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

[David van der Spoel]

Christopher Daub wrote:
> 
> 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 ?


try running the programs outside the demo script.

In the worst case you can run grompp on another box, and only use mdrun 
on the HP.
>>
> 
> 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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> 
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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