[Trilinos-Users] Cygwin Build Problems
Michael Sielemann
michael.sielemann at gmail.com
Thu Jan 15 02:09:27 MST 2009
Dear Ross,
I am trying to get a separate Windows computer from our IT guys with only
plain Windows installed (not the usual procedure of dumping some image with
OS+software but formatting and installing from original media). Then, I'll
try the standard procedure of building Trilinos. For that, I'd like to ask
for your confirmation on the procedure I described earlier using the
do-configure script shown below (your script minus some flags enabling
packages that did not make it into the general release yet):
1. Install latest Cygwin with
- Section 'devel': Adding several items by hand to the default such
that the complete set ends up as
autoconf wrapper scripts, autoconf 2.1, automake 1.5, binutils,
cmake, doxygen, e2fsprogs, gcc-core, gcc-g++, gcc-g77, gcc-mingw-core,
gcc-mingw-g++, gcc-mingw-g77, gettext, gtk2-x11, gtk-x11-runtime,
libfpx-devel, libfreetype2, libgdbm-devel, libhdf5-devel, libhdf5-runtime,
libiconv, lib-jasper-devel, liblcms-devel, libwmf-devel?!, libxml2,
libxml-devel, make, mingw-runtime, pango, pango-runtime
- Section 'math': The LAPACK package (includes BLAS)
- All others left on default
2. In the Cygwin Bash Console, do the following
Admin at Laptop ~
$ cd /cygdrive/c/tmp/
Admin at Laptop /cygdrive/c/tmp
$ gunzip trilinos-9.0.2.tar.gz
Admin at Laptop /cygdrive/c/tmp
$ tar xf trilinos-9.0.2.tar
Admin at Laptop /cygdrive/c/tmp
$ cd trilinos-9.0.2
Admin at Laptop /cygdrive/c/tmp/trilinos-9.0.2
$ mkdir cygwin_serial
Admin at Laptop /cygdrive/c/tmp/trilinos-9.0.2
$ cd cygwin_serial/
Admin at Laptop /cygdrive/c/tmp/trilinos-9.0.2/cygwin_serial
$ bash do-configure.sh
(...)
$ make everything
(...)
Thanks for your input,
Best regards MICHAEL
-----8<---------------------------------------------------------------------------------------------------------
#!/bin/sh
rm config.cache
../configure --prefix=/cygdrive/f/C_Sandbox/tribox/trilinoslib
\--cache-file=config.cache
\
--with-install="/usr/bin/install -p" \
CXXFLAGS="-g -O0 -ansi -pedantic -Wall -fexceptions" \
CFLAGS="-g -O0 -ansi -pedantic -Wall -fexceptions" \
FFLAGS="-g -O0 " \
--enable-export-makefiles \
--with-gnumake \
--disable-default-packages \
--enable-teuchos --enable-teuchos-extended --enable-teuchos-debug
--enable-teuchos-abc --disable-teuchos-blasfloat \
--enable-thyra \
--enable-epetra --enable-epetra-abc \
--enable-triutils --disable-triutils-tests --disable-triutils-examples \
--enable-epetraext \
--enable-amesos \
--enable-aztecoo \
--enable-belos \
--enable-ifpack \
--enable-ml \
--enable-nox --enable-nox-epetra --enable-nox-epetraext --enable-nox-thyra
--enable-nox-thyra-tests --enable-nox-tests \
--enable-loca \
--enable-stratimikos \
--enable-rythmos \
--enable-moocho \
--enable-sacado \
--enable-meros \
--enable-new_package \
--enable-galeri \
--enable-isorropia \
--enable-moertel \
--enable-anasazi \
--enable-didasko
On Wed, Jan 14, 2009 at 3:44 PM, Michael Sielemann <
michael.sielemann at gmail.com> wrote:
>
> Dear Ross,
> Thanks for your reply and also for your interest.
>
> Using the following GCC...
