May 2018 - petsc-dev - mailman3.cels.anl.gov

Segfaults on DMPlexGenerate_Triangle
by Dener, Alp 31 May '18

31 May '18

The latest master branch is segfaulting on three tao tests (two of which don’t actually use tao at all). The errors trace to DMPLex. The output is below: [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors [0]PETSC ERROR: likely location of problem given in stack below [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, [0]PETSC ERROR: INSTEAD the line number of the start of the function [0]PETSC ERROR: is given. [0]PETSC ERROR: [0] DMPlexGenerate_Triangle line 74 /Users/adener/Developer/petsc/src/dm/impls/plex/generators/triangle/trigenerate.c [0]PETSC ERROR: [0] DMPlexGenerate line 155 /Users/adener/Developer/petsc/src/dm/impls/plex/plexgenerate.c [0]PETSC ERROR: [0] DMPlexCreateBoxMesh_Simplex_Internal line 495 /Users/adener/Developer/petsc/src/dm/impls/plex/plexcreate.c [0]PETSC ERROR: [0] DMPlexCreateBoxMesh line 1022 /Users/adener/Developer/petsc/src/dm/impls/plex/plexcreate.c [0]PETSC ERROR: [0] CreateMesh line 54 /Users/adener/Developer/petsc/src/tao/examples/tutorials/ex1.c [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Signal received [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Development GIT revision: v3.9.2-548-ge8e5c7cd70 GIT Date: 2018-05-25 12:11:26 -0500 [0]PETSC ERROR: ./ex1 on a arch-darwin-c-debug named Calculon by adener Thu May 31 12:52:17 2018 [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --download-suitesparse --download-superlu --download-mumps --download-hdf5 --download-metis --download-parmetis --download-superlu_dist --download-triangle --download-netcdf --download-viennacl --download-chaco --download-ctetgen --download-exodusii --download-pnetcdf --with-fortran-interfaces=1 --download-p4est --download-pragmatic --download-eigen --download-scalapack [0]PETSC ERROR: #1 User provided function() line 0 in unknown file application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59 : system msg for write_line failure : Bad file descriptor The specific tests that are failing are: * tao_tutorial-ex1 * tao_tutorial-ex2 * tao_tutorial-ex3 These live under src/tao/examples/tutorials. Is this just a local problem for me related to my configuration, or is there something actually broken here? ________________________________ Alp Dener Postdoctoral Appointee Argonne National Laboratory Mathematics and Computer Science Division

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hang while saving non-distributed Exodus mesh
by Vaclav Hapla 24 May '18

24 May '18

Hello I wanted to load an Exodus mesh and immediately save it into HDF5 (i.e. use PETSc just for the conversion) without distributing (needed for reproducing another issue). See https://bitbucket.org/petsc/petsc/branch/haplav/fix-dmplex-immediate-exodus…. But then there's a problem with labels created by the reader (e.g. "Cell Sets"). Only rank 0 has them. This in turn leads to the HDF5 writer hanging in DMPlexWriteLabels_HDF5_Static. I think this should be fixed somehow and I will gladly do that. But my question is, what should be fixed? Should DMPlexCreateExodus produce consistent labels (I mean the number of labels and their names being the same on all ranks of the DM's communicator), or DMPlexWriteLabels_HDF5_Static cope somehow with inconsistent labels? I mean in longer term it would be nice to enforce labels being always consistent (e.g. DMSetLabelValue being collective) ... Thanks for opinions, Vaclav

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Re: [petsc-dev] Mat updating from 3.7 to 3.9.2 Fortran
by Hector E Barrios Molano 23 May '18

