dolfin team mailing list archive

[Shawn Walker <walker@xxxxxxxxxxxxxxx>]

I can't figure this out.  I have put a bunch of print messages, but all I 
can tell is that cpp_test_version does not get compiled.  I don't 
understand how a 0.02 s future timestamp skew is messing it up.  I have 
rebuilt PETSc.

I can just remove PETSC from compiling dolfin.  But I would like to know 
why this is happening.

- Shawn

On Tue, 14 Jul 2009, Garth N. Wells wrote:

> Shawn Walker wrote:
> > I've done a couple of these already.  But how do I fix the time?  Is this 
> > the date?  I'm not sure how I fix this... or what I am fixing exactly.
>
> The time error is usually due to files which have timestamps in the 'future'. 
> Make uses timestamps to decide if one file is newer than another. The problem 
> can be due a system clock time which has been changed. Check that 'date' give 
> the correct time, and check the timestamp on some PETSc file ('ls -lt').
>
> Garth
>
> > - Shawn
> >
> > On Tue, 14 Jul 2009, Garth N. Wells wrote:
> >
> > > Here are some tips:
> > >
> > > - Fix the time on your computer and rebuild PETSc if necessary to get rid 
> > > of the clock skew message
> > > - Try compiling without PETSc.
> > > - Test that your PETSc installation is working ('make test' in the PETSc 
> > > directory)
> > > - Test your mpi compiler by compiling a 'hello world' program
> > > - Run
> > >    python scons/simula-scons/simula_scons/pkgconfiggenerators/petsc.py
> > > and add some print statements to find out where the error crops up.
> > >
> > > Garth
> > >
> > > Shawn Walker wrote:
> > > > I tried enabling and disabling MPI when configuring DOLFIN.  I still get 
> > > > an error:
> > > >
> > > > $ scons configure prefix=$INSTALL_PATH withBoostDir=$BOOST_DIR 
> > > > withUmfpackDir=$UMFPACK_DIR withPetscDir=$PETSC_DIR 
> > > > withSlepcDir=$SLEPC_DIR enableDemos=yes enableScotch=no enableTrilinos=no 
> > > > enableMpi=yes enablePetsc=yes enableSlepc=yes enableUmfpack=yes 
> > > > enableParmetis=no enableMtl4=no enableDebug=yes enablePython=yes
> > > > scons: Reading SConscript files ...
> > > > Using options from /home/walker/FENICS/dolfin/scons/options.cache
> > > > Checking for pkg-config... yes
> > > > Checking for boost_filesystem... yes
> > > > Checking for numpy-1... yes
> > > > Checking for slepc... yes
> > > > sh: -c: line 0: unexpected EOF while looking for matching ``'
> > > > sh: -c: line 3: syntax error: unexpected end of file
> > > >   Trying to re-generate pkg-config file for slepc... failed
> > > > Checking for ufc-1... yes
> > > > Checking for umfpack... yes
> > > >   Trying to re-generate pkg-config file for umfpack... done
> > > >   Found UMFPACK and generated pkg-config file in
> > > >   '/home/walker/FENICS/dolfin/scons/pkgconfig'
> > > > Checking for python-2... yes
> > > > Checking for petsc... yes
> > > > sh: -c: line 0: unexpected EOF while looking for matching ``'
> > > > sh: -c: line 3: syntax error: unexpected end of file
> > > >   Trying to re-generate pkg-config file for petsc... Does not know about 
> > > > any alternates for mpicxx
> > > > make: warning:  Clock skew detected.  Your build may be incomplete., so 
> > > > that is used
> > > > sh: -c: line 0: unexpected EOF while looking for matching ``'
> > > > sh: -c: line 3: syntax error: unexpected end of file
> > > > Does not know about any alternates for mpicxx
> > > > make: warning:  Clock skew detected.  Your build may be incomplete., so 
> > > > that is used
> > > > sh: -c: line 2: unexpected EOF while looking for matching `''
