[mpich-discuss] compiling MPICH2 with intel compilers

[Anthony Chan]

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"