23 May '18

Thanks Barry, I did that, the problem was when setting values to the matrix. The matrix is set row by row, although only the first element of the vectors is given. Here is how I modified it: call MatSetValuesBlocked(mat,1,[N-1],IROW,LC(nnz:IROW),BB(nnz:IROW),INSERT_VALUES,ierr) Thanks for the help, Hector On 05/23/2018 07:15 PM, Smith, Barry F. wrote: > Use -mat_view on the new and old code to verify that the same matrix is actually being generated. > > Barry > > >> On May 23, 2018, at 6:18 PM, Hector E Barrios Molano <hectorb(a)utexas.edu> wrote: >> >> Thanks Jed for the Answer. >> >> I am still having problems with this code. In summary what I changed from PETSc 3.7 to 3.9 was: >> >> - use of PETSC_NULL_MAT to evaluate if the matrix was defined >> >> mat = PETSC_NULL_MAT >> ... >> if(mat .eq. PETSC_NULL_MAT)then >> create matrix,vectors, ksp >> else >> KSPSetInitialGuessNonzero >> VecResetArray >> end if >> >> - modified MatSetValuesBlocked call >> Previously it was: >> >> call MatSetValuesBlocked(mat,1,N-1,IROW,LC(nnz),BB(nnz),INSERT_VALUES,ierr) >> >> with N-1, LC(nnz), and BB(nnz) scalar values, the elements where inserted one at a time >> >> Modified to: >> >> call MatSetValuesBlocked(mat,1,[N-1],IROW,[LC(nnz)],[BB(nnz)],INSERT_VALUES,ierr) >> >> After the matrix is built there is a call to >> >> KSPSolve >> >> When I run the program I get a lot of these errors: >> >> [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- >> [0]PETSC ERROR: Object is in wrong state >> [0]PETSC ERROR: Matrix is missing diagonal entry 1 >> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. >> [0]PETSC ERROR: Petsc Release Version 3.9.2, unknown >> [0]PETSC ERROR: ../../../UTCOMPRS on a named bandera by hector Wed May 23 18:08:07 2018 >> [0]PETSC ERROR: Configure options --prefix=/home/hector/installed/petsc_git-intel-debug --PETSC_DIR=/home/hector/dwnld_prog/petsc --PETSC_ARCH=linux-intel-debug --CC=mpiicc --FC=mpiifort --CXX=mpiicpc --with-openmp=1 --with-valgrind=1 --with-valgrind-dir=/home/hector/installed --with-parmetis-dir=/home/hector/installed/parmetis/ --with-metis-dir=/home/hector/installed/parmetis/ --with-zoltan-dir=/home/hector/installed/zoltan/ --with-hypre-dir=/home/hector/installed/hypre --download-ptscotch --with-blaslapack-lib="[/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_intel_lp64.a,/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_core.a,/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_intel_thread.a]" --with-scalapack-include=/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/include --with-scalapack-lib="[/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a,/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a]" --with-shared-libraries=0 --FC_LINKER_FLAGS="-qopenmp -qopenmp-link static" --FFLAGS="-qopenmp -qopenmp-link static" --LIBS="-Wl,--start-group /home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_intel_lp64.a /home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_core.a /home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_intel_thread.a -Wl,--end-group -liomp5 -ldl -lpthread -lm" >> [0]PETSC ERROR: #305869 MatILUFactorSymbolic_SeqBAIJ() line 369 in /home/hector/dwnld_prog/petsc/src/mat/impls/baij/seq/baijfact2.c >> [0]PETSC ERROR: #305870 MatILUFactorSymbolic() line 6522 in /home/hector/dwnld_prog/petsc/src/mat/interface/matrix.c >> [0]PETSC ERROR: #305871 PCSetUp_ILU() line 144 in /home/hector/dwnld_prog/petsc/src/ksp/pc/impls/factor/ilu/ilu.c >> [0]PETSC ERROR: #305872 PCSetUp() line 923 in /home/hector/dwnld_prog/petsc/src/ksp/pc/interface/precon.c >> [0]PETSC ERROR: #305873 KSPSetUp() line 381 in /home/hector/dwnld_prog/petsc/src/ksp/ksp/interface/itfunc.c >> [0]PETSC ERROR: #305874 KSPSolve() line 612 in /home/hector/dwnld_prog/petsc/src/ksp/ksp/interface/itfunc.c >> >> >> What could be the problem? >> >> Thanks for your help, >> >> Hector >> >> >> >> On 05/22/2018 06:28 PM, Jed Brown wrote: >>> Hector E Barrios Molano <hectorb(a)utexas.edu> >>> writes: >>> >>> >>>> Hi PETSc Experts! >>>> >>>> I am updating a Fortran code that use PETSc 3.7 to version 3.9.2 (from >>>> git repository). >>>> >>>> Such code declares: >>>> >>>> Mat mat >>>> >>>> and used it as an integer, for example, to assign an initial value and >>>> test it to know if the matrix has been created by PETSc. >>>> >>>> data mat/-1/ >>>> if (mat .eq. -1) then >>>> >>> You can use PETSC_NULL_MAT >>> >>> >>>> With the new PETSc Fortran modules the compiler complains about this and >>>> stops. >>>> >>>> Is there a better way to achieve this? So that I do not have to set an >>>> predefined value to Mat type to test if it was already created by PETSc? >>>> >>>> If not, Is there a way to access the value in mat? >>>> Looking at the source code type(tMat) has "v" variable, so could I used >>>> as mat%v? >>>> >>> Please no. >>>

