[gmx-users] still some problems with HP-UX... grompp acting weird
David van der Spoel
spoel at xray.bmc.uu.se
Tue Sep 9 21:31:39 CEST 2008
Christopher Daub wrote:
>
> 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.
>
I'm afraid this is going to be hard to reproduce because as far as I
know neither of the developers has a HPUX system. It sounds like a
problem in the getenv C-library function...
>>
>> 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?
Yes, these files are portable.
>
> 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
>>>> _______________________________________________
>>>> gmx-users mailing list gmx-users at gromacs.org
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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
>> http://www.gromacs.org/mailman/listinfo/gmx-users
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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
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