Paul,
./configure is trying to compile a trivial Fortran program with
/home/hzh225/LIB_CFD/openmpi-1.8.3/bin/mpif90 and failing. See full output from
below. You can try the same thing from the command line and see that there is
something wrong with the MPI install.
Barry
TEST checkFortranCompiler from
config.setCompilers(/home/hzh225/LIB_CFD/nP/petsc-3.5.2/config/BuildSystem/config/setCompilers.py:910)
TESTING: checkFortranCompiler from
config.setCompilers(config/BuildSystem/config/setCompilers.py:910)
Locate a functional Fortran compiler
Checking for program /home/hzh225/LIB_CFD/openmpi-1.8.3/bin/mpif90...found
Defined make macro "FC" to
"/home/hzh225/LIB_CFD/openmpi-1.8.3/bin/mpif90"
Executing: /home/hzh225/LIB_CFD/openmpi-1.8.3/bin/mpif90 -c -o
/tmp/petsc-rVaKfJ/config.setCompilers/conftest.o
-I/tmp/petsc-rVaKfJ/config.setCompilers
/tmp/petsc-rVaKfJ/config.setCompilers/conftest.F
Successful compile:
Source:
program main
end
Executing: /home/hzh225/LIB_CFD/openmpi-1.8.3/bin/mpif90 -o
/tmp/petsc-rVaKfJ/config.setCompilers/conftest
/tmp/petsc-rVaKfJ/config.setCompilers/conftest.o
Executing: /tmp/petsc-rVaKfJ/config.setCompilers/conftest
Executing: /tmp/petsc-rVaKfJ/config.setCompilers/conftest
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
> On Dec 1, 2014, at 1:02 PM, paul zhang <[email protected]> wrote:
>
> I should have installed openmpi successfully...
>
>
> 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
> >
>
>
> <configure.log>