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Re: [petsc-dev] Mat updating from 3.7 to 3.9.2 Fortran
by Smith, Barry F. 23 May '18

23 May '18

Use -mat_view on the new and old code to verify that the same matrix is actually being generated. Barry > On May 23, 2018, at 6:18 PM, Hector E Barrios Molano <hectorb(a)utexas.edu> wrote: > > Thanks Jed for the Answer. > > I am still having problems with this code. In summary what I changed from PETSc 3.7 to 3.9 was: > > - use of PETSC_NULL_MAT to evaluate if the matrix was defined > > mat = PETSC_NULL_MAT > ... > if(mat .eq. PETSC_NULL_MAT)then > create matrix,vectors, ksp > else > KSPSetInitialGuessNonzero > VecResetArray > end if > > - modified MatSetValuesBlocked call > Previously it was: > > call MatSetValuesBlocked(mat,1,N-1,IROW,LC(nnz),BB(nnz),INSERT_VALUES,ierr) > > with N-1, LC(nnz), and BB(nnz) scalar values, the elements where inserted one at a time > > Modified to: > > call MatSetValuesBlocked(mat,1,[N-1],IROW,[LC(nnz)],[BB(nnz)],INSERT_VALUES,ierr) > > After the matrix is built there is a call to > > KSPSolve > > When I run the program I get a lot of these errors: > > [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > [0]PETSC ERROR: Object is in wrong state > [0]PETSC ERROR: Matrix is missing diagonal entry 1 > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. > [0]PETSC ERROR: Petsc Release Version 3.9.2, unknown > [0]PETSC ERROR: ../../../UTCOMPRS on a named bandera by hector Wed May 23 18:08:07 2018 > [0]PETSC ERROR: Configure options --prefix=/home/hector/installed/petsc_git-intel-debug --PETSC_DIR=/home/hector/dwnld_prog/petsc --PETSC_ARCH=linux-intel-debug --CC=mpiicc --FC=mpiifort --CXX=mpiicpc --with-openmp=1 --with-valgrind=1 --with-valgrind-dir=/home/hector/installed --with-parmetis-dir=/home/hector/installed/parmetis/ --with-metis-dir=/home/hector/installed/parmetis/ --with-zoltan-dir=/home/hector/installed/zoltan/ --with-hypre-dir=/home/hector/installed/hypre --download-ptscotch --with-blaslapack-lib="[/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_intel_lp64.a,/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_core.a,/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_intel_thread.a]" --with-scalapack-include=/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/include --with-scalapack-lib="[/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a,/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a]" --with-shared-libraries=0 --FC_LINKER_FLAGS="-qopenmp -qopenmp-link static" --FFLAGS="-qopenmp -qopenmp-link static" --LIBS="-Wl,--start-group /home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_intel_lp64.a /home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_core.a /home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_intel_thread.a -Wl,--end-group -liomp5 -ldl -lpthread -lm" > [0]PETSC ERROR: #305869 MatILUFactorSymbolic_SeqBAIJ() line 369 in /home/hector/dwnld_prog/petsc/src/mat/impls/baij/seq/baijfact2.c > [0]PETSC ERROR: #305870 MatILUFactorSymbolic() line 6522 in /home/hector/dwnld_prog/petsc/src/mat/interface/matrix.c > [0]PETSC ERROR: #305871 PCSetUp_ILU() line 144 in /home/hector/dwnld_prog/petsc/src/ksp/pc/impls/factor/ilu/ilu.c > [0]PETSC ERROR: #305872 PCSetUp() line 923 in /home/hector/dwnld_prog/petsc/src/ksp/pc/interface/precon.c > [0]PETSC ERROR: #305873 KSPSetUp() line 381 in /home/hector/dwnld_prog/petsc/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: #305874 KSPSolve() line 612 in /home/hector/dwnld_prog/petsc/src/ksp/ksp/interface/itfunc.c > > > What could be the problem? > > Thanks for your help, > > Hector > > > > On 05/22/2018 06:28 PM, Jed Brown wrote: >> Hector E Barrios Molano <hectorb(a)utexas.edu> >> writes: >> >> >>> Hi PETSc Experts! >>> >>> I am updating a Fortran code that use PETSc 3.7 to version 3.9.2 (from >>> git repository). >>> >>> Such code declares: >>> >>> Mat mat >>> >>> and used it as an integer, for example, to assign an initial value and >>> test it to know if the matrix has been created by PETSc. >>> >>> data mat/-1/ >>> if (mat .eq. -1) then >>> >> You can use PETSC_NULL_MAT >> >> >>> With the new PETSc Fortran modules the compiler complains about this and >>> stops. >>> >>> Is there a better way to achieve this? So that I do not have to set an >>> predefined value to Mat type to test if it was already created by PETSc? >>> >>> If not, Is there a way to access the value in mat? >>> Looking at the source code type(tMat) has "v" variable, so could I used >>> as mat%v? >>> >> Please no. >> >

