[Trilinos-Users] Cygwin Build Problems

Michael Sielemann michael.sielemann at gmail.com
Fri Jan 16 09:42:59 MST 2009 

Dear Ross,
I got a separate computer to do the tests I mentioned. It uses, just like my
laptop, the Core 2 Duo platform. Is this possibly the reason for the trouble
I am having (64 bit)? One of the other computers I tested earlier was a
Centrino, however.

Just for the record:
1. Started Cygwin Setup 2.573.2.3
   Installation for current user only
   Unix file type
   Downloaded from mirror http://www.gtlib.gatech.edu
   List of packages is in the attached ZIP file (cygwin.packages.log)
2. Configured using do-configure-orig.sh as suggested
3. Log of configure, screen dump of configure and make are also included in
the ZIP file.
4. Errors as reported before.

Best regards,

And have a great weekend,

Michael


On Thu, Jan 15, 2009 at 10:09 AM, Michael Sielemann <
michael.sielemann at gmail.com> wrote:

> 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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> http://software.sandia.gov/mailman/listinfo/trilinos-users
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>
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