[petsc-users] [Ext] Re: error: identifier "MatCreateMPIAIJMKL" is undefined in 3.10.4
Kun Jiao
KJiao at slb.com
Tue Mar 26 20:15:04 CDT 2019
Hi Richard,
Understood! Thanks very much for you advice.
Regards,
Kun
Schlumberger-Private
From: Mills, Richard Tran <rtmills at anl.gov>
Sent: Tuesday, March 26, 2019 8:11 PM
To: petsc-users at mcs.anl.gov
Cc: Kun Jiao <KJiao at slb.com>
Subject: Re: [petsc-users] [Ext] Re: error: identifier "MatCreateMPIAIJMKL" is undefined in 3.10.4
Hi Kun,
I'm the author of most of the AIJMKL stuff in PETSc. My apologies for having inadvertently omitted these function prototypes for these interfaces; I'm glad that Satish's patch has fixed this.
I want to point out that -- though I can envision some scenarios in which one would want to use the MatCreateXXXAIJMKL interfaces -- most of the time I would recommend against using these directly. Instead, I would recommend simply creating AIJ matrices and then setting them to the AIJMKL sub-types via the PETSc options database. (Via the command line, this could be done by specifying something like "-mat_seqaij_type seqaijmkl" to indicate that all of the "sequential" AIJ matrices that make up an "MPI" AIJ matrix should be of type SEQAIJMKL.) Because this is how I usually do things, my testing had not uncovered the missing function prototypes.
Best regards,
Richard
On 3/26/19 2:37 PM, Kun Jiao via petsc-users wrote:
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><mailto:balay at mcs.anl.gov>
Sent: Tuesday, March 26, 2019 3:42 PM
To: Kun Jiao <KJiao at slb.com><mailto:KJiao at slb.com>
Cc: petsc-users <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
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><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,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><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
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