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

[David van der Spoel]

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 ?

> 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