AMBER Archive (2009)

Subject: Re: [AMBER] amber10 parallel compiling error

From: nam kim (namkkim_at_gmail.com)
Date: Mon Jul 20 2009 - 12:24:14 CDT

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
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>>
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>

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