Prof Ross Walker,
I am using the right executable,
/usr/bin/mpirun -np 2 /usr/local/amber9/exe/sander.MPI -ng 2
Error: specified more groups ( 2 ) than the number of processors (
1 ) !
I've also verified that the sander.MPI does execute in parallel when I don't
use the -ng option.(When I use it for MD without TI)
I did run the parallel test cases.
Most tests pass, but there are a few failures:
export TESTsander=/Users/srana/AmberTest/amber9/exe/sander.MPI; make
test.sander
.BASIC
cd dmp; ./Run.dmp
This test not set up for parallel
cannot run in parallel with #residues < #pes
cd adenine; ./Run.adenine
This test not set up for parallel
cannot run in parallel with #residues < #pes
==============================================================
cd cytosine; ./Run.cytosine
diffing cytosine.out.save with cytosine.out
PASSED
...
cd dhfr; ./Run.dhfr.min
diffing mdout.dhfr.min.save with mdout.dhfr.min
possible FAILURE: check mdout.dhfr.min.dif
...
cd dna_pol; ./Run.dna_pol
diffing mdout.dna_pol.save with mdout.dna_pol
possible FAILURE: check mdout.dna_pol.dif
...
cd rdc; ./Run.dip
./Run.dip: Program error
The tests exit on the last error.
This is on an OSX 10.5.5 system, but we've verified the same runtime error
with the -ng flag on other architectures.
thanks
sadhna
> Hi Sadhna,
>
>> Error: specified more groups ( 2 ) than the number of
>> processors ( 1 ) !
>>
>> inspite of specifying 2 processors through -np 2 option
>>
>> I am not sure where I am going wrong. If anyone can give some hints
>> that
>> would be great.
>
> Are you using sander.MPI as the executable? You must do this which means
> you
> must have compiled the parallel version of the code. So you would do
> something like:
>
> mpirun -np 2 $AMBERHOME/exe/sander.MPI .....
>
> Also did you run the parallel test cases? You should really do this - make
> sure you set DO_PARALLEL='mpirun -np 2' and then do
>
> cd $AMBERHOME/test/
> make test.parallel
>
> If this gives errors then please post these to the list since this is the
> best way for us to help you debug.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | 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
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Received on Fri Oct 03 2008 - 05:10:43 PDT
