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Old 06-16-2006, 09:55 AM   #1
martinr
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How do I get gaussian 03 (a quantum chemical program) to work on Fedora Core 5?


Is there any quantum chemist out there?

I know that Fedora Core 5 is frequently updated, and for this reason it appears that Gaussian03 won't work. Is there any way of installing a fix of some sort, some kind of older "library" or something like that? I'm currently using an AMD-2600+ CPU with FC5-i386-(kernel 133 I think). The error I get is shown below.

-----------------
nohup.out:
Erroneous write during file extend. write 1728 instead of 4096
Probably out of disk space.
Write error in NtrExt1
-------------------

I'm REALLY thankful for any help.

/A desperate quantum chemist
 
Old 06-18-2006, 08:26 AM   #2
Theorist
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Hi martinr,
I have not used g03. May we know what was the command that you ran?

Also, what about the file permission of g03? Is it world readable? If yes, then please try changing the permissions.

With Regards,
Theorist
 
Old 06-19-2006, 05:11 AM   #3
martinr
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Hello,

g03 is run from a folder avalible on the office network. It has not been compiled on my system directly. I've just added some info to my bash.profile. It starts nicely just before giving the error shown above. This should work and does so for both suse and several redhat distros. After googling the issue my hopes were somewhat shattered. It appears that with fedora (atleast with FC4), the compilers, the libraries...I'm not really sure what is is, they are too new anyway. It's updated too frequently.

If anyone EVER finds the answer, please let me know. Fedora is after all great in all other aspects.
cheers,
 
Old 08-01-2006, 02:47 PM   #4
johnnyg
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???

Has anyone ever answered this question? I am having the same problems
 
Old 08-28-2006, 06:46 AM   #5
phenolholic
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where do you guys do research and what area do you use g03? i'm in FIU and it's for PES calculations
 
Old 09-06-2006, 04:21 PM   #6
martinr
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Gaussian is the most widely spread and used program for doing quantum chemical calulations, i.e. calculations on chemical reactions. Most people in physical/physical-organic chemistry that do compuational work uses it, or have come across it. Sadly it doesn't work on any of the newer releases of fedora.
 
Old 09-12-2006, 12:37 AM   #7
phenolholic
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does it work on ubuntu? i tried running an already compiled version and this is what I get:

./g98: error while loading shared libraries: util.so: cannot open shared object file: No such file or directory

however, the util.so is there in my g98 directory. i'd really like to use it in ubuntu
 
Old 09-17-2006, 07:06 AM   #8
martinr
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I really have no idear... My advice is google. Please let us know if you succeed. Good luck!
 
Old 09-17-2006, 07:12 AM   #9
Nylex
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Quote:
Originally Posted by phenolholic
./g98: error while loading shared libraries: util.so: cannot open shared object file: No such file or directory

however, the util.so is there in my g98 directory. i'd really like to use it in ubuntu
You get that message (presumably) because the file isn't in a directory listed in your /etc/ld.so.conf. You can put the directory in there and then run ldconfig.
 
Old 09-17-2006, 01:02 PM   #10
phenolholic
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Ok in /etc there was no ld.so.conf file, so I created one and added ~/g98 (pointing to my g98 folder). i then ran ldconfig, and tried running g98 again and got the same error message. any instructions would be greatly appreciated. thanks
 
Old 09-26-2006, 08:24 PM   #11
danrod
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Hi. I am actually having the same problem with g03 running in Fedora Core 5 on a Dell PowerEdge 2800 (and I have to say, Fedora Core 5 is not supported by Dell, nor by Gaussian), I was having the exact problem running any of the kernels provided by Fedora, but I downloaded and recompiled one of the kernel.org kernels and g03 ran with no problems. I think either Red Hat or Fedora engineers changed in some way some of the i/o system calls in the kernel, and It affected the functioning of Gaussian, and perhaps other programs. Well, aside from that, gaussian works fine with my new kernel, but suddenly, I have problems with my flash drives, they don't automount anymore, must be something I miss in the kernel, if anyone has any input, will be much appreciated.
 
Old 09-27-2006, 01:02 AM   #12
Nylex
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Quote:
Originally Posted by phenolholic
Ok in /etc there was no ld.so.conf file, so I created one and added ~/g98 (pointing to my g98 folder). i then ran ldconfig, and tried running g98 again and got the same error message. any instructions would be greatly appreciated. thanks
No idea. You should have had an ld.so.conf, it's a standard file :/.
 
Old 11-17-2006, 08:55 AM   #13
fedorie
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Hi,
Don't know if you guys are still having these problems, but the official answer of Gaussian is, that they do not support FC, although their suggested solution:

echo 0 > /proc/sys/kernel/randomize_va_space

works (normally it reads 1).
If you don't want to this everytime you reboot, you can add this line to
/etc/rc.local
G03 works fine with that solution on both FC4 & FC5 (don't know about FC6 yet though)
Hope this helps,
Fedor
 
Old 12-14-2006, 03:43 PM   #14
VincentV
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don't know if this will help

hi,
Just (finally) got g03 built myself, system is Red Hat Linux Advanced Server release 2.1AS (Pensacola). I also had trouble running it at first, but luckily had been scouring forums for days trying to get it built, so I had some tricks to try. First, make sure you're running it under csh (either have csh as your login shell, have your job script change shells to csh, etc.), I kept forgetting that. Then, since I built my own copy of g03 in my home directory I added the following sort of thing to my PATH in my .cshrc file:
setenv LD_LIBRARY_PATH "/home/VincentV/g03root/g03:$LD_LIBRARY_PATH"

Now my new g03 seems able to find the right util.so just fine, and so far it runs great. I didn't mess with ld.so.conf at all, in building or running g03. Anyway, that's what worked for me, hope some of the info here is helpful. Good luck!
johnny
 
  


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