[Trilinos-Users] Cygwin Build Problems
Michael Sielemann
michael.sielemann at gmail.com
Sun Jan 11 10:24:51 MST 2009
Dear all,
I am sending a quick update: I tried to adapt the settings I found in
http://trilinos.sandia.gov/packages/docs/r9.0/packages/nox/doc/html/step1.html
So I ran...
../configure --prefix=/cygdrive/f/C_Sandbox/tribox/trilinoslib \
--disable-tests \
--disable-examples \
--enable-nox \
--enable-nox-tests \
--enable-nox-examples \
--enable-prerelease \
--enable-nox-lapack \
--enable-nox-epetra \
--with-nox-epetraext \
--enable-loca \
--enable-epetra \
--enable-epetraext \
--enable-ifpack \
--enable-aztecoo \
--enable-triutils \
--enable-anasazi \
--enable-teuchos --enable-teuchos-complex \
--disable-default-packages \
--disable-python \
--with-lapack="-L/cygdrive/f/C_Sandbox/tribox/atlaslib/lib/ -llapack"
--with-blas="-L/cygdrive/f/C_Sandbox/tribox/atlaslib/lib -lf77blas -lcblas
-latlas" \ CXXFLAGS="-DMPICH_SKIP_MPICXX -g -ansi -Wall" CFLAGS="-g -ansi
-Wall" FFLAGS="-g -ansi -Wall" \
--with-gnumake --cache-file=config.cache
...without --enable-prerelease, because the include files used in
\trilinos-9.0.1\packages\nox\src\NOX_Direction_Factory.C for that option are
not provided right now (NOX_Direction_Tensor.H etc.).
Now, I get many errors of the following type:
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/stl_uninitialized.h:(.text$_Z
NSt6vectorISsSaISsEE20_M_allocate_and_copyIN9__gnu_cxx17__normal_iteratorIPKSsS1
_EEEEPSsjT_S9_[std::basic_string<char, std::char_traits<char>,
std::allocator<ch
ar> >* std::vector<std::basic_string<char, std::char_traits<char>,
std::allocato
r<char> >, std::allocator<std::basic_string<char, std::char_traits<char>,
std::a
llocator<char> > >
>::_M_allocate_and_copy<__gnu_cxx::__normal_iterator<std::bas
ic_string<char, std::char_traits<char>, std::allocator<char> > const*,
std::vect
or<std::basic_string<char, std::char_traits<char>, std::allocator<char> >,
std::
allocator<std::basic_string<char, std::char_traits<char>,
std::allocator<char> >
> > > >(unsigned int, __gnu_cxx::__normal_iterator<std::basic_string<char,
std:
:char_traits<char>, std::allocator<char> > const*,
std::vector<std::basic_string
<char, std::char_traits<char>, std::allocator<char> >,
std::allocator<std::basic
_string<char, std::char_traits<char>, std::allocator<char> > > > >,
__gnu_cxx::_
_normal_iterator<std::basic_string<char, std::char_traits<char>,
std::allocator<
char> > const*, std::vector<std::basic_string<char, std::char_traits<char>,
std:
:allocator<char> >, std::allocator<std::basic_string<char,
std::char_traits<char
>, std::allocator<char> > > > >)]+0xc): undefined reference to
`___gxx_personali
ty_sj0'
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/stl_uninitialized.h:(.text$_Z
NSt6vectorISsSaISsEE20_M_allocate_and_copyIN9__gnu_cxx17__normal_iteratorIPKSsS1
_EEEEPSsjT_S9_[std::basic_string<char, std::char_traits<char>,
std::allocator<ch
ar> >* std::vector<std::basic_string<char, std::char_traits<char>,
std::allocato
r<char> >, std::allocator<std::basic_string<char, std::char_traits<char>,
std::a
llocator<char> > >
>::_M_allocate_and_copy<__gnu_cxx::__normal_iterator<std::bas
ic_string<char, std::char_traits<char>, std::allocator<char> > const*,
std::vect
or<std::basic_string<char, std::char_traits<char>, std::allocator<char> >,
std::
allocator<std::basic_string<char, std::char_traits<char>,
std::allocator<char> >
> > > >(unsigned int, __gnu_cxx::__normal_iterator<std::basic_string<char,
std:
:char_traits<char>, std::allocator<char> > const*,
std::vector<std::basic_string
<char, std::char_traits<char>, std::allocator<char> >,
std::allocator<std::basic
_string<char, std::char_traits<char>, std::allocator<char> > > > >,
__gnu_cxx::_
_normal_iterator<std::basic_string<char, std::char_traits<char>,
std::allocator<
char> > const*, std::vector<std::basic_string<char, std::char_traits<char>,
std:
:allocator<char> >, std::allocator<std::basic_string<char,
std::char_traits<char
>, std::allocator<char> > > > >)]+0x80): undefined reference to
`___cxa_begin_ca
tch'
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/stl_uninitialized.h:(.text$_Z
NSt6vectorISsSaISsEE20_M_allocate_and_copyIN9__gnu_cxx17__normal_iteratorIPKSsS1
_EEEEPSsjT_S9_[std::basic_string<char, std::char_traits<char>,
std::allocator<ch
ar> >* std::vector<std::basic_string<char, std::char_traits<char>,
std::allocato
r<char> >, std::allocator<std::basic_string<char, std::char_traits<char>,
std::a
llocator<char> > >
>::_M_allocate_and_copy<__gnu_cxx::__normal_iterator<std::bas
ic_string<char, std::char_traits<char>, std::allocator<char> > const*,
std::vect
or<std::basic_string<char, std::char_traits<char>, std::allocator<char> >,
std::
allocator<std::basic_string<char, std::char_traits<char>,
std::allocator<char> >
> > > >(unsigned int, __gnu_cxx::__normal_iterator<std::basic_string<char,
std:
:char_traits<char>, std::allocator<char> > const*,
