[petsc-users] configuration option for PETSc on cluster

[Satish Balay]

BTW: In this case configure succeed - but your example compile command failed.

Configure is using:

BLAS/LAPACK: -Wl,-rpath,/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -L/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -lmkl_blas95_lp64 -Wl,-rpath,/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -L/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -lmkl_lapack95_lp64 -Wl,--start-group -Wl,-rpath,/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -L/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -lmkl_intel_lp64 -Wl,-rpath,/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -L/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -lmkl_sequential -Wl,-rpath,/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -L/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -lmkl_core -Wl,--end-group -lpthread -lm -ldl

however your link command has:

ftn -O   -o ex5f ex5f.o -L/users/lanthale/petsc-git/arch-complex/lib -Wl,-rpath,/users/lanthale/petsc-git/arch-complex/lib -Wl,-rpath,/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -L/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -Wl,--start-group -Wl,--end-group -lpetsc -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lsuperlu -lmkl_blas95_lp64 -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl -lstdc++ -ldl

This does not match configure detected list.

PETSC_WITH_EXTERNAL_LIB = -L/users/lanthale/petsc-git/arch-complex/lib -Wl,-rpath,/users/lanthale/petsc-git/arch-complex/lib -Wl,-rpath,/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -L/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -Wl,--start-group -Wl,--end-group -lpetsc -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lsuperlu -lmkl_blas95_lp64 -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl -lstdc++ -ldl

Ok - this formatting got changed [a potential bug in petsc configure] - and perhaps the reason for this failure.


 If you still have this build - you could manually edit
arch-complex/lib/petsc/conf/petscvariables and change the above to the
following and see if it makes a difference

PETSC_WITH_EXTERNAL_LIB = -L/users/lanthale/petsc-git/arch-complex/lib -Wl,-rpath,/users/lanthale/petsc-git/arch-complex/lib -Wl,-rpath,/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -L/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -lpetsc -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lsuperlu -lmkl_blas95_lp64 -lmkl_lapack95_lp64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread -lm -ldl -lstdc++ -ldl

Satish

On Tue, 24 Apr 2018, Samuel Lanthaler wrote:

> Hi there,
> 
> I was wondering if you could help me with the correct configuration of
> PETSc-dev version on a cluster (https://www.cscs.ch/)? I'm not sure which
> information would be useful to you, but basically the problem seems to be in
> correctly compiling it with intel compiler and the existing mkl library.
> 
> The pre-installed mkl version is
> 
> intel/17.0.4.196
> 
> I have tried various things and finally, I got it at least to compile with the
> following options (options chosen in reference to the mkl link advisor...):
> 
> ./configure --with-fc=ftn --with-cc=cc --with-cxx=CC --with-debugging=0
> --with-scalar-type=complex --download-scalapack --download-mumps=yes
> --download-superlu --with-batch --known-mpi-shared-libraries=1
> *--with-blaslapack-lib=*" ${MKLROOT}/lib/intel64/libmkl_blas95_lp64.a
> ${MKLROOT}/lib/intel64/libmkl_lapack95_lp64.a -Wl,--start-group
> ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a
> ${MKLROOT}/lib/intel64/libmkl_sequential.a
> ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl"
> *--with-blaslapack-include*="[/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/include,/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/include/intel64/lp64]"
> --known-64-bit-blas-indices=0
> 
> After compilation, when trying to compile
> /users/lanthale/petsc-git/src/snes/examples/tutorials/ex5f I get linking
> errors (attached). Would anyone be able to help me out here? I really don't
> have a good understanding of this.
> 
> I'm attaching the configuration.log file, as well as the linking errors when
> trying to compile ex5f.
> 
> Thank you very much in advance!
> 
> Best regards,
> Samuel
>