Re: octave install

[Tatsuro MATSUOKA]

--- On Thu, 2014/4/10, Tatsuro MATSUOKA <address@hidden> wrote:

> --- On Thu, 2014/4/10, Tatsuro MATSUOKA <address@hidden> wrote:
> 
> > --- On Wed, 2014/4/9, address@hidden <address@hidden> wrote:
> > 
> > > On Wednesday, April 09, 2014 05:57 PM, Tatsuro MATSUOKA wrote:
> > > > --- On Wed, 2014/4/9, Tatsuro MATSUOKA <address@hidden> o
> > > >> Sorry my build was lack of lighdf
> > > >>
> > > >
> > > > I checked config.log
> > > >
> > > > configure:15393: gcc -c -g -O2 -pthread    conftest.c >&5
> > > > In file included from /usr/include/hdf5.h:24:0,
> > > >                   from conftest.c:90:
> > > > /usr/include/H5public.h:57:20: fatal error: mpi.h: No such file or 
> > > > directory
> > > > compilation terminated.
> > > > configure:15393: $? = 1
> > > >
> > > > The lack of mpi.h from openmpi is the origin of misdectioning 
> > > > libhdf5openmpi-dev.
> > > 
> > > Ah, thanks!
> > > 
> > > >
> > > > According to the synaptic package manager, openmpi on Ubuntu 12.04 LTS 
> > > > does not have dev package.  The version of openmpi bundled with gmsh is 
> > > > 1.4.3.  I have build openmpi-1.4.3 from source and installed to 
> > > > /usr/local.
> > > 
> > > Strange! Ubuntu quantal does have libopenmpi-dev and mpi.h lives in 
> > > /usr/include/mpi (a symlink created by update-alternatives). Therefore 
> > > passing CPPFLAGS=-I/usr/include/mpi to "configure" should have it 
> > > detected. Or maybe simply use setting CXX=mpic++ will be good enough.
> > > 
> > > >
> > > > The configure of octave-3.8.1 successfully detected hdf5.
> > > > Now I am executing "make".
> > > >
> > > > After "make" finished I will report the results.
> > > 
> > > I'll wait for your results. Building octave takes too long a time on my 
> > > rather old box. :-(
> > > 
> > > Regards,
> > > ST
> > > -- 
> > 
> > 
> > > Strange! Ubuntu quantal does have libopenmpi-dev and mpi.h lives in 
> > > /usr/include/mpi (a symlink created by update-alternatives). 
> > 
> > Thanks.  I will search them.
> > 
> > > I'll wait for your results. Building octave takes too long a time on my 
> > > rather old box. :-(
> > 
> > Unfortunately build was unsuccessful at compling __fltk_uigetfile__.cc
> > 
> > /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. 
> > -I..  -pthread -I/usr/include/cairo -I/usr/include/glib-2.0 
> > -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 
> > -I/usr/include/freetype2 -I/usr/include/libpng12   -fstack-protector 
> > --param=ssp-buffer-size=4 -Wformat -Wformat-security 
> > -Werror=format-security -DCP936  -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE 
> > -D_FILE_OFFSET_BITS=64 -D_THREAD_SAFE -D_REENTRANT -I/usr/include/freetype2 
> >   -I../liboctave/cruft/misc -I../liboctave/array -I../liboctave/numeric 
> > -I../liboctave/numeric -I../liboctave/operators -I../liboctave/operators 
> > -I../liboctave/system -I../liboctave/util -I./octave-value -I./operators 
> > -Iparse-tree -I./parse-tree -Icorefcn -I./corefcn -I../libgnu -I../libgnu  
> > -mieee-fp -Wall -W -Wshadow -Wold-style-cast -Wformat -Wpointer-arith 
> > -Wwrite-strings -Wcast-align -Wcast-qual -g -O2 -pthread -MT
 dldfcn/dldfcn___fltk_uigetfile___la-__fltk_uigetfile__.lo -MD -MP -MF
> >  dldfcn/.deps/dldfcn___fltk_uigetfile___la-__fltk_uigetfile__.Tpo -c -o 
> >dldfcn/dldfcn___fltk_uigetfile___la-__fltk_uigetfile__.lo `test -f 
> >'dldfcn/__fltk_uigetfile__.cc' || echo './'`dldfcn/__fltk_uigetfile__.cc
> > libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread 
> > -I/usr/include/cairo -I/usr/include/glib-2.0 
> > -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 
> > -I/usr/include/freetype2 -I/usr/include/libpng12 -fstack-protector 
> > --param=ssp-buffer-size=4 -Wformat -Wformat-security 
> > -Werror=format-security -DCP936 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE 
> > -D_FILE_OFFSET_BITS=64 -D_THREAD_SAFE -D_REENTRANT -I/usr/include/freetype2 
> > -I../liboctave/cruft/misc -I../liboctave/array -I../liboctave/numeric 
> > -I../liboctave/numeric -I../liboctave/operators -I../liboctave/operators 
