November 2011 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] How to configure parallel petsc on windows?
by John R. Cary 21 Nov '11

21 Nov '11

On 11/20/2011 9:45 PM, Satish Balay wrote: > On Sun, 20 Nov 2011, John R. Cary wrote: > >> On 11/20/2011 11:09 AM, Satish Balay wrote: >>> On Sun, 20 Nov 2011, Satish Balay wrote: >>> >>>> Executing: mingw32-gfortran -o conftest.exe -Wall -Wno-unused-variable >>>> -O -I/winsame/contrib-mingw/microsoft-hpc-mingw/Include conftest.o >>>> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib >>>> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib >>>> -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/lib/gcc/mingw32/4.6.1 >>>> -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/lib/gcc >>>> -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/mingw32/lib >>>> -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/lib >>>> -L/mingw/lib -lmingw32 -lgcc_eh -lmoldname -lmingwex -lmsvcrt -ladvapi32 >>>> -lshell32 -luser32 >>>> sh: >>>> Possible ERROR while running linker: Warning: .drectve >>>> `/DEFAULTLIB:"uuid.lib" /DEFAULTLIB:"uuid.lib" ' unrecognized >>>> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_recv_]+0x1f): >>>> undefined reference to `_imp__MPI_F_STATUS_IGNORE' >>>> ... (repetitions of the last line) >>>> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpirinitc]+0x25): >>>> undefined reference to `_imp__MPI_F_STATUSES_IGNORE' >>>> collect2: ld returned 1 exit status >>>> >>>> >>>> Source: >>>> program main >>>> include 'mpif.h' >>>> integer ierr >>>> call mpi_init(ierr) >>>> end >>>> >>>> <<<<<<<<<<<<< >>>> >>>> Perhaps msmpi libs are using some internal notation that >>>> mingw-gfortran is unable to interpret? The unresolved symbols are >>>> coming from >>>> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib and I >>>> think should be resolved by either >>>> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib or >>>> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib >>>> >>>> I would check with: >>>> >>>> nm -Ao /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib >>>> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib |grep >>>> _imp__MPI_F_STATUS_IGNORE >>> Should also try to compile that simple mpi fortran code snippet >>> directly with mingw32-gfortran - and see if that works. >>> >>> mingw32-gfortran conftest.f -o conftest.exe >>> -I/winsame/contrib-mingw/microsoft-hpc-mingw/Include >>> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib >>> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib >> So I confirm what you found. I also found >> >> http://social.microsoft.com/Forums/is/windowshpcmpi/thread/fa213e91-5b83-41… >> >> which indicates this is a known problem. The basic symbol is in msmpi.lib: >> >> xena.cary$ link /dump /exports msmpi.lib | grep -i mpi_f_st >> _MPI_F_STATUSES_IGNORE >> _MPI_F_STATUS_IGNORE >> >> But not the symbol desired by msmpifec.lib: >> >> xena.cary$ nm msmpifec.lib | grep -i mpi_f_st >> U __imp__MPI_F_STATUSES_IGNORE >> U __imp__MPI_F_STATUS_IGNORE >> >> So seems not to be mingw but just a fact of the msmpi package. > Hm - but I guess this error doesn't show up with ifort. > > So my initial guess about 'extra notation/metadata' in the lib file > that nm/gnu-ld sounds more feasible. [and gnu tools nm, gnu-ld are > unable to parse this stuff. However MS's linker might be resolving > this stuff correctly] > > Perhaps 'dumpbin /symbols foo.lib' shows what MS linker is looking at. xena.cary$ dumpbin.exe /symbols C:"\winsame\contrib-mingw\microsoft-hpc-mingw\Lib\i386\msmpifec.lib" | grep F_STATUS_IGNORE 01B 00000000 UNDEF notype External | __imp__MPI_F_STATUS_IGNORE > Either way - looks like msmpi is unuseable from mingw-gfortran. Agreed. Seems that ifort and MS-Link can resolve what gfortran cannot. I have a summary on these issues that I will send to the list. John

