[petsc-users] valgrind

paul zhang paulhuaizhang at gmail.com
Mon Dec 1 12:55:44 CST 2014 

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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20141201/46c9aebc/attachment.html>

More information about the petsc-users mailing list