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Chapter3.txt
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Chapter3.txt
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>vmd
>su
>sudo yum update
>sudo yum install libcudart.so.4 libexpat.so.0 libsqlite3.so.0
>sudo yum install libcudart.so.4 libexpat.so.0 libsqlite3.so.0 libGL.so.1
>sudo yum install libGLU.so.1 csh libXinerama.so.1 libXi.so.6 libXft.so.2
>sudo su
>sh ./vmdInstall.sh
#Required for VMD install on Fedora. VMD requires old graphical
#user interface information not standard in present linux version
#csh is required for the installation procedure.
>sudo yum install compat-libstdc++-33 csh
>cd Documents
>tar -zxvf
>cd vmd-1.9.1
>./configure LINUX
>cd src
>make install
>wget ftp://plasma-gate/weizmann.ac.il/pub/grace/src/grace-latest.tar.gz
>tar -xzf ./grace-latest.tar.gz
>cd ./grace-5.1.23
>./configure --enable-grace-home=/opt/grace --with-extra-incpath=/usr/local/include:/opt/include --with-extra-ldpath=/usr/local/lib:/opt/lib --prefix=/usr
>xmgrace
sudo yum install grace
>module load cmake/2.8.10.2
>tar xfz GROMACS-4.6.5.tar.gz
>cd GROMACS-4.6.5
>mkdir build
>cd build
>module load cmake/2.8.10.2
>module load cuda
>module load fftw3/3.3
>cmake ..
>cmake .. -DGMX_BUILD_OWN=ON
>make gmxfftw
>make
>cmake .. -DGMX_GPU=ON -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/marydoe/programs --program-suffix=-4.6.5-MPI_GPU
#!/bin/bash
#The purpose of this script is to install GROMACS and its supporting packages.
#It downloads the required packages directly from the in-ternet when required.
#obtaining root privileges
>sudo su
#Check if the GROMACS engine is functioning [expected fails].
>luck
grompp
#This is where the engine commands will be stored.
>cd $Home/Documents
#To display a list of available updates type
>yum list updates
#To update packages
>yum update
#Installing other packages that GROMACS users will likely find themselves utilizing.
>sudo yum install avogadro-1.0.3-16.fc19 avogadro-libs-1.0.3-16.fc19
sudo yum install fftw2-2.1.5-25.fc19 fftw-doc-3.3.3-5.fc19
#Installing the GROMACS packages available in the soft-ware center
>sudo yum install GROMACS-4.6.3-1.fc19 GROMACS-bash-4.6.3-1.fc19 GROMACS-common-4.6.3-1.fc19 GROMACS-csh-4.6.3-1.fc19 GROMACS-devel-4.6.c-1.fc19 GROMACS-libs-4.6.3-1.fc19 GROMACS-mpich2-4.6.3-1.fc19 GROMACS-mpich2-devel-4.6.3-1.fc19 GROMACS-mpich2-libs-4.6.3-1.fc19 GROMACS-ngmx-4.6.3-1.fc19 GROMACS-openmpi-4.6.3-1.fc19 GROMACS-openmpi-devel-4.6.3-1.fc19 GROMACS-openmpi-libs-4.6.3-1.fc19 GROMACS-zdh-4.6.3-1.fc19 xdrfile-1.1.1-4.fc19
#Installing cmake (a program the installs other programs - including GROMACS)
>sudo yum install catkin-0.4.5-7.gitd4f1f24.fc19 cmake-2.8.11-1.fc19 cmake-fedora-1.0.5-2.fc19 cmake-gui-2.8.11-1.fc19
#Installing wget (a file downloading program to obtain the GROMACS tarball)
>sudo yum install wget-1.14-8.fc19 gwget
#Testing g_energy [expected pass]
>g_energy
#Testing grompp and mdrun [expected fail]
>grompp
>mdrun
#Download the GROMACS package from the site
#There are many newer and older versions available. So pick a GROMACS
#version and source, then place them here.
>wget ftp://ftp.GROMACS.org/pub/GROMACS/GROMACS-4.6.3.tar.gz
>tar xvzf GROMACS-4.6.3.tar.gz
>cd GROMACS-4.6.3
#Alternative code sequence for GROMACS download#
#git clone >git://git.GROMACS.org/GROMACS.git
#cd GROMACS
#git checkout --track -b release-4-6 origin/release-4-6
#There are several different ways to compile GROMACS and some of them were tested
#and are commented out here. Some knowledge of compiling software is required to
#figure out which commented out sections go together.
>mkdir build
>cd build
>cmake .. -DGMX_BUILD_OWN_FFTW=ON
>make
>sudo make install
>cd ./GROMACS-4.6.3/
#Without sudo in the second of these two lines a folder is not created
#Can use make -j N where N is the number of cores or threads to speed up make
>sudo cmake ../GROMACS-4.6.3/
#For compilation on multiple cores within a single node run [untested]
http://www.GROMACS.org/Documentation/Installation_Instructions_4.5/Cmake#OpenMP_enabled_build_(default)
>cmake -DGMX_OPENMP=ON ../GROMACS-src
>sudo make
#This line should by modified for multiprocessor instal-lations
#Speeding up the make commands can be done by make -j N (N is #cores) [untested]
>sudo make install-mdrun
>make mdrun
>make &> log
>sudo make install
>sudo make install-mdrun
>g_energy
#The linking of the library commands and bin which we created
#after installation are not present in this filecd /usr/local/bin
>cd ./Documents/
>cd ./GROMACS-4.6.3/
>source /home/sabri/Documents/GROMACS-4.6.3/src/kernel
#Checking to see if editconf is here [success]
>g_editconf
>sudo ln -s $HOME/Documents/GROMACS-4.6.3/src/kernel /bin
>sudo PATH=$HOME/Documents/GROMACS-4.6.3/src/kernel:$PATH
>PATH=$HOME/Documents/GROMACS-4.6.3/src/kernel:$PATH
#Checked for grompp [success]
>grompp
#Checking for mdrun [success]
>mdrun
>tar -xvf GROMACS-5.0-beta2-tar.gz
>cd ./GROMACS-5.0-beta2
>module load cuda
>module load cmake/2.8.10.2
>module load fftw3
>module load intel/14.0.0.080
>cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_5.0 -DGMX_LIBS_SUFFIX=_5.0
>make install DESTDIR=/nfs/05/cwr0408/GROMACS-5.0/
>rpm -qa > installed-software.log
>yum -y install $(cat /home/user/installed-software.log)
>echo "Look at all of this Good data..." | mail -s "Good data" [email protected] –a uuencode attachment-file | mail -s "Mail subject" "[email protected]" < body.txt