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Re: [petsc-dev] Mat updating from 3.7 to 3.9.2 Fortran
by Matthew Knepley 23 May '18

23 May '18

On Wed, May 23, 2018 at 7:18 PM, Hector E Barrios Molano <hectorb(a)utexas.edu > wrote: > Thanks Jed for the Answer. > > I am still having problems with this code. In summary what I changed from > PETSc 3.7 to 3.9 was: > > - use of PETSC_NULL_MAT to evaluate if the matrix was defined > > mat = PETSC_NULL_MAT > ... > if(mat .eq. PETSC_NULL_MAT)then > create matrix,vectors, ksp > else > KSPSetInitialGuessNonzero > VecResetArray > end if > > - modified MatSetValuesBlocked call > Previously it was: > > call MatSetValuesBlocked(mat,1,N-1,IROW,LC(nnz),BB(nnz),INSERT_ > VALUES,ierr) > > with N-1, LC(nnz), and BB(nnz) scalar values, the elements where inserted > one at a time > > Modified to: > > call MatSetValuesBlocked(mat,1,[N-1],IROW,[LC(nnz)],[BB(nnz)], > INSERT_VALUES,ierr) > > After the matrix is built there is a call to > > KSPSolve > > When I run the program I get a lot of these errors: > > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Object is in wrong state > [0]PETSC ERROR: Matrix is missing diagonal entry 1 > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > [0]PETSC ERROR: Petsc Release Version 3.9.2, unknown > [0]PETSC ERROR: ../../../UTCOMPRS on a named bandera by hector Wed May 23 > 18:08:07 2018 > [0]PETSC ERROR: Configure options --prefix=/home/hector/ > installed/petsc_git-intel-debug --PETSC_DIR=/home/hector/dwnld_prog/petsc > --PETSC_ARCH=linux-intel-debug --CC=mpiicc --FC=mpiifort --CXX=mpiicpc > --with-openmp=1 --with-valgrind=1 --with-valgrind-dir=/home/hector/installed > --with-parmetis-dir=/home/hector/installed/parmetis/ > --with-metis-dir=/home/hector/installed/parmetis/ --with-zoltan-dir=/home/hector/installed/zoltan/ > --with-hypre-dir=/home/hector/installed/hypre --download-ptscotch > --with-blaslapack-lib="[/home/hector/installed/intel/ > compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/ > libmkl_intel_lp64.a,/home/hector/installed/intel/ > compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/ > libmkl_core.a,/home/hector/installed/intel/compilers_and_ > libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_intel_thread.a]" > --with-scalapack-include=/home/hector/installed/intel/ > compilers_and_libraries_2019.0.046/linux/mkl/include > --with-scalapack-lib="[/home/hector/installed/intel/ > compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/ > libmkl_scalapack_lp64.a,/home/hector/installed/intel/ > compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a]" > --with-shared-libraries=0 --FC_LINKER_FLAGS="-qopenmp -qopenmp-link static" > --FFLAGS="-qopenmp -qopenmp-link static" --LIBS="-Wl,--start-group > /home/hector/installed/intel/compilers_and_libraries_2019. > 0.046/linux/mkl/lib/intel64/libmkl_intel_lp64.a > /home/hector/installed/intel/compilers_and_libraries_2019. > 0.046/linux/mkl/lib/intel64/libmkl_core.a /home/hector/installed/intel/ > compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_intel_thread.a > -Wl,--end-group -liomp5 -ldl -lpthread -lm" > [0]PETSC ERROR: #305869 MatILUFactorSymbolic_SeqBAIJ() line 369 in > /home/hector/dwnld_prog/petsc/src/mat/impls/baij/seq/baijfact2.c > [0]PETSC ERROR: #305870 MatILUFactorSymbolic() line 6522 in > /home/hector/dwnld_prog/petsc/src/mat/interface/matrix.c > [0]PETSC ERROR: #305871 PCSetUp_ILU() line 144 in > /home/hector/dwnld_prog/petsc/src/ksp/pc/impls/factor/ilu/ilu.c > [0]PETSC ERROR: #305872 PCSetUp() line 923 in > /home/hector/dwnld_prog/petsc/src/ksp/pc/interface/precon.c > [0]PETSC ERROR: #305873 KSPSetUp() line 381 in > /home/hector/dwnld_prog/petsc/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: #305874 KSPSolve() line 612 in > /home/hector/dwnld_prog/petsc/src/ksp/ksp/interface/itfunc.c > > > What could be the problem? > For all factorizations, you must have diagonal entries, even if they are 0. Thanks, Matt > Thanks for your help, > > Hector > > > > On 05/22/2018 06:28 PM, Jed Brown wrote: > > Hector E Barrios Molano <hectorb(a)utexas.edu> <hectorb(a)utexas.edu> writes: > > > Hi PETSc Experts! > > I am updating a Fortran code that use PETSc 3.7 to version 3.9.2 (from > git repository). > > Such code declares: > > Mat mat > > and used it as an integer, for example, to assign an initial value and > test it to know if the matrix has been created by PETSc. > > data mat/-1/ > if (mat .eq. -1) then > > You can use PETSC_NULL_MAT > > > With the new PETSc Fortran modules the compiler complains about this and > stops. > > Is there a better way to achieve this? So that I do not have to set an > predefined value to Mat type to test if it was already created by PETSc? > > If not, Is there a way to access the value in mat? > Looking at the source code type(tMat) has "v" variable, so could I used > as mat%v? > > Please no. > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>