>
> $ gcc -v
> Reading specs from /usr/lib/gcc/i686-pc-cygwin/3.4.4/specs
> Configured with: /usr/build/package/orig/test.respin/gcc-3.4.4-3/configure
> --verbose --prefix=/usr --exec-prefix=/usr --
> sysconfdir=/etc --libdir=/usr/lib --libexecdir=/usr/lib
> --mandir=/usr/share/man --infodir=/usr/share/info --enable-langu
> ages=c,ada,c++,d,f77,pascal,java,objc --enable-nls
> --without-included-gettext --enable-version-specific-runtime-libs --w
> ithout-x --enable-libgcj --disable-java-awt --with-system-zlib
> --enable-interpreter --disable-libgcj-debug --enable-thre
> ads=posix --enable-java-gc=boehm --disable-win32-registry
> --enable-sjlj-exceptions --enable-hash-synchronization --enabl
> e-libstdcxx-debug
> Thread model: posix
> gcc version 3.4.4 (cygming special, gdc 0.12, using dmd 0.125)
>
>
> ...I compiled all package libraries successfully ('make -i') except Zoltan.
> Most warnings were regarding ISO C90 compatibility, implicit declarations,
> xyz will be initialized after abc, ISO C compatibility. I hope that this is
> expected in spite of supplying -ansi -pedantic. The actual errors are
> http://pastebin.com/m26cf085c
>
>
> Whenever I then try to build the tests or examples too many errors are
> reported. At some point I interrupt via Ctrl-C.
>
> Tests via 'make -i tests':
> http://pastebin.com/m19aeaac3
>
>
> Examples via 'make -i examples':
> http://pastebin.com/m205199a8
>
> To me, Zoltan is not of primary interest but as building the examples and
> tests fails, too, I expect that the build is corrupted, too.
>
> Even though I only have gcc, g++, g77 in exactly the same version in the
> present Cygwin installation (no 4.x versions or gfortran installed) I tried
> the --disable-fortran flag suggested earlier.
>
> In this case I do get a warning from teuchos/configure and others but that
> seems to be related to Fortran and thus shouldn't be a problem.
> checking for dgecon_... no
> checking for dgecon_ in -llapack... yes
> checking how to get verbose linking output from ... configure: WARNING:
> compilation failed
>
> checking for Fortran 77 libraries of ...
> checking for template-specific object files to be linked... none
>
> In teuchos/config.log:
> configure:16399: checking how to get verbose linking output from
> configure:16415: -c -g -O0 conftest.f >&5
> ../../../packages/teuchos/configure: line 16416: -c: command not found
> configure:16421: $? = 127
> configure: failed program was:
> | program main
> |
> | end
> configure:16502: WARNING: compilation failed
> configure:16509: result:
> configure:16511: checking for Fortran 77 libraries of
> configure:16534: -o conftest.exe -g -O0 conftest.f
> ../../../packages/teuchos/configure: line 16535: -o: command not found
> configure:16708: result:
> configure:16740: checking for template-specific object files to be linked
> configure:16743: result: none
>
> I ran this one (without Fortran code) with 'make' only. I got the same
> error message on Zoltan as before and stopped.
>
> I also tried downgrading to gcc 3.3.3-3. The error message was exactly the
> same as using 3.4.4-3.
>
> This is very weird. Is it possible that one of the tools used in the
> configure / make scripts behaves differently in the latest Cygwin version?
>
> I have lots of software on my computer that shows up in the environment
> variables under Cygwin (Services for Unix, Open Watcom installed by Maple,
> VS 8 etc.) that could potentially conflict with Cygwin/Gcc. Still, I
> reproduced the same error message on two other Windows computers (even one
> outside of our facility, DLR). So I expect that the source of the trouble is
> not the additional software. Just for fun I set PATH to only
> /usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/usr/bin:/usr/lib/lapack but
> nothing changed either. Once again, I got the strdup() undeclared error in
> some Zoltan code.
