Send configure.log for the ./configure with ./configure --download-fblaslapack --with-valgrind-dir=/share/cluster/RHEL6.2/x86_64/apps/valgrind/3.9.0 --with-mpi=1 --with-mpi-dir=/home/hzh225/LIB_CFD/openmpi-1.8.3
Barry > On Dec 1, 2014, at 12:55 PM, paul zhang <[email protected]> wrote: > > Matt, > > Sorry to poke you again. I am in a dilemma. > > If I use > > ./configure --with-cc=mpicc --with-cxx=mpiCC --with-fc=mpif77 > --download-fblaslapack > --with-valgrind-dir=/share/cluster/RHEL6.2/x86_64/apps/valgrind/3.9.0 > --with-mpi=1 --with-mpi-dir=/home/hzh225/LIB_CFD/openmpi-1.8.3/ > > > Then I am told to > > TESTING: checkMPICompilerOverride from > config.setCompilers(config/BuildSystem/config/setCompilers.py:1501) > > > ******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > details): > ------------------------------------------------------------------------------- > --with-cc=mpicc is specified with > --with-mpi-dir=/home/hzh225/LIB_CFD/openmpi-1.8.3. However > /home/hzh225/LIB_CFD/openmpi-1.8.3/bin/mpicc exists and should be the > prefered compiler! Suggest not specifying --with-cc option so that configure > can use /home/hzh225/LIB_CFD/openmpi-1.8.3/bin/mpicc instead. > ******************************************************************************* > > > However if I skip those compilers, > > ./configure --download-fblaslapack > --with-valgrind-dir=/share/cluster/RHEL6.2/x86_64/apps/valgrind/3.9.0 > --with-mpi=1 --with-mpi-dir=/home/hzh225/LIB_CFD/openmpi-1.8.3 > > > My problem now is > > =============================================================================== > Configuring PETSc to compile on your system > > =============================================================================== > TESTING: checkFortranCompiler from > config.setCompilers(config/BuildSystem/config/setCompilers.py:910) > > > ******************************************************************************* > UNABLE to EXECUTE BINARIES for ./configure > ------------------------------------------------------------------------------- > Cannot run executables created with FC. If this machine uses a batch system > to submit jobs you will need to configure using ./configure with the > additional option --with-batch. > Otherwise there is problem with the compilers. Can you compile and run code > with your C/C++ (and maybe Fortran) compilers? > > > > > > > > > > > > > > Huaibao (Paul) Zhang > Gas Surface Interactions Lab > Department of Mechanical Engineering > University of Kentucky, > Lexington, > KY, 40506-0503 > Office: 216 Ralph G. Anderson Building > Web:gsil.engineering.uky.edu > > On Mon, Dec 1, 2014 at 1:34 PM, Matthew Knepley <[email protected]> wrote: > On Mon, Dec 1, 2014 at 12:33 PM, paul zhang <[email protected]> wrote: > That is my new configuration. Is that OK? > > export PETSC_DIR=`pwd` > export PETSC_ARCH=linux-gnu-intel > ./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran > --download-fblaslapack --download-mpich > --with-valgrind-dir=/share/cluster/RHEL6.2/x86_64/apps/valgrind/3.9.0 > --with-mpi=1 --with-mpi-dir=/home/hzh225/LIB_CFD/openmpi-1.8.3/ > > That looks correct. > > When I say "using PETSc makefiles", I mean for your own project. You appear > to be using CMake. > > Matt > > > Huaibao (Paul) Zhang > Gas Surface Interactions Lab > Department of Mechanical Engineering > University of Kentucky, > Lexington, > KY, 40506-0503 > Office: 216 Ralph G. Anderson Building > Web:gsil.engineering.uky.edu > > On Mon, Dec 1, 2014 at 1:28 PM, paul zhang <[email protected]> wrote: > I did use the PETSc makefiles. Should I include the valgrind path in my own > make file again? > > [hzh225@dlxlogin2-2 petsc-3.5.2]$ pwd > /home/hzh225/LIB_CFD/nP/petsc-3.5.2 > [hzh225@dlxlogin2-2 petsc-3.5.2]$ make getincludedirs > -I/home/hzh225/LIB_CFD/nP/petsc-3.5.2/include > -I/home/hzh225/LIB_CFD/nP/petsc-3.5.2/linux-gnu-intel/include > -I/share/cluster/RHEL6.2/x86_64/apps/valgrind/3.9.0/include > > Huaibao (Paul) Zhang > Gas Surface Interactions Lab > Department of Mechanical Engineering > University of Kentucky, > Lexington, > KY, 40506-0503 > Office: 216 Ralph G. Anderson Building > Web:gsil.engineering.uky.edu > > On Mon, Dec 1, 2014 at 11:55 AM, Matthew Knepley <[email protected]> wrote: > On Mon, Dec 1, 2014 at 10:43 AM, paul zhang <[email protected]> wrote: > Matt, > > Thanks for your reply. I am able to compile PETSc. And I went through the > default tests. Now when I go to my code, I got problems. > > I am assuming that you put flags in your makefiles rather than using the > PETSc makefiles. You need all the includes you get from > > make getincludedirs > > Matt > > [hzh225@dlxlogin2-1 petsc-3.5]$ make all > [100%] Building CXX object CMakeFiles/kats.dir/main.cc.o > /home/hzh225/LIB_CFD/nP/petsc-3.5.2/include/petscsys.h(1760): catastrophic > error: cannot open source file "valgrind/valgrind.h" > # include <valgrind/valgrind.h> > ^ > > compilation aborted for /home/hzh225/CMake/petsc/petsc-3.5/main.cc (code 4) > make[2]: *** [CMakeFiles/kats.dir/main.cc.o] Error 4 > make[1]: *** [CMakeFiles/kats.dir/all] Error 2 > make: *** [all] Error 2 > > > Huaibao (Paul) Zhang > Gas Surface Interactions Lab > Department of Mechanical Engineering > University of Kentucky, > Lexington, > KY, 40506-0503 > Office: 216 Ralph G. Anderson Building > Web:gsil.engineering.uky.edu > > On Mon, Dec 1, 2014 at 11:28 AM, Matthew Knepley <[email protected]> wrote: > On Mon, Dec 1, 2014 at 10:21 AM, paul zhang <[email protected]> wrote: > Hi All, > > How to enable the valgrind flag? I installed that by myself locally. > > It appears you do not have valgrind installed on your system. > > > We HIGHLY recommend you install it from www.valgrind.org > > > Or install valgrind-devel or equivalent using your package > manager. > > Then rerun ./configure > > > > > We could not find the valgrind header (valgrind.h). You can use > > --with-valgrind-dir=<path> > > so that it can find the path/include/valgrind/valgrind.h > > Thanks, > > Matt > > Thanks, > Paul > > > Huaibao (Paul) Zhang > > > > > -- > What most experimenters take for granted before they begin their experiments > is infinitely more interesting than any results to which their experiments > lead. > -- Norbert Wiener > > > > > -- > What most experimenters take for granted before they begin their experiments > is infinitely more interesting than any results to which their experiments > lead. > -- Norbert Wiener > > > > > > -- > What most experimenters take for granted before they begin their experiments > is infinitely more interesting than any results to which their experiments > lead. > -- Norbert Wiener >