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Re: [petsc-dev] Mat updating from 3.7 to 3.9.2 Fortran
by Hector E Barrios Molano 23 May '18

23 May '18

Thanks Jed for the Answer. I am still having problems with this code. In summary what I changed from PETSc 3.7 to 3.9 was: - use of PETSC_NULL_MAT to evaluate if the matrix was defined mat = PETSC_NULL_MAT ... if(mat .eq. PETSC_NULL_MAT)then create matrix,vectors, ksp else KSPSetInitialGuessNonzero VecResetArray end if - modified MatSetValuesBlocked call Previously it was: call MatSetValuesBlocked(mat,1,N-1,IROW,LC(nnz),BB(nnz),INSERT_VALUES,ierr) with N-1, LC(nnz), and BB(nnz) scalar values, the elements where inserted one at a time Modified to: call MatSetValuesBlocked(mat,1,[N-1],IROW,[LC(nnz)],[BB(nnz)],INSERT_VALUES,ierr) After the matrix is built there is a call to KSPSolve When I run the program I get a lot of these errors: [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Object is in wrong state [0]PETSC ERROR: Matrix is missing diagonal entry 1 [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.9.2, unknown [0]PETSC ERROR: ../../../UTCOMPRS on a named bandera by hector Wed May 23 18:08:07 2018 [0]PETSC ERROR: Configure options --prefix=/home/hector/installed/petsc_git-intel-debug --PETSC_DIR=/home/hector/dwnld_prog/petsc --PETSC_ARCH=linux-intel-debug --CC=mpiicc --FC=mpiifort --CXX=mpiicpc --with-openmp=1 --with-valgrind=1 --with-valgrind-dir=/home/hector/installed --with-parmetis-dir=/home/hector/installed/parmetis/ --with-metis-dir=/home/hector/installed/parmetis/ --with-zoltan-dir=/home/hector/installed/zoltan/ --with-hypre-dir=/home/hector/installed/hypre --download-ptscotch --with-blaslapack-lib="[/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_intel_lp64.a,/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_core.a,/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_intel_thread.a]" --with-scalapack-include=/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/include --with-scalapack-lib="[/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a,/home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a]" --with-shared-libraries=0 --FC_LINKER_FLAGS="-qopenmp -qopenmp-link static" --FFLAGS="-qopenmp -qopenmp-link static" --LIBS="-Wl,--start-group /home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_intel_lp64.a /home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_core.a /home/hector/installed/intel/compilers_and_libraries_2019.0.046/linux/mkl/lib/intel64/libmkl_intel_thread.a -Wl,--end-group -liomp5 -ldl -lpthread -lm" [0]PETSC ERROR: #305869 MatILUFactorSymbolic_SeqBAIJ() line 369 in /home/hector/dwnld_prog/petsc/src/mat/impls/baij/seq/baijfact2.c [0]PETSC ERROR: #305870 MatILUFactorSymbolic() line 6522 in /home/hector/dwnld_prog/petsc/src/mat/interface/matrix.c [0]PETSC ERROR: #305871 PCSetUp_ILU() line 144 in /home/hector/dwnld_prog/petsc/src/ksp/pc/impls/factor/ilu/ilu.c [0]PETSC ERROR: #305872 PCSetUp() line 923 in /home/hector/dwnld_prog/petsc/src/ksp/pc/interface/precon.c [0]PETSC ERROR: #305873 KSPSetUp() line 381 in /home/hector/dwnld_prog/petsc/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: #305874 KSPSolve() line 612 in /home/hector/dwnld_prog/petsc/src/ksp/ksp/interface/itfunc.c What could be the problem? Thanks for your help, Hector On 05/22/2018 06:28 PM, Jed Brown wrote: > Hector E Barrios Molano <hectorb(a)utexas.edu> writes: > >> Hi PETSc Experts! >> >> I am updating a Fortran code that use PETSc 3.7 to version 3.9.2 (from >> git repository). >> >> Such code declares: >> >> Mat mat >> >> and used it as an integer, for example, to assign an initial value and >> test it to know if the matrix has been created by PETSc. >> >> data mat/-1/ >> if (mat .eq. -1) then > You can use PETSC_NULL_MAT > >> With the new PETSc Fortran modules the compiler complains about this and >> stops. >> >> Is there a better way to achieve this? So that I do not have to set an >> predefined value to Mat type to test if it was already created by PETSc? >> >> If not, Is there a way to access the value in mat? >> Looking at the source code type(tMat) has "v" variable, so could I used >> as mat%v? > Please no.

