AMBER Archive (2009)

Subject: Re: [AMBER] amber10 parallel compiling error

From: nam kim (namkkim_at_gmail.com)
Date: Mon Jul 20 2009 - 13:34:41 CDT

Ross,

In the second try, I can pass the test without any error, there are
several failures to pass in module tests though.

The reason I got a test error before might be PATH and LD_LIBRARY_PATH issues.
I have multiple versions of openmpi and the one I need to test is not
in the PATH and LD_LIBRARY_PATH.

Thanks
-Nam

On Mon, Jul 20, 2009 at 11:15 AM, nam kim<namkkim_at_gmail.com> wrote:
> Ross,
>
> There is no .out file in rdc directory.
>
> Thanks
> -Nam
>
> On Mon, Jul 20, 2009 at 10:33 AM, Ross Walker<ross_at_rosswalker.co.uk> wrote:
>> 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,
>>> may not
>>> >> be read every day, and should not be used for urgent or sensitive
>>> issues.
>>> >>
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>>> >
>>>
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