Need Help Installing Gaussian on SUSE 10

flanker12k · 07-25-2006, 12:31 AM

I'm a complete noob when it comes to linux let alone suse

okay for chemistry molecular modeling software theres a program called gaussian

and I'm following the instructions on the website, but I can't seem to get too far

http://www.gaussian.com/g_tech/install_binary.htm

on step three when I got to type cd $g03root it says no such directory exists when I type the commands in su mode....

help!

here's what I had from command line if it helps diagnose the problem

/home/> setenv mntpnt "/mnt/cdrom"
/home/> setenv g03root "dir"
/home/> cd $g03root
dir: No such file or directory.
/home/> setenv g03root
/home/> setenv mntpnt "/mnt/cd"
/home/> setenv g03root "dir"
/home/> cd g03root
g03root: No such file or directory.
/home/ad> cd $g03root
dir: No such file or directory.
/home/> mkdir /mnt/cd
mkdir: cannot create directory `/mnt/cd': File exists
/home/> cd $g03root
dir: No such file or directory.
/home/> ls
bin Desktop Documents public_html
/home/> cd bin
/bin> ls
/bin> cd..
/home/> $ /bin/csh
$: Command not found.
/home/> cd g03root
g03root: No such file or directory.
/home/> /bin
/bin: Permission denied.
/home/> root

CORRECT>rootv (y|n|e|a)? no
root: Command not found.
/home/> su
Password:
linux-drw4:/home/ # /bin
bash: /bin: is a directory
linux-drw4:/home/ # /bin/csh
naveed has logged on :0 from console.
naveed has logged on pts/0 from local.
naveed has logged on pts/1 from local.
linux-drw4 /home/ setenv mntpnt "/mnt/cdrom"
linux-drw4 /home/ setenv g03root "dir"
linux-drw4 /home/ cd $g03root
dir: No such file or directory.
linux-drw4 /home/

Nylex · 07-25-2006, 01:05 AM

Quote:

Originally Posted by flanker12k

/home/naveed> setenv mntpnt "/mnt/cdrom"
/home/naveed> setenv g03root "dir"
/home/naveed> cd $g03root
dir: No such file or directory.

The problem is that you don't have a directory called dir. Looking at that link, when you run "setenv g03root "dir"", you're giving the variable g03root the value of the directory you want to install to. So, replace dir with the directory you want to install to (and if it doesn't exist, create it first).

Quote:

/home/naveed> $ /bin/csh
$: Command not found.

Here, you don't need to type the $. That's just the usual prompt you have.

flanker12k · 07-25-2006, 07:23 PM

ohhhh, cool! Thank you.

alright now i'm stuck at step 4. here's what i did so far. the CD was already in when I booted into suse 10.1....

/home/naveed> setenv mntpnt "/mnt/cdrom"
/home/naveed> mk dir g03root

CORRECT>mv dir g03root (y|n|e|a)? yes
mv: cannot stat `dir': No such file or directory
/home/naveed> mkdir g03root
/home/naveed> ls
bin Desktop Documents g03root public_html
/home/naveed> setenv g03root "dir"
/home/naveed> cd $g03root
dir: No such file or directory.
/home/naveed> cd g03root
naveed/g03root> cat $mntpnt/tar/*.taz | zcat | tar xvf
cat: No match.

zcat: stdin: unexpected end of file
tar: Old option `f' requires an argument.
Try `tar --help' or `tar --usage' for more information.
naveed/g03root> cat $mntpnt/tar/*.taz | zcat | tar xvf -
cat: No match.

zcat: stdin: unexpected end of file
naveed/g03root> cat mntpnt/tar/*.taz | zcat |tar xvf
cat: No match.
tar: Old option `f' requires an argument.
Try `tar --help' or `tar --usage' for more information.

zcat: stdin: unexpected end of file
naveed/g03root>

Nylex · 07-25-2006, 11:50 PM

Quote:

Originally Posted by flanker12k

/home/naveed> mkdir g03root
/home/naveed> ls
bin Desktop Documents g03root public_html
/home/naveed> setenv g03root "dir"
/home/naveed> cd $g03root
dir: No such file or directory.

