Hi Lee and Ross,
I have been following your discussion about the problem with running
sander.mpi in amber 9.
I am having the same problem and I posted this to the amber mailing list
on 20.10.06.
David Case replied to me and asked me to run the jac benchmarks which I
did but the same problem exists again and it crashes after some steps.
Regards
Rafi
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of Ross Walker
Sent: 2. november 2006 01:04
To: amber.scripps.edu
Subject: RE: AMBER: Problem of QM/MM calculation with amber 9 parallel
version
Dear Lee,
>I installed parallel version of amber9 in intel itanium server
>usaually called white box with intel compiler 9.
>Installing amber9 went well without a error message.
>When I runned QM/MM calculation with 2 process (mpich option is -np 2),
>it's not working. For long time, sander don't stop itself and don't
make
any data.
>In running with 1 cpu (mpich option is -np 1), sander are working
normally.
This is definately not right it shouldn't hang. I suspect this may be
related to a bug I have been seeing with Intel's 9.1 compilers on my
x86_64
box with our amber10 development code. There was an issue with the Intel
compiler generating incorrect machine code for a loop over MPI_sends
that
are in the ewald setup routines in the QM/MM code.
A couple of questions. Can you post the input file that you are using
for
QM/MM - are you using ewald or pme?
Can you post the output file up to the point where it hangs?
Did you run the QM/MM test cases in parallel? Do the first test cases
(crambin_2) run correctly but the later ones 1NLN_periodic_lnk_atoms
hang?
Or do they all hang?
If it is the former then I have a potential work around that you can
try,
get back to me and let me know. If it is the later (i.e. they all hang)
then
I will have to investigate it further. Having the output file up to the
point where the calculation hung would be very useful here.
All the best
Ross
/\
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|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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Received on Sun Nov 05 2006 - 06:07:24 PST
