[Developers] beta compile failure on Ubuntu?
Johnoel Ancheta
johnoel at hawaii.edu
Fri Nov 12 14:09:01 PST 2010
Opps... Sorry...
I accidentally committed the Makefile without the -O3 option.
I'll correct and commit the changes.
Thanks Dave for catching that.
Johnoel
On 11/12/10 4:09 AM, dave fournier wrote:
> 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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>>>
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