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Re: [petsc-dev] Error while compiling PETSC from git repo
by Satish Balay 23 May '18

23 May '18

you must be using an incompatible version of hypre. 'maint' branch is compatible with: [from config/BuildSystem/config/packages/hypre.py] self.gitcommit = 'v2.14.0' self.download = ['git://https://github.com/LLNL/hypre','https://github.com/LLNL/hypre/archive/'+self.gitcommit+'.tar.gz'] Satish On Wed, 23 May 2018, Hector E Barrios Molano wrote: > Hi PETSc Experts! > > I am compiling PETSc from git repository and I am getting the following error, > attached you will find make.log: > > ï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œ CC linux-intel-debug/obj/mat/impls/hypre/mhypre.o > /home/hector/dwnld_prog/petsc/src/mat/impls/hypre/mhypre.c(1453): error #55: > too many arguments in invocation of macro"hypre_TFree" > ï¿œï¿œï¿œï¿œ hypre_TFree(ptr,HYPRE_MEMORY_HOST); > ï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œ ^ > > compilation aborted for > /home/hector/dwnld_prog/petsc/src/mat/impls/hypre/mhypre.c (code 2) > gmakefile:150: recipe for target > 'linux-intel-debug/obj/mat/impls/hypre/mhypre.o' failed > make[2]: *** [linux-intel-debug/obj/mat/impls/hypre/mhypre.o] Error 2 > make[2]: *** Waiting for unfinished jobs.... > ï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œ CC linux-intel-debug/obj/mat/impls/composite/mcomposite.o > ï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œ CC linux-intel-debug/obj/mat/impls/nest/ftn-auto/matnestf.o > ï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œï¿œ CC linux-intel-debug/obj/mat/impls/nest/matnest.o > make[2]: Leaving directory '/home/hector/dwnld_prog/petsc' > /home/hector/dwnld_prog/petsc/lib/petsc/conf/rules:81: recipe for target > 'gnumake' failed > make[1]: *** [gnumake] Error 2 > make[1]: Leaving directory '/home/hector/dwnld_prog/petsc' > **************************ERROR************************************* > ï¿œ Error during compile, check linux-intel-debug/lib/petsc/conf/make.log > ï¿œ Send it and linux-intel-debug/lib/petsc/conf/configure.log to > petsc-maint(a)mcs.anl.gov > ******************************************************************** > makefile:30: recipe for target 'all' failed > > Configure.log is about 14.4 MB and in tar.gz form is 1.2MB is it ok to send it > to the mail list? > > Here is the configure command I am using: > > ./configure --prefix=/home/hector/installed/petsc_git-intel-debug > --PETSC_DIR=/home/hector/dwnld_prog/petsc --PETSC_ARCH=linux-intel-debug > --CC=mpiicc --FC=mpiifort --CXX=mpiicpc --with-openmp=1 --with-valgrind=1 > --with-valgrind-dir=/home/hector/installed > --with-parmetis-dir=/home/hector/installed/parmetis/ > --with-metis-dir=/home/hector/installed/parmetis/ > --with-zoltan-dir=/home/hector/installed/zoltan/ > --with-hypre-dir=/home/hector/installed/hypre --download-ptscotch > --with-blas-lapack-lib=\[${MKLROOT}/lib/intel64/libmkl_intel_lp64.a,${MKLROOT}/lib/intel64/libmkl_core.a,${MKLROOT}/lib/intel64/libmkl_intel_thread.a\] > --with-scalapack-include=${MKLROOT}/include > --with-scalapack-lib=\[${MKLROOT}/lib/intel64/libmkl_scalapack_lp64.a,${MKLROOT}/lib/intel64/libmkl_blacs_intelmpi_lp64.a\] > --with-shared-libraries=0 --FC_LINKER_FLAGS="-qopenmp -qopenmp-link static" > --FFLAGS="-qopenmp -qopenmp-link static" --LIBS="-Wl,--start-group > ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a > ${MKLROOT}/lib/intel64/libmkl_core.a > ${MKLROOT}/lib/intel64/libmkl_intel_thread.a -Wl,--end-group -liomp5 -ldl > -lpthread -lm" > > > What could be the problem? > > Thanks for your help! > > Hector >

