[CIG-LONG] compiling Gale on a supercomputer

[Robert Gray]

Hey Walter,
Now I'm trying to compile Gale on the supercomputer with a mumps.  I've
loaded the appropriate module, and the configuration process works fine
with:

./configure.sh --hdf5-dir=$SCINET_HDF5_BASE --cxxflags="-std=c++0x"
--linkflags="-lX11 -L/scinet/gpc/intel/mkl/lib/em64t -lmkl_lapack
-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -pthread -lm"
--cxx=mpicxx

but the compilation process fails with a load of warnings:

icpc: warning #10315: specifying -lm before files may supercede the
Intel(R) math library and affect performance
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/linux-gnu-c-opt/lib/libpetsc.a(mumps.c.o):
In function `MatDestroy_MUMPS':
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/mat/impls/aij/mpi/mumps/mumps.c:(.text+0x1ef9):
undefined reference to `dmumps_c'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/linux-gnu-c-opt/lib/libpetsc.a(mumps.c.o):
In function `MatSolve_MUMPS':
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/mat/impls/aij/mpi/mumps/mumps.c:(.text+0x22ca):
undefined reference to `dmumps_c'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/linux-gnu-c-opt/lib/libpetsc.a(mumps.c.o):
In function `MatSolveTranspose_MUMPS':
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/mat/impls/aij/mpi/mumps/mumps.c:(.text+0x2919):
undefined reference to `dmumps_c'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/linux-gnu-c-opt/lib/libpetsc.a(mumps.c.o):
In function `MatFactorNumeric_MUMPS':
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/mat/impls/aij/mpi/mumps/mumps.c:(.text+0x316c):
undefined reference to `dmumps_c'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/linux-gnu-c-opt/lib/libpetsc.a(mumps.c.o):
In function `MatLUFactorSymbolic_AIJMUMPS':
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/mat/impls/aij/mpi/mumps/mumps.c:(.text+0x4b9a):
undefined reference to `dmumps_c'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/linux-gnu-c-opt/lib/libpetsc.a(mumps.c.o):/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/mat/impls/aij/mpi/mumps/mumps.c:(.text+0x61ce):
more undefined references to `dmumps_c' follow
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/linux-gnu-c-opt/lib/libpetsc.a(ml.c.o):
In function `MatMult_ML':
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0xbc7):
undefined reference to `ML_Operator_Apply'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/linux-gnu-c-opt/lib/libpetsc.a(ml.c.o):
In function `MatMultAdd_ML':
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0xf1c):
undefined reference to `ML_Operator_Apply'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x102c):
undefined reference to `ML_Operator_Apply'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/linux-gnu-c-opt/lib/libpetsc.a(ml.c.o):
In function `PCReset_ML':
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x17c1):
undefined reference to `ML_Aggregate_Destroy'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x17c9):
undefined reference to `ML_Destroy'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/linux-gnu-c-opt/lib/libpetsc.a(ml.c.o):
In function `PCSetUp_ML':
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x1e78):
undefined reference to `ML_Init_Amatrix'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x1e89):
undefined reference to `ML_Set_Amatrix_Matvec'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x1ed9):
undefined reference to `ML_Operator_Clean'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x1eed):
undefined reference to `ML_Operator_Init'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x1efc):
undefined reference to `ML_Gen_AmatrixRAP'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x2013):
undefined reference to `ML_Aggregate_Destroy'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x201b):
undefined reference to `ML_Destroy'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x2535):
undefined reference to `ML_Create'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x254a):
undefined reference to `ML_Comm_Set_UsrComm'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x256a):
undefined reference to `ML_Init_Amatrix'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x2585):
undefined reference to `ML_Set_Amatrix_Getrow'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x2596):
undefined reference to `ML_Set_Amatrix_Matvec'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x25ae):
undefined reference to `ML_Set_Symmetrize'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x25b8):
undefined reference to `ML_Aggregate_Create'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x25d6):
undefined reference to `ML_Aggregate_Set_NullSpace'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x25e4):
undefined reference to `ML_Aggregate_Set_MaxCoarseSize'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x25fc):
undefined reference to `ML_Aggregate_Set_CoarsenScheme_MIS'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x260d):
undefined reference to `ML_Aggregate_Set_CoarsenScheme_METIS'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x2619):
undefined reference to `ML_Aggregate_Set_CoarsenScheme_Coupled'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x2629):
undefined reference to `ML_Aggregate_Set_Threshold'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x2639):
undefined reference to `ML_Aggregate_Set_DampingFactor'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x264a):
undefined reference to `ML_Set_SpectralNormScheme_Anorm'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x26c4):
undefined reference to `ML_Gen_MGHierarchy_UsingAggregation'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x26dc):
undefined reference to `ML_Gen_MultiLevelHierarchy_UsingAggregation'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/linux-gnu-c-opt/lib/libpetsc.a(ml.c.o):
In function `MatWrapML_MPIAIJ':
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x523f):
undefined reference to `ML_build_global_numbering'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x531c):
undefined reference to `ml_void_mem_ptr'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/linux-gnu-c-opt/lib/libpetsc.a(ml.c.o):
In function `PCDestroy_ML':
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x5b42):
undefined reference to `ML_Aggregate_Destroy'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x5b4a):
undefined reference to `ML_Destroy'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/linux-gnu-c-opt/lib/libpetsc.a(ml.c.o):
In function `PCSetFromOptions_ML':
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/ksp/pc/impls/ml/ml.c:(.text+0x619a):
undefined reference to `ML_Set_PrintLevel'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/linux-gnu-c-opt/lib/libpetsc.a(pmetis.c.o):
In function `MatPartitioningApply_Parmetis':
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/mat/partition/impls/pmetis/pmetis.c:(.text+0x33b):
undefined reference to `ParMETIS_V3_PartKway'
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/linux-gnu-c-opt/lib/libpetsc.a(pmetis.c.o):
In function `MatMeshToCellGraph':
/scinet/gpc/Libraries/petsc-3.2-p2-openmpi-mumps/src/mat/partition/impls/pmetis/pmetis.c:(.text+0x10c3):
undefined reference to `ParMETIS_V3_Mesh2Dual'
scons: *** [build/bin/Gale] Error 1
scons: building terminated because of errors.

Any advice is greatly appreciated.
Cheers,
Rob



On Thu, May 24, 2012 at 6:15 PM, Robert Gray <graywacke at gmail.com> wrote:

> Alright, the yielding.json model works!
> Thanks for your tireless help with this Walter.
> Cheers,
> Rob
>
>
> On Thu, May 24, 2012 at 4:51 PM, Walter Landry <wlandry at caltech.edu>wrote:
>
>> Robert Gray <graywacke at gmail.com> wrote:
>> > Hey Walter,
>> > Success with the compilation process!  Thank you.  However, when I try
>> to
>> > run the yielding.json model it crashes immediately with the error
>> message:
>> >
>> > ./Gale: error while loading shared libraries: libmkl_lapack.so: cannot
>> open
>> > shared object file: No such file or directory
>>
>> Normally, loading the module should set the appropriate variables so
>> that you do not get this error.  In any case, if you set
>>
>>  export LD_LIBRARY_PATH=/scinet/gpc/intel/mkl/lib/em64t:$LD_LIBRARY_PATH
>>
>> it should fix this error.
>>
>> Cheers,
>> Walter Landry
>>
>>
>
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