure -cuda gnu | tee -a amber16-install.log 2>& | ./configure -cuda gnu | tee -a amber16-install.log 2>& | ||
+ | source / | ||
+ | make install | tee -a amber16-install.log 2>&1 | ||
+ | Installation of pmemd.cuda complete | ||
+ | |||
+ | | ||
+ | source / | ||
+ | make install | tee -a amber16-install.log 2>&1 | ||
+ | Installation of pmemd.cuda.MPI complete | ||
+ | |||
+ | [hmeij@n37 amber16]$ ls -l bin/pmemd* | ||
+ | -rwxr-xr-x 1 hmeij its 3097968 Aug 22 10:12 bin/pmemd | ||
+ | lrwxrwxrwx 1 hmeij its 15 Aug 22 15:19 bin/ | ||
+ | pmemd.cuda_SPFP | ||
+ | -rwxr-xr-x 1 hmeij its 38851928 Aug 22 15:25 bin/ | ||
+ | -rwxr-xr-x 1 hmeij its 39436704 Aug 22 16:04 bin/ | ||
+ | lrwxrwxrwx 1 hmeij its 19 Aug 22 15:57 bin/ | ||
+ | pmemd.cuda_SPFP.MPI | ||
+ | -rwxr-xr-x 1 hmeij its 32950848 Aug 22 15:19 bin/ | ||
+ | -rwxr-xr-x 1 hmeij its 33531456 Aug 22 15:57 bin/ | ||
+ | -rwxr-xr-x 1 hmeij its 33405504 Aug 22 15:31 bin/ | ||
+ | -rwxr-xr-x 1 hmeij its 33990208 Aug 22 16:10 bin/ | ||
+ | -rwxr-xr-x 1 hmeij its 3647784 Aug 22 10:36 bin/ | ||
</ | </ | ||
+ | |||
+ | **Tests** | ||
+ | |||
+ | Although the 9.2 cuda compiled Amber passed all tests please double check your results. | ||
+ | |||
+ | < | ||
+ | export DO_PARALLEL=" | ||
+ | make test >> amber16-test.log 2>&1 | ||
+ | </ | ||
+ | |||
+ | **Finish** | ||
+ | * [root@n37 /]# tar -cvf / | ||
+ | * [root@n37 /]# scp / | ||
+ | |||
+ | |||
+ | ==== Gromacs ==== | ||
+ | |||
+ | As root install | ||
+ | |||
+ | * cmake, latest version, never understand why so far ahead of distro... | ||
+ | |||
+ | Download and extract source. Using same environment as Amber compilation. | ||
+ | |||
+ | < | ||
+ | |||
+ | cd gromacs-2018/ | ||
+ | mkdir build | ||
+ | cd build | ||
+ | |||
+ | which mpicc mpicxx | ||
+ | / | ||
+ | / | ||
+ | |||
+ | | ||
+ | / | ||
+ | -DCMAKE_INSTALL_PREFIX=/ | ||
+ | -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_GPU=ON | ||
+ | | ||
+ | | ||
+ | |||
+ | </ | ||
+ | ==== Lammps ==== | ||
+ | |||
+ | As root install | ||
+ | |||
+ | * yum install libjpeg libjpeg-devel libjpeg-turbo libjpeg-turbo-devel | ||
+ | * yum install blas blas-devel lapack lapack-devel boost boost-devel | ||
+ | |||
+ | For Lammps-22Aug18 I followed the top installation instructions at this page | ||
+ | |||
+ | * [[cluster: | ||
+ | |||
+ | The only difference in my approach was | ||
+ | |||
+ | * to stay with openmpi-1.8.4 (not mpich3...) | ||
+ | * consulting the ARCH web page I choose -arch=sm_35 | ||
+ | |||
+ | Good thing we're doing this now, future versions of CUDA will not support the K20s anymore. In fact on that web site they are not mentioned, only the K40/K80 gpus. So we'll see what testing reveals. | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@n37 src]$ ll / | ||
+ | total 104356 | ||
+ | -rwxr-xr-x 1 hmeij its 35739800 Aug 23 08:49 lmp_mpi-double-double-with-cuda | ||
+ | -rwxr-xr-x 1 hmeij its 35555672 Aug 23 09:11 lmp_mpi-single-double-with-cuda | ||
+ | -rwxr-xr-x 1 hmeij its 35559552 Aug 23 09:53 lmp_mpi-single-single-with-cuda | ||
+ | |||
+ | </ | ||
+ | |||
+ | ==== mapd ==== | ||
+ | |||
+ | * https:// | ||
+ | |||
+ | < | ||
+ | |||
+ | useradd -U mapd | ||
+ | |||
+ | # mapd.repo | ||
+ | [mapd-ce-cuda] | ||
+ | name=mapd ce - cuda | ||
+ | baseurl=https:// | ||
+ | gpgcheck=1 | ||
+ | gpgkey=https:// | ||
+ | |||
+ | yum install \ | ||
+ | copy-jdk-configs java-1.8.0-openjdk-headless \ | ||
+ | javapackages-tools libxslt \ | ||
+ | lksctp-tools python-javapackages \ | ||
+ | python-lxml tzdata-java \ | ||
+ | mapd | ||
+ | # n37:/ | ||
+ | |||
+ | # User specific aliases and functions | ||
+ | export MAPD_USER=mapd | ||
+ | export MAPD_GROUP=mapd | ||
+ | export MAPD_STORAGE=/ | ||
+ | export MAPD_PATH=/ | ||
+ | # The $MAPD_STORAGE directory must be dedicated to MapD | ||
+ | |||
+ | </ | ||
+ | |||
+ | ==== Finish ==== | ||
+ | |||
+ | * Make the final tar file for /usr/local and post with CHROOT | ||
+ | * Install all the packages of this page in CHROOT | ||
\\ | \\ | ||
**[[cluster: | **[[cluster: |