[petsc-users] valgrind
Matthew Knepley
knepley at gmail.com
Mon Dec 1 13:06:25 CST 2014
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?
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > 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
>> >
>>
>>
>
--
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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