There does not appear to be any "make clean" or similar thing being called in
exodusii.py hence it is buggy. (see below)
Would who ever wrote this monstrosity, please fix it off of maint and get it
back into maint and eventually next and master
Thanks
Barry
BTW: Now that BuildSystem is a sub-something like thing of petsc would it be
possible to get all the packages/*.py files into one packages directory rather
than in two confusing locations?
Begin forwarded message:
> From: Barry Smith <[email protected]>
> Subject: Re: [petsc-users] How to understand these error messages
> Date: June 23, 2013 11:05:32 PM CDT
> To: Jed Brown <[email protected]>
> Cc: Fande Kong <[email protected]>, PETSc users list
> <[email protected]>
>
>
> On Jun 23, 2013, at 10:35 PM, Jed Brown <[email protected]> wrote:
>
>> Fande Kong <[email protected]> writes:
>>
>>> When I switch to gnu compiler, I can not install petsc, I got the following
>>> errors:
>>
>> Looks like an environment problem:
>>
>> Possible ERROR while running linker:
>> /glade/p/work/fandek/petsc/arch-linux2-cxx-opt_gnu/lib/libexodus.a(ex_err.o):
>> In function `ex_err':
>> ex_err.c:(.text+0xbc): undefined reference to `__intel_sse2_strcpy'
>> ex_err.c:(.text+0xe3): undefined reference to `__intel_sse2_strcpy'
>>
>> /glade/p/work/fandek/petsc/arch-linux2-cxx-opt_gnu/lib/libexodus.a(ex_utils.o):
>> In function `ex_put_names_internal':
>> ex_utils.c:(.text+0x247): undefined reference to `__intel_sse2_strlen'
>> ex_utils.c:(.text+0x292): undefined reference to `__intel_sse2_strlen'
>>
>> Did you load the wrong modules?
>
> Fande,
>
> The error you got listed below can happen when some of the code is
> compiled with the Intel compilers (which insert those funky symbols) but
> then linked with GNU which doesn't know about those symbols since they are
> hidden away inside the Intel compiler libraries.
>
> ex_err.c:(.text+0xbc): undefined reference to `__intel_sse2_strcpy'
> ex_err.c:(.text+0xe3): undefined reference to `__intel_sse2_strcpy'
> /glade/p/work/fandek/petsc/arch-linux2-cxx-opt_gnu/lib/libexodus.a(ex_utils.o):
> In function `ex_put_names_internal':
> ex_utils.c:(.text+0x247): undefined reference to `__intel_sse2_strlen'
> ex_utils.c:(.text+0x292): undefined reference to `__intel_sse2_strlen'
>
> Looking closer at the configure output I see
>
> sh: cd /glade/p/work/fandek/petsc/externalpackages/exodus-5.24/exodus && make
> -f Makefile.standalone libexodus.a RANLIB="/usr/bin/ranlib" AR="/usr/bin/ar
> cr" NETCDF="/glade/p/work/fandek/petsc/arch-linux2-cxx-opt_gnu" CC="mpicc"
> CCOPTIONS=" -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing
> -Wno-unknown-pragmas -O -DADDC_ " FC="mpif90" F77OPTIONS=" -fPIC -Wall
> -Wno-unused-variable -Wno-unused-dummy-argument -O "
> Executing: cd /glade/p/work/fandek/petsc/externalpackages/exodus-5.24/exodus
> && make -f Makefile.standalone libexodus.a RANLIB="/usr/bin/ranlib"
> AR="/usr/bin/ar cr"
> NETCDF="/glade/p/work/fandek/petsc/arch-linux2-cxx-opt_gnu" CC="mpicc"
> CCOPTIONS=" -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing
> -Wno-unknown-pragmas -O -DADDC_ " FC="mpif90" F77OPTIONS=" -fPIC -Wall
> -Wno-unused-variable -Wno-unused-dummy-argument -O "
> sh: echo "making exodus in cbind/src"
> making exodus in cbind/src
> (cd cbind/src && make -f Makefile.standalone "AR=/usr/bin/ar cr" "CC=mpicc"
> "CFLAGS=-O2 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing
> -Wno-unknown-pragmas -O -DADDC_ -DVERBOSE -I../../cbind/include
> -I../../forbind/include
> -I/glade/p/work/fandek/petsc/arch-linux2-cxx-opt_gnu/include "
> "RANLIB=/usr/bin/ranlib" libexodus.a)
> make[1]: Entering directory
> `/glade/p/work/fandek/petsc/externalpackages/exodus-5.24/exodus/cbind/src'
> make[1]: `libexodus.a' is up to date.
> make[1]: Leaving directory
> `/glade/p/work/fandek/petsc/externalpackages/exodus-5.24/exodus/cbind/src'
> cp cbind/src/libexodus.a .
> /usr/bin/ranlib libexodus.a
>
> it is NOT actually recompiling the libraries so the old library (compiled
> with Intel) is just reused resulting in the problem.
>
> Please do the following, rm -rf petsc/externalpackages/exodus-5.24 and then
> run the configure again and it should go through.
>
> Barryt
>
>
>
