[petsc-users] configure problems

Thu Jul 22 15:45:55 CDT 2010

On Thu, 22 Jul 2010, Dominik Szczerba wrote:

> Thanks a lot.
> But now there is no meaningful output...

What do you mean? Have you run the examples manually? You just show the
'compile' step - which looks successful.

> > > > mpiexec -n 2 ./ex2.exe
> > > > mpiexec -localonly -n 2 ./ex2.exe

Satish

> 
> Dominik at Tharsis/cygdrive/c/Users/Dominik/Programs/petsc-3.1-p3/src/ksp/ksp/examples/tutorials
> $ make PETSC_DIR=/cygdrive/c/Users/Dominik/Programs/petsc-3.1-p3
> PETSC_ARCH=win64-msvc-release ex2
> /cygdrive/c/Users/Dominik/Programs/petsc-3.1-p3/bin/win32fe/win32fe cl -o
> ex2.o -c -MT -wd4996
> -I/cygdrive/c/Users/Dominik/Programs/petsc-3.1-p3/src/dm/mesh/sieve
> -I/cygdrive/c/Users/Dominik/Programs/
> petsc-3.1-p3/win64-msvc-release/include
> -I/cygdrive/c/Users/Dominik/Programs/petsc-3.1-p3/include
> -I/cygdrive/c/Program Files/MPICH2/include
> -D__INSDIR__=src/ksp/ksp/examples/tutorials/ ex2.c
> ex2.c
> /cygdrive/c/Users/Dominik/Programs/petsc-3.1-p3/bin/win32fe/win32fe cl -MT
> -wd4996  -o ex2 ex2.o
> -L/cygdrive/c/Users/Dominik/Programs/petsc-3.1-p3/win64-msvc-release/lib
> -L/cygdrive/c/Users/Dominik/P
> rograms/petsc-3.1-p3/win64-msvc-release/lib -lpetsc
> -L/cygdrive/c/Users/Dominik/Programs/petsc-3.1-p3/win64-msvc-release/lib
> -lf2clapack -lf2cblas /cygdrive/c/Program\ Files/MPICH2/lib/fmpich2.lib /
> cygdrive/c/Program\ Files/MPICH2/lib/fmpich2g.lib /cygdrive/c/Program\
> Files/MPICH2/lib/mpi.lib Gdi32.lib User32.lib Advapi32.lib Kernel32.lib
> Ws2_32.lib
> /usr/bin/rm -f ex2.o
> 
> 
> 
> 
> 
> 
> On Thu, Jul 22, 2010 at 10:23 PM, Satish Balay <balay at mcs.anl.gov> wrote:
> 
> > Sorry - you need PETSC_ARCH and PETSC_DIR with make. [normally these are
> > set as env variables]
> >
> > make PETSC_DIR=/cygdrive/c/Users/Dominik/Programs/petsc-3.1-p3
> > PETSC_ARCH=win64-msvc-release ex2
> >
> > Satish
> >
> > On Thu, 22 Jul 2010, Dominik Szczerba wrote:
> >
> > > Hmmm I get the following errors:
> > >
> > > $ cd src/ksp/ksp/examples/tutorials
> > >
> > > Dominik at Tharsis
> > /cygdrive/c/Users/Dominik/Programs/petsc-3.1-p3/src/ksp/ksp/examples/tutorials
> > > $ make ex2
> > > makefile:16: /conf/variables: No such file or directory
> > > makefile:17: /conf/rules: No such file or directory
> > > makefile:856: /conf/test: No such file or directory
> > > make: *** No rule to make target `/conf/test'.  Stop.
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > On Thu, Jul 22, 2010 at 10:11 PM, Satish Balay <balay at mcs.anl.gov>
> > wrote:
> > >
> > > > Should have said:
> > > >
> > > > cd src/ksp/ksp/examples/tutorials
> > > > make ex2
> > > > mpiexec -n 2 ./ex2.exe
> > > > mpiexec -localonly -n 2 ./ex2.exe
> > > >
> > > > Satish
> > > >
> > > > On Thu, 22 Jul 2010, Satish Balay wrote:
> > > >
> > > > > Try running manually. MPICH2 install by default insists on passwd -
> > > > > and this process isn't handled by petsc scripts properly.
> > > > >
> > > > > [or use '--with-mpiexec=mpiexec --localonly']
> > > > >
> > > > > Satish
> > > > >
> > > > > On Thu, 22 Jul 2010, Dominik Szczerba wrote:
> > > > >
> > > > > > Dear all,
> > > > > >
> > > > > > The problem was apparently that I was trying to configure Petsc
> > under
> > > > the 32
> > > > > > bit terminal with the 64 bit MPI system installation.
> > > > > >
> > > > > > I managed to invoke the 64 bit terminal and configure and build
> > Petsc
> > > > as
> > > > > > follows:
> > > > > >
> > > > > > ./config/configure.py PETSC_DIR=$PWD PETSC_ARCH=win64-msvc-release
> > > > > > --download-c-blas-lapack=1 --with-x=0 --with-debugging=0
> > > > --with-cc='win32fe
