[Trilinos-Users] Cygwin Build Problems

[Michael Sielemann]

Dear all,
A quick update: I removed several flags from the configure call suggested by
Ross...

the ones enabling Intrepid, TPetra, RBGen, CTrilinos
--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

...to get a setup that compiles under Suse (Linux 2.6). I took that as a
basis for a configure call under current Cygwin. But still no success. The
error message I get is still the same


make  all-recursive
make[1]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial'
Making all in packages
make[2]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages'
Making all in teuchos
make[3]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/teuchos'
Making all in src
make[4]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/teuchos/src'
make  all-am
make[5]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/teuchos/src'

Trilinos package teuchos subdirectory src built successfully.

make[5]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/teuchos/src'
make[4]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/teuchos/src'
make[4]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/teuchos'
Trilinos package teuchos built successfully
make[4]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/teuchos'
make[3]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/teuchos'
Making all in rtop
make[3]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/rtop'
Making all in src
make[4]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/rtop/src'
make  all-am
make[5]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/rtop/src'

Trilinos package rtop subdirectory src built successfully.

make[5]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/rtop/src'
make[4]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/rtop/src'
make[4]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/rtop'
Trilinos package rtop built successfully
make[4]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/rtop'
make[3]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/rtop'
Making all in zoltan
make[3]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan'
Making all in siMPI
make[4]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan/siMPI'
Making all in pyMPI
make[5]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan/siMPI/pyMPI'
Making all in siMPI
make[6]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan/siMPI/pyMPI/siMPI'
make[6]: Nothing to be done for `all'.
make[6]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan/siMPI/pyMPI/siMPI'
make[6]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan/siMPI/pyMPI'
make[6]: Nothing to be done for `all-am'.
make[6]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan/siMPI/pyMPI'
make[5]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan/siMPI/pyMPI'
make[5]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan/siMPI'
make[5]: Nothing to be done for `all-am'.
make[5]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan/siMPI'
make[4]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan/siMPI'
Making all in src
make[4]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan/src'
Making all in .
make[5]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan/src'

Trilinos package Zoltan subdirectory src built successfully.

make[5]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan/src'
Making all in driver
make[5]: Entering directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan/src/driver'
CC -DHAVE_CONFIG_H -I. -I../../src/include
-I../../../../../packages/zoltan/src/driver
-I/cygdrive/f/C_Sandbox/tribox/t
rilinos-9.0.2/Cygwin_serial/packages/zoltan/src/include
-I/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/packages/zoltan/sr
c/include
-I/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/packages/zoltan/siMPI/pyMPI/siMPI
-I../../../../../packages/zolt
an/src/driver/ -I../../../../../packages/zoltan/src/ch/   -g -O0 -ansi
-pedantic -Wall -fexceptions -MT zCPPdrive-dr_mai
nCPP.o -MD -MP -MF .deps/zCPPdrive-dr_mainCPP.Tpo -c -o
zCPPdrive-dr_mainCPP.o `test -f '../../../../../packages/zoltan/
src/driver/dr_mainCPP.cpp' || echo
'../../../../../packages/zoltan/src/driver/'`../../../../../packages/zoltan/src/drive
r/dr_mainCPP.cpp
In file included from
../../../../../packages/zoltan/src/driver/dr_loadbal_const.h:22,
                 from
../../../../../packages/zoltan/src/driver/dr_mainCPP.cpp:27:
/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/packages/zoltan/src/include/zoltan_cpp.h:
In member function `int Zoltan::Generate_Files(std::string&, const int&,
const int&, const int&, const int&)':
/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/packages/zoltan/src/include/zoltan_cpp.h:606:
error: `strdup' undeclared (first use this function)
/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/packages/zoltan/src/include/zoltan_cpp.h:606:
error: (Each undeclared identifier is reported only once for each function
it appears in.)
make[5]: *** [zCPPdrive-dr_mainCPP.o] Error 1
make[5]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan/src/driver'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan/src'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages/zoltan'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial/packages'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.2/Cygwin_serial'
make: *** [all] Error 2


Before that many warnings of different type appear, including the following.


