[Developers] beta compile failure on Ubuntu?
dave fournier
davef at otter-rsch.com
Fri Nov 12 06:09:06 PST 2010
Ian Taylor wrote:
Just a thought Re speed. I don't see a -O3 flag for gcc for optimization.
> Hi Johnoel and others,
>
> Compiling ADMB 10 Beta on with 64-bit linux worked perfectly for me
> with the files in the download.
>
> However, the new script you sent by email failed. From the commands
> below (fuller notes attached), it looks like for Ubuntu at least, it
> would be better to test for 64 vs 32 using uname -m rather than uname -p.
>
> ~/admb/admb-10.0Beta $ uname -a
> Linux ian-laptop 2.6.32-25-generic #45-Ubuntu SMP Sat Oct 16
> 19:52:42 UTC 2010 x86_64 GNU/Linux
> ~/admb/admb-10.0Beta $ uname -s
> Linux
> ~/admb/admb-10.0Beta $ uname -p
> unknown
> ~/admb/admb-10.0Beta $ uname -m
> x86_64
>
> Aside from the good news of the successful install, this version 10
> Beta also produced identical results, which is also good news.
> However, it seems to be running slower than version 9, by a large
> margin, at least for a single model that I tried. Perhaps related to
> this, when I compiled using GCC in and ADMB version 9, the safe
> executable was about double the size of the optimized. Compiling with
> ADMB version 10, the file sizes are similar, and in between the old
> sizes. Perhaps the speed and file size differences are related to
> changes in the compile scripts? My old script was dated "23 May 2009".
>
> Finally, thank you, Johnoel, and all the others who've contributed to
> the developments that have gone into this new beta release.
> -Ian
>
> On 11/10/2010 02:44 PM, Johnoel Ancheta wrote:
>> Updated configure script is available.
>>
>> http://admb-project.googlecode.com/files/configure
>>
>> Download and replace the configure script in the admb-10.0Beta
>> distribution.
>>
>>
>> On 11/10/10 11:09 AM, Ben Bolker wrote:
>>> (running under VMWare Fusion on Mac OS X.6, but I don't think that
>>> matters)
>>>
>>> It looks like configure is getting confused and thinking my
>>> system is
>>> 64-bit ... ?
>>>
>>>> uname -a
>>> Linux ubuntu-10 2.6.32-25-generic #45-Ubuntu SMP Sat Oct 16 19:48:22
>>> UTC
>>> 2010 i686 GNU/Linux
>>>
>>> uname -m
>>> i686 ## indicates 32-bit kernel
>>>
>>> $ gcc -v
>>> Using built-in specs.
>>> Target: i486-linux-gnu
>>> Configured with: ../src/configure -v --with-pkgversion='Ubuntu
>>> 4.4.3-4ubuntu5' --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs
>>> --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
>>> --enable-shared --enable-multiarch --enable-linker-build-id
>>> --with-system-zlib --libexecdir=/usr/lib --without-included-gettext
>>> --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4
>>> --program-suffix=-4.4 --enable-nls --enable-clocale=gnu
>>> --enable-libstdcxx-debug --enable-plugin --enable-objc-gc
>>> --enable-targets=all --disable-werror --with-arch-32=i486
>>> --with-tune=generic --enable-checking=release --build=i486-linux-gnu
>>> --host=i486-linux-gnu --target=i486-linux-gnu
>>> Thread model: posix
>>> gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5)
>>>
>>>
>>>
>>> bolker at ubuntu-10:/usr/local/src/admb-10.0Beta$
>>> <mailto:bolker at ubuntu-10:/usr/local/src/admb-10.0Beta$> sudo
>>> ./configure
>>> checking for gcc... gcc
>>> checking whether the C compiler works... yes
>>> checking for C compiler default output file name... a.out
>>> checking for suffix of executables...