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Re: [petsc-dev] Parmetis / Metis changes
by Sean Farley 21 Nov '11

21 Nov '11

> > > Can you pass it in through the CFLAGS environment variable as is? (Ugly, > but I think CMake claims to respect that variable.) > > This appears to work. I have pushed a change to metis.py to do this define > the Mac. We should eventually have BuildSystem check for __thread but I'm > too lazy to do that today. This doesn't work on cray, it seems. I went ahead and reverted Barry's change while adding support for "cflags=blah."

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Re: [petsc-dev] How to configure parallel petsc on windows?
by Satish Balay 20 Nov '11

20 Nov '11

On Sun, 20 Nov 2011, John R. Cary wrote: > On 11/20/2011 11:09 AM, Satish Balay wrote: > > On Sun, 20 Nov 2011, Satish Balay wrote: > > > > > > > > > > > > > > > > > > > > > . > > > Executing: mingw32-gfortran -o conftest.exe -Wall -Wno-unused-variable > > > -O -I/winsame/contrib-mingw/microsoft-hpc-mingw/Include conftest.o > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib > > > -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/lib/gcc/mingw32/4.6.1 > > > -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/lib/gcc > > > -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/mingw32/lib > > > -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/lib > > > -L/mingw/lib -lmingw32 -lgcc_eh -lmoldname -lmingwex -lmsvcrt -ladvapi32 > > > -lshell32 -luser32 > > > sh: > > > Possible ERROR while running linker: Warning: .drectve > > > `/DEFAULTLIB:"uuid.lib" /DEFAULTLIB:"uuid.lib" ' unrecognized > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_recv_]+0x1f): > > > undefined reference to `_imp__MPI_F_STATUS_IGNORE' > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_wait_]+0x1f): > > > undefined reference to `_imp__MPI_F_STATUS_IGNORE' > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_test_]+0x20): > > > undefined reference to `_imp__MPI_F_STATUS_IGNORE' > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_waitany_]+0x20): > > > undefined reference to `_imp__MPI_F_STATUS_IGNORE' > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_testany_]+0x21): > > > undefined reference to `_imp__MPI_F_STATUS_IGNORE' > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_waitall_]+0x1f): > > > undefined reference to `_imp__MPI_F_STATUSES_IGNORE' > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_testall_]+0x20): > > > undefined reference to `_imp__MPI_F_STATUSES_IGNORE' > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_waitsome_]+0x1f): > > > undefined reference to `_imp__MPI_F_STATUSES_IGNORE' > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_testsome_]+0x1f): > > > undefined reference to `_imp__MPI_F_STATUSES_IGNORE' > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_iprobe_]+0x20): > > > undefined reference to `_imp__MPI_F_STATUS_IGNORE' > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_probe_]+0x1f): > > > undefined reference to `_imp__MPI_F_STATUS_IGNORE' > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_sendrecv_]+0x1f): > > > undefined reference to `_imp__MPI_F_STATUS_IGNORE' > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_sendrecv_replace_]+0x1f): > > > undefined reference to `_imp__MPI_F_STATUS_IGNORE' > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpirinitc]+0xa): > > > undefined reference to `_imp__MPI_F_STATUS_IGNORE' > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpirinitc]+0x25): > > > undefined reference to `_imp__MPI_F_STATUSES_IGNORE' > > > collect2: ld returned 1 exit status > > > > > > > > > Source: > > > program main > > > include 'mpif.h' > > > integer ierr > > > call mpi_init(ierr) > > > end > > > > > > <<<<<<<<<<<<< > > > > > > Perhaps msmpi libs are using some internal notation that > > > mingw-gfortran is unable to interpret? The unresolved symbols are > > > coming from > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib and I > > > think should be resolved by either > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib or > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib > > > > > > I would check with: > > > > > > nm -Ao /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib > > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib |grep > > > _imp__MPI_F_STATUS_IGNORE > > > > Should also try to compile that simple mpi fortran code snippet > > directly with mingw32-gfortran - and see if that works. > > > > mingw32-gfortran conftest.f -o conftest.exe > > -I/winsame/contrib-mingw/microsoft-hpc-mingw/Include > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib > > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib > > > > > > So I confirm what you found. I also found > > http://social.microsoft.com/Forums/is/windowshpcmpi/thread/fa213e91-5b83-41… > > which indicates this is a known problem. The basic symbol is in msmpi.lib: > > xena.cary$ link /dump /exports msmpi.lib | grep -i mpi_f_st > _MPI_F_STATUSES_IGNORE > _MPI_F_STATUS_IGNORE > > But not the symbol desired by msmpifec.lib: > > xena.cary$ nm msmpifec.lib | grep -i mpi_f_st > U __imp__MPI_F_STATUSES_IGNORE > U __imp__MPI_F_STATUS_IGNORE > > So seems not to be mingw but just a fact of the msmpi package. Hm - but I guess this error doesn't show up with ifort. So my initial guess about 'extra notation/metadata' in the lib file that nm/gnu-ld sounds more feasiable. [and gnu tools nm, gnu-ld are unable to parse this stuff. However MS's linker might be resolving this stuff correctly] Perhaps 'dumpbin /symbols foo.lib' shows what MS linker is looking at. Either way - looks like msmpi is unuseable from mingw-gfortran. Satish

