[petsc-users] valgrind

Mon Dec 1 13:28:07 CST 2014

  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 <paulhuaizhang at gmail.com> 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
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> 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 <knepley at gmail.com> wrote:
> On Mon, Dec 1, 2014 at 1:02 PM, paul zhang <paulhuaizhang at gmail.com> 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 <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?
> >
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> > 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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> 
> -- 
> 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
> 