[petsc-users] Compiling PETSc 3.1-p3, gcc-4.4.4

Fri Jul 9 10:41:06 CDT 2010

1) With any error report you MUST send configure.log, or we know nothing
about your build. Send
    it to petsc-maint at mcs.anl.gov

2) Where are the error lines from UMFPack coming from? Not from the PETSc
build.

3) I have no idea why Dolfin segfaults. YOu should mail the Dolfin list

    Matt

On Fri, Jul 9, 2010 at 4:57 PM, Frantisek Fridrich <frafridr at gmail.com>wrote:

> Hello.
>
> Please could anybody help me?
>
> I compiled PETSc 3.1-p3 in Scientific Linux 5, gcc-4.4.4 with options:
> =========================================================== beg
>  --prefix=${P_petsc_INSTALL} \
>  --with-external-packages-dir=${P_extpckg_INSTALL} \
>  --PETSC_ARCH=${PETSC_ARCH} \
>  --PETSC_DIR=${PETSC_DIR} \
>  --with-clanguage=c++ \
>  --with-c-support=yes \
>  --with-shared=yes \
>  --with-large-file-io=yes \
>  --CFLAGS=${CFLAGS} \
>  --CXXFLAGS=${CXXFLAGS} \
>  --FFLAGS=${FCFLAGS} \
>  --with-ar=ar \
>  --AR_FLAGS=cr \
>  --with-ranlib=ranlib \
>  --COPTFLAGS=${COPTFLAGS} \
>  --CXXOPTFLAGS=${CXXOPTFLAGS} \
>  --FOPTFLAGS=${FOPTFLAGS} \
>  --with-mpi-dir=${P_MPI_INSTALL} \
>  --with-mpi-shared=yes \
>  --with-spooles=yes \
>  --download-spooles=yes \
>  --with-blas-lapack-dir=${ATLAS} \
>  --with-blacs=yes \
>  --download-blacs=yes \
>  --with-parmetis=yes \
>  --with-parmetis-dir=${P_parmetis_INSTALL} \
>  --with-scalapack=yes \
>  --download-scalapack=yes \
>  --with-mumps=yes \
>  --download-mumps=yes \
>  --with-hypre=yes \
>  --with-hypre-dir=${P_hypre_INSTALL} \
>  --with-umfpack=yes \
>  --download-umfpack=yes \
> =========================================================== end
>
> I got 1600 lines of the following warnings:
> =========================================================== beg
> ../Source/umf_analyze.c: In function ‘umf_i_analyze’:
> ../Source/umf_analyze.c:94: warning: ignoring #pragma ivdep
> ../Source/umf_analyze.c:581: warning: ignoring #pragma novector
> ../Source/umf_analyze.c: In function ‘umf_l_analyze’:
> ../Source/umf_analyze.c:94: warning: ignoring #pragma ivdep
>
>
> ../Source/umf_blas3_update.c: In function ‘umfdi_blas3_update’:
> ../Source/umf_blas3_update.c:81: warning: ignoring #pragma ivdep
> ../Source/umf_blas3_update.c:100: warning: passing argument 1 of
> ‘dtrsm_’ discards qualifiers from pointer target type
> ../Source/cholmod_blas.h:243: note: expected ‘char *’ but argument is
> of type ‘const char *’
> ../Source/umf_blas3_update.c:100: warning: passing argument 2 of
> ‘dtrsm_’ discards qualifiers from pointer target type
> ../Source/cholmod_blas.h:243: note: expected ‘char *’ but argument is
> of type ‘const char *’
>
>
> ../Source/umfpack_report_info.c: In function ‘umfpack_di_report_info’:
> ../Source/umfpack_report_info.c:403: warning: passing argument 1 of
> ‘print_ratio’ discards qualifiers from pointer target type
> ../Source/umfpack_report_info.c:33: note: expected ‘char *’ but
> argument is of type ‘const char *’
> ../Source/umfpack_report_info.c:403: warning: passing argument 2 of
> ‘print_ratio’ discards qualifiers from pointer target type
> ../Source/umfpack_report_info.c:33: note: expected ‘char *’ but
> argument is of type ‘const char *’
> ../Source/umfpack_report_info.c:405: warning: passing argument 1 of
> ‘print_ratio’ discards qualifiers from pointer target type
> ../Source/umfpack_report_info.c:33: note: expected ‘char *’ but
> argument is of type ‘const char *’
>
>
> ../Source/umf_blas3_update.c:152: warning: ignoring #pragma ivdep
> ../Source/umf_create_element.c: In function ‘copy_column’:
> ../Source/umf_create_element.c:31: warning: ignoring #pragma ivdep
> ../Source/umf_create_element.c: In function ‘umfdl_create_element’:
>
> ../Source/umfpack_report_info.c:403: warning: passing argument 1 of
> ‘print_ratio’ discards qualifiers from pointer target type
> ../Source/umfpack_report_info.c:33: note: expected ‘char *’ but
> argument is of type ‘const char *’
> ../Source/umfpack_report_info.c:403: warning: passing argument 2 of