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Re: [petsc-dev] How to configure parallel petsc on windows?
by John R. Cary 20 Nov '11

20 Nov '11

On 11/20/2011 11:09 AM, Satish Balay wrote: > On Sun, 20 Nov 2011, Satish Balay wrote: > >>>>>>>>>>>>>>>>>> . >> Executing: mingw32-gfortran -o conftest.exe -Wall -Wno-unused-variable -O -I/winsame/contrib-mingw/microsoft-hpc-mingw/Include conftest.o /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/lib/gcc/mingw32/4.6.1 -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/lib/gcc -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/mingw32/lib -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/lib -L/mingw/lib -lmingw32 -lgcc_eh -lmoldname -lmingwex -lmsvcrt -ladvapi32 -lshell32 -luser32 >> sh: >> Possible ERROR while running linker: Warning: .drectve `/DEFAULTLIB:"uuid.lib" /DEFAULTLIB:"uuid.lib" ' unrecognized >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_recv_]+0x1f): undefined reference to `_imp__MPI_F_STATUS_IGNORE' >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_wait_]+0x1f): undefined reference to `_imp__MPI_F_STATUS_IGNORE' >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_test_]+0x20): undefined reference to `_imp__MPI_F_STATUS_IGNORE' >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_waitany_]+0x20): undefined reference to `_imp__MPI_F_STATUS_IGNORE' >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_testany_]+0x21): undefined reference to `_imp__MPI_F_STATUS_IGNORE' >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_waitall_]+0x1f): undefined reference to `_imp__MPI_F_STATUSES_IGNORE' >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_testall_]+0x20): undefined reference to `_imp__MPI_F_STATUSES_IGNORE' >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_waitsome_]+0x1f): undefined reference to `_imp__MPI_F_STATUSES_IGNORE' >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_testsome_]+0x1f): undefined reference to `_imp__MPI_F_STATUSES_IGNORE' >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_iprobe_]+0x20): undefined reference to `_imp__MPI_F_STATUS_IGNORE' >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_probe_]+0x1f): undefined reference to `_imp__MPI_F_STATUS_IGNORE' >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_sendrecv_]+0x1f): undefined reference to `_imp__MPI_F_STATUS_IGNORE' >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_sendrecv_replace_]+0x1f): undefined reference to `_imp__MPI_F_STATUS_IGNORE' >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpirinitc]+0xa): undefined reference to `_imp__MPI_F_STATUS_IGNORE' >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpirinitc]+0x25): undefined reference to `_imp__MPI_F_STATUSES_IGNORE' >> collect2: ld returned 1 exit status >> >> >> Source: >> program main >> include 'mpif.h' >> integer ierr >> call mpi_init(ierr) >> end >> >> <<<<<<<<<<<<< >> >> Perhaps msmpi libs are using some internal notation that >> mingw-gfortran is unable to interpret? The unresolved symbols are >> coming from >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib and I >> think should be resolved by either >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib or >> /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib >> >> I would check with: >> >> nm -Ao /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib |grep _imp__MPI_F_STATUS_IGNORE > > Should also try to compile that simple mpi fortran code snippet > directly with mingw32-gfortran - and see if that works. > > mingw32-gfortran conftest.f -o conftest.exe -I/winsame/contrib-mingw/microsoft-hpc-mingw/Include /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib > > So I confirm what you found. I also found http://social.microsoft.com/Forums/is/windowshpcmpi/thread/fa213e91-5b83-41… which indicates this is a known problem. The basic symbol is in msmpi.lib: xena.cary$ link /dump /exports msmpi.lib | grep -i mpi_f_st _MPI_F_STATUSES_IGNORE _MPI_F_STATUS_IGNORE But not the symbol desired by msmpifec.lib: xena.cary$ nm msmpifec.lib | grep -i mpi_f_st U __imp__MPI_F_STATUSES_IGNORE U __imp__MPI_F_STATUS_IGNORE So seems not to be mingw but just a fact of the msmpi package. ???? John

