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Re: scons configure error

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The time on my computer is correct. I couldn't change it anyway because this computer is managed by the IT people. I have also already upgraded PETSc from 2.3.3 to 3.0.0 and the error message was the same for scons.
I also ran make test with petsc and that ran fine. I then ran this python pkgconfiggen thing and got the stuff below. It basically says that my petsc_makefile is 0.02 s in the future. What the hell? 

- Shawn
walker@box227 ~/FENICS/dolfin/scons/simula-scons/simula_scons/pkgconfiggenerators 
$ python petsc.py

** Warning **
pkg-config files may be generated in the directory:

/home/walker/FENICS/dolfin/scons/simula-scons/simula_scons/pkgconfiggenerators.
Consider updating your PKG_CONFIG_PATH variable with this directoy.
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 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 0: unexpected EOF while looking for matching ``'
sh: -c: line 3: syntax error: unexpected end of file
Traceback (most recent call last):
  File "petsc.py", line 242, in <module>
    generatePkgConf(directory=".")
  File "petsc.py", line 225, in generatePkgConf
    version, compiler, linker, libs, cflags = pkgTests(sconsEnv=sconsEnv)
  File "petsc.py", line 215, in pkgTests
    compiler=compiler, linker=linker, sconsEnv=sconsEnv)
  File "petsc.py", line 157, in pkgVersion
    program=cpp_test_version_str, errormsg=cmdoutput)
commonPkgConfigUtils.UnableToCompileException: Unable to compile a PETSc test program. 
Compilation command was:
make: Warning: File `petsc_makefile' has modification time 0.02 s in the future 
/home/walker/build/bin/mpicxx
make: warning: Clock skew detected. Your build may be incomplete. -I/home/walker/src/petsc-3.0.0-p7/linux-gnu-cxx-opt/include -I/home/walker/src/petsc-3.0.0-p7/include -I/home/walker/build/include -I/home/walker/build/lib -c petsc_config_test_version.cpp 
Failed test program was:

#include <stdio.h>
#include <petsc.h>

int main() {
  #ifdef PETSC_VERSION_MAJOR
    #ifdef PETSC_VERSION_MINOR
      #ifdef PETSC_VERSION_SUBMINOR
printf("%d.%d.%d", PETSC_VERSION_MAJOR, PETSC_VERSION_MINOR, PETSC_VERSION_SUBMINOR); 
      #else
        printf("%d.%d", PETSC_VERSION_MAJOR, PETSC_VERSION_MINOR);
      #endif
    #else
      printf("%d", PETSC_VERSION_MAJOR);
    #endif
  #endif
  return 0;
}

- 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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