AMBER Archive (2006)

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

From: Ross Walker (
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

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | 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
To unsubscribe, send "unsubscribe amber" to