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

Tue Mar 26 16:29:59 CDT 2019

One strange thing I just found out.

Compile a *.c file make it work.
mpiicc -o ex5.o -c -fPIC -wd1572 -Ofast -xHost -I /NFS/home/home3/kjiao/software/petsc_3.10.4/include/ -I/wgdisk/hy3300/source_code_dev/imaging/kjiao/software/intel/compilers_and_libraries_2019.2.187/linux/mkl/include -I/wgdisk/hy3300/source_code_dev/imaging/kjiao/software/intel/compilers_and_libraries_2019.2.187/linux/mpi/intel64/include lsqr.c

Compile a *.cpp file does not work, even though .cpp file is exactly same as .c file.
mpiicc -o ex5.o -c -Ofast -xHost -I /NFS/home/home3/kjiao/software/petsc_3.10.4/include/ -I/wgdisk/hy3300/source_code_dev/imaging/kjiao/software/intel/compilers_and_libraries_2019.2.187/linux/mkl/include -I/wgdisk/hy3300/source_code_dev/imaging/kjiao/software/intel/compilers_and_libraries_2019.2.187/linux/mpi/intel64/include lsqr.cpp

From: Mark Adams <mfadams at lbl.gov>
Sent: Tuesday, March 26, 2019 3:38 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



On Tue, Mar 26, 2019 at 3:00 PM Kun Jiao <KJiao at slb.com<mailto:KJiao at slb.com>> 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'm not sure I follow what you are doing exactly but look at the compile lines (good and bad) and compare them. If one works and one does not then they must be different.

Anyway, as Satish said this interface was not enabled in any version that we see. (So we are puzzled that any version works.) You can wait for a fix to get pushed but using the method that I showed you should work now.


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 <balay at mcs.anl.gov<mailto:balay at mcs.anl.gov>>
Sent: Tuesday, March 26, 2019 10:19 AM
To: Kun Jiao <KJiao at slb.com<mailto:KJiao at slb.com>>
Cc: Mark Adams <mfadams at lbl.gov<mailto:mfadams at lbl.gov>>; petsc-users at mcs.anl.gov<mailto: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,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 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.cc
> (code 2)
>
> Thanks.
>
>
> From: Mark Adams <mfadams at lbl.gov<mailto:mfadams at lbl.gov>>
> Sent: Tuesday, March 26, 2019 9:22 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: 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><mailto: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><mailto: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><mailto:KJiao at slb.com<mailto:KJiao at slb.com>>>
> Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov><mailto: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><mailto: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
>


Schlumberger-Private
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