AMBER Archive (2006)

Subject: RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Nov 01 2006 - 18:04:28 CST

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_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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