>>> checking whether we are cross compiling... no
>>> checking for suffix of object files... o
>>> checking whether we are using the GNU C compiler... yes
>>> checking whether gcc accepts -g... yes
>>> checking for gcc option to accept ISO C89... none needed
>>> checking for g++... g++
>>> checking whether we are using the GNU C++ compiler... yes
>>> checking whether g++ accepts -g... yes
>>> checking how to run the C++ preprocessor... g++ -E
>>> checking for grep that handles long lines and -e... /bin/grep
>>> checking for egrep... /bin/grep -E
>>> checking for ANSI C header files... yes
>>> checking for sys/types.h... yes
>>> checking for sys/stat.h... yes
>>> checking for stdlib.h... yes
>>> checking for string.h... yes
>>> checking for memory.h... yes
>>> checking for strings.h... yes
>>> checking for inttypes.h... yes
>>> checking for stdint.h... yes
>>> checking for unistd.h... yes
>>> checking iostream usability... yes
>>> checking iostream presence... yes
>>> checking for iostream... yes
>>> checking for flex... flex
>>> checking lex output file root... lex.yy
>>> checking lex library... none needed
>>> checking whether yytext is a pointer... no
>>> checking for sed... yes
>>> checking whether C++ compiler is 64-bit enabled... yes
>>> checking for svnversion... yes
>>> configure: creating ./config.status
>>> config.status: creating GNUmakefile
>>> config.status: creating admb_configure.h
>>> config.status: creating scripts/bash/admb-bin
>>>
>>> Configure completed for admb10.0Beta-linux-gcc4.4.3-64bit
>>> To build ADMB, type 'make'
>>> bolker at ubuntu-10:/usr/local/src/admb-10.0Beta$
>>> <mailto:bolker at ubuntu-10:/usr/local/src/admb-10.0Beta$> sudo make
>>> CXX=g++ CXXFLAGS="-m64"
>>> LIBPATH=../build/admb10.0Beta-linux-gcc4.4.3-64bit/objects
>>> DISK=../build/admb10.0Beta-linux-gcc4.4.3-64bit/dist ADMB_CONFIGURE=1
>>> make --directory=src --file=linux.mak
>>> make[1]: Entering directory `/usr/local/src/admb-10.0Beta/src'
>>> rm -rf ../build/admb10.0Beta-linux-gcc4.4.3-64bit/dist
>>> mkdir -p
>>> ../build/admb10.0Beta-linux-gcc4.4.3-64bit/dist/{bin,lib,include,docs,docs/manuals,examples}
>>>
>>> mkdir -p ../build/admb10.0Beta-linux-gcc4.4.3-64bit/objects/linad99-olp
>>> mkdir -p ../build/admb10.0Beta-linux-gcc4.4.3-64bit/objects/linad99-slp
>>> mkdir -p ../build/admb10.0Beta-linux-gcc4.4.3-64bit/objects/nh99-olp
>>> mkdir -p
>>> ../build/admb10.0Beta-linux-gcc4.4.3-64bit/objects/nh99-olp-stub
>>> mkdir -p ../build/admb10.0Beta-linux-gcc4.4.3-64bit/objects/tools99-olp
>>> mkdir -p
>>> ../build/admb10.0Beta-linux-gcc4.4.3-64bit/objects/df1b2-separable-slp
>>> mkdir -p
>>> ../build/admb10.0Beta-linux-gcc4.4.3-64bit/objects/df1b2-separable-olp
>>> make --directory=df1b2-separable CC=gcc CXXFLAGS="-c -m64 -Wall
>>> -Wno-deprecated -DUSE_LAPLACE -fpermissive -I../df1b2-separable
>>> -I../nh99 -I../linad99 -I../tools99 -D__SPDLL__ -D__GNUDOS__ -Dlinux
>>> -DOPT_LIB"
>>> LIBPATH=../../build/admb10.0Beta-linux-gcc4.4.3-64bit/objects/df1b2-separable-olp
>>>
>>> DISKDIR=../../build/admb10.0Beta-linux-gcc4.4.3-64bit/dist -f
>>> optg32-rh8-laplace.mak disk
>>> make[2]: Entering directory
>>> `/usr/local/src/admb-10.0Beta/src/df1b2-separable'
>>> g++ -c -m64 -Wall -Wno-deprecated -DUSE_LAPLACE -fpermissive
>>> -I../df1b2-separable -I../nh99 -I../linad99 -I../tools99 -D__SPDLL__
>>> -D__GNUDOS__ -Dlinux -DOPT_LIB df1b2impspf.cpp -o
>>> ../../build/admb10.0Beta-linux-gcc4.4.3-64bit/objects/df1b2-separable-olp/df1b2impspf.obj
>>>
>>> In file included from /usr/include/features.h:378,
>>> from /usr/include/unistd.h:26,
>>> from ../linad99/fvar.hpp:173,
>>> from ../nh99/admodel.h:69,
>>> from df1b2impspf.cpp:8:
>>> /usr/include/gnu/stubs.h:9:27: error: gnu/stubs-64.h: No such file or
>>> directory
>>> df1b2impspf.cpp: In function ‘double
>>> calculate_importance_sample_shess(const dvector&, const dvector&, const
>>> dmatrix&, const dvector&, const dvector&, const dmatrix&,
>>> function_minimizer*)’:
>>> df1b2impspf.cpp:20: warning: unused variable ‘Hessadjoint’
>>> df1b2impspf.cpp:44: warning: unused variable ‘onvar’
>>> df1b2impspf.cpp:49: warning: unused variable ‘j’
>>> make[2]: *** [df1b2impspf.obj] Error 1
>>> make[2]: Leaving directory
>>> `/usr/local/src/admb-10.0Beta/src/df1b2-separable'
>>> make[1]: *** [dist] Error 2
>>> make[1]: Leaving directory `/usr/local/src/admb-10.0Beta/src'
>>> make: *** [all] Error 2
>>> _______________________________________________
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>>> Developers at admb-project.org <mailto:Developers at admb-project.org>
>>> http://lists.admb-project.org/mailman/listinfo/developers
>>
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