AMBER Archive (2004)

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

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Wed Dec 01 2004 - 21:04:31 CST

Hi Ilyas,

Glad to hear you have recently installed amber8 on
your laptop.
 
One way or the other amber8 installs well on Linux
Suse 9.1. My installation guide is for those who have
a full Suse package (5 CDs). It has worked for me..

Cheers,

Jenk.

--- Ilyas Yildirim <yildirim_at_pas.rochester.edu> wrote:

> 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
> >
>
=== message truncated ===

                
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