std::vector<std::basic_string
<char, std::char_traits<char>, std::allocator<char> >,
std::allocator<std::basic
_string<char, std::char_traits<char>, std::allocator<char> > > > >,
__gnu_cxx::_
_normal_iterator<std::basic_string<char, std::char_traits<char>,
std::allocator<
char> > const*, std::vector<std::basic_string<char, std::char_traits<char>,
std:
:allocator<char> >, std::allocator<std::basic_string<char,
std::char_traits<char
>, std::allocator<char> > > > >)]+0xa5): undefined reference to
`___cxa_rethrow'
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/stl_uninitialized.h:(.text$_Z
NSt6vectorISsSaISsEE20_M_allocate_and_copyIN9__gnu_cxx17__normal_iteratorIPKSsS1
_EEEEPSsjT_S9_[std::basic_string<char, std::char_traits<char>,
std::allocator<ch
ar> >* std::vector<std::basic_string<char, std::char_traits<char>,
std::allocato
r<char> >, std::allocator<std::basic_string<char, std::char_traits<char>,
std::a
llocator<char> > >
>::_M_allocate_and_copy<__gnu_cxx::__normal_iterator<std::bas
ic_string<char, std::char_traits<char>, std::allocator<char> > const*,
std::vect
or<std::basic_string<char, std::char_traits<char>, std::allocator<char> >,
std::
allocator<std::basic_string<char, std::char_traits<char>,
std::allocator<char> >
> > > >(unsigned int, __gnu_cxx::__normal_iterator<std::basic_string<char,
std:
:char_traits<char>, std::allocator<char> > const*,
std::vector<std::basic_string
<char, std::char_traits<char>, std::allocator<char> >,
std::allocator<std::basic
_string<char, std::char_traits<char>, std::allocator<char> > > > >,
__gnu_cxx::_
_normal_iterator<std::basic_string<char, std::char_traits<char>,
std::allocator<
char> > const*, std::vector<std::basic_string<char, std::char_traits<char>,
std:
:allocator<char> >, std::allocator<std::basic_string<char,
std::char_traits<char
>, std::allocator<char> > > > >)]+0xc8): undefined reference to
`___cxa_end_catc
h'
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/stl_uninitialized.h:(.text$_Z
St6__copyIPSsS0_ET0_T_S2_S1_St26random_access_iterator_tag[std::basic_string<cha
r, std::char_traits<char>, std::allocator<char> >*
std::__copy<std::basic_string
<char, std::char_traits<char>, std::allocator<char> >*,
std::basic_string<char,
std::char_traits<char>, std::allocator<char> >*>(std::basic_string<char,
std::ch
ar_traits<char>, std::allocator<char> >*, std::basic_string<char,
std::char_trai
ts<char>, std::allocator<char> >*, std::basic_string<char,
std::char_traits<char
>, std::allocator<char> >*, std::random_access_iterator_tag)]+0x28):
undefined r
eference to `std::basic_string<char, std::char_traits<char>,
std::allocator<char
> >::operator=(std::basic_string<char, std::char_traits<char>,
std::allocator<ch
ar> > const&)'
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/stl_uninitialized.h:(.text$_Z
St15__copy_backwardIPSsS0_ET0_T_S2_S1_St26random_access_iterator_tag[std::basic_
string<char, std::char_traits<char>, std::allocator<char> >*
std::__copy_backwar
d<std::basic_string<char, std::char_traits<char>, std::allocator<char> >*,
std::
basic_string<char, std::char_traits<char>, std::allocator<char>
>*>(std::basic_s
tring<char, std::char_traits<char>, std::allocator<char> >*,
std::basic_string<c
har, std::char_traits<char>, std::allocator<char> >*,
std::basic_string<char, st
d::char_traits<char>, std::allocator<char> >*,
std::random_access_iterator_tag)]
+0x34): undefined reference to `std::basic_string<char,
std::char_traits<char>,
std::allocator<char> >::operator=(std::basic_string<char,
std::char_traits<char>
, std::allocator<char> > const&)'
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/stl_uninitialized.h:(.text$_Z
St6__copyIPKSsPSsET0_T_S4_S3_St26random_access_iterator_tag[std::basic_string<ch
ar, std::char_traits<char>, std::allocator<char> >*
std::__copy<std::basic_strin
g<char, std::char_traits<char>, std::allocator<char> > const*,
std::basic_string
<char, std::char_traits<char>, std::allocator<char>
>*>(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const*,
std::basic_string<char, s
td::char_traits<char>, std::allocator<char> > const*,
std::basic_string<char, st
d::char_traits<char>, std::allocator<char> >*,
std::random_access_iterator_tag)]
+0x28): undefined reference to `std::basic_string<char,
std::char_traits<char>,
std::allocator<char> >::operator=(std::basic_string<char,
std::char_traits<char>
, std::allocator<char> > const&)'
collect2: ld returned 1 exit status
make[5]: *** [rosenbrock.exe] Error 1
make[5]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_s
erial/packages/nox/examples/lapack/NOX_SimpleExamples'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_s
erial/packages/nox/examples/lapack'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_s
erial/packages/nox/examples'
make[2]: *** [examples] Error 2
make[2]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_s
erial/packages/nox'
Error, the make of target examples failed for the package !
