AMBER Archive (2006)

Subject: Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft

From: Ross Walker (
Date: Fri Nov 03 2006 - 10:39:22 CST

Dear Yu,

>>Assuming that you did not compile in support for binary trajectories,
>>the -bintraj option to configure, then you can >>safely ignore the first
>>The second error is strange. Are you certain DO_PARALLEL is set to 'mpirun
-np 4'?

>Yeah, I ignored the first error, and I am certain DO_PARALLEL is set to
"mpirun -np 4".
> Afterwards, I commented it out, and everything finished nicely.

>Here is the interesting part. I did the tests. it passed on np=2, 8, 32,
>but failed on np=4,16,64 with the "ASSERTion 'processor == numtasks' failed
>in spatial_fft.f " error. And, just for try, it all failed on nps not power
of 2.

Yes, this is a function of the way things are spatially decomposed for doing
a spatial FFT. Mike Crowley should probably look into the restrictions here
to work out exactly what they are so that we can put together a bug fix that
will skip that test case if the number of cpus aren't within the acceptable

>BTW, any other programs in Amber require number of processors be set to
power of 2?

The only programs in Amber that are parallel are sander.MPI and pmemd.
Neither strictly require a power of two (except the spatial FFT above)
although sander will likely run more efficiently if you have a power of two
cpus available. PMEMD should be efficient with almost all combinations of
processors although I would stick to even numbers. The parallel performance
is very dependent on interconnect, cpu speed, processors per node,
interconnect within a node, mpi implementation, compilers, cluster load
etc... As such I would recommend that you take some example problems of
different sizes and run them on various cpus counts on your cluster. This
will aid you in picking efficient cpu counts when you run production jobs.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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