You're doing the same thing as before. Again, with "setenv g03root "dir"", you're setting the value of an environment variable, $g03root with the value enclosed in the double quotes (i.e. dir). You do not have a directory called dir and the shell tells you so. You've created a directory called g03root, so if you want to use that, substitute "g03root" in place of "dir".

flanker12k · 07-26-2006, 12:10 AM

okay this is what i've done so far am I on the right track this time?

naveed@linux-drw4:~> /bin/csh
/home/naveed> setenv mntpnt "/mnt/cdrom"
/home/naveed> setenv g03root "g03root
Unmatched ".
/home/naveed> setenv g03root "g03root"
/home/naveed> cd g03root
naveed/g03root> cat mnt/pnt/tar*.taz | zcat | tar xvf
cat: No match.

zcat: stdin: unexpected end of file
tar: Old option `f' requires an argument.
Try `tar --help' or `tar --usage' for more information.
naveed/g03root> cat mnt/pnt/tar*.taz | zcat | tar xvf -
cat: No match.

zcat: stdin: unexpected end of file
naveed/g03root> chgrp -R grp g03
chgrp: invalid group `grp'
naveed/g03root>

Nylex · 07-26-2006, 12:15 AM

Quote:

Originally Posted by flanker12k

naveed/g03root> cat mnt/pnt/tar*.taz | zcat | tar xvf

Those instructions say you're supposed to use the variable you called $mntpnt here (it'd also work if you used the value of that variable, which you've set as /mnt/cdrom). You're also missing a slash (/) between "tar" and "*" and a dash (-) after "xvf".

rhodium · 08-08-2006, 07:22 PM

Quote:

Originally Posted by Nylex

Those instructions say you're supposed to use the variable you called $mntpnt here (it'd also work if you used the value of that variable, which you've set as /mnt/cdrom). You're also missing a slash (/) between "tar" and "*" and a dash (-) after "xvf".

Hello people...
I am having the same problem as the previous user. The command line is this one:
candeias/G03> cat $mntpnt/tar/*.taz | zcat | tar xvf -
cat: No match.

zcat: stdin: unexpected end of file

why is this happening?... I have already set all the variables.

Help, please!!!

phenolholic · 08-28-2006, 05:48 AM

where do you do research and what topics? i'm in FIU and we do PES

flanker12k · 08-28-2006, 10:09 PM

forgive my retardedness, PES?? what's that?

I'm a Wichita State University primarily doing semi empircal with Cache 6.0 but I thought I would give it a shot at gaussian on a linux system on an athlon 64 machine running 64bit

This actually is a can of worms and for a linux newbie is a double can of worms because you don't understand what the hell is going on in linux! <sigh> its something to do with the way the permissions are set of gaussian and all goes back to some stupid copyright related issue (well thats what a graduate student told me anyway)

phenolholic · 08-28-2006, 11:53 PM

PES = potential energy surfaces. it calculates a gradient of the surface potential energy of atomic structures of reactions and intermediates using atomic and molecular geometries as parameters.

marcelo61 · 09-26-2006, 12:36 PM

Anyone got Gaussian 03 to work under suse 10.1?

When compiling it stop with this error:

util.so: undefined reference to `pthread_kill_other_threads_np'

Any ideas?

Thanks, Marcelo.

guiri · 09-29-2006, 12:42 AM

Gaussian 03 under SUSE 10 ENT (which is like SUSE 10.1) on a AMD Opteron 280 systems (Tyan GT24) and Portland PGI 5.1 Fortran. I am having some problems with this library lpgthread. Just to get Gaussian 03 D02 to start to compile I had to install the comtat-g77 rpm and create a file called localrc in /usr/pgi/linux86-64/5.1/bin that looked like this...

set LFC=-lg2c;
set LDSO=/lib64/ld-linux-x86-64.so.2;
set GCCDIR=/usr/lib64/gcc/x86_64-suse-linux/4.1.0;
set GCCINC=/usr//include;
set G77DIR=usr/lib64/gcc/x86_64-suse-linux/4.1.0;
set THROW=__THROW=;

But it would hang at -lpgthread library part. I then downloaded the
PGI 6.2 compiler from Portland and installed. Was then able to get Gaussian 03 D02 to compile. But when I went to check if it works I get
this error. ( I do get all 80 *.exe files). I set my env

GAUSS_SCRDIR=/home/scratch/(username)
export GAUSS_SCRDIR

g03root=/usr/local/
export g03root

source "$g03root/g03/bsd/g03.profile"

$> g03 test001.com
Segmentation fault

Anybody have any ideas ...

marcelo61 · 09-29-2006, 06:24 AM

please see this post:

http://www.linuxquestions.org/questi...d.php?t=487167

Marcelo.