>
> BTW, for each 'configure' and 'make' run I have always been deleting the
> whole build tree to avoid extra trouble.
>
> Do you learn anything from all this?
>
> Thanks again for your time and input,
>
> Best regards,
>
> Michael
>
>
>
> On Tue, Jan 13, 2009 at 9:33 PM, Bartlett, Roscoe A <rabartl at sandia.gov>wrote:
>
>> Michael,
>>
>> This is very troubling. I have never seen errors like this.
>>
>> If you build with 'make -i everything' what packages build and which ones
>> do not?
>>
>> Cheers,
>>
>> - Ross
>>
>>
>> ------------------------------
>> *From:* Michael Sielemann [mailto:michael.sielemann at gmail.com]
>> *Sent:* Tuesday, January 13, 2009 7:47 AM
>> *To:* Trilinos-Users at software.sandia.gov; Bartlett, Roscoe A
>> *Subject:* Re: [Trilinos-Users] Cygwin Build Problems
>>
>>
>>
>>
>> Dear Ross,
>> By now I did two successful builds on Linux (one on OpenSuse 10.2 and one
>> on a Centos 5.2 node). But none on Cygwin. I tested on my laptop, a second
>> laptop and my home computer, which has a pretty fresh Windows XP
>> installation. They all failed. I made Cygwin installations as user and as
>> admin, with all packages in section "devel" selected and with a hand-picked
>> set only. I tried Trilinos versions 9.0.2 and 8.0.7.
>>
>> I understand that you did not have any trouble with this so I would like
>> to ask you whether I am missing out on a crucial step. This is what I do:
>> 1. Install latest Cygwin with
>> - All items in the devel section enabled ---or--- adding several
>> items by hand to the default such that the complete set ends up as
>> autoconf wrapper scripts, autoconf 2.1, automake 1.5, binutils,
>> cmake, doxygen, e2fsprogs, gcc-core, gcc-g++, gcc-g77, gcc-mingw-core,
>> gcc-mingw-g++, gcc-mingw-g77, gettext, gtk2-x11, gtk-x11-runtime,
>> libfpx-devel, libfreetype2, libgdbm-devel, libhdf5-devel, libhdf5-runtime,
>> libiconv, lib-jasper-devel, liblcms-devel, libwmf-devel!!, libxml2,
>> libxml-devel, make, mingw-runtime, pango, pango-runtime
>> - the LAPACK package from the math section (includes BLAS)
>> 2. In the Cygwin Bash Console, do the following (this one is from my home
>> computer)
>>
>> Admin at Laptop ~
>> $ cd /cygdrive/c/tmp/
>>
>> Admin at Laptop /cygdrive/c/tmp
>> $ gunzip trilinos-9.0.2.tar.gz
>>
>> Admin at Laptop /cygdrive/c/tmp
>> $ tar xf trilinos-9.0.2.tar
>>
>> Admin at Laptop /cygdrive/c/tmp
>> $ cd trilinos-9.0.2
>>
>> Admin at Laptop /cygdrive/c/tmp/trilinos-9.0.2
>> $ mkdir cygwin_serial
>>
>> Admin at Laptop /cygdrive/c/tmp/trilinos-9.0.2
>> $ cd cygwin_serial/
>>
>> Admin at Laptop /cygdrive/c/tmp/trilinos-9.0.2/cygwin_serial
>> $ bash do-configure.sh
>> rm: cannot remove `config.cache': No such file or directory
>>
>> (...)
>>
>> $ make everything
>>
>> (...)
