initial petsc ex47cu.cu example build with:

SCRGP2$ module show petsc/3.3/gcc-4.4.3-mpich2-1.2-epd-sm_10-dbg
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/usr/local/Modules/3.2.8/modulefiles/petsc/3.3/gcc-4.4.3-mpich2-1.2-epd-sm_10-dbg:

module-whatis            download petsc with
module-whatis            wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.3-p4.tar.gz
module-whatis            petsc configured with
module-whatis            config/configure.py --with-precision=single --with-clanguage=C++ --with-mpi-dir=/usr --with-shared-libraries --CFLAGS='-O0' --CXXFLAGS='-O0' --CUDAFLAGS='-O0' --with-etags=1 --with-mpi4py=0 --with-blas-lapack-lib=[/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_rt.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_intel_thread.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_core.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libiomp5.so] --download-metis --with-cuda=1 --with-cusp=1 --with-thrust=1 --with-cuda-dir=$CUDA_DIR  --with-boost=1 --with-boost-dir=/usr --download-fiat=yes --download-generator --download-scientificpython
module-whatis            cd $PETSC_DIR/externalpackages/petsc4py-1.2; python setup.py build ; python setup.py install --home=$PETSC_DIR/$PETSC_ARCH
module           load epd/7.3.1
module           load cuda/4.2
setenv           PETSC_ARCH gcc-4.4.3-mpich2-1.2-epd-sm_10-dbg
setenv           PETSC_DIR /opt/apps/PETSC/petsc-3.3-p4
prepend-path     PYTHONPATH /opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_10-dbg/lib/python
prepend-path     PYTHONPATH /opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_10-dbg/lib/python2.7/site-packages
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utility file
cuda updates
running but 70 % time spent in jacobian.

need bug fix

Event                Count      Time (sec)     Flops                             --- Global ---  --- Stage ---   Total
                   Max Ratio  Max     Ratio   Max  Ratio  Mess   Avg len Reduct  %T %f %M %L %R  %T %f %M %L %R Mflop/s
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--- Event Stage 0: Main Stage

ComputeFunction       52 1.0 4.2100e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 3.0e+00  0  0  0  0  1   0  0  0  0  1     0
VecDot                50 1.0 2.6836e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 0.0e+00  0  4  0  0  0   0  4  0  0  0   362
VecMDot               50 1.0 2.0384e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 0.0e+00  0  4  0  0  0   0  4  0  0  0   476
VecNorm              150 1.0 7.7771e-01 1.0 2.91e+08 1.0 0.0e+00 0.0e+00 0.0e+00  1 12  0  0  0   1 12  0  0  0   374
VecScale             100 1.0 1.6661e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 0.0e+00  0  4  0  0  0   0  4  0  0  0   582
VecCopy              250 1.0 9.9133e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  1  0  0  0  0   1  0  0  0  0     0
VecSet               113 1.0 4.2281e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
VecAXPY               50 1.0 4.0780e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 0.0e+00  0  4  0  0  0   0  4  0  0  0   238
VecWAXPY              50 1.0 4.0663e-01 1.0 4.85e+07 1.0 0.0e+00 0.0e+00 0.0e+00  0  2  0  0  0   0  2  0  0  0   119
VecMAXPY             100 1.0 8.5455e-01 1.0 1.94e+08 1.0 0.0e+00 0.0e+00 0.0e+00  1  8  0  0  0   1  8  0  0  0   227
VecScatterBegin      102 1.0 4.0932e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
VecReduceArith       101 1.0 4.0903e-01 1.0 1.96e+08 1.0 0.0e+00 0.0e+00 0.0e+00  0  8  0  0  0   0  8  0  0  0   479
VecReduceComm         51 1.0 1.3709e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
VecNormalize         100 1.0 3.9175e-01 1.0 1.94e+08 1.0 0.0e+00 0.0e+00 0.0e+00  0  8  0  0  0   0  8  0  0  0   495
VecCUSPCopyTo        152 1.0 5.9921e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
VecCUSPCopyFrom      151 1.0 7.5544e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  1  0  0  0  0   1  0  0  0  0     0
MatMult              100 1.0 6.9635e-01 1.0 1.25e+09 1.0 0.0e+00 0.0e+00 0.0e+00  0 53  0  0  0   0 53  0  0  0  1795
MatAssemblyBegin     101 1.0 1.3471e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
MatAssemblyEnd       101 1.0 3.3193e+01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 23  0  0  0  0  23  0  0  0  0     0
MatZeroEntries        50 1.0 1.1296e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  1  0  0  0  0   1  0  0  0  0     0
MatCUSPCopyTo        101 1.0 2.7970e+01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 19  0  0  0  0  19  0  0  0  0     0
SNESSolve              1 1.0 1.2806e+02 1.0 2.37e+09 1.0 0.0e+00 0.0e+00 3.2e+02 89100  0  0 87  89100  0  0 87    18
SNESFunctionEval      51 1.0 4.1588e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
SNESJacobianEval      50 1.0 1.0154e+02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 70  0  0  0  0  70  0  0  0  0     0
SNESLineSearch        50 1.0 1.0205e+01 1.0 1.16e+09 1.0 0.0e+00 0.0e+00 5.0e+01  7 49  0  0 14   7 49  0  0 14   114
KSPGMRESOrthog        50 1.0 5.4782e-01 1.0 1.94e+08 1.0 0.0e+00 0.0e+00 5.0e+01  0  8  0  0 14   0  8  0  0 14   354
KSPSetUp              50 1.0 3.9054e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 1.5e+01  0  0  0  0  4   0  0  0  0  4     0
KSPSolve              50 1.0 1.4356e+01 1.0 1.21e+09 1.0 0.0e+00 0.0e+00 2.6e+02 10 51  0  0 72  10 51  0  0 72    84
PCSetUp               50 1.0 3.7909e-05 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
PCApply              100 1.0 3.9783e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
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compute jacobian only once
Location of data members
STYLE: organizing files to PetscFiniteDifferenceExample/
Merge branch 'branchfromsecondrepo'