Zuzana Benkova wrote:
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Zuzana Benkova
Sent: Tuesday, November 04, 2008 3:11 PM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] running a simulation without production
Dear Mark,
Thank you very much for valuable advice.
Previously, I run some simulations and I obtained what I had expected. For
instance, instead of the plate I have just used one single chain which was
treated as frozen and the simulations were running. I obtained all output
files containing appropriate information.
I have GMX version 3.3.3. I have just tried gmxtest.pl test first in sthe
ingle precision. The output I got was
All 16 simple tests PASSED
FAILED. Check files in dec+water
FAILED. Check files in fe_test
2 out of 14 complex tests FAILED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED
I am not very familiar with programming language C++. As I wanted to test
also the double precision I did some changes in the gmxtest.pl file. I am
not sure if I did it correctly. I have installed GMX with _mpi suffix, so I
have changed the sub setup_vars section
sub setup_vars {
my $mdprefix = "";
if ( $parallel > 0 ) {
$mdprefix = "mpirun -c $parallel ";
}
if ( $double > 0 ) {
$grompp = "grompp_mpi";
$mdrun = $mdprefix . "mdrun_mpi";
$ref = "reference_d";
}
and after applying command gmxtest.pl -double all I have obtained
sh: line 1: 30240 Segmentation fault mdrun_mpi >mdrun.out 2>&1
FAILED. Check files in rb1
1 out of 16 simple tests FAILED
All 14 complex tests PASSED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED
In the case of the single precision test I can not figure out the error
since I do not have any new files produced after the test in corresponding
directories. In the case of double precision test I have also log file in
rb1 directory which has been terminated exactly in the same way as my
attempts to run simulation of plate-chain system.
Please, could you give me some explanation and hints how to proceed further?
It would be very helpful for me. I have checked the mailing list but did not
find something that could help me. Thank you in advance.
Something's wrong, but you've got too many variables going on to make
for ready diagnosis. Start with single-precision non-MPI and unmodified
gmxtest.pl in a fresh test directory and see if that works properly. If
not, then you have a fundamental problem. If it works, then gradually
test a new variable until you can isolate the problem.
Mark
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