[petsc-users] valgrind

Mon Dec 1 12:57:40 CST 2014

On Mon, 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?
>

It looks like your Fortran is broken here. Send configure.log so we can see
what the problem is. If you do not need
Fortran, use --with-fc=0 in the configuration.

 Thanks,

    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 1:34 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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