Re: problems installing openmpi_ext

[Francis Poulin]

Hello,

Thanks to both of you for looking into this.  I am happy to try this in the 
debugger but I admit that I've never used it before and I'm having problems 
getting started. 

First, you don't mean to use the debugger in octave I bather?  I tried starting 

octave --debug

and that give a lot of output, none of which seemed at all useful.

Second ,you suggest running octave in a debugger and show 'run-octave -g'.  I 
did not know you could run octave in a debugger and am not sure exactly how to 
do that.  If you could get me started I'm happy to share the output.

Thanks again,
Francis


On 2013-09-08, at 3:42 AM, c. <address@hidden>
 wrote:

> 
> On 8 Sep 2013, at 09:28, c. <address@hidden> wrote:
> 
>> 
>> On 8 Sep 2013, at 00:55, Alexander Hansen <address@hidden> wrote:
>> 
>>>>> Fink's build process for the general package is pretty much identical to
>>>>> just installing it manually, and it appears to produce the same failure.
>>>>> :-(
>>>>> 
>>>>> My assumption is that some of the options that I'm using to build Octave
>>>>> aren't the best.  Here's what Fink uses (at least for the variant that
>>>>> uses untuned LAPACK):
>>>>> 
>>>>> octave:2> octave_config_info.config_opts
>>>>> ans = '--prefix=/sw' '--with-lapack=-L/sw/lib/lapack/3.4.2 -lreflapack'
>>>>> '--with-blas=-L/sw/lib/lapack/3.4.2 -lrefblas' '--with-framework-carbon'
>>>>> '--with-x' '--x-libraries=/usr/X11/lib' '--x-includes=/usr/X11/include'
>>>>> '--with-magick=GraphicsMagick'
>>>>> '--with-qhull-includedir=/sw/include/libqhull'
>>>>> '--host=x86_64-apple-darwin' '--build=x86_64-apple-darwin'
>>>>> '--infodir=/sw/share/info' '--mandir=/sw/share/man'
>>>>> '--libexecdir=/sw/lib' '--enable-shared' '--enable-dl'
>>>>> '--disable-static' '--disable-docs' '--enable-dependency-tracking'
>>>>> 'build_alias=x86_64-apple-darwin' 'host_alias=x86_64-apple-darwin'
>>>>> 'CC=flag-sort -r gcc' 'CFLAGS=-O3 -MD' 'LDFLAGS=-Wl,-dead_strip_dylibs
>>>>> -L/sw/lib' 'CPPFLAGS=-I/sw/include' 'CXX=flag-sort -r g++' 'CXXFLAGS=-O3
>>>>> -MD -I/usr/X11/include' 'F77=/sw/bin/gfortran-fsf-4.8' 'FFLAGS=-O3'
>>>> 
>>>> I should have added that "flag-sort" is a script that sorts the flags
>>>> fed to the compiler, and that "g++" and "gcc" are Apple's clang++ and
>>>> clang in this case.
>>>> 
>>> 
>>> Following up:
>>> 
>>> I tried rebuilding Octave (followed by rebuilding general) changing -O3 to 
>>> -O0 in the CFLAGS and CXXFLAGS, as well as switching the C and C++ 
>>> compilers to our FSF gcc-4.8, but I'm still getting the malloc() error that 
>>> Francis reported
>>> 
>>> octave:1> parcellfun_example
>>> Elapsed time is 9.4712 seconds.
>>> parcellfun: child process 46393 created
>>> parcellfun: child process 46394 created
>>> parcellfun: 0/200 jobs doneoctave(46386,0x7fff7479d180) malloc: *** error 
>>> for object 0x10c7f07e0: pointer being freed was not allocated
>>> *** set a breakpoint in malloc_error_break to debug
>>> panic: Abort trap: 6 -- stopping myself...
>>> 
>> 
>> 
>> Hi,
>> 
>> Sorry it took me long to respond but it's been a while since I 
>> last built the 3.6 version and it took me a few attempts to get 
>> it to work.
>> 
>> Here's my configure options:
>> 
>> ./configure                                                \
>>   CC=/opt/local/bin/gcc-mp-4.7                           \
>>   CFLAGS="-pipe -O2 -m64"                                \
>>   CPPFLAGS="-D_THREAD_SAFE -I/opt/local/include"         \
>>   LDFLAGS="-L/opt/local/lib -m64 /opt/local/lib/libsuitesparseconfig.a" \
>>   CXX=/opt/local/bin/g++-mp-4.7                          \
>>   CXXFLAGS="-pipe -O2 -m64"                              \
>>   F77=/opt/local/bin/gfortran-mp-4.7                     \
>>   FFLAGS="-pipe -O2 -m64"                                \
>>   LLVM_CONFIG=/opt/local/bin/llvm-config-mp-3.1          \
>>   --prefix=/opt/octave/3.6                               \
>>   --without-framework-carbon                             \
>>   --with-arpack                                          \
>>   --with-lapack="/opt/local/lib/liblapack.a /opt/local/lib/libatlas.a 
>> -lgfortran" \
>>   --with-blas="/opt/local/lib/libcblas.a /opt/local/lib/libf77blas.a 
>> /opt/local/lib/libatlas.a -lgfortran"   
>> 
>> Notice in particular I had to change blas/lapack as configure seemed to have 
>> problems detecting atlas
>> and that I had to add "libsuitesparseconfig.a" explicitely.
>> 
>> Finally I had to disable framework Carbon to avoid use of deprecated 
>> function CGDisplayBitsPerPixel.
>> 
>> All my  dependencies are installed via MacPorts.
>> 
>> With these options I get:
>> 
>>>> parcellfun_example
>> Elapsed time is 10.2874 seconds.
>> parcellfun: child process 87208 created
>> parcellfun: child process 87209 created
>> parcellfun: 200/200 jobs done
>> parcellfun: waiting for child process 87208 to close
>> parcellfun: waiting for child process 87209 to close
>> Elapsed time is 7.35937 seconds.
>>>> 
>> 
>> I attach parcellfun_example.m jus to make sure we are using the same example.
>> 
>> c.
> 
> As our configure options are not much different I suspect the error might not 
> be in Octave itself
> but rather in some of the linked libraries.
> 
> If you run Octave in a debugger (run-octave -g) and look at the backtrace of 
> the crash, that may give some hint ...
> c.