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.
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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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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