Strange things, when I compile my code in the test dir in PETSC, it works.
After I "make install" PETSC, and try to compile my code against the installed
PETSC, it doesn't work any more.
I guess this is what you means.
Is there any way to reenable MatCreateMPIAIJMKL public interface?
And, I am using intel MKL, here is my configure option:
Configure Options: --configModules=PETSc.Configure
--optionsModule=config.compilerOptions PETSC_ARCH=linux-gnu-intel
--with-precision=single --with-cc=mpiicc --with-cxx=mpiicc --with-fc=mpiifort
--with-mpi-include=/wgdisk/hy3300/source_code_dev/imaging/kjiao/software/intel/compilers_and_libraries_2019.2.187/linux/mpi/intel64/include
--with-mpi-lib="-L/wgdisk/hy3300/source_code_dev/imaging/kjiao/software/intel//compilers_and_libraries_2019.2.187/linux/mpi/intel64/lib
-lmpifort -lmpi_ilp64"
--with-blaslapack-lib="-L/wgdisk/hy3300/source_code_dev/imaging/kjiao/software/intel/compilers_and_libraries_2019.2.187/linux/mkl/lib/intel64
-Wl, --no-as-needed -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm
-ldl"
--with-scalapack-lib="-L/wgdisk/hy3300/source_code_dev/imaging/kjiao/software/intel/compilers_and_libraries_2019.2.187/linux/mkl/lib/intel64
-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64"
--with-scalapack-include=/wgdisk/hy3300/source_code_dev/imaging/kjiao/software/intel/compilers_and_libraries_2019.2.187/linux/mkl/include
--with-mkl_pardiso-dir=/wgdisk/hy3300/source_code_dev/imaging/kjiao/software/intel/compilers_and_libraries_2019.2.187/linux/mkl
--with-mkl_sparse=1
--with-mkl_sparse-dir=/wgdisk/hy3300/source_code_dev/imaging/kjiao/software/intel/compilers_and_libraries_2019.2.187/linux/mkl
--with-mkl_cpardiso=1
--with-mkl_cpardiso-dir=/wgdisk/hy3300/source_code_dev/imaging/kjiao/software/intel/compilers_and_libraries_2019.2.187/linux/mkl
--with-mkl_sparse_optimize=1
--with-mkl_sparse_optimize-dir=/wgdisk/hy3300/source_code_dev/imaging/kjiao/software/intel/compilers_and_libraries_2019.2.187/linux/mkl
--with-mkl_sparse_sp2m=1
--with-mkl_sparse_sp2m-dir=/wgdisk/hy3300/source_code_dev/imaging/kjiao/software/intel/compilers_and_libraries_2019.2.187/linux/mkl
--with-cmake=1
--prefix=/wgdisk/hy3300/source_code_dev/imaging/kjiao/software/petsc_3.9.4
--known-endian=big --with-debugging=0 --COPTFLAGS=" -Ofast -xHost"
--CXXOPTFLAGS=" -Ofast -xHost" --FOPTFLAGS=" -Ofast -xHost" --with-x=0
Working directory: /wgdisk/hy3300/source_code_dev/imaging/kjiao/petsc-3.10.4
Schlumberger-Private
-----Original Message-----
From: Balay, Satish <ba...@mcs.anl.gov>
Sent: Tuesday, March 26, 2019 10:19 AM
To: Kun Jiao <kj...@slb.com>
Cc: Mark Adams <mfad...@lbl.gov>; petsc-users@mcs.anl.gov
Subject: Re: [petsc-users] [Ext] Re: error: identifier "MatCreateMPIAIJMKL" is
undefined in 3.10.4
>>>>>>>
balay@sb /home/balay/petsc (maint=)
$ git grep MatCreateMPIAIJMKL maint-3.8
maint-3.8:src/mat/impls/aij/mpi/aijmkl/mpiaijmkl.c: MatCreateMPIAIJMKL -
Creates a sparse parallel matrix whose local
maint-3.8:src/mat/impls/aij/mpi/aijmkl/mpiaijmkl.c:PetscErrorCode
MatCreateMPIAIJMKL(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt
N,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[],Mat
*A)
maint-3.8:src/mat/impls/aij/mpi/aijmkl/mpiaijmkl.c:.seealso:
MatCreateMPIAIJMKL(), MATSEQAIJMKL, MATMPIAIJMKL
maint-3.8:src/mat/impls/aij/seq/aijmkl/aijmkl.c:.seealso: MatCreate(),
MatCreateMPIAIJMKL(), MatSetValues() balay@sb /home/balay/petsc (maint=) $ git
grep MatCreateMPIAIJMKL maint
maint:src/mat/impls/aij/mpi/aijmkl/mpiaijmkl.c: MatCreateMPIAIJMKL - Creates
a sparse parallel matrix whose local
maint:src/mat/impls/aij/mpi/aijmkl/mpiaijmkl.c:PetscErrorCode
MatCreateMPIAIJMKL(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt
N,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[],Mat
*A)
maint:src/mat/impls/aij/mpi/aijmkl/mpiaijmkl.c:.seealso: MatCreateMPIAIJMKL(),
MATSEQAIJMKL, MATMPIAIJMKL
maint:src/mat/impls/aij/seq/aijmkl/aijmkl.c:.seealso: MatCreate(),
MatCreateMPIAIJMKL(), MatSetValues() balay@sb /home/balay/petsc (maint=) $
<<<<<<<<<<<
MatCreateMPIAIJMKL() exists in both petsc-3.8 and petsc-3.10. However the
public interface is missing from both of these versions. So I'm surprised you
don't get the same error with petsc-3.8
Can you try the following change?
