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-- Ilyas Yildirim --------------------------------------------------------------- - Department of Chemisty - - - University of Rochester - - - Hutchison Hall, Office B10 - Ph.:(585) 503 44 00 (Cell) - - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) - - http://www.pas.rochester.edu/~yildirim/ - --------------------------------------------------------------- On Tue, 16 Nov 2004, Cenk Andac wrote: > I am sending you my personal guide flines for installation of ifort and amber8 > in Linux Suse 9.1. Let me know it works for you. *********************************************************************************** > Installation of ifort in Linux Suse 9.1 > jenk directory can be your personal home directory > > > Installation requirements: > > make sure you have pre-installed kernel and glibc libraries > > fromSuse Linux installation disks > > > > > > # now untar fortran compiler > > cd /home/jenk > > tar -zxvf l_fc_p_8.0.034.tar.gz > > > > # create licenses directory in home/jenk/opt/ifort/ (if not available there!) > > mkdir home/jenk/opt/ifort/licenses > > > > #copy intel evaluation license file (xxx.lic) to ../ifort/licenses directory as ifort.lic > > #become a root user > > cd home/jenk/l_fc_p_8.0.034 > > cp intel-ifort8-8.0-40.i386.rpm /home/jenk/opt/ifort/intel-ifort8-8.0-40.i386.rpm > > # using SuSe File manager open home/jenk/opt/ifort > > # click on the rpm file and allow Suse handle installation as root (enter root password). > > # source ifort > > cd /home/jenk/opt/ifort/bin > > source ifortvars.sh > > ifortvars.sh > > #or better yet > > # become a root user > > #add path lines in /etc/profile > > #to eliminate sourcing ifort each time system is restarted > > # (see the following /etc/profile file) > > cd /etc > > # you may want to use vi or other editors (kate , emacs, etc.) to edit /etc/profile > > # say you use vi. then > > vi profile > > # add the following red path lines in /etc/profile and save and quit > > # here are some quick tips on using vi for beginners: > > # hit insert on your keyboard to make additions > > # Backspace has never worked for me, so use delete instead when necessary > > # hit ESC on your keybord to quit insert mode > > # type " :wq " to save and quit > > # here is the red path lines you should add in /etc/profile > > Make path more comfortable > > > > if test -z "$PROFILEREAD" ; then > > PATH=/home/jenk/opt/ifort/bin:/usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin > > if test "$HOME" != "/" ; then > > for dir in $HOME/bin/$CPU $HOME/bin ; do > > test -d $dir && PATH=$dir:$PATH > > done > > fi > > test "$UID" = 0 && PATH=/sbin:/usr/sbin:/usr/local/sbin:/home/jenk/opt/ifort/bin:$PATH > > for dir in /var/lib/dosemu \ > > /usr/games \ > > /home/jenk/opt/ifort/bin\ > > /opt/bin \ > > /opt/gnome/bin \ > > /opt/kde3/bin \ > > /opt/kde2/bin \ > > /opt/kde/bin \ > > /usr/openwin/bin \ > > /opt/cross/bin > > do > > test -d $dir && PATH=$PATH:$dir > > done > > unset dir > > export PATH > > fi > > > > #You may now proceed to install amber8 > > > > ************************************************************************************* > > Installation of Amber 8 in Linux Suse 9.1 > jenk directory can be your personal home directory > > > Installation requirements: > > 1) make sure that files involving gcc, cc, c, c++, mpich are all installed from Suse-Linux disks > > 2) make sure that g77 that is installed from Suse-Linux disks > > 3) make sure that ifort (f90) is properly installed and sourced > > 4) make sure that yacc is installed from Suse-Linux disks > > suggested files involving yacc are > > bison, global, gob2,pccts > > 5) Before installing amber8, you need to source ifort (see the guide above for > > sourcing ifort) > > > > INSTALLATION of AMBER8: > > #DO NOT run any other application while amber8 installs > > # untar amber 8 in /home/jenk directory > > tar -zxvf amber8.tar.gz > > # configure amber8 > > cd /home/jenk/amber8/src > > ./configure ifort > > # ignore warning message of unset path for MKL_HOME > > make serial > > #make sure instalation is complete > > #update amber8 > > #download the most recent bugfix.all patch from Amber website > > #into $AMBERHOME (/home/jenk/amber8 > > #then patch bugfix.all > > cd /home/jenk/amber8 > > patch -p0 -N -r patch_rejects <bugfix.all > > > > #test amber > > cd /home/jenk/amber8/test > > make test > > > > #make sure amber8 passes all tests > > #some failure messages regarding xxx.dif files may be listed > > #while testing SANDER and ANTECHAMBER > > #They do not however seem to affect amber functionality! > > #So amber should be fine with the xxx.dif files. > > #other failure messages could be problematic and > > #hence the installation must be revised. > > > > #set AMBERHOME environment and path in cshell (csh) > > #so that $AMBERHOME/exe/.. commands work in csh with no requirement for path definition > > #for instance; xleap executes xleap in any directory in csh > > # > > #become a root user > > #create or open /etc/csh.cshrc.local and /etc/csh.login.local > > #add and save following red path lines in /etc/csh.cshrc.local and /etc/csh.login.local > > # using any available editor > > > > setenv AMBERHOME /home/jenk/amber8 > > set path=($path $AMBERHOME/exe) > > #set AMBERHOME environment in bash > > # > > #so that $AMBERHOME/exe/.. commands work in bash but requires path definition > > #for instance; $AMBERHOME/exe/xleap executes xleap in any directory in bash > > # > > #become a root user > > #create or open /etc/bash.bashrc.local > > #add and save the following line in /etc/bash.bashrc.local > > # > > #setenv AMBERHOME /home/jenk/amber8 > > > > *************************************************************************** > That is about all from me. Let me know if things work out allright for you. > > Cheers, > > Jenk. > > > Cenk Andac > M.S., Ph.D. candidate > Faculty candiate in Turkey > > > > Ilyas Yildirim <yildirim.pas.rochester.edu> wrote: > > Dear Amber members, > Did anyone install AMBER 8 to a SUSE 9.1 Personal system? If yes, can you > give me the address of the compiler u have used? I have tried Intel > Fortran Compiler 8.1, and pgf90, but they did not work. There were a lot > of other problems, which I could not solve using internet. Thanks in > advance. > Ciao, > > ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Wed Dec 01 2004 - 21:53:00 PST