[petsc-users] valgrind

Mon Dec 1 13:13:34 CST 2014

  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 <paulhuaizhang at gmail.com> 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 <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
> >
> 
> 
> <configure.log>