diff --git a/include/petscmat.h b/include/petscmat.h index
1b8ac69377..c66f727994 100644
--- a/include/petscmat.h
+++ b/include/petscmat.h
@@ -223,7 +223,8 @@ typedef enum
{DIFFERENT_NONZERO_PATTERN,SUBSET_NONZERO_PATTERN,SAME_NONZERO_PATT
#if defined PETSC_HAVE_MKL_SPARSE
PETSC_EXTERN PetscErrorCode
MatCreateBAIJMKL(MPI_Comm,PetscInt,PetscInt,PetscInt,PetscInt,PetscInt,PetscInt,const
PetscInt[],PetscInt,const PetscInt[],Mat*); -PETSC_EXTERN PetscErrorCode
MatCreateSeqBAIJMKL(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt
nz,const PetscInt nnz[],Mat *A);
+PETSC_EXTERN PetscErrorCode
+MatCreateSeqBAIJMKL(MPI_Comm,PetscInt,PetscInt,PetscInt,PetscInt,const
+PetscInt[],Mat*); PETSC_EXTERN PetscErrorCode
+MatCreateMPIAIJMKL(MPI_Comm,PetscInt,PetscInt,PetscInt,PetscInt,PetscIn
+t,const PetscInt[],PetscInt,const PetscInt[],Mat*);
#endif
PETSC_EXTERN PetscErrorCode
MatCreateSeqSELL(MPI_Comm,PetscInt,PetscInt,PetscInt,const PetscInt[],Mat*);
Also note: - this routine is available only when PETSc is built with Intel MKL
Satish
On Tue, 26 Mar 2019, Kun Jiao via petsc-users wrote:
> [kjiao@hyi0016 src/lsqr]% make
> [ 50%] Building CXX object lsqr/CMakeFiles/p_lsqr.dir/lsqr.cc.o
> /wgdisk/hy3300/source_code_dev/imaging/kjiao/src/git/src/lsqr/lsqr.cc(318):
> error: identifier "MatCreateMPIAIJMKL" is undefined
> ierr =
> MatCreateMPIAIJMKL(comm,m,n,M,N,maxnz,dialens,maxnz,offlens,&A);CHKERRQ(ierr);
> ^
>
> /wgdisk/hy3300/source_code_dev/imaging/kjiao/src/git/src/lsqr/lsqr.cc(578):
> error: identifier "MatCreateMPIAIJMKL" is undefined
> ierr =
> MatCreateMPIAIJMKL(comm,m,n,M,N,maxnz,dialens,maxnz,offlens,&A);CHKERRQ(ierr);
> ^
>
> compilation aborted for
> /wgdisk/hy3300/source_code_dev/imaging/kjiao/src/git/src/lsqr/lsqr.cc
> (code 2)
>
> Thanks.
>
>
> From: Mark Adams <mfad...@lbl.gov>
> Sent: Tuesday, March 26, 2019 9:22 AM
> To: Kun Jiao <kj...@slb.com>
> Cc: petsc-users@mcs.anl.gov
> Subject: Re: [Ext] Re: [petsc-users] error: identifier
> "MatCreateMPIAIJMKL" is undefined in 3.10.4
>
> I assume the whole error message will have the line of code. Please send the
> whole error message and line of offending code if not included.
>
> On Tue, Mar 26, 2019 at 10:08 AM Kun Jiao
> <kj...@slb.com<mailto:kj...@slb.com>> wrote:
> It is compiling error, error message is:
>
> error: identifier "MatCreateMPIAIJMKL" is undefined.
>
>
>
>
>
> From: Mark Adams <mfad...@lbl.gov<mailto:mfad...@lbl.gov>>
> Sent: Tuesday, March 26, 2019 6:48 AM
> To: Kun Jiao <kj...@slb.com<mailto:kj...@slb.com>>
> Cc: petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>
> Subject: [Ext] Re: [petsc-users] error: identifier
> "MatCreateMPIAIJMKL" is undefined in 3.10.4
>
> Please send the output of the error (runtime, compile time, link
> time?)
>
> On Mon, Mar 25, 2019 at 10:50 PM Kun Jiao via petsc-users
> <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> wrote:
> Hi Petsc Experts,
>
> Is MatCreateMPIAIJMKL retired in 3.10.4?
>
> I got this error with my code which works fine in 3.8.3 version.
>
> Regards,
> Kun
>
>
>
> Schlumberger-Private
>
>
> Schlumberger-Private
>
>
> Schlumberger-Private
>
