dolfin team mailing list archive

["Garth N. Wells" <gnw20@xxxxxxxxx>]

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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