If you don't need fortran than just use your (already compiled) OpenMPI but pass to PETSc's ./configure --with-fc=0 and PETSc should configure.
Barry > On Dec 1, 2014, at 1:22 PM, paul zhang <[email protected]> wrote: > > Thanks for checking. > > My program is coded with C++ actually, so fortran may not be necessary. I > compiled PETSc on our university cluster, where a MPI package has already > been installed as universal module. It seems not compatible with PETSc. So I > am trying to install my own version of MPI and link it to PETSc. > > As compile PETSc using its default configuration, it automatically downloaded > the mpi . > ./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran > --download-fblaslapack --download-mpich > > I was wondering if it does the same thing as I installed MPI by my own. > > Thanks again. > Paul > > > > > > > > > > > > > > > > > > > > > > > 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 2:06 PM, Matthew Knepley <[email protected]> wrote: > On Mon, Dec 1, 2014 at 1:02 PM, paul zhang <[email protected]> wrote: > I should have installed openmpi successfully... > > The Fortran wrapper does not seem to correctly link the libraries: > > ERROR while running executable: Could not execute > "/tmp/petsc-rVaKfJ/config.setCompilers/conftest": > /tmp/petsc-rVaKfJ/config.setCompilers/conftest: symbol lookup error: > /home/hzh225/LIB_CFD/openmpi-1.8.3/lib/libmpi_mpifh.so.2: undefined symbol: > mpi_fortran_weights_empty > > Or else you need something in your LD_LIBRARY_PATH. Either way, so you need > Fortran? If so, > use --download-mpich, otherwise use --with-fc=0. > > Thanks, > > Matt > > Attached. > > Thanks, > Paul > > 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 1:59 PM, Barry Smith <[email protected]> wrote: > > 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 > > > > > > > > -- > 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 >
