Ah, this could be the issue.
Depending on how you configure the double precision binaries
could have the same names as the single precision ones,
or they could have _d appended.
I guess the test scripts can not figure out what they should use,
but currently they apparently request the _d appended names.
Berk.
From: Chris Snook <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Subject: Re: [gmx-users] Double precision test failure
Date: Fri, 30 Nov 2007 08:20:11 -0500
The gromacs commands are in my search path as both the commands suggested
worked. The single precision tests worked but it was the double precision
tests that completely failed.
All of the grompp.out files contain the single line error :
sh: line 1: grompp_d: command not found
Checking the bin directory, indeed there is no grompp_d binary. Was the Mac
OS X binaries only compiled for single precision?
Chris
David van der Spoel wrote:
Chris Snook wrote:
Yes,
The paths for GMXBIN, GMXLDLIB, GMXDATA and GMXMAN are correctly defined
whether
I use sh or bash as the shell. I do get the following errors when I run
GMXRC in
either shell:
../bin/GMXRC: line 35: return: can only `return' from a function or
sourced
script
../bin/GMXRC: line 44: CSH:: command not found
../bin/GMXRC: /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near
unexpected token `setenv'
../bin/GMXRC: /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (!
$?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ""'
you should in sh or bash type
. GMXRC
the important question is whether the gromacs commands are in your search
path. this is best test by typing
grompp -h
or
luck
If they are there then something else is wrong in the test set. Please
check the grompp.out files in the subdirectories.
Regards
Chris
Quoting David van der Spoel <[EMAIL PROTECTED]>:
Chris Snook wrote:
I am trying to use gromacs on a Mac OS X 10.4.11 with an Intel 2.16GHz
Core 2
Duo processor.
I have downloaded and installed the v 3.3.2 binaries of gromacs for
this OS and
run the test program. The single precision tests run OK. But the double
precision tests completely fail with the following output (partial):
No topol.tpr file in angles1. grompp failed
FAILED. Check files in angles1
No topol.tpr file in angles125. grompp failed
FAILED. Check files in angles125
No topol.tpr file in bham. grompp failed
FAILED. Check files in bham
etc
No topol.tpr file in kernel334. grompp failed
FAILED. Check files in kernel334
63 out of 63 kernel tests FAILED
readline() on closed filehandle PIPE at ./gmxtest.pl line 353.
etc
I've checked the archives and the manual and haven't seen anything
relevant to
this. Any help would be appreciated.
did you source GMXRC?
Regards
Chris
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X-ray Crystallography Core Manager
Dept. of Biochemistry & Molecular Biology
Medical University of South Carolina
173 Ashley Avenue
Charleston
SC 29425
USA
Phone: 843-792-5848
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email: [EMAIL PROTECTED]
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