make test

[Yixun Liu]

Hi,
I use the command,
./config/configure.py --with-cc=gcc --with-fc=gfortran --download-f-blas-lapack=1 --download-mpich=1

 and make test success.

But when I compile my Petsc-based application I got the following errors,


Linking CXX executable ../../../bin/PETScSolver
/home/scratch/yixun/petsc-3.0.0-p3/linux-gnu-c-debug/lib/libpetscvec.a(vpscat.o):
In function `VecScatterCreateCommon_PtoS':
/home/scratch/yixun/petsc-3.0.0-p3/src/vec/vec/utils/vpscat.c:1770:
undefined reference to `MPI_Type_create_indexed_block'
/home/scratch/yixun/petsc-3.0.0-p3/src/vec/vec/utils/vpscat.c:1792:
undefined reference to `MPI_Type_create_indexed_block'
collect2: ld returned 1 exit status
/usr/bin/mpiCC: No such file or directory
gmake[2]: *** [bin/PETScSolver] Error 1
gmake[1]: ***
[PersoPkgs/oclatzPkg/MeshRegister/CMakeFiles/PETScSolver.dir/all] Error 2
gmake: *** [all] Error 2



Does it mean that I need to set LD_LIBRARY_PATH to MPICH2 installation path?

Thanks.












Satish Balay wrote:
> On Sun, 5 Jul 2009, Yixun Liu wrote:
>
>   
>> I run it on my computer.
>>
>> md[/home/scratch/yixun/petsc-3.0.0-p3/src/ksp/ksp/examples/tutorials>make
>> ex2
>>
>> mpicc -o ex2.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -g3
>> -I/home/scratch/yixun/petsc-3.0.0-p3/src/dm/mesh/sieve
>> -I/home/scratch/yixun/petsc-3.0.0-p3/linux-gnu-c-debug/include
>> -I/home/scratch/yixun/petsc-3.0.0-p3/include
>> -I/usr/lib64/mpi/gcc/openmpi/include -I/usr/lib64/mpi/gcc/openmpi/lib64
>> -D__SDIR__="src/ksp/ksp/examples/tutorials/" ex2.c
>> mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -g3 -o ex2 ex2.o
>> -Wl,-rpath,/home/scratch/yixun/petsc-3.0.0-p3/linux-gnu-c-debug/lib
>> -L/home/scratch/yixun/petsc-3.0.0-p3/linux-gnu-c-debug/lib -lpetscksp
>> -lpetscdm -lpetscmat -lpetscvec -lpetsc -lX11 -llapack -lblas
>> -L/usr/lib64/mpi/gcc/openmpi/lib64
>> -L/usr/lib64/gcc/x86_64-suse-linux/4.3 -L/usr/lib64 -L/lib64
>> -L/usr/x86_64-suse-linux/lib -ldl -lmpi -lopen-rte -lopen-pal -lnsl
>> -lutil -lgcc_s -lpthread -lmpi_f90 -lmpi_f77 -lgfortranbegin -lgfortran
>> -lm -lm -L/usr/lib64/gcc/x86_64-suse-linux -L/usr/x86_64-suse-linux/bin
>> -L/lib -lm -lm -ldl -lmpi -lopen-rte -lopen-pal -lnsl -lutil -lgcc_s
>> -lpthread -ldl
>> /bin/rm -f ex2.o
>>     
>
> Did you install this OpenMPI - or did someone-else/sysadmin install it for you?
>
>   
>> md[/home/scratch/yixun/petsc-3.0.0-p3/src/ksp/ksp/examples/tutorials>mpiexec
>> -n 2 ./ex2
>>
>> DAT: library load failure: /usr/lib64/libdaplcma.so.1: undefined symbol:
>> dat_registry_add_provider
>> DAT: library load failure: /usr/lib64/libdaplcma.so.1: undefined symbol:
>> dat_registry_add_provider
>>     
>
>   
>> --------------------------------------------------------------------------
>>
>> WARNING: Failed to open "OpenIB-cma"
>> [DAT_PROVIDER_NOT_FOUND:DAT_NAME_NOT_REGISTERED].
>> This may be a real error or it may be an invalid entry in the uDAPL
>> Registry which is contained in the dat.conf file. Contact your local
>> System Administrator to confirm the availability of the interfaces in
>> the dat.conf file.
>>     
>
> Your mpiexec is trying to run on infiniban and failing?
>
>   
>> --------------------------------------------------------------------------
>> [0,1,1]: uDAPL on host md was unable to find any NICs.
>> Another transport will be used instead, although this may result in
>> lower performance.
>> --------------------------------------------------------------------------
>> Norm of error 0.000411674 iterations 7
>>     
>
> And then it attempts 'sockets' - and then successfully runs the PETSc example..
>
> So something is wrong with your mpi usage. I guess - you'll have to
> check with your sysadmin - how to correctly use infiniband..
>
> Satish
>
>