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

Christopher Daub cdaub at vcu.edu
Tue Sep 9 22:05:13 CEST 2008


On Sep 9, 2008, at 3:31 PM, David van der Spoel wrote:

> 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...

Hmm.  getenv seems to work elsewhere in the codes (finding $GMXLIB  
etc)... I wonder why it messes up here? Maybe I could compile grompp  
with lower optimization, or with gcc instead of the HP compilers...  
I'll try that sometime.

>>>
>>> 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.

OK, I tried this and it does work.  Thanks! For now I guess this will  
be our M.O...

Thanks again for all the help,
Chris.

>> 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
>>> _______________________________________________
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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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