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cluster:172 [2018/08/22 13:22] hmeij07 [Amber 16] |
cluster:172 [2018/08/22 20:18] hmeij07 [Amber] |
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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 | + | yum install gcc gcc-devel gcc-gfortran |
# download runfiles from https:// | # download runfiles from https:// | ||
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* [root@n37 /]# scp / | * [root@n37 /]# scp / | ||
- | ==== Amber 16 ==== | + | ==== Amber ==== |
+ | |||
+ | ** Requirements ** | ||
< | < | ||
- | #As root check requirements | + | # As root check requirements |
rpm -qa | grep ^gcc | rpm -qa | grep ^gcc | ||
+ | rpm -qa | grep ^g++ | ||
rpm -qa | grep ^flex | rpm -qa | grep ^flex | ||
rpm -qa | grep ^tcsh | rpm -qa | grep ^tcsh | ||
Line 187: | Line 190: | ||
</ | </ | ||
+ | |||
+ | ** 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: |