[mpich-discuss] compiling MPICH2 with intel compilers

Thu Jul 17 02:44:26 CDT 2008

Dear Anthony,

Thanks for your answer. In the meantime I have found the problem. My 
mpich build was not complete. For some reason several header files were 
not installed by make install. When I compiled AMBER10, it found an 
mpif.h file which was installed in /usr/include. I solved the problem by 
recompiling mpich2 and everything works fine now

Best wishes
vlad

Anthony Chan wrote:
> Did you compile AMBER10 with mpif90 from the install directory of 1.0.7 ?
> if you can use mpif90 to compile AMBER, make sure the 1.0.7's mpi.h/mpif.h
> and libraries are used in building AMBER.
>
> Just to be sure that your mpich2 is installed correctly, try running
> the example programs, cpi/fpi and pi3f90, in your build directoy.
> If you see any problem, send us the configure output as seen on
> your screen (the instruction is written in MPICH2 installer's guide).
>
> A.Chan
> ----- "Vlad Cojocaru" <Vlad.Cojocaru at eml-r.villa-bosch.de> wrote:
>
>   
>> Dear MPICH2 users,
>>
>> I am trying to build a parallel version of AMBER10 (a molecular
>> dynamics 
>> package) with MPICH2.
>> I downloaded the mpich2 from your site, I compiled it with the intel 
>> compiler suite 10.1. Apparently everything went smoothly (the tests
>> from 
>> the mpich2 installation guide were correctly executed). However after
>> I 
>> successfully compiled AMBER10 I tried to run the tests and I got the 
>> error below which obviously comes from the mpich2 build. I used the 
>> correct mpiexec script when executing my application, and apparently I
>>
>> have to interference from a pre-installed mpich.
>>
>> Looking back at the configuration logfile from the mpich2 compilation
>>
>> (see attached) I noticed some errors. Could you please take a look at
>>
>> the config.log attached and tell me if you see anything obviously
>> wrong. 
>> I also attached the compilation flags I set as environmental variables
>>
>> (maybe there is something wrong there). Also, if you have any idea why
>> I 
>> get the error below, I would be grateful for any advices.
>>
>> Thanks in advance
>>
>> Best wishes
>> vlad
>>
>> --------------------------------------------error upo testing 
>> --------------------------------------------------------------------------------------------
>>
>>
>> export 
>> TESTsander=/scratch/node-06-01/cojocavd/Software/amber10_intel_mpich2/exe/sander.MPI;
>>
>> make test.sander.BASIC
>> make[1]: Entering directory 
>> `/exports/scratch/cojocavd/Software/amber10_intel_mpich2/test'
>> cd cytosine && ./Run.cytosine
>> Fatal error in MPI_Comm_rank: Invalid communicator, error stack:
>> MPI_Comm_rank(107): MPI_Comm_rank(comm=0x0, rank=0x14150f0) failed
>> MPI_Comm_rank(65).: Invalid communicator[cli_0]: aborting job:
>> Fatal error in MPI_Comm_rank: Invalid communicator, error stack:
>> MPI_Comm_rank(107): MPI_Comm_rank(comm=0x0, rank=0x14150f0) failed
>> MPI_Comm_rank(65).: Invalid communicator
>> Fatal error in MPI_Comm_rank: Invalid communicator, error stack:
>> MPI_Comm_rank(107): MPI_Comm_rank(comm=0x0, rank=0x14150f0) failed
>> MPI_Comm_rank(65).: Invalid communicator[cli_1]: aborting job:
>> Fatal error in MPI_Comm_rank: Invalid communicator, error stack:
>> MPI_Comm_rank(107): MPI_Comm_rank(comm=0x0, rank=0x14150f0) failed
>> MPI_Comm_rank(65).: Invalid communicator
>> Fatal error in MPI_Comm_rank: Invalid communicator, error stack:
>> MPI_Comm_rank(107): MPI_Comm_rank(comm=0x0, rank=0x14150f0) failed
>> MPI_Comm_rank(65).: Invalid communicator[cli_2]: aborting job:
>> Fatal error in MPI_Comm_rank: Invalid communicator, error stack:
>> MPI_Comm_rank(107): MPI_Comm_rank(comm=0x0, rank=0x14150f0) failed
>> MPI_Comm_rank(65).: Invalid communicator
>> Fatal error in MPI_Comm_rank: Invalid communicator, error stack:
>> MPI_Comm_rank(107): MPI_Comm_rank(comm=0x0, rank=0x14150f0) failed
>> MPI_Comm_rank(65).: Invalid communicator[cli_3]: aborting job:
>> Fatal error in MPI_Comm_rank: Invalid communicator, error stack:
>> MPI_Comm_rank(107): MPI_Comm_rank(comm=0x0, rank=0x14150f0) failed
>> MPI_Comm_rank(65).: Invalid communicator
>> rank 3 in job 10  node-06-01_60831   caused collective abort of all
>> ranks
>>  exit status of rank 3: return code 1
>> rank 1 in job 10  node-06-01_60831   caused collective abort of all
>> ranks
>>  exit status of rank 1: return code 1
>> rank 0 in job 10  node-06-01_60831   caused collective abort of all
>> ranks
>>  exit status of rank 0: return code 1
>>  ./Run.cytosine:  Program error
>> make[1]: *** [test.sander.BASIC] Error 1
>> make[1]: Leaving directory 
>> `/exports/scratch/cojocavd/Software/amber10_intel_mpich2/test'
>> make: *** [test.sander.BASIC.MPI] Error 2
>>
>> -- 
>> ----------------------------------------------------------------------------
>> Dr. Vlad Cojocaru
>>
>> EML Research gGmbH
>> Schloss-Wolfsbrunnenweg 33
>> 69118 Heidelberg
>>
>> Tel: ++49-6221-533266
>> Fax: ++49-6221-533298
>>
>> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>>
>> http://projects.villa-bosch.de/mcm/people/cojocaru/
>>
>> ----------------------------------------------------------------------------
>> EML Research gGmbH
>> Amtgericht Mannheim / HRB 337446
>> Managing Partner: Dr. h.c. Klaus Tschira
>> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
>> http://www.eml-r.org
>> ----------------------------------------------------------------------------
>>
>>
>>
>> export INTELC=/exports/scratch/cojocavd/Software/intel/cce/10.1.015
>> export INTELF=/exports/scratch/cojocavd/Software/intel/fce/10.1.015
>> export LD_LIBRARY_PATH=$INTELC/lib:$INTELF/lib:$LD_LIBRARY_PATH
>> export CFLAGS="-O2 -I$INTELC/include:$INTELF/include
>> -L$LD_LIBRARY_PATH"
>> export CXXFLAGS="-O2 -I$INTELC/include:$INTELF/include
>> -L$LD_LIBRARY_PATH"
>> export FFFLAGS="-O2 -I$INTELC/include:$INTELF/include
>> -L$LD_LIBRARY_PATH"
>> export F90FLAGS="-O2 -I$INTELC/include:$INTELF/include
>> -L$LD_LIBRARY_PATH"
>> export LDFLAGS="-O2 -L$LD_LIBRARY_PATH"
>> export CPPFLAGS="-O2 -I$INTELC/include:$INTELF/include"
>> export CC="$INTELC/bin/icc"
>> export CXX="$INTELC/bin/icc"
>> export F90="$INTELF/bin/ifort"
>> export FC="$INTELF/bin/ifort"
>> export CPP="$INTELC/bin/icc -E"
>>     
>
>   

-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru

EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Tel: ++49-6221-533266
Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

----------------------------------------------------------------------------
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
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