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cluster:172 [2018/08/22 11:58] hmeij07 [Note] |
cluster:172 [2018/08/22 20:18] hmeij07 [Amber] |
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* check polkit user ... screws up systemd-logind | * check polkit user ... screws up systemd-logind | ||
* connectX mlx4_0 IB interface breaks in CentOS 7.3+ | * connectX mlx4_0 IB interface breaks in CentOS 7.3+ | ||
+ | * unmount NFS mounts while installing nvidia as root | ||
+ | * install other software as regular user | ||
==== Nvidia ==== | ==== Nvidia ==== | ||
+ | |||
+ | ** Installation ** | ||
< | < | ||
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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 gcc-gfortran gcc-gfortran-devel | + | yum install gcc gcc-devel gcc-gfortran gcc-c++ |
# download runfiles from https:// | # download runfiles from https:// | ||
Line 82: | Line 86: | ||
* export PATH=/ | * export PATH=/ | ||
* export LD_LIBRARY_PATH=/ | * export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | **Verification** | ||
+ | |||
+ | < | ||
+ | |||
+ | [root@n37 cuda-9.2]# / | ||
+ | / | ||
+ | |||
+ | CUDA Device Query (Runtime API) version (CUDART static linking) | ||
+ | |||
+ | Detected 4 CUDA Capable device(s) | ||
+ | |||
+ | Device 0: "Tesla K20m" | ||
+ | CUDA Driver Version / Runtime Version | ||
+ | CUDA Capability Major/Minor version number: | ||
+ | ... | ||
+ | > Peer access from Tesla K20m (GPU0) -> Tesla K20m (GPU1) : Yes | ||
+ | > Peer access from Tesla K20m (GPU0) -> Tesla K20m (GPU2) : No | ||
+ | > Peer access from Tesla K20m (GPU0) -> Tesla K20m (GPU3) : No | ||
+ | > Peer access from Tesla K20m (GPU1) -> Tesla K20m (GPU0) : Yes | ||
+ | > Peer access from Tesla K20m (GPU1) -> Tesla K20m (GPU2) : No | ||
+ | > Peer access from Tesla K20m (GPU1) -> Tesla K20m (GPU3) : No | ||
+ | > Peer access from Tesla K20m (GPU2) -> Tesla K20m (GPU0) : No | ||
+ | > Peer access from Tesla K20m (GPU2) -> Tesla K20m (GPU1) : No | ||
+ | > Peer access from Tesla K20m (GPU2) -> Tesla K20m (GPU3) : Yes | ||
+ | > Peer access from Tesla K20m (GPU3) -> Tesla K20m (GPU0) : No | ||
+ | > Peer access from Tesla K20m (GPU3) -> Tesla K20m (GPU1) : No | ||
+ | > Peer access from Tesla K20m (GPU3) -> Tesla K20m (GPU2) : Yes | ||
+ | |||
+ | deviceQuery, | ||
+ | CUDA Runtime Version = 9.2, NumDevs = 4, | ||
+ | Device0 = Tesla K20m, Device1 = Tesla K20m, | ||
+ | Device2 = Tesla K20m, Device3 = Tesla K20m | ||
+ | Result = PASS | ||
+ | |||
+ | </ | ||
+ | |||
+ | ** BandWithTest ** | ||
+ | |||
+ | < | ||
+ | |||
+ | [root@n37 cuda-9.2]# / | ||
+ | [CUDA Bandwidth Test] - Starting... | ||
+ | Running on... | ||
+ | |||
+ | | ||
+ | Quick Mode | ||
+ | |||
+ | Host to Device Bandwidth, 1 Device(s) | ||
+ | | ||
+ | | ||
+ | | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | |||
+ | Result = PASS | ||
+ | |||
+ | </ | ||
+ | |||
+ | ** Finish ** | ||
+ | |||
+ | * yum install freeglut-devel libX11-devel libXi-devel libXmu-devel \ make mesa-libGLU-devel | ||
+ | * check for / | ||
+ | * [root@n37 /]# tar -cvf / | ||
+ | * [root@n37 /]# scp / | ||
+ | |||
+ | ==== Amber ==== | ||
+ | |||
+ | ** Requirements ** | ||
+ | |||
+ | < | ||
+ | # As root check requirements | ||
+ | rpm -qa | grep ^gcc | ||
+ | rpm -qa | grep ^g++ | ||
+ | rpm -qa | grep ^flex | ||
+ | rpm -qa | grep ^tcsh | ||
+ | rpm -qa | grep ^zlib | ||
+ | rpm -qa | grep ^zlib-devel | ||
+ | rpm -qa | grep ^bzip2 | ||
+ | rpm -qa | grep ^bzip2-devel | ||
+ | rpm -qa | grep ^bzip | ||
+ | rpm -qa | grep ^bzip-devel | ||
+ | rpm -qa | grep ^libXt | ||
+ | rpm -qa | grep ^libXext | ||
+ | rpm -qa | grep ^libXdmcp | ||
+ | rpm -qa | grep ^tkinter # weird one need python 2.6.6_something | ||
+ | rpm -qa | grep ^openmpi | ||
+ | rpm -qa | grep ^perl | egrep " | ||
+ | rpm -qa | grep ^patch | ||
+ | rpm -qa | grep ^bison | ||
+ | |||
+ | # As root install missing | ||
+ | yum install flex bzip2-devel libXdmcp zlib zlib-devel | ||
+ | yum install tkinter openmpi perl-ExtUtils-MakeMaker patch bison | ||
+ | |||
+ | </ | ||
+ | |||
+ | ** Compilations ** | ||
+ | |||
+ | < | ||
+ | |||
+ | # as regular user | ||
+ | # amber16 dir will be created | ||
+ | cd /usr/local | ||
+ | tar xvfj / | ||
+ | tar xvfj / | ||
+ | export AMBERHOME=/ | ||
+ | cd $AMBERHOME | ||
+ | |||
+ | # to preserve existing work flows | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export PATH=/ | ||
+ | |||
+ | # use gnu, Y to patches, Y to miniconda | ||
+ | # bundled netcdf, fftw | ||
+ | ./configure gnu | tee -a amber16-install.log 2>&1 | ||
+ | source / | ||
+ | make install | tee -a amber16-install.log 2>&1 | ||
+ | Installation of Amber16 (serial) is complete at Wed Aug 22 10:12:55 EDT 2018. | ||
+ | |||
+ | ./configure -mpi gnu | tee -a amber16-install.log 2>&1 | ||
+ | source / | ||
+ | make install | tee -a amber16-install.log 2>&1 | ||
+ | Installation of Amber16 (parallel) is complete at Wed Aug 22 10:36:45 EDT 2018. | ||
+ | |||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | # $AMBERHOME/ | ||
+ | # edit and bypass cuda test for 9.0 -> 9.2 version | ||
+ | # please be sure to verify any results against known outcomes | ||
+ | export CUDA_HOME=/ | ||
+ | |||
+ | ./configure -cuda gnu | tee -a amber16-install.log 2>& | ||
+ | source / | ||
+ | make install | tee -a amber16-install.log 2>&1 | ||
+ | Installation of pmemd.cuda complete | ||
+ | |||
+ | | ||
+ | source / | ||
+ | make install | tee -a amber16-install.log 2>&1 | ||
+ | Installation of pmemd.cuda.MPI complete | ||
+ | |||
+ | [hmeij@n37 amber16]$ 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/ | ||
+ | |||
+ | </ | ||
+ | |||
+ | ==== Gromacs ==== | ||
+ | |||
+ | |||
\\ | \\ | ||
**[[cluster: | **[[cluster: |