>>
>> cc -DHAVE_CONFIG_H -I. -I../../src/include
>> -I../../../../../packages/zoltan/src/
>> driver
>> -I/cygdrive/c/tmp/trilinos-9.0.2/cygwin_serial/packages/zoltan/src/include
>> -I/cygdrive/c/tmp/trilinos-9.0.2/packages/zoltan/src/include
>> -I/cygdrive/c/tmp/
>> trilinos-9.0.2/packages/zoltan/siMPI/pyMPI/siMPI
>> -I../../../../../packages/zolta
>> n/src/driver/ -I../../../../../packages/zoltan/src/ch/ -g -O0 -ansi
>> -pedantic
>> -Wall -fexceptions -MT zCPPdrive-ch_input_read.o -MD -MP -MF
>> .deps/zCPPdrive-ch_
>> input_read.Tpo -c -o zCPPdrive-ch_input_read.o `test -f
>> '../../../../../packages
>> /zoltan/src/ch/ch_input_read.c' || echo
>> '../../../../../packages/zoltan/src/driv
>> er/'`../../../../../packages/zoltan/src/ch/ch_input_read.c
>> mv -f .deps/zCPPdrive-ch_input_read.Tpo .deps/zCPPdrive-ch_input_read.Po
>> CC -DHAVE_CONFIG_H -I. -I../../src/include
>> -I../../../../../packages/zoltan/src/
>> driver
>> -I/cygdrive/c/tmp/trilinos-9.0.2/cygwin_serial/packages/zoltan/src/include
>> -I/cygdrive/c/tmp/trilinos-9.0.2/packages/zoltan/src/include
>> -I/cygdrive/c/tmp/
>> trilinos-9.0.2/packages/zoltan/siMPI/pyMPI/siMPI
>> -I../../../../../packages/zolta
>> n/src/driver/ -I../../../../../packages/zoltan/src/ch/ -g -O0 -ansi
>> -pedantic
>> -Wall -fexceptions -MT zCPPdrive-dr_mainCPP.o -MD -MP -MF
>> .deps/zCPPdrive-dr_mai
>> nCPP.Tpo -c -o zCPPdrive-dr_mainCPP.o `test -f
>> '../../../../../packages/zoltan/s
>> rc/driver/dr_mainCPP.cpp' || echo
>> '../../../../../packages/zoltan/src/driver/'`.
>> ./../../../../packages/zoltan/src/driver/dr_mainCPP.cpp
>> In file included from
>> ../../../../../packages/zoltan/src/driver/dr_loadbal_const
>> .h:22,
>> from
>> ../../../../../packages/zoltan/src/driver/dr_mainCPP.cpp:2
>> 7:
>> /cygdrive/c/tmp/trilinos-9.0.2/packages/zoltan/src/include/zoltan_cpp.h:
>> In memb
>> er function `int Zoltan::Generate_Files(std::string&, const int&, const
>> int&, co
>> nst int&, const int&)':
>> */cygdrive/c/tmp/trilinos-9.0.2/packages/zoltan/src/include/zoltan_cpp.h:606:
>> err
>> or: `strdup' undeclared (first use this function)*
>> /cygdrive/c/tmp/trilinos-9.0.2/packages/zoltan/src/include/zoltan_cpp.h:606:
>> err
>> or: (Each undeclared identifier is reported only once for each function it
>> appea
>> $
>> make[5]: *** [zCPPdrive-dr_mainCPP.o] Error 1
>> make[5]: Leaving directory
>> `/cygdrive/c/tmp/trilinos-9.0.2/cygwin_serial/packages/
>> zoltan/src/driver'
>> make[4]: *** [all-recursive] Error 1
>> make[4]: Leaving directory
>> `/cygdrive/c/tmp/trilinos-9.0.2/cygwin_serial/packages/
>> zoltan/src'
>> make[3]: *** [all-recursive] Error 1
>> make[3]: Leaving directory
>> `/cygdrive/c/tmp/trilinos-9.0.2/cygwin_serial/packages/
>> zoltan'
>> make[2]: *** [all-recursive] Error 1
>> make[2]: Leaving directory
>> `/cygdrive/c/tmp/trilinos-9.0.2/cygwin_serial/packages'
>>
>> make[1]: *** [everything] Error 2
>> make[1]: Leaving directory
>> `/cygdrive/c/tmp/trilinos-9.0.2/cygwin_serial/packages'
>>
>> make: *** [everything] Error 2
>>
>>
>>
>> Configure almost never complains about anything but during 'make' or 'make
>> everything' the build process fails. GCC, G77, G++ are 3.4.4 as on your
>> Cygwin, too.
