#! /bin/bash ## Assumed CENTOS 7 or higher ## All of the following installations are supposed to be installed in automated mode without the need for manual intervention. #0. testdir='/share/apps/configrepo' if [ ! -d "$testdir" ] ; then echo "$testdir" not found echo "Abort. Please create the $testdir directory and try again" exit 1 else #if needed #also: elif [new condition] echo "$testdir" found. Proceed. fi echo ' ' ###### END OF PRELIMINARY ################################ #1 ## install openmpi using intel compilers, assuming intel compilers have been successfully installed and sourced cd /share/apps/configrepo wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/intel/auto_source_XE17_sa.txt chmod +x auto_source_XE17_sa.txt ./auto_source_XE17_sa.txt wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/openmpi/inst_openmpi_3.1.2i.txt chmod +x inst_openmpi_3.1.2i.txt ./inst_openmpi_3.1.2i.txt #2 ## install openmpi using gpu compilers. cd /share/apps/configrepo wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/openmpi/inst_openmpi_3.1.2g.txt chmod +x inst_openmpi_3.1.2g.txt ./inst_openmpi_3.1.2g.txt #3 install tunned atlas libraries (lapack and gnu) with gnu compilers (potentially fail due to setlinux/throttling issues) ### yummed installation of lapack and blas lib development yum install -y lapack.x86_64 lapack-devel.x86_64 lapack-static.x86_64 lapack64.x86_64 lapack64-devel.x86_64 lapack64-static.x86_64 ### install optimised atlas libraries ver 3.10.2 in /share/apps/atlas-3-10-2/gnu wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/BLAS_and_LAPACK/inst_atlas chmod +x inst_atlas ./inst_atlas #4 install fftw 3.3.6 in /share/apps/fftw-3.3.6/intel using intel compilers wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/fftw/inst_fftw336_intel.txt chmod +x inst_fftw336_intel.txt ./inst_fftw336_intel.txt #5 install fftw 3.3.6 in /share/apps/fftw-3.3.6/gnu using gnu compilers wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/fftw/inst_fftw336_gnu.txt chmod +x inst_fftw336_gnu.txt ./inst_fftw336_gnu.txt #6 Install lammps version 16Mar18 using intel compilers in /share/apps/lammps_16Mar18_intel cd /share/apps/configrepo; wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/lammps/inst_lammps_intel_16Mar18.txt ; chmod +x inst_lammps_intel_16Mar18.txt ./inst_lammps_intel_16Mar18.txt #7 Install lammps version 16Mar18 using gnu compilers in /share/apps/lammps_16Mar18_gnu cd /share/apps/configrepo; wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/lammps/inst_lammps_gnu_16Mar18.txt ; chmod +x inst_lammps_gnu_16Mar18.txt ./inst_lammps_gnu_16Mar18.txt #8 Install qe-6.3 (using intel compiler) cd /share/apps/configrepo; wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/qe/inst_qe.6.3.txt chmod +x inst_qe.6.3.txt ./inst_qe.6.3.txt #9 install qe-6.1-gpu ## Mandatory requirement: cuda-9.2 is required for qe-6.1-gpu, pgi compiler is installed in /share/apps/pgi ## Assumed cuda-9.2 has been installed ## install cuda-9.2 by following http://developer.download.nvidia.com/compute/cuda/9.2/Prod/docs/sidebar/CUDA_Installation_Guide_Linux.pdf wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/qe/qe-6.1-gpu/inst_qe-6.1-gpu chmod +x inst_qe-6.1-gpu #### qe-6.1-gpu is known to work with cuda-9.2. #### If this installation fails try to set the default cuda path in ~/.bashrc from ############# # export PATH=/usr/local/cuda/bin:$PATH # export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH # export CUDA_HOME=/usr/local/cuda # To # export PATH=/usr/local/cuda-9.2/bin:$PATH # export LD_LIBRARY_PATH=/usr/local/cuda-9.2/lib64:$LD_LIBRARY_PATH # export CUDA_HOME=/usr/local/cuda-9.2 #### If this installation fails try to set the default cuda path in ~/.bashrc from ############# #10 ### Install ASE cd /share/apps wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/inst_ase.txt chmod +x inst_ase.txt ./inst_ase.txt #11 ## Install dftb+ (version 1.3.0) cd /share/apps/configrepo; wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/inst_dftb+; sh inst_dftb+ #12. Install netcdf version 4.3.2 cd /share/apps/configrepo; wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/inst_netcdf_4.3.2; sh inst_netcdf_4.3.2 # yum -y install netcdf.x86_64 #13. Install abinit 7.6.4 cd /share/apps/configrepo; wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/inst_abinit_7.6.4; sh inst_abinit_7.6.4 ############# optional ######################## #16 ## Install ptmbhga cd /share/apps/configrepo; wget https://staffusm-my.sharepoint.com/personal/tlyoon_usm_my/Documents/Downloads/ptmbhga_v2.1.tar ; mv ptmbhga_v2.1.tar ../ ; mkdir ptmbhga ; cd ptmbhga; mv ../ptmbhga_v2.1.tar . ; tar -zxvf ptmbhga_v2.1.tgz ; cd template; ./config.make; cd ../VER2.1/; make #17 ## Install pev6.0 ## Note that pev6.0 is equivalent to p0 ### cd /share/apps; scp root@comsics.usm.my:/share/apps/pe/VER6.0.tar.gz . ; mkdir pe; cd pe; mv ../VER6.0.tar.gz . ; tar -zxvf VER6.0.tar.gz; cd VER6.0/ ; make -f Makefile.centos7 ; ln -s /share/apps/pe/VER6.0/pev6.0 /share/apps/local/bin ; ./config.make #18. Install wien2k 14.2 cd /share/apps/configrepo; wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/inst_wien2k_14.2_intel; sh inst_wien2k_14.2_intel ## this may not work #### #19 ## install tensorflow-gpu from nvdia portal (for centos 7 version) using cuDNN v7.5.0.56 Library for Linux (as of 20 Apr 2019) for cuda driver version 10.1 for CentOS from https://developer.nvidia.com/compute/machine-learning/cudnn/secure/v7.5.0.56/prod/10.1_20190225/cudnn-10.1-linux-x64-v7.5.0.56.tgz # Installation proven to work in jaws (CentOS 7.5), with cuda driver version 10.1, GPU GTX 750i cd /share/apps/configrepo wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/inst_tensorflow-gpu-centos.txt chmod +inst_tensorflow-gpu-centos.txt ./inst_tensorflow-gpu-centos.txt