AMBER Archive (2009)

Subject: RE: [AMBER] amber10 parallel compiling error

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jul 20 2009 - 12:33:08 CDT

Hi Nam,

Can you send the .out file produced in the rdc directory please so I can see
where it crashes.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of nam kim
> Sent: Monday, July 20, 2009 10:24 AM
> To: amber_at_ambermd.org
> Subject: Re: [AMBER] amber10 parallel compiling error
>
> Ross,
>
> I can compile amber10 without netCDF option in success.
> But, when I test it, there is Run.dip error.
> My cluster use openmpi 1.2.8 with Infiniband connection and PBS.
> Do you think I should use PBS when testing " setenv DO_PARALLEL
> 'mpirun -np 4' make test.parallel.MM < /dev/null"?
>
> Here is the error:
>
> cd rdc && ./Run.dip
> [MPI_ABORT invoked on rank 0 in
> communicator MPI_COMM_WORLD with errorcode 1
> mpirun noticed that job rank 1 with PID 31846 on node
> exited on signal 15 (Terminated).
> 2 additional processes aborted (not shown)
>  ./Run.dip:  Program error
> make[1]: *** [test.sander.BASIC] Error 1
> make[1]: Leaving directory `/apps/amber10/test'
> make: *** [test.sander.BASIC.MPI] Error 2
>
>
>  Many Thanks
> -Nam
>
> > On Sat, Jul 18, 2009 at 10:57 AM, vitor.felix<vitor.felix_at_ua.pt>
> wrote:
> >>
> >>
> >> Sent from my HTC Android phone.
> >>
> >> ----- Reply message -----
> >> From: "nam kim" <namkkim_at_gmail.com>
> >> Date: Sat, Jul 18, 2009 5:19 PM
> >> Subject: [AMBER] amber10 parallel compiling error
> >> To: <amber_at_ambermd.org>
> >>
> >> Ross,
> >>
> >> I will try when I get back to the office.
> >>
> >> Thanks
> >> -Nam
> >>
> >>
> >> Hi Nam,
> >>
> >>> I have successfully compiled amber10 with g95 in serial, but for
> the
> >>> parallel mode, I failed with the error message:
> >>> /share/apps/openmpi/bin/mpif90 -c -O3 -fno-second-underscore
> >>> -ffree-form -o ncsu-umbrella.o _
> >>>
> >>> ncsu-umbrella.f
> >>>
> >>> Fatal Error: Reading module netcdf at line 3 column 1: Expected
> left
> >>> parenthesis
> >>>
> >>> make[1]: *** [ncsu-umbrella.o] Error 1
> >>>
> >>> make[1]: Leaving directory `/share/apps/amber10/src/sander'
> >>>
> >>> make: *** [parallel] Error 2
> >>
> >> I have not seen this error before but a couple of things to try.
> >>
> >> 1) As a work around you could compile without NetCDF support:
> >>
> >> ../configure_amber -mpich2 -nobintraj g95
> >>
> >> 2) If you want to keep the netcdf support try doing a full clean of
> both
> >> amber and ambertools before configuring for parallel. E.g.
> >>
> >> cd $AMBERHOME/src/
> >> make -f Makefile_at clean
> >> make clean
> >> ./configure_amber -mpich2 g95
> >> make parallel
> >>
> >> Obviously adjusting the options (mpich2) above for the MPI version
> you are
> >> using.
> >>
> >> Good luck,
> >> Ross
> >>
> >> /\
> >> \/
> >> |\oss Walker
> >>
> >> | Assistant Research Professor |
> >> | 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 |
> >>
> >> Note: Electronic Mail is not secure, has no guarantee of delivery,
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> >>
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>
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