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Re: [petsc-dev] Parmetis / Metis changes
by Barry Smith 20 Nov '11

20 Nov '11

On Nov 20, 2011, at 11:53 AM, Jed Brown wrote: > On Sun, Nov 20, 2011 at 11:51, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > I think you should "patch the top-level makefile to take a "cflags='-blah'" argument and hope that George accepts the patch." > > Can you pass it in through the CFLAGS environment variable as is? (Ugly, but I think CMake claims to respect that variable.) This appears to work. I have pushed a change to metis.py to do this define the Mac. We should eventually have BuildSystem check for __thread but I'm too lazy to do that today. Barry

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Re: [petsc-dev] How to configure parallel petsc on windows?
by Satish Balay 20 Nov '11

20 Nov '11

On Sun, 20 Nov 2011, Satish Balay wrote: > >>>>>>>>>>>>>>>>. > Executing: mingw32-gfortran -o conftest.exe -Wall -Wno-unused-variable -O -I/winsame/contrib-mingw/microsoft-hpc-mingw/Include conftest.o /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/lib/gcc/mingw32/4.6.1 -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/lib/gcc -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/mingw32/lib -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/lib -L/mingw/lib -lmingw32 -lgcc_eh -lmoldname -lmingwex -lmsvcrt -ladvapi32 -lshell32 -luser32 > sh: > Possible ERROR while running linker: Warning: .drectve `/DEFAULTLIB:"uuid.lib" /DEFAULTLIB:"uuid.lib" ' unrecognized > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_recv_]+0x1f): undefined reference to `_imp__MPI_F_STATUS_IGNORE' > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_wait_]+0x1f): undefined reference to `_imp__MPI_F_STATUS_IGNORE' > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_test_]+0x20): undefined reference to `_imp__MPI_F_STATUS_IGNORE' > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_waitany_]+0x20): undefined reference to `_imp__MPI_F_STATUS_IGNORE' > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_testany_]+0x21): undefined reference to `_imp__MPI_F_STATUS_IGNORE' > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_waitall_]+0x1f): undefined reference to `_imp__MPI_F_STATUSES_IGNORE' > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_testall_]+0x20): undefined reference to `_imp__MPI_F_STATUSES_IGNORE' > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_waitsome_]+0x1f): undefined reference to `_imp__MPI_F_STATUSES_IGNORE' > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_testsome_]+0x1f): undefined reference to `_imp__MPI_F_STATUSES_IGNORE' > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_iprobe_]+0x20): undefined reference to `_imp__MPI_F_STATUS_IGNORE' > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_probe_]+0x1f): undefined reference to `_imp__MPI_F_STATUS_IGNORE' > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_sendrecv_]+0x1f): undefined reference to `_imp__MPI_F_STATUS_IGNORE' > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_sendrecv_replace_]+0x1f): undefined reference to `_imp__MPI_F_STATUS_IGNORE' > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpirinitc]+0xa): undefined reference to `_imp__MPI_F_STATUS_IGNORE' > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpirinitc]+0x25): undefined reference to `_imp__MPI_F_STATUSES_IGNORE' > collect2: ld returned 1 exit status > > > Source: > program main > include 'mpif.h' > integer ierr > call mpi_init(ierr) > end > > <<<<<<<<<<<<< > > Perhaps msmpi libs are using some internal notation that > mingw-gfortran is unable to interpret? The unresolved symbols are > coming from > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib and I > think should be resolved by either > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib or > /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib > > I would check with: > > nm -Ao /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib |grep _imp__MPI_F_STATUS_IGNORE Should also try to compile that simple mpi fortran code snippet directly with mingw32-gfortran - and see if that works. mingw32-gfortran conftest.f -o conftest.exe -I/winsame/contrib-mingw/microsoft-hpc-mingw/Include /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib Satish

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Re: [petsc-dev] How to configure parallel petsc on windows?
by Satish Balay 20 Nov '11

20 Nov '11

On Sun, 20 Nov 2011, John R. Cary wrote: > On 11/20/2011 7:13 AM, Satish Balay wrote: > > You might have to do step 6 [edit MPI.py] before 5 [run configure]. > > > > 6.(only 32bit version). > > > > edit python/BuildSystem/config/packages/MPI.py and comment out the line > > > > self.functions = ['MPI_Init', 'MPI_Comm_create' > > <<<<< > > > > The issue is: MSMPI mangles function names. And configure should use > > mpi.h in all mpi function tests - to be able to use the correct name > > mangling [which it doesn't] > > Thanks. Now configured. A few more questions. > > Wenming's web page mentions patching: > > "The patch file basically puts a MPIAPI macro in front of all their calls. > This patch is either available upon request or by emailing petsc support and > refer to [PETSC #17869]" > > Is that still needed? (I ran make test, and it did not complain.) That page is for petsc-2.3.3-p13. Subsequent releases have this fix included. > > 2. If I want to use mingw, do I use > > --with-cc="win32fe mingw32-gcc" > > ? We've not had support for mingw compilers. > > (BTW, what does win32fe do?) Win32fe translates 'gcc' type compile/link command to MS cl notation [and translates options with paths of cygwin notation into native notation with cl understands]. It also does this type of tranlation from 'ar' to ms 'lib' command for archiving libraries etc. > > 3. When I add in fortran (with mingw32) I now get a failure in looking for > mpi_init: > > =============================================================================== > TESTING: FortranMPICheck from > config.packages.MPI(config/BuildSystem/config/pack******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > details): > ------------------------------------------------------------------------------- > Fortran error! mpi_init() could not be located! > ******************************************************************************* > > > I finally got both libs on the link line, but there seems to be a > similar link error as before, perhaps with the name mangling. > > Is there a quick suggestion for this? >>>>>>>>>>>>>>>> compilers: Checking arg -Lc:/mingw/bin/../lib/gcc/mingw32/4.6.1 compilers: Found library directory: -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/lib/gcc/mingw32/4.6.1 <<<<<<<<<<<<<< Here configure is goofing up trying resolve this c:/ notation path. [peraps its a bug - as this is a valid cygwin notation - and configure is supporsed to work with cygwin notation]. But perhaps this is not the reason for the eror below.. >>>>>>>>>>>>>>>>. Executing: mingw32-gfortran -o conftest.exe -Wall -Wno-unused-variable -O -I/winsame/contrib-mingw/microsoft-hpc-mingw/Include conftest.o /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/lib/gcc/mingw32/4.6.1 -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/lib/gcc -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/mingw32/lib -L/winsame/builds-mingw/facetsall-mingw/petsc-3.1-p8/par/c:/mingw/lib -L/mingw/lib -lmingw32 -lgcc_eh -lmoldname -lmingwex -lmsvcrt -ladvapi32 -lshell32 -luser32 sh: Possible ERROR while running linker: Warning: .drectve `/DEFAULTLIB:"uuid.lib" /DEFAULTLIB:"uuid.lib" ' unrecognized /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_recv_]+0x1f): undefined reference to `_imp__MPI_F_STATUS_IGNORE' /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_wait_]+0x1f): undefined reference to `_imp__MPI_F_STATUS_IGNORE' /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_test_]+0x20): undefined reference to `_imp__MPI_F_STATUS_IGNORE' /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_waitany_]+0x20): undefined reference to `_imp__MPI_F_STATUS_IGNORE' /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_testany_]+0x21): undefined reference to `_imp__MPI_F_STATUS_IGNORE' /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_waitall_]+0x1f): undefined reference to `_imp__MPI_F_STATUSES_IGNORE' /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_testall_]+0x20): undefined reference to `_imp__MPI_F_STATUSES_IGNORE' /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_waitsome_]+0x1f): undefined reference to `_imp__MPI_F_STATUSES_IGNORE' /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_testsome_]+0x1f): undefined reference to `_imp__MPI_F_STATUSES_IGNORE' /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_iprobe_]+0x20): undefined reference to `_imp__MPI_F_STATUS_IGNORE' /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_probe_]+0x1f): undefined reference to `_imp__MPI_F_STATUS_IGNORE' /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_sendrecv_]+0x1f): undefined reference to `_imp__MPI_F_STATUS_IGNORE' /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpi_sendrecv_replace_]+0x1f): undefined reference to `_imp__MPI_F_STATUS_IGNORE' /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpirinitc]+0xa): undefined reference to `_imp__MPI_F_STATUS_IGNORE' /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib(obj/i386/mpif.obj):(.text[_mpirinitc]+0x25): undefined reference to `_imp__MPI_F_STATUSES_IGNORE' collect2: ld returned 1 exit status Source: program main include 'mpif.h' integer ierr call mpi_init(ierr) end <<<<<<<<<<<<< Perhaps msmpi libs are using some internal notation that mingw-gfortran is unable to interpret? The unresolved symbols are coming from /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib and I think should be resolved by either /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib or /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib I would check with: nm -Ao /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpifec.lib /winsame/contrib-mingw/microsoft-hpc-mingw/lib/i386/msmpi.lib |grep _imp__MPI_F_STATUS_IGNORE Satish > > Thx...John > > > > > > > Satish > > > > On Sun, 20 Nov 2011, John R. Cary wrote: > > > > > Is this still possible? > > > > > > I followed the example at > > > > > > http://blogs.msdn.com/b/hpctrekker/archive/2008/09/07/running-petsc-on-wind… > > > > > > by doing > > > > > > config/configure.py --with-cc="win32fe cl" --with-fc=0 > > > --download-c-blas-lapack=1 --with-mpi-include="/cygdrive/c/Program > > > Files/Microsoft HPC Pack 2008 SDK/Include" > > > --with-mpi-lib="/cygdrive/c/Program > > > Files/Microsoft HPC Pack 2008 SDK/Lib/i386/msmpi.lib" --useThreads=0 > > > --with-shared=0 > > > > > > which ended with > > > > > > =============================================================================== > > > Configuring PETSc to compile on your system > > > =============================================================================== > > > TESTING: check from > > > config.libraries(config/BuildSystem/config/libraries.py:133)******************************************************************************* > > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > > > details): > > > > > > ------------------------------------------------------------------------------- > > > --with-mpi-lib=['/cygdrive/c/Program Files/Microsoft HPC Pack 2008 > > > SDK/Lib/i386/msmpi.lib'] and > > > --with-mpi-include=/cygdrive/c/Program Files/Microsoft HPC Pack 2008 > > > SDK/Include did not work > > > ******************************************************************************* > > > > > > > > > > > > My configure.log is attached. > > > > > > Thx for any help.....John > > > > >