> > > > > > cl' --with-fc=0
> > > > > >
> > > > > > (with the official MPICH2 64bitinstallation):
> > > > > >
> > > > > > MPI:
> > > > > >   Includes: -I/cygdrive/c/Program\ Files/MPICH2/include
> > > > > >   Library:  /cygdrive/c/Program\ Files/MPICH2/lib/fmpich2.lib
> > > > > > /cygdrive/c/Program\ Files/MPICH2/lib/fmpich2g.lib
> > /cygdrive/c/Program\
> > > > > > Files/MPICH2/lib/mpi.lib
> > > > > >
> > > > > > However, I am getting errors when executing "make test": (errors
> > below)
> > > > > > Any ideas how to proceed? (I clicked some 'yes when Windows popped
> > up a
> > > > > > yes/no security window)
> > > > > >
> > > > > > Regards,
> > > > > > Dominik
> > > > > >
> > > > > >
> > > > > > $ make PETSC_DIR=/cygdrive/c/Users/Dominik/Programs/petsc-3.1-p3
> > > > > > PETSC_ARCH=win64-msvc-release test
> > > > > > Running test examples to verify correct installation
> > > > > > Possible error running C/C++ src/snes/examples/tutorials/ex19 with
> > 1
> > > > MPI
> > > > > > process
> > > > > > See
> > > >
> > http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html
> > > > > > Error while connecting to host, No connection could be made because
> > the
> > > > > > target machine actively refused it. (10061)
> > > > > > Connect on sock (host=Tharsis, port=8676) failed, exhaused all end
> > > > points
> > > > > > Unable to connect to 'Tharsis:8676',
> > > > > > sock error: Error = -1
> > > > > >
> > > > > > Possible error running C/C++ src/snes/examples/tutorials/ex19 with
> > 2
> > > > MPI
> > > > > > processes
> > > > > > See
> > > >
> > http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html
> > > > > > Error while connecting to host, No connection could be made because
> > the
> > > > > > target machine actively refused it. (10061)
> > > > > > Connect on sock (host=Tharsis, port=8676) failed, exhaused all end
> > > > points
> > > > > > Unable to connect to 'Tharsis:8676',
> > > > > > sock error: Error = -1
> > > > > >
> > > > > > Completed test examples
> > > > > >
> > > > > >
> > > > > > On Thu, Jul 22, 2010 at 4:13 PM, Satish Balay <balay at mcs.anl.gov>
> > > > wrote:
> > > > > >
> > > > > > > On Thu, 22 Jul 2010, Dominik Szczerba wrote:
> > > > > > >
> > > > > > > > Many thanks for your precious feedback.
> > > > > > > > My MPICH install is 64 bit but it seems that for some reason 32
> > bit
> > > > VC
> > > > > > > > compiler is invoked (I have both 32 and 64 installed).
> > > > > > >
> > > > > > > As mentioned - whichever compiler is first in the PATH is used
> > > > > > > cl
> > > > > > >
> > > > > > > > I am clarifying with a local MSVC expert how to control this,
> > will
> > > > update
> > > > > > > > you later today.
> > > > > > >
> > > > > > > One way to control this - is to run the desired 'build env' cmd -
> > as
> > > > > > > mentioned in the installation instructions.
> > > > > > >
> > > > > > >
> > > >
> > http://www.mcs.anl.gov/petsc/petsc-as/documentation/installation.html#Windows
> > > > > > >
> > > > > > > Satish
> > > > > > >
> > > > > > > > Dominik
> > > > > > > >
> > > > > > > > On Thu, Jul 22, 2010 at 3:45 PM, Satish Balay <
> > balay at mcs.anl.gov>
> > > > wrote:
> > > > > > > >
> > > > > > > > > > sh: Warning: win32fe: File Not Found: /cygdrive/c/Program
> > > > > > > > > > Files/MPICH2/lib/amd64/msmpi.lib
> > > > > > > > >
> > > > > > > > > Looks like - if win32fe doesn't find the file - it doesn't
> > try to
> > > > > > > > > convert the path. This is not the cause of his configure
> > failure.
> > > > > > > > >
> > > > > > > > > The primary issue is: [which is much ahead in configure.log]
> > > > > > > > >
> > > > > > > > > >>>>>>>>>>>
