[petsc-users] [Ext] Re: error: identifier "MatCreateMPIAIJMKL" is undefined in 3.10.4

Kun Jiao KJiao at slb.com
Tue Mar 26 16:37:59 CDT 2019 

And yes, by applying the patch in the petscmat.h, everything works.
Thanks for the help.

Regards,
Kun



Schlumberger-Private

-----Original Message-----
From: Balay, Satish <balay at mcs.anl.gov> 
Sent: Tuesday, March 26, 2019 3:42 PM
To: Kun Jiao <KJiao at slb.com>
Cc: petsc-users <petsc-users at mcs.anl.gov>
Subject: Re: [petsc-users] [Ext] Re: error: identifier "MatCreateMPIAIJMKL" is undefined in 3.10.4

Please apply the patch I sent earlier and retry.

Satish

On Tue, 26 Mar 2019, Kun Jiao via petsc-users wrote:

> 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/softwa
> re/intel/compilers_and_libraries_2019.2.187/linux/mpi/intel64/include 
> --with-mpi-lib="-L/wgdisk/hy3300/source_code_dev/imaging/kjiao/softwar
> e/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/intel6
> 4 -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/s
> oftware/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/so
> ftware/intel/compilers_and_libraries_2019.2.187/linux/mkl 
> --with-mkl_sparse=1 
> --with-mkl_sparse-dir=/wgdisk/hy3300/source_code_dev/imaging/kjiao/sof
> tware/intel/compilers_and_libraries_2019.2.187/linux/mkl 
> --with-mkl_cpardiso=1 
> --with-mkl_cpardiso-dir=/wgdisk/hy3300/source_code_dev/imaging/kjiao/s
> oftware/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/kjia
> o/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 <balay at mcs.anl.gov>
> Sent: Tuesday, March 26, 2019 10:19 AM
> To: Kun Jiao <KJiao at slb.com>
> Cc: Mark Adams <mfadams at lbl.gov>; petsc-users at mcs.anl.gov
> Subject: Re: [petsc-users] [Ext] Re: error: identifier 
> "MatCreateMPIAIJMKL" is undefined in 3.10.4
> 
> >>>>>>>
> balay at 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 at 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 at 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,cons
> +t PetscInt[],Mat*); PETSC_EXTERN PetscErrorCode 
> +MatCreateMPIAIJMKL(MPI_Comm,PetscInt,PetscInt,PetscInt,PetscInt,Petsc
> +In 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 at 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.c
> > c
> > (code 2)
> > 
> > Thanks.
> > 
> > 
> > From: Mark Adams <mfadams at lbl.gov>
> > Sent: Tuesday, March 26, 2019 9:22 AM
> > To: Kun Jiao <KJiao at slb.com>
> > Cc: petsc-users at 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 <KJiao at slb.com<mailto:KJiao at slb.com>> wrote:
> > It is compiling error, error message is:
> > 
> > error: identifier "MatCreateMPIAIJMKL" is undefined.
> > 
> > 
> > 
> > 
> > 
> > From: Mark Adams <mfadams at lbl.gov<mailto:mfadams at lbl.gov>>
> > Sent: Tuesday, March 26, 2019 6:48 AM
> > To: Kun Jiao <KJiao at slb.com<mailto:KJiao at slb.com>>
> > Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at 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 at mcs.anl.gov<mailto:petsc-users at 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
> > 
>

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