Re: problem building geometry package, Ubuntu 14.04

[Juan Pablo Carbajal]

On Sat, Jun 7, 2014 at 1:56 AM, Robin Urselli <address@hidden> wrote:
>
> Hi Juan Pablo,
> we already tried the version from apt, but we also had problems installing
> octave packages.
> But your other way seems to work. I have tried on a Ubuntu 14.04 multicore
> virtual machine, and with CPPFLAGS=-I/usr/include/mpi make -j8 I'm able to
> compile and later to install geometry dev and all other packages without
> problems.
> I will soon try on my real pc.
>
> Thank you very much in the meantime!!
>
> Robin
>
>
>
> Sent: Friday, June 06, 2014 at 11:38 PM
>
> From: "Juan Pablo Carbajal" <address@hidden>
> To: "Robin Urselli" <address@hidden>, "Octave Help"
> <address@hidden>
>
> Subject: Re: problem building geometry package, Ubuntu 14.04
> On Fri, Jun 6, 2014 at 11:29 PM, Robin Urselli <address@hidden>
> wrote:
>> Hi Juan Pablo,
>> thanks for your answer. I tried your suggestion but octave comes out with
>> the very same error we already had installing it from the forge.
>> I spent a little time trying to understand the problem. When we installed
>> octave, we had to configure it with the -enable-openmp flag, otherwise it
>> didn't want to build.
>> GOMP_parallel_start is an openmp related symbol. I read that to make the
>> packages using openmp working, they should be compiled with the -fopenmp
>> flag. I tried to set it in the makefile of the geometry package, but I
>> found
>> in an old bug report that -f options are not supported by octave. Don't
>> know
>> if it's still the truth
>>
>> Here are two interesing posts about the argument. The first one is
>> explicitly about geometry and nurbs, which have the same problem
>>
>> http://www.marshut.com/iutwmv/build-with-openmp-by-default.html#iuuwkt
>> http://comments.gmane.org/gmane.comp.gnu.octave.general/50101
>>
>> Robin
>>
>>
>> Sent: Friday, June 06, 2014 at 12:40 AM
>> From: "Juan Pablo Carbajal" <address@hidden>
>> To: "Robin Urselