[gmx-users] still some problems with HP-UX... grompp acting weird

[Christopher Daub]

On Sep 9, 2008, at 2:53 AM, David van der Spoel wrote:

> Christopher Daub wrote:
>> Hey again!
>> The install of gromacs 3.3.3 on HP-UX is mostly working fine, but  
>> I'm getting some weird behaviour from grompp where it doesn't set  
>> the output filename correctly.  Here is the grompp output from  
>> when I run the demo program, for example (the demo works fine  
>> until it gets to this step, after pdb2gmx and genbox):
>> --------------------------------------------------------------------- 
>> ------- checking input for internal consistency...
>> sh: /grace/bin/: Cannot create the specified file.
>
> grompp uses a temporary file and for the the environment variable  
> $TMPDIR is read. Is that pointing to /grace/bin ?
>

Thanks a lot for the suggestion.  This variable is not set.  I tried  
to set it to the current directory (export TMPDIR=./), but it didn't  
make a difference.  Where is this set? I grep'd for TMPDIR in the src/ 
kernel directory and couldn't find any reference to it... are you  
sure this is right? Maybe there's another variable getting set  
somewhere... is there a list somewhere of environment variables used  
by gromacs?

I tried other preprocessors other than the default cpp (m4, and a  
cpp.ansi I found in /usr/lib) but get the same error... so it does  
seem to be grompp, not the cpp...

Cheers,
Chris.

>> Cleaning up temporary file gromppa11751
>> -------------------------------------------------------
>> Program grompp, VERSION 3.3.3
>> Source code file: topio.c, line: 312
>> Fatal error:
>> Could not open /grace/bin/
>> -------------------------------------------------------
>> "If Life Seems Jolly Rotten, There's Something You've  
>> Forgotten !" (Monty Python
>> )
>>                          :-)  G  R  O  M  A  C  S  (-:
>>                GRoups of Organic Molecules in ACtion for Science
>>                             :-)  VERSION 3.3.3  (-:
>>       Written by David van der Spoel, Erik Lindahl, Berk Hess, and  
>> others.
>>        Copyright (c) 1991-2000, University of Groningen, The  
>> Netherlands.
>>              Copyright (c) 2001-2008, The GROMACS development team,
>>             check out http://www.gromacs.org for more information.
>>          This program is free software; you can redistribute it  
>> and/or
>>           modify it under the terms of the GNU General Public License
>>          as published by the Free Software Foundation; either  
>> version 2
>>              of the License, or (at your option) any later version.
>>                                 :-)  grompp  (-:
>> creating statusfile for 1 node...
>> calling /usr/bin/cpp...
>> cpp exit code: 256
>> Tried to execute: '/usr/local/bin/cpp  -I/home/snoop/gmacs/share/ 
>> gromacs/top -DFLEX_SP
>> C cpeptide.top > /grace/bin/'
>> The '/usr/bin/cpp' command is defined in the .mdp file
>> processing topology...
>> ---------------------------------------------------------
>> I think it's getting the /grace/bin thing from my PATH variable of  
>> all things! Why it sticks it in there as the output filename is  
>> beyond me.  I've looked at grompp.c and topio.c to see if I can  
>> find the problem, but my C coding skills are not great and I'm not  
>> sure what to do with all those pointers... can anyone suggest an  
>> easy fix for this? I tried an ugly hack to set outfile =  
>> "cppoutput" in topio.c, but that didn't work...
>> Thanks for any suggestions (other than getting rid of HP-UX...),
>> Chris.
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>
>
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala  
> University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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