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Re: [petsc-dev] Error while compiling PETSC from git repo
by Matthew Knepley 23 May '18

23 May '18

On Wed, May 23, 2018 at 5:26 PM, Hector E Barrios Molano <hectorb(a)utexas.edu > wrote: > Hi PETSc Experts! > > I am compiling PETSc from git repository and I am getting the following > error, attached you will find make.log: > The release 3.9.2 uses Hypre 2.14.0 (so does master) https://bitbucket.org/petsc/petsc/src/v3.9.2/config/BuildSystem/config/pack… This looks like a version mismatch for Hypre. Thanks, Matt > CC linux-intel-debug/obj/mat/impls/hypre/mhypre.o > /home/hector/dwnld_prog/petsc/src/mat/impls/hypre/mhypre.c(1453): error > #55: too many arguments in invocation of macro"hypre_TFree" > hypre_TFree(ptr,HYPRE_MEMORY_HOST); > ^ > > compilation aborted for /home/hector/dwnld_prog/petsc/src/mat/impls/hypre/mhypre.c > (code 2) > gmakefile:150: recipe for target 'linux-intel-debug/obj/mat/impls/hypre/mhypre.o' > failed > make[2]: *** [linux-intel-debug/obj/mat/impls/hypre/mhypre.o] Error 2 > make[2]: *** Waiting for unfinished jobs.... > CC linux-intel-debug/obj/mat/impls/composite/mcomposite.o > CC linux-intel-debug/obj/mat/impls/nest/ftn-auto/matnestf.o > CC linux-intel-debug/obj/mat/impls/nest/matnest.o > make[2]: Leaving directory '/home/hector/dwnld_prog/petsc' > /home/hector/dwnld_prog/petsc/lib/petsc/conf/rules:81: recipe for target > 'gnumake' failed > make[1]: *** [gnumake] Error 2 > make[1]: Leaving directory '/home/hector/dwnld_prog/petsc' > **************************ERROR************************************* > Error during compile, check linux-intel-debug/lib/petsc/conf/make.log > Send it and linux-intel-debug/lib/petsc/conf/configure.log to > petsc-maint(a)mcs.anl.gov > ******************************************************************** > makefile:30: recipe for target 'all' failed > > Configure.log is about 14.4 MB and in tar.gz form is 1.2MB is it ok to > send it to the mail list? > > Here is the configure command I am using: > > ./configure --prefix=/home/hector/installed/petsc_git-intel-debug > --PETSC_DIR=/home/hector/dwnld_prog/petsc --PETSC_ARCH=linux-intel-debug > --CC=mpiicc --FC=mpiifort --CXX=mpiicpc --with-openmp=1 --with-valgrind=1 > --with-valgrind-dir=/home/hector/installed --with-parmetis-dir=/home/hector/installed/parmetis/ > --with-metis-dir=/home/hector/installed/parmetis/ --with-zoltan-dir=/home/hector/installed/zoltan/ > --with-hypre-dir=/home/hector/installed/hypre --download-ptscotch > --with-blas-lapack-lib=\[${MKLROOT}/lib/intel64/libmkl_ > intel_lp64.a,${MKLROOT}/lib/intel64/libmkl_core.a,${ > MKLROOT}/lib/intel64/libmkl_intel_thread.a\] --with-scalapack-include=${MKLROOT}/include > --with-scalapack-lib=\[${MKLROOT}/lib/intel64/libmkl_ > scalapack_lp64.a,${MKLROOT}/lib/intel64/libmkl_blacs_intelmpi_lp64.a\] > --with-shared-libraries=0 --FC_LINKER_FLAGS="-qopenmp -qopenmp-link static" > --FFLAGS="-qopenmp -qopenmp-link static" --LIBS="-Wl,--start-group > ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a > ${MKLROOT}/lib/intel64/libmkl_intel_thread.a -Wl,--end-group -liomp5 -ldl > -lpthread -lm" > > > What could be the problem? > > Thanks for your help! > > Hector > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>