../../../../packages/zoltan/src/zz/zz_coord.c: In function
`Zoltan_Get_Coordinates':
../../../../packages/zoltan/src/zz/zz_coord.c:338: warning: ISO C90 does not
support the `%lf' printf format
../../../../packages/zoltan/src/zz/zz_coord.c:338: warning: ISO C90 does not
support the `%lf' printf format


I also tried removing the --enable-export-makefiles flag because I got some
other errors otherwise.


I'll put Cygwin onto another Windows XP computer now and try to build
Trilinos there. If, in the meantime, someone posted some additional
information I'd be happy to read about it.

Aron, you mentioned that you went through certain steps with Cygwin. Are
there any deviations from the cookbook recipe given in the Users' Guide?

Thanks again and

Best regards MICHAEL




On Mon, Jan 12, 2009 at 1:09 PM, Michael Sielemann <
michael.sielemann at gmail.com> wrote:

> Dear all,
> Thanks for all the replies. Unfortunately I still did not succeeded to
> finish the compilation.
>
> First, I followed Ross' suggestions:
>
> Earlier, in the Cygwin setup utility (1.5-25), I selected everything in the
> section "devel". Due to this or as a default, LAPACK was active in the
> "math" section. I did not notice this until your email, though.
> In the Cygwin Bash consolve, I went to lapack-3.0-6. In the make file I had
> to correct the backward slash in lines 33 and 48 to a forward slash (strip
> $(LAPACK_DIR)/cyglapack.dll, strip $(LAPACK_DIR)/cygblas.dll). Otherwise the
> make failed. Ran 'make && make dist' as suggested in the readme. Extracted
> the lapack-3.0-5.tar.bz2 distribution into the Cygwin installation. Ran the
> script /etc/profile.d/lapack.sh to set paths properly.
> Ran the trilinos configure script as you suggested (only changed one flag
> to --prefix=/cygdrive/f/C_Sandbox/tribox/trilinoslib). Configure succeeded.
> Make everything failed because of strdup(), which should be available after
> including string.h, shouldn't it?
>
> cc -DHAVE_CONFIG_H -I. -I../../src/include
> -I../../../../../packages/zoltan/src/
> driver
> -I/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_serial3/packages/zo
> ltan/src/include
> -I/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/packages/zoltan/s
> rc/include
> -I/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/packages/zoltan/siMPI/p
> yMPI/siMPI -I../../../../../packages/zoltan/src/driver/
> -I../../../../../package
> s/zoltan/src/ch/   -g -O0 -ansi -pedantic -Wall -fexceptions -MT
> zdrive-dr_param
> _file.o -MD -MP -MF .deps/zdrive-dr_param_file.Tpo -c -o
> zdrive-dr_param_file.o
> `test -f '../../../../../packages/zoltan/src/driver/dr_param_file.c' ||
> echo '..
>
> /../../../../packages/zoltan/src/driver/'`../../../../../packages/zoltan/src/dri
> ver/dr_param_file.c
> ../../../../../packages/zoltan/src/driver/dr_param_file.c: In function
> `zoltanPa
> rams_hier_set_param':
> ../../../../../packages/zoltan/src/driver/dr_param_file.c:156: warning:
> implicit
>  declaration of function `strdup'
> ../../../../../packages/zoltan/src/driver/dr_param_file.c:156: warning:
> assignme
> nt makes pointer from integer without a cast
> ../../../../../packages/zoltan/src/driver/dr_param_file.c:157: warning:
> assignme
> nt makes pointer from integer without a cast
>
> (...)
>
> 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/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_serial3/packages/zo
> ltan/src/include
> -I/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/packages/zoltan/s
> rc/include
> -I/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/packages/zoltan/siMPI/p
> yMPI/siMPI -I../../../../../packages/zoltan/src/driver/
> -I../../../../../package
> s/zoltan/src/ch/   -g -O0 -ansi -pedantic -Wall -fexceptions -MT
> zCPPdrive-dr_ma
> inCPP.o -MD -MP -MF .deps/zCPPdrive-dr_mainCPP.Tpo -c -o
> zCPPdrive-dr_mainCPP.o
> `test -f '../../../../../packages/zoltan/src/driver/dr_mainCPP.cpp' || echo
> '../
>
> ../../../../packages/zoltan/src/driver/'`../../../../../packages/zoltan/src/driv
> er/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/f/C_Sandbox/tribox/trilinos-9.0.1/packages/zoltan/src/include/zoltan_c
> pp.h: In member function `int Zoltan::Generate_Files(std::string&, const
