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
/\
\/
|\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 |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Nov 05 2006 - 06:07:18 PST