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Error while compiling PETSC from git repo
by Hector E Barrios Molano 23 May '18

23 May '18

Hi PETSc Experts! I am compiling PETSc from git repository and I am getting the following error, attached you will find make.log: CC linux-intel-debug/obj/mat/impls/hypre/mhypre.o /home/hector/dwnld_prog/petsc/src/mat/impls/hypre/mhypre.c(1453): error #55: too many arguments in invocation of macro"hypre_TFree" hypre_TFree(ptr,HYPRE_MEMORY_HOST); ^ compilation aborted for /home/hector/dwnld_prog/petsc/src/mat/impls/hypre/mhypre.c (code 2) gmakefile:150: recipe for target 'linux-intel-debug/obj/mat/impls/hypre/mhypre.o' failed make[2]: *** [linux-intel-debug/obj/mat/impls/hypre/mhypre.o] Error 2 make[2]: *** Waiting for unfinished jobs.... CC linux-intel-debug/obj/mat/impls/composite/mcomposite.o CC linux-intel-debug/obj/mat/impls/nest/ftn-auto/matnestf.o CC linux-intel-debug/obj/mat/impls/nest/matnest.o make[2]: Leaving directory '/home/hector/dwnld_prog/petsc' /home/hector/dwnld_prog/petsc/lib/petsc/conf/rules:81: recipe for target 'gnumake' failed make[1]: *** [gnumake] Error 2 make[1]: Leaving directory '/home/hector/dwnld_prog/petsc' **************************ERROR************************************* Error during compile, check linux-intel-debug/lib/petsc/conf/make.log Send it and linux-intel-debug/lib/petsc/conf/configure.log to petsc-maint(a)mcs.anl.gov ******************************************************************** makefile:30: recipe for target 'all' failed Configure.log is about 14.4 MB and in tar.gz form is 1.2MB is it ok to send it to the mail list? Here is the configure command I am using: ./configure --prefix=/home/hector/installed/petsc_git-intel-debug --PETSC_DIR=/home/hector/dwnld_prog/petsc --PETSC_ARCH=linux-intel-debug --CC=mpiicc --FC=mpiifort --CXX=mpiicpc --with-openmp=1 --with-valgrind=1 --with-valgrind-dir=/home/hector/installed --with-parmetis-dir=/home/hector/installed/parmetis/ --with-metis-dir=/home/hector/installed/parmetis/ --with-zoltan-dir=/home/hector/installed/zoltan/ --with-hypre-dir=/home/hector/installed/hypre --download-ptscotch --with-blas-lapack-lib=\[${MKLROOT}/lib/intel64/libmkl_intel_lp64.a,${MKLROOT}/lib/intel64/libmkl_core.a,${MKLROOT}/lib/intel64/libmkl_intel_thread.a\] --with-scalapack-include=${MKLROOT}/include --with-scalapack-lib=\[${MKLROOT}/lib/intel64/libmkl_scalapack_lp64.a,${MKLROOT}/lib/intel64/libmkl_blacs_intelmpi_lp64.a\] --with-shared-libraries=0 --FC_LINKER_FLAGS="-qopenmp -qopenmp-link static" --FFLAGS="-qopenmp -qopenmp-link static" --LIBS="-Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a -Wl,--end-group -liomp5 -ldl -lpthread -lm" What could be the problem? Thanks for your help! Hector

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23 May '18

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