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cluster:172 [2018/08/22 20:18] hmeij07 [Amber] |
cluster:172 [2018/09/25 12:30] hmeij07 [Finish] |
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yum update kernel kernel-tools kernel-tools-libs | yum update kernel kernel-tools kernel-tools-libs | ||
yum install kernel-devel kernel-headers (remove old headers after reboot) | yum install kernel-devel kernel-headers (remove old headers after reboot) | ||
- | yum install gcc gcc-devel | + | yum install gcc gcc-gfortran gcc-c++ |
# download runfiles from https:// | # download runfiles from https:// | ||
- | sh cuda_name_of_runfile | + | # files in / |
- | sh cuda_name_of_runfile_patch | + | sh cuda_9.2.148_396.37_linux.run |
Install NVIDIA Accelerated Graphics Driver for Linux-x86_64 396.26? | Install NVIDIA Accelerated Graphics Driver for Linux-x86_64 396.26? | ||
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(y)es/ | (y)es/ | ||
- | #/ | + | # / |
+ | # reboot before driver | ||
blacklist nouveau | blacklist nouveau | ||
options nouveau modeset=0 | options nouveau modeset=0 | ||
Line 60: | Line 62: | ||
# nvidia driver | # nvidia driver | ||
- | ./ | + | ./ |
# backup | # backup | ||
Line 71: | Line 73: | ||
[root@n37 src]# find / | [root@n37 src]# find / | ||
[root@n37 src]# | [root@n37 src]# | ||
- | [root@n37 src]# scp n78:/ | + | [root@n37 src]# scp n78:/ |
# Device files/ | # Device files/ | ||
Line 79: | Line 81: | ||
# new kernel initramfs, load | # new kernel initramfs, load | ||
dracut --force | dracut --force | ||
+ | |||
+ | # for mapd graphics support needs to be enabled | ||
+ | nvidia-smi --gom=0 | ||
+ | # have left persistence and exclusivity at defaults for now | ||
+ | |||
reboot | reboot | ||
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* export PATH=/ | * export PATH=/ | ||
* export LD_LIBRARY_PATH=/ | * export LD_LIBRARY_PATH=/ | ||
+ | * export CUDA_HOME=/ | ||
**Verification** | **Verification** | ||
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** Finish ** | ** Finish ** | ||
- | * yum install freeglut-devel libX11-devel libXi-devel libXmu-devel \ make mesa-libGLU-devel | + | * yum install freeglut-devel libX11-devel libXi-devel libXmu-devel \ make mesa-libGLU-devel |
* check for / | * check for / | ||
* [root@n37 /]# tar -cvf / | * [root@n37 /]# tar -cvf / | ||
Line 165: | Line 173: | ||
< | < | ||
- | # As root check requirements | + | # As root check requirements |
rpm -qa | grep ^gcc | rpm -qa | grep ^gcc | ||
rpm -qa | grep ^g++ | rpm -qa | grep ^g++ | ||
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rpm -qa | grep ^bison | rpm -qa | grep ^bison | ||
- | # As root install missing | + | # As root install missing |
yum install flex bzip2-devel libXdmcp zlib zlib-devel | yum install flex bzip2-devel libXdmcp zlib zlib-devel | ||
yum install tkinter openmpi perl-ExtUtils-MakeMaker patch bison | yum install tkinter openmpi perl-ExtUtils-MakeMaker patch bison | ||
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</ | </ | ||
+ | |||
+ | **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 ==== | ==== 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 # CHROOT done | ||
+ | * yum install blas blas-devel lapack lapack-devel boost boost-devel # CHROOT done | ||
+ | |||
+ | 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 (on n37 for K20) | ||
+ | |||
+ | 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-gpu | ||
+ | -rwxr-xr-x 1 hmeij its 35555672 Aug 23 09:11 lmp_mpi-single-double-with-gpu | ||
+ | -rwxr-xr-x 1 hmeij its 35559552 Aug 23 09:53 lmp_mpi-single-single-with-gpu | ||
+ | |||
+ | </ | ||
+ | |||
+ | ==== 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 | ||
+ | |||
+ | yum install 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 # done | ||
+ | * Install all the packages of this page in CHROOT # marked done | ||
+ | |||
+ | |||
+ | To do another node, the steps are | ||
+ | |||
+ | * add node in deploy.txtof n37.chroot/ | ||
+ | * ./ | ||
+ | * scp in place passwd, shadow, group, hosts, fstab from global archive | ||
+ | * umount -a | ||
+ | * ONBOOT=no, ib0 ??? connectX mlx4_0 IB interface breaks in CentOS 7.3+ | ||
+ | * reboot then check polkit user … screws up systemd-logind | ||
+ | * hostnamectl set-hostname node_name (logout/ | ||
+ | * tar in place n37.chroot.ul.tar.gz in / FIRST | ||
+ | * REMOVE / | ||
+ | * Nvidia install: files in / | ||
+ | * sh cuda_name_of_runfile | ||
+ | * nvidia-modprobe.sh | ||
\\ | \\ | ||
**[[cluster: | **[[cluster: |