[petsc-users] valgrind

[Barry Smith]

  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
>