> > > > > > > > > sh:
> > > > /cygdrive/c/Users/Dominik/Programs/petsc-3.1-p3/bin/win32fe/win32fe
> > > > > > > cl
> > > > > > > > >  -o conftest.exe    -MT -wd4996  conftest.o
> >  /cygdrive/c/Program\
> > > > > > > > > Files/MPICH2/lib/mpi.lib Ws2_32.lib
> > > > > > > > > Executing:
> > > > > > > > >
> > > > /cygdrive/c/Users/Dominik/Programs/petsc-3.1-p3/bin/win32fe/win32fe cl
> > > > > > >  -o
> > > > > > > > > conftest.exe    -MT -wd4996  conftest.o  /cygdrive/c/Program\
> > > > > > > > > Files/MPICH2/lib/mpi.lib Ws2_32.lib
> > > > > > > > > sh: conftest.obj : error LNK2019: unresolved external symbol
> > > > _MPI_Init
> > > > > > > > > referenced in function _main^M
> > > > > > > > > C:\Users\Dominik\Programs\PETSC-~1.1-P\conftest.exe : fatal
> > error
> > > > > > > LNK1120:
> > > > > > > > > 1 unresolved externals^M
> > > > > > > > > <<<<<<<<<<<
> > > > > > > > >
> > > > > > > > > Here cl is finding the correct library - but not MPI_Init
> > symbol
> > > > in it.
> > > > > > > > > For whatever reason - libmpi.lib is not compatible.
> > > > > > > > >
> > > > > > > > > Satish
> > > > > > > > >
> > > > > > > > > On Thu, 22 Jul 2010, Farshid Mossaiby wrote:
> > > > > > > > >
> > > > > > > > > > I doubt 'cl' can interpret Cygwin paths:
> > > > > > > > > >
> > > > > > > > > > cl : Command line warning D9002 : ignoring unknown option
> > > > > > > > > > '/cygdrive/c/Program Files/MPICH2/lib/amd64/msmpi.lib'
> > > > > > > > > >
> > > > > > > > > > Shouldn't win32fe convert this path first?
> > > > > > > > > >
> > > > > > > > > > Hope this helps.
> > > > > > > > > >
> > > > > > > > > > --- On Wed, 7/21/10, Dominik Szczerba <
> > dominik at itis.ethz.ch>
> > > > wrote:
> > > > > > > > > >
> > > > > > > > > > > From: Dominik Szczerba <dominik at itis.ethz.ch>
> > > > > > > > > > > Subject: Re: [petsc-users] configure problems
> > > > > > > > > > > To: "PETSc users list" <petsc-users at mcs.anl.gov>
> > > > > > > > > > > Date: Wednesday, July 21, 2010, 7:01 PM
> > > > > > > > > > > Coming back to the original problem:
> > > > > > > > > > > I tried to compile MPICH2 myself
> > > > > > > > > > > and failed because of wrong version of automake in
> > Cygwin.
> > > > > > > > > > > I then
> > > > > > > > > > > installed the Windows binary available on the mpich2
> > > > > > > > > > > webpage. I
> > > > > > > > > > > configure petsc with:
> > > > > > > > > > >
> > > > > > > > > > > $ ./config/configure.py PETSC_DIR=$PWD
> > > > > > > > > > > PETSC_ARCH=win64-msvc-release
> > > > > > > > > > > --download-c-blas-lapack=1
> > > > > > > > > > > --with-mpi-dir='/cygdrive/c/Program
> > > > > > > > > > > Files/MPICH2' --with-x=0 --with-debugging=0
> > > > > > > > > > > --with-cc='win32fe cl'
> > > > > > > > > > > --with-fc=0
> > > > > > > > > > >
> > > > > > > > > > > to hear at the end (of a very long configuration
> > > > > > > > > > > process...):
> > > > > > > > > > >
> > > > > > > > > > > sh:
> > > > > > > > > > >
> > > > /cygdrive/c/Users/Dominik/Programs/petsc-3.1-p3/bin/win32fe/win32fe
> > > > > > > > > > > cl  -o conftest.exe    -MT -wd4996
> > > > > > > > > > > conftest.o  /cygdrive/c/Program\
> > > > > > > > > > > Files/MPICH2/lib/amd64/msmpi.lib Ws2_32.lib
> > > > > > > > > > > Executing:
> > > > > > > > > > >
> > > > /cygdrive/c/Users/Dominik/Programs/petsc-3.1-p3/bin/win32fe/win32fe
> > > > > > > > > > > cl  -o conftest.exe    -MT -wd4996
> > > > > > > > > > > conftest.o  /cygdrive/c/Program\
> > > > > > > > > > > Files/MPICH2/lib/amd64/msmpi.lib Ws2_32.lib
> > > > > > > > > > > sh: Warning: win32fe: File Not Found: /cygdrive/c/Program
> > > > > > > > > > > Files/MPICH2/lib/amd64/msmpi.lib