> ‘print_ratio’ discards qualifiers from pointer target type
> ../Source/umfpack_report_info.c:33: note: expected ‘char *’ but
> argument is of type ‘const char *’
> ../Source/umfpack_report_info.c:405: warning: passing argument 1 of
> ‘print_ratio’ discards qualifiers from pointer target type
> ../Source/umfpack_report_info.c:33: note: expected ‘char *’ but
> argument is of type ‘const char *’
>
> umfpack_zl_demo.c:547: warning: format ‘%ld’ expects type ‘long int’,
> but argument 2 has type ‘long long int’
> umfpack_zl_demo.c:547: warning: format ‘%ld’ expects type ‘long int’,
> but argument 3 has type ‘long long int’
>
> umfpack_zl_demo.c:719: warning: passing argument 1 of ‘error’ discards
> qualifiers from pointer target type
> umfpack_zl_demo.c:75: note: expected ‘char *’ but argument is of type
> ‘const char *’
> umfpack_zl_demo.c:728: warning: passing argument 1 of ‘error’ discards
> qualifiers from pointer target type
> umfpack_zl_demo.c:75: note: expected ‘char *’ but argument is of type
> ‘const char *’
> make[1]: [run] Error 1 (ignored)
> make[1]: [run] Error 1 (ignored)
> make[1]: [run] Error 1 (ignored)
> make[1]: [run] Error 1 (ignored)
> ********End of Output of running make on UMFPACK *******
> =========================================================== end
>
> When running DOLFIN 0.9.8 demos I got error:
> =========================================================== beg
>    Newton iteration 8: r (abs) = 1.509e-14 (tol = 1.000e-10) r (rel)
> = 3.674e-15 (tol = 1.000e-09)
>    Newton solver finished in 8 iterations and 8 linear solver iterations.
> Plot active, press 'q' to continue.
> [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/petsc-as/documentation/troubleshooting.html#Signal[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: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 3, Fri Jun  4
> 15:34:52 CDT 2010
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Unknown Name on a linux-gnu named juniper by fridrich
> Fri Jul  9 11:27:30 2010
> [0]PETSC ERROR: Libraries linked from
> /home/rose/OpenMPI/openmpi-1.4.2/utils/petsc-3.1-p3/lib
> [0]PETSC ERROR: Configure run at Thu Jul  8 19:49:50 2010
> [0]PETSC ERROR: Configure options
> --prefix=/home/rose/OpenMPI/openmpi-1.4.2/utils/petsc-3.1-p3
>
> --with-external-packages-dir=/home/rose/OpenMPI/openmpi-1.4.2/utilsRepo/petsc-3.1-p3/petscUtilsRepo
> --PETSC_ARCH=linux-gnu
>
> --PETSC_DIR=/home/rose/OpenMPI/openmpi-1.4.2/utilsRepo/petsc-3.1-p3/petsc-3.1-p3
> --with-clanguage=c++ --with-c-support=yes --with-shared=yes
> --with-large-file-io=yes --CFLAGS= -Wall -march=opteron -m64 -O2
> -fno-reorder-blocks -fno-reorder-functions -pipe -fPIC --CXXFLAGS=
> -Wall -march=opteron -m64 -O2 -fno-reorder-blocks
> -fno-reorder-functions -pipe -fPIC --FFLAGS= -Wall -march=opteron -m64
> -O2 -fno-reorder-blocks -fno-reorder-functions -pipe -fPIC
> --with-ar=ar --AR_FLAGS=cr --with-ranlib=ranlib --COPTFLAGS= -O2
> -fno-reorder-blocks -fno-reorder-functions --CXXOPTFLAGS= -O2
> -fno-reorder-blocks -fno-reorder-functions --FOPTFLAGS= -O2
> -fno-reorder-blocks -fno-reorder-functions
> --with-mpi-dir=/home/rose/OpenMPI/openmpi-1.4.2/install
> --with-mpi-shared=yes --with-spooles=yes --download-spooles=yes
>
> --with-blas-lapack-dir=/home/rose/OpenMPI/openmpi-1.4.2/utils/atlas-3.9.24/lib
> --with-blacs=yes --download-blacs=yes --with-parmetis=yes
> --with-parmetis-dir=/home/rose/OpenMPI/openmpi-1.4.2/utils/ParMetis-3.1.1
> --with-scalapack=yes --download-scalapack=yes --with-mumps=yes
> --download-mumps=yes --with-hypre=yes
> --with-hypre-dir=/home/rose/OpenMPI/openmpi-1.4.2/utils/hypre-2.6.0b
> --with-umfpack=yes --download-umfpack=yes
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> --------------------------------------------------------------------------
> =========================================================== end
>
> Thank you for response.
> Frantisek
>

-- 
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
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