Jones de Andrade wrote:
Hi Justin.
Well, bothering again. Good and bad news.
The good news: I found a strange "work-around" for my problems here. For
some reason, the perl script updates the path, environments and
everything else when runs. So, the variables I placed on the script I
was usin
Hi Justin.
On Mon, May 11, 2009 at 11:10 PM, Justin A. Lemkul wrote:
> All of the above can be fixed by changing the appropriate .mdp option.
Yes, I agree. I'll try that. Probably that's what will solve that problem.
If that's ok, I'll send to the site a "revised" version of the test set. :)
Jones de Andrade wrote:
Ok, summary of errors begin here.
First, errors with MPI in double precision:
1 Simple Test:
bham: ns type Simple is not supported with domain decomposition, use
particle decomposition: mdrun -pd
7 Complex Tests:
acetonitrilRF: ns type Simple is not supported with d
Ok, summary of errors begin here.
First, errors with MPI in double precision:
1 Simple Test:
bham: ns type Simple is not supported with domain decomposition, use
particle decomposition: mdrun -pd
7 Complex Tests:
acetonitrilRF: ns type Simple is not supported with domain decomposition,
use parti
Hi Justin.
Well, bothering again. Good and bad news.
The good news: I found a strange "work-around" for my problems here. For
some reason, the perl script updates the path, environments and everything
else when runs. So, the variables I placed on the script I was using where
simply lost. Workarou
Jones de Andrade wrote:
Hi Justin.
Thanks a lot for that. It helped, but enough yet. :( Just made 4.0.4
tests reach the same "range of errors" that I'm getting with 3.3.3. :P
Using openMPI, it just complains that it can't find orted. That would
mean that the paths are not in there, BUT they
Hi Justin.
Thanks a lot for that. It helped, but enough yet. :( Just made 4.0.4 tests
reach the same "range of errors" that I'm getting with 3.3.3. :P
Using openMPI, it just complains that it can't find orted. That would mean
that the paths are not in there, BUT they are. :P If I just try to run
Justin A. Lemkul wrote:
Jones de Andrade wrote:
Hi Justin
This has been discussed several times on the list. The -np flag is
no longer necessary with grompp. You don't get an mdrun.out because
the .tpr file is likely never created, since grompp fails.
Yes, I know that and th
Hi Justin
This has been discussed several times on the list. The -np flag is no
> longer necessary with grompp. You don't get an mdrun.out because the .tpr
> file is likely never created, since grompp fails.
Yes, I know that and that is what I would have expected. But what I'm
running is the g
Jones de Andrade wrote:
Using just the "simple" tests now to try to find out where is the error.
Since the error goes everywhere, it just simplify things.
It outputs everything ok with the serial part, but it all gets really
messy in the mpi section.
In version 4.0.4, it's complaining tha
Thanks Justin. ;)
Well, I'm using a simple script to run the tests. The script follows:
**
#!/bin/tcsh
source ../../tcshrc
source /opt/chemistry/gmx404.ompi/bin/GMXRC.csh
set path=( $path /opt/mpi/ompi131/bin )
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/opt/mpi/ompi131/lib
se
Jones de Andrade wrote:
Hi everyone.
Well, lets go straight to the point: last time I've installed gromacs,
it was still 3.3.x and there was no testbed available yet. I've done
some tests of my own and everything gone fine.
I'm doing some new installations now, both gmx3.3.3 and gmx4.0.4.
Hi everyone.
Well, lets go straight to the point: last time I've installed gromacs, it
was still 3.3.x and there was no testbed available yet. I've done some tests
of my own and everything gone fine.
I'm doing some new installations now, both gmx3.3.3 and gmx4.0.4. They weem
to work pretty well i
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