> > > > > > > > > > > cl : Command line warning D9002 : ignoring unknown option
> > > > > > > > > > > '/cygdrive/c/Program Files/MPICH2/lib/amd64/msmpi.lib'
> > > > > > > > > > > conftest.obj : error LNK2019: unresolved external symbol
> > > > > > > > > > > _MPI_Init
> > > > > > > > > > > referenced in function _main
> > > > > > > > > > > C:\Users\Dominik\Programs\PETSC-~1.1-P\conftest.exe :
> > fatal
> > > > > > > > > > > error
> > > > > > > > > > > LNK1120: 1 unresolved externals
> > > > > > > > > > >
> > > > > > > > > > > Any directions why would the configuration look for a
> > > > > > > > > > > nonexistent
> > > > > > > > > > > library? The contents of the installation folder are:
> > > > > > > > > > >
> > > > > > > > > > > $ ls -la /cygdrive/c/Program\ Files/MPICH2/lib/
> > > > > > > > > > > total 808
> > > > > > > > > > > drwx------+ 1 SYSTEM SYSTEM   4096
> > > > > > > > > > > 2010-07-21 15:54 .
> > > > > > > > > > > drwx------+ 1 SYSTEM SYSTEM   4096
> > > > > > > > > > > 2010-07-21 15:54 ..
> > > > > > > > > > > -rwx------+ 1 SYSTEM SYSTEM   4644
> > > > > > > > > > > 2010-02-22 17:13 TraceInput.lib
> > > > > > > > > > > -rwx------+ 1 SYSTEM SYSTEM 322820 2010-02-22 17:09
> > > > > > > > > > > cxx.lib
> > > > > > > > > > > -rwx------+ 1 SYSTEM SYSTEM 131316 2010-02-22 17:11
> > > > > > > > > > > fmpich2.lib
> > > > > > > > > > > -rwx------+ 1 SYSTEM SYSTEM 136382 2010-02-22 17:13
> > > > > > > > > > > fmpich2g.lib
> > > > > > > > > > > -rwx------+ 1 SYSTEM SYSTEM   1936
> > > > > > > > > > > 2010-02-22 17:13 irlog2rlog.lib
> > > > > > > > > > > -rwx------+ 1 SYSTEM SYSTEM  10430 2010-02-22 16:30
> > > > > > > > > > > mpe.lib
> > > > > > > > > > > -rwx------+ 1 SYSTEM SYSTEM 132128 2010-02-22 16:29
> > > > > > > > > > > mpi.lib
> > > > > > > > > > > -rwx------+ 1 SYSTEM SYSTEM  61286 2010-02-22 16:30
> > > > > > > > > > > rlog.lib
> > > > > > > > > > >
> > > > > > > > > > > Best regards,
> > > > > > > > > > > Dominik
> > > > > > > > > > >
> > > > > > > > > > > On Tue, Jul 20, 2010 at 12:44 AM, Jed Brown <
> > jed at 59a2.org>
> > > > > > > > > > > wrote:
> > > > > > > > > > > > On Tue, 20 Jul 2010 08:37:18 +1000, Matthew Knepley
> > > > > > > > > > > <knepley at gmail.com>
> > > > > > > > > > > wrote:
> > > > > > > > > > > >> This would do you absolutely no good. Even Jed's
> > > > > > > > > > > thing needs all the
> > > > > > > > > > > >> information that the configure provides. CMake is
> > > > > > > > > > > exactly what it
> > > > > > > > > > > >> says, make. It does no configuration
> > > > > > > > > > > >
> > > > > > > > > > > > This isn't true, CMake isn't a build system at all, it
> > > > > > > > > > > does
> > > > > > > > > > > > configuration and produces build files for another
> > > > > > > > > > > tool (like make or an
> > > > > > > > > > > > IDE).  I see no point in maintaining duplicate
> > > > > > > > > > > configuration systems,
> > > > > > > > > > > > and CMake's scripting language is so attrocious that
> > > > > > > > > > > "replacing"
> > > > > > > > > > > > BuildSystem with CMake script would be a disaster.
> > > > > > > > > > >  It's
> > > > > > > > > > > > cross-compilation support is also a bit weak, and
> > > > > > > > > > > there are a pile of
> > > > > > > > > > > > other things that it does poorly (mostly related to
> > > > > > > > > > > pathologically
> > > > > > > > > > > > dysfunctional "Find*.cmake" modules).  That doesn't
> > > > > > > > > > > mean it isn't useful
> > > > > > > > > > > > for producing build files.
> > > > > > > > > > > >
> > > > > > > > > > > > Jed
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > > >
> > >
> >
> >
> 