[Trilinos-Users] Cygwin Build Problems

[Michael Sielemann]

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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