[petsc-users] valgrind
paul zhang
paulhuaizhang at gmail.com
Mon Dec 1 13:02:32 CST 2014
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 <bsmith at mcs.anl.gov> 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 <paulhuaizhang at gmail.com> 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 <knepley at gmail.com>
> wrote:
> > On Mon, Dec 1, 2014 at 12:33 PM, paul zhang <paulhuaizhang at gmail.com>
> 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 <paulhuaizhang at gmail.com>
> wrote:
> > I did use the PETSc makefiles. Should I include the valgrind path in my
> own make file again?
> >
> > [hzh225 at dlxlogin2-2 petsc-3.5.2]$ pwd
> > /home/hzh225/LIB_CFD/nP/petsc-3.5.2
> > [hzh225 at 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 <knepley at gmail.com>
> wrote:
> > On Mon, Dec 1, 2014 at 10:43 AM, paul zhang <paulhuaizhang at gmail.com>
> 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 at 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 <knepley at gmail.com>
> wrote:
> > On Mon, Dec 1, 2014 at 10:21 AM, paul zhang <paulhuaizhang at gmail.com>
> 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
> >
>
>
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