>>
>> siel_mi at rmlap069/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial
>> $ gcc --version
>> gcc (GCC) 3.4.4 (cygming special, gdc 0.12, using dmd 0.125)
>> Copyright (C) 2004 Free Software Foundation, Inc.
>> This is free software; see the source for copying conditions. There is NO
>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
>> PURPOSE.
>>
>>
>> siel_mi at rmlap069/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial
>> $ g++ --version
>> g++ (GCC) 3.4.4 (cygming special, gdc 0.12, using dmd 0.125)
>> Copyright (C) 2004 Free Software Foundation, Inc.
>> This is free software; see the source for copying conditions. There is NO
>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
>> PURPOSE.
>>
>>
>> siel_mi at rmlap069/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial
>> $ g77 --version
>> GNU Fortran (GCC) 3.4.4 (cygming special, gdc 0.12, using dmd 0.125)
>> Copyright (C) 2004 Free Software Foundation, Inc.
>>
>> GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
>> You may redistribute copies of GNU Fortran
>> under the terms of the GNU General Public License.
>> For more information about these matters, see the file named COPYING
>> or type the command `info -f g77 Copying'.
>>
>> Below, I am sending you the do-configure script I am using, which is
>> essentially yours after removing some --enable-xyz's for packages that I
>> think are not included in the general release.
>>
>> I also tried several modifications. This one is my favorite error message
>>
>>
>> /cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/teuchos/example/BLAS/../../../../../packages/teuchos/
>> example/BLAS/cxx_main.cpp:18: undefined reference to `std::cout'
>>
>> As you mentioned that you never had any trouble I am wondering what I am
>> doing wrong repeatedly. And I hope that you have some hints for me.
>>
>> Thanks in advance, and best regards MICHAEL
>>
>>
>>
>> -----8<---------------------------------------------------------------------------------------------------------
>>
>>
>> #!/bin/sh
>> rm config.cache
>> ../configure --prefix=/cygdrive/f/C_Sandbox/tribox/trilinoslib \
>> --cache-file=config.cache \
>> --with-install="/usr/bin/install -p" \
>> CXXFLAGS="-g -O0 -ansi -pedantic -Wall -fexceptions" \
>> CFLAGS="-g -O0 -ansi -pedantic -Wall -fexceptions" \
>> FFLAGS="-g -O0 " \
>> --enable-export-makefiles \
>> --with-gnumake \
>> --disable-default-packages \
>> --enable-teuchos --enable-teuchos-extended --enable-teuchos-debug
>> --enable-teuchos-abc --disable-teuchos-blasfloat \
>> --enable-thyra \
>> --enable-epetra --enable-epetra-abc \
>> --enable-triutils --disable-triutils-tests --disable-triutils-examples \
>> --enable-epetraext \
>> --enable-amesos \
>> --enable-aztecoo \
>> --enable-belos \
>> --enable-ifpack \
>> --enable-ml \
>> --enable-nox --enable-nox-epetra --enable-nox-epetraext --enable-nox-thyra
>> --enable-nox-thyra-tests --enable-nox-tests \
>> --enable-loca \
>> --enable-stratimikos \
>> --enable-rythmos \
>> --enable-moocho \
>> --enable-sacado \
>> --enable-meros \
>> --enable-new_package \
>> --enable-galeri \
>> --enable-isorropia \
>> --enable-moertel \
>> --enable-anasazi \
>> --enable-didasko
>>
>>
>>
>>
>>
>
> _______________________________________________
> Trilinos-Users mailing list
> Trilinos-Users at software.sandia.gov
> http://software.sandia.gov/mailman/listinfo/trilinos-users
>
>
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