> > > > sh: -c: line 5: syntax error: unexpected end of file
> > > > failed
> > > > Checking for boost_program_options... yes
> > > > Checking for gts... yes
> > > > Checking for cholmod... yes
> > > > Checking for boost... yes
> > > >   Trying to re-generate pkg-config file for boost... done
> > > >   Found Boost and generated pkg-config file in
> > > >   '/home/walker/FENICS/dolfin/scons/pkgconfig'
> > > > Checking for libxml-2.0... yes
> > > > Resolving compiler... done
> > > > Found optional package: umfpack
> > > > Found optional package: gts
> > > > Found optional package: cholmod
> > > > Unable to find optional package: petsc
> > > > Unable to find optional package: slepc
> > > > Enabling compilation of Python wrappers
> > > > ---------------------------------------------------------
> > > >
> > > > I have no idea what to do.
> > > >
> > > > - Shawn
> > > >
> > > > On Tue, 14 Jul 2009, Johannes Ring wrote:
> > > >
> > > > > On Tue, July 14, 2009 15:02, Shawn Walker wrote:
> > > > > > Do I need to install the newest PETSC and SLEPC?  I'm running 2.3.3 
> > > > > > right
> > > > > > now.  Was there a change recently where this matters?
> > > > > Both PETSc 2.3.3 and 3.0.0 are supported. I see in one of your other 
> > > > > posts
> > > > > that you set enableMpi=no during configure. This will not work if PETSc 
> > > > > is
> > > > > built with MPI. Try to enable MPI or rebuild PETSc without MPI.
> > > > >
> > > > > Johannes
> > > > >
> > > > > > - Shawn
> > > > > >
> > > > > > On Tue, 14 Jul 2009, Johannes Ring wrote:
> > > > > >
> > > > > > > Hi Shawn,
> > > > > > >
> > > > > > > I have never seen this error before but some googling suggests that
> > > > > > > there
> > > > > > > is something wrong with your time, however, it shouldn't be a problem.
> > > > > > >
> > > > > > > I'm not sure why it fails to generate a pkg-config file for PETSc but 
> > > > > > > it
> > > > > > > might be that you need to set PETSC_ARCH before running "scons
> > > > > > > configure".
> > > > > > > Try that and look in scons/simula_scons.log in case of any failures.
> > > > > > >
> > > > > > > Johannes
> > > > > > >
> > > > > > > On Mon, July 13, 2009 15:33, Shawn Walker wrote:
> > > > > > > > Does anyone know what this error is when I run "scons configure" for
> > > > > > > > DOLFIN:
> > > > > > > >
> > > > > > > > Checking for petsc... yes
> > > > > > > > sh: -c: line 0: unexpected EOF while looking for matching ``'
> > > > > > > > sh: -c: line 3: syntax error: unexpected end of file
> > > > > > > >   Trying to re-generate pkg-config file for petsc... Does not know
> > > > > > > > about
> > > > > > > > any alternates for mpicxx
> > > > > > > > make: warning:  Clock skew detected.  Your build may be incomplete., 
> > > > > > > > so
> > > > > > > > that is used
> > > > > > > > sh: -c: line 0: unexpected EOF while looking for matching ``'
> > > > > > > > sh: -c: line 3: syntax error: unexpected end of file
> > > > > > > > Does not know about any alternates for mpicxx
> > > > > > > > make: warning:  Clock skew detected.  Your build may be incomplete., 
> > > > > > > > so
> > > > > > > > that is used
> > > > > > > > sh: -c: line 2: unexpected EOF while looking for matching `''
> > > > > > > > sh: -c: line 5: syntax error: unexpected end of file
> > > > > > > > failed
> > > > > > > >
> > > > > > > > =================================
> > > > > > > >
> > > > > > > > I tried erasing the DOLFIN dir and re-cloning it and I still get that
> > > > > > > > error.
> > > > > > > >
> > > > > > > > - Shawn
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