> > -I../liboctave/system -I../liboctave/util -I./octave-value -I./operators 
> > -Iparse-tree -I./parse-tree -Icorefcn -I./corefcn -I../libgnu -I../libgnu 
> > -mieee-fp -Wall -W -Wshadow -Wold-style-cast -Wformat -Wpointer-arith 
> > -Wwrite-strings -Wcast-align -Wcast-qual -g -O2 -pthread -MT 
> > dldfcn/dldfcn___fltk_uigetfile___la-__fltk_uigetfile__.lo -MD -MP -MF
> >  dldfcn/.deps/dldfcn___fltk_uigetfile___la-__fltk_uigetfile__.Tpo -c 
> >dldfcn/__fltk_uigetfile__.cc  -fPIC -DPIC -o 
> >dldfcn/.libs/dldfcn___fltk_uigetfile___la-__fltk_uigetfile__.o
> > In file included from /usr/local/include/mpi.h:1886:0,
> >                  from /usr/include/H5public.h:57,
> >                  from /usr/include/hdf5.h:24,
> >                  from corefcn/oct-hdf5.h:27,
> >                  from ./octave-value/ov.h:42,
> >                  from corefcn/oct-obj.h:34,
> >                  from ./octave-value/ov-fcn.h:32,
> >                  from ./octave-value/ov-builtin.h:28,
> >                  from corefcn/defun-int.h:28,
> >                  from corefcn/defun-dld.h:30,
> >                  from dldfcn/__fltk_uigetfile__.cc:44:
> > /usr/local/include/openmpi/ompi/mpi/cxx/mpicxx.h:186:9: error: expected 
> > identifier before 'int'
> > /usr/local/include/openmpi/ompi/mpi/cxx/mpicxx.h:186:9: error: multiple 
> > types in one declaration
> > In file included from 
> > /usr/local/include/openmpi/ompi/mpi/cxx/mpicxx.h:231:0,
> >                  from /usr/local/include/mpi.h:1886,
> >                  from /usr/include/H5public.h:57,
> >                  from /usr/include/hdf5.h:24,
> >                  from corefcn/oct-hdf5.h:27,
> >                  from ./octave-value/ov.h:42,
> >                  from corefcn/oct-obj.h:34,
> >                  from ./octave-value/ov-fcn.h:32,
> >                  from ./octave-value/ov-builtin.h:28,
> >                  from corefcn/defun-int.h:28,
> >                  from corefcn/defun-dld.h:30,
> >                  from dldfcn/__fltk_uigetfile__.cc:44:
> > /usr/local/include/openmpi/ompi/mpi/cxx/status.h:22:7: error: expected 
> > identifier before 'int'
> > /usr/local/include/openmpi/ompi/mpi/cxx/status.h:22:14: error: expected 
> > unqualified-id before '{' token
> > dldfcn/__fltk_uigetfile__.cc:142:1: error: expected '}' at end of input
> > make[3]: *** [dldfcn/dldfcn___fltk_uigetfile___la-__fltk_uigetfile__.lo] 
> > Error 1
> > make[3]: Leaving directory 
> > `/home/tatsuromatsuoka/work/octave/octave-3.8.1/libinterp'
> > make[2]: *** [all] Error 2
> > make[2]: Leaving directory 
> > `/home/tatsuromatsuoka/work/octave/octave-3.8.1/libinterp'
> > make[1]: *** [all-recursive] Error 1
> > make[1]: Leaving directory `/home/tatsuromatsuoka/work/octave/octave-3.8.1'
> > make: *** [all] Error 2
> > 
> > I watched /usr/local/include/openmpi/ompi/mpi/cxx/status.h but I could not 
> > find the origin of errors.
> > 
> 
> I found the libopenmpi-dev in /usr/lib/openmpi and carried out configure  
> like :
> 
> CPPFLAGS='-I/usr/lib/openmpi/include' \
> LDFLAGS='-L/usr/lib/openmpi/lib' \
> ./configure --enable-jit LLVM_CONFIG=/usr/bin/llvm-config-3.2
> 
> configure could detect libhdf5.
> 
> However, at "make" the same errors occured.
> 
> I will consider another option.
> 
> Regards
> Tatsuro
 Help-octave mailing list
> address@hidden
> https://lists.gnu.org/mailman/listinfo/help-octave


I have found another solution.
I have built hdf-1.8.4-patch1 (the same version of hdfopenmpi-dev on the Ubuntu 
12.04 LTS)  in the static way in order to avoid confiliction of dynamic link 
library.

(I had tried hdf-1.8.14(the latest verion) but confiure of octave did not go 
well due to "undefined reference to `dlclose" etcs. )

The configure condition for of hdf-5 is :

cd ~/work/hdf5/hdf5-1.8.4-patch1
./configure --disable-shared --enable-static --prefix=/usr/local/hdf5

The confiure condition of octave-3.8.1 is :
CPPFLAGS='-I/usr/local/hdf5/include' \
LDFLAGS='-L/usr/local/hdf5/lib' \
./configure --enable-jit LLVM_CONFIG=/usr/bin/llvm-config-3.2

The build was successful.

make check reult:
Summary:

  PASS     11539
  FAIL         0
  XFAIL        7

Hope the above helps.

Regards
Tatsuro