make[1]: *** [examples] Error 2
make[1]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_s
erial/packages'
make: *** [examples] Error 2
I notices messages of this type...
undefined reference to `___gxx_personality_sj0'
... which might indicate trouble due to different compiler versions in
ATLAS, LAPACK on one hand and Trilinos on the other!?! Is this correct?
Currently, I am trying to get the compiler selection of ATLAS, LAPACK and
Trilinos right.
If someone posted working compiler flags for ATLAS, netlib's LAPACK and
Trilinos under current Cygwin I'd appreciate that very much.
Best regards
Michael
---------- Forwarded message ----------
From: Michael Sielemann <michael.sielemann at gmail.com>
Date: Fri, Jan 9, 2009 at 3:57 PM
Subject: Cygwin Build Problems
To: Trilinos-Users at software.sandia.gov
Dear all,
I read through the last six months of compile problem emails on
Trilinos-Users but still have trouble compiling on Cygwin.
Configure works fine with the following flags. Also, I succeed to compile
the libraries. But the examples won't compile.
___
$ ../configure F77=g77 CC=gcc CXX=g++ --with-gnumake
--with-blas="-L/cygdrive/f
/C_Sandbox/tribox/atlaslib/lib -lf77blas -lcblas -latlas"
--with-lapack="-L/cyg
drive/f/C_Sandbox/tribox/atlaslib/lib/ -llapack"
--prefix=/cygdrive/f/C_Sandbox
/tribox/trilinoslib/ --enable-didasko --enable-nox --enable-nox-epetra
--enable
-nox-examples --cache-file=config.cache
$ make
$ make examples
leads to
Making all in HBMatrices
make[4]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_
serial/packages/didasko/examples/HBMatrices'
make[4]: *** No rule to make target `GetNecessaryFiles.exe', needed by
`all-am'.
Stop.
make[4]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_s
erial/packages/didasko/examples/HBMatrices'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_s
erial/packages/didasko/examples'
make[2]: *** [examples] Error 2
make[2]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_s
erial/packages/didasko'
Error, the make of target examples failed for the package !
make[1]: *** [examples] Error 2
make[1]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_s
erial/packages'
make: *** [examples] Error 2
Earlier I tried --enable-sacado, too. But then "make everything" complained
that
/trilinos-9.0.1/packages/nox/examples/epetra/System_Sacado_FEApp/AppModelEval.H
was missing, which does not seem to be included in the tar of 9.0.1 nor
9.0.2.
Earlier this week, I compiled netlib's LAPACK with g77 and ATLAS following
the guidelines with gcc-4.
Is this incompatible with the Trilinos flags above? I tried to change this
but both
../configure F77=g77 CC=gcc-4 CXX=g++-4 (...)
and
../configure F77=gfortran-4 CC=gcc-4 CXX=g++-4 (...)
report trouble finding BLAS.
checking for dgemm_ in -L/cygdrive/f/C_Sandbox/tribox/atlaslib/lib -lf77blas
-lcblas -latlas... no
checking for dgemm in -L/cygdrive/f/C_Sandbox/tribox/atlaslib/lib -lf77blas
-lcblas -latlas... no
checking for DGEMM in -L/cygdrive/f/C_Sandbox/tribox/atlaslib/lib -lf77blas
-lcblas -latlas... no
checking for DGEMM_ in -L/cygdrive/f/C_Sandbox/tribox/atlaslib/lib -lf77blas
-lcblas -latlas... no
configure: error: Cannot find blas library, specify a path using
--with-blas=DIR
/LIB (for example --with-blas=/usr/path/lib/libcxml.a)
I did not find the hints mentioned in the documentation for trouble due to
different compiler versions ("personality error" etc.) so I did not
elaborate more on this.
Does someone have an idea of what is going wrong on my computer?
Thanks, in advance, for any input,
Best regards MICHAEL
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://software.sandia.gov/mailman/private/trilinos-users/attachments/20090111/ed0c9fff/attachment-0001.html
More information about the Trilinos-Users
mailing list