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Re: [petsc-dev] Parmetis / Metis changes
by Jed Brown 20 Nov '11

20 Nov '11

On Sun, Nov 20, 2011 at 11:51, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > I think you should "patch the top-level makefile to take a > "cflags='-blah'" argument and hope that George accepts the patch." Can you pass it in through the CFLAGS environment variable as is? (Ugly, but I think CMake claims to respect that variable.)

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Re: [petsc-dev] Parmetis / Metis changes
by Barry Smith 20 Nov '11

20 Nov '11

On Nov 20, 2011, at 2:22 AM, Sean Farley wrote: > It appears that George is still living in the Linux desert and Sean has so pimped out his Mac it is barely running OS X. > > > Actually, you'd want to pass -D__thread= which is how metis handles it with other compilers. I don't know why llvm is reporting __thread incorrectly. Apple simply doesn't support __thread. > > Any ideas on how to pass it from metis.py?????? > > This is an annoying fact of the way that metis's makefile passes variables to cmake. We could circumvent the top-level makefile entirely, but that would lock us into a permanent battle with doing the same with every metis release. Or I could just patch the top-level makefile to take a "cflags='-blah'" argument and hope that George accepts the patch. I'm leaning towards the patch. I've implemented both but will see how I feel about it tomorrow before I push any changes. I think you should "patch the top-level makefile to take a "cflags='-blah'" argument and hope that George accepts the patch." Thanks Barry

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Re: [petsc-dev] How to configure parallel petsc on windows?
by Satish Balay 20 Nov '11

20 Nov '11

You might have to do step 6 [edit MPI.py] before 5 [run configure]. >>>>> 6.(only 32bit version). edit python/BuildSystem/config/packages/MPI.py and comment out the line > > self.functions = ['MPI_Init', 'MPI_Comm_create' <<<<< The issue is: MSMPI mangles function names. And configure should use mpi.h in all mpi function tests - to be able to use the correct name mangling [which it doesn't] Satish On Sun, 20 Nov 2011, John R. Cary wrote: > Is this still possible? > > I followed the example at > > http://blogs.msdn.com/b/hpctrekker/archive/2008/09/07/running-petsc-on-wind… > > by doing > > config/configure.py --with-cc="win32fe cl" --with-fc=0 > --download-c-blas-lapack=1 --with-mpi-include="/cygdrive/c/Program > Files/Microsoft HPC Pack 2008 SDK/Include" --with-mpi-lib="/cygdrive/c/Program > Files/Microsoft HPC Pack 2008 SDK/Lib/i386/msmpi.lib" --useThreads=0 > --with-shared=0 > > which ended with > > =============================================================================== > Configuring PETSc to compile on your system > =============================================================================== > TESTING: check from > config.libraries(config/BuildSystem/config/libraries.py:133)******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > details): > ------------------------------------------------------------------------------- > --with-mpi-lib=['/cygdrive/c/Program Files/Microsoft HPC Pack 2008 > SDK/Lib/i386/msmpi.lib'] and > --with-mpi-include=/cygdrive/c/Program Files/Microsoft HPC Pack 2008 > SDK/Include did not work > ******************************************************************************* > > > > My configure.log is attached. > > Thx for any help.....John >

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