AMBER Archive (2004)

Subject: AMBER: Re: INSTALLATION GUIDE FOR IFORT AND AMBER8 IN LINUX SUSE 9.1 ....Re: AMBER: SUSE 9.1 and AMBER 8

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Dec 01 2004 - 15:12:49 CST

Dear AMBER List Members,

I could not respond you back for the last two weeks. I have installed
AMBER 8 to my laptop. I am writing this email to people who are using SUSE
Linux 9.1 and having trouble with AMBER 8 installation. I have a DELL 5100
Inspiron, and will use my computer to prepare amber .pdb files using
xleap, before doing the simulations in a cluster. So, if you are a
beginner like me in SUSE 9.1, I hope this will be useful for you.

The SUSE Linux 9.1 version I am using is the personal version. After
installing SUSE 9.1, it was clear that not everything was installed (like
gcc lib. files) The Personal SUSE Linux 9.1 is just 1 CD and does not
install a lot of things. In order to include the libraries needed to
compile AMBER 8, you have to install the packages using YaST. YaST is the
most important program (at least it seems for me) in SUSE 9.1 which lets u
install the packages. It is like Windows XP Update. The only problem is
that you have to specify the Source of Installation. If you do not specify
the source (a new source), it will use the CD. Again, the 1 CD of SUSE 9.1
does not have all the packages.

So, what you have to do is go to

YaST > Change Source of Installation
Add > FTP
server: (chose the best server from
http://www.suse.com/en/private/download/ftp/int_mirrors.html)
directory: pub/suse/i386/9.1

This will add a new source to your installation. Then, use the search
option of 'Install and Remove Software' module of YaST. For instance, if
you need to install gcc, write gcc in the search area, and press enter.
This will show you the packages installed or not installed. So, chose the
ones you need, and install those packages. One other thing, if you have
trouble with SUSE 9.1, the best thing is to go to some linux forums, like
http://www.linuxquestions.org. It is very helpful because there are people
who had the same problems. Moreover, you can ask any questions you want
and someone will respond you back. (Like AMBER Mailing List)

Another important thing is the Intel Fortran Compiler. I have tried the
ifort ver.8.1 but could not compile AMBER 8. (PS: I tried this 2 weeks
ago, before installing the missing lib files. Maybe it will work) I have
installed the ifort 8.0 and the compilation went well. I tried to follow
Cenk's Installation Manual for ifort, but could not install it. The best
thing is to follow the README file of ifort, step by step. (In Cenk's
procedure, there was this DIRECTORY problem, which is the directory ifort
is installed. It did not show the installed directory, and as a result,
gave a directory problem)

I do not remember where I have downloaded the ifort ver.8.0; someone gave
the website in this mailing list. The reason why I am telling you this is
because when you go to the INTEL's website, they will let you download the
latest version of ifort, namely ver.8.1. As I said above, maybe this
version of ifort will compiler AMBER 8 after installing all the lib files
needed, but I did not try it. ver. 8.0 definitely works.

There was another problem while I was compiling AMBER 8. It gave an error
on X11/Intrinsic.h and X11/ShellP.h files, saying that it cannot find
those files. These are x windows files, and the package needs to be
installed. The name of the package that needs to be installed using YaST
is Xfree86 (or Xfree86-devel, not sure about the name). After installing
this package, I did not have any trouble. And compiled AMBER 8.

I hope this will help to people who are using SUSE 9.1. Ciao... 

-- 
  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_at_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,
>
>

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