> int&, c
> onst int&, const int&, const int&)':
>
> /cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/packages/zoltan/src/include/zoltan_c
> pp.h:601: error: `strdup' undeclared (first use this function)
>
> /cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/packages/zoltan/src/include/zoltan_c
> pp.h:601: error: (Each undeclared identifier is reported only once for each
> func
> tion it appears in.)
> make[5]: *** [zCPPdrive-dr_mainCPP.o] Error 1
> make[5]: Leaving directory
> `/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_s
> erial3/packages/zoltan/src/driver'
> make[4]: *** [all-recursive] Error 1
> make[4]: Leaving directory
> `/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_s
> erial3/packages/zoltan/src'
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory
> `/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_s
> erial3/packages/zoltan'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory
> `/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_s
> erial3/packages'
> make[1]: *** [everything] Error 2
> make[1]: Leaving directory
> `/cygdrive/f/C_Sandbox/tribox/trilinos-9.0.1/Cygwin_s
> erial3/packages'
> make: *** [everything] Error 2
>
> I think that pasting the config.log doesnt help here, does it? Not finding
> strdup() sounds strange to me.
>
> BTW, I stopped using gcc-4, g++-4 and gfortran because they all are
> included in Cygwin as
> "version 4.3.2 20080827 (alpha-testing) 1 (GCC)"
>
> gcc, g++ and g77 seem to be more mature (all 3.4.4).
> $ 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
> --ver
> bose --prefix=/usr --exec-prefix=/usr --sysconfdir=/etc --libdir=/usr/lib
> --libe
> xecdir=/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 --without-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-exceptio
> ns --enable-hash-synchronization --enable-libstdcxx-debug
> Thread model: posix
> gcc version 3.4.4 (cygming special, gdc 0.12, using dmd 0.125)
>
>
> Mike,
> As always I deleted the whole build directory and used the same call to
> configure but with --disable-fortran and removing the FFLAGS flag.
>
> This got me the same error as before. Instead of disabling Zoltan I chose
> to try 9.0.2. This resulted in the same error, though. Then, I disabled
> Zoltan using --disable-zoltan on the configure line. However, the same error
> is reported (probably some other package depends on Zoltan?).
>
> I keep on getting all kinds of errors that do not give me much information.
> Do you suggest to re-install Cygwin considering that you "never had a
> problem building Trilinos under cygwin/gcc on any Windows laptop that [you]
> have ever had"!?
>
> Aron,
> I am posting a recent config.log to
> http://pastebin.com/m35d90bf6.Additionally, Zoltan's config.log is here
> http://pastebin.com/m7afffd07.
>
> Thanks to everybody for helping me,
>
> Best regards MICHAEL
>
>
>
>
> On Mon, Jan 12, 2009 at 12:03 AM, Bartlett, Roscoe A <rabartl at sandia.gov>wrote:
>
>>  Micheal,
>>
>> I have built Trilinos under Cygwin/gcc on a Windoxs XP laptop many times.
>> What I did was to use the BLAS and LAPACK that you can install with the
>> cygwin_setup.exe program (or whatever you call it).  Just run your's again
>> and select BLAS and LAPACK to install.
>>
>> Here is a configure script for cygwin that I have used fairly recently:
>>
>>
>> $ cat do-configure
>> #!/bin/sh
>> rm config.cache
>> $HOME/PROJECTS/Trilinos.base/Trilinos/configure \
>> --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-tpetra \
>> --enable-meros \
>> --enable-new_package \
>> --enable-galeri \
>> --enable-isorropia \
>> --enable-rbgen \
>> --enable-moertel \
>> --enable-anasazi \
>> --enable-intrepid \
>> --enable-ctrilinos \
>> --enable-didasko \
>>
>> --prefix=/home/rabartl/PROJECTS/install-dir/gcc-3.4.6/trilinos/dev/serial/dbg
>>
>>
>> Also, the version of g++ running on that system is:
>>
>>
>> $ gcc --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.
>>
>>
>>
>> I have never had a problem building Trilinos under cygwin/gcc on any
>> Windows laptop that I have ever had.
>>
>> I hope that helps,
>>
>> - Ross
>>
>>
>>
>>
>
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