[gmx-users] still some problems with HP-UX... grompp acting weird
Christopher Daub
cdaub at vcu.edu
Tue Sep 9 20:24:17 CEST 2008
On Sep 9, 2008, at 12:43 PM, David van der Spoel wrote:
> 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.
Yep, tried that... makes no difference. I've tried a different HP
box, and another user also tried, in which case, the attempted output
directory is a different mangled piece of our respective $PATH
variables. Every attempt to run grompp does the same weird thing.
>
> In the worst case you can run grompp on another box, and only use
> mdrun on the HP.
Thanks, we may have to do that... but will it work? grompp will make
a binary .tpr file, I don't think I'll be able to read that with
mdrun running somewhere else, or will I?
Thanks again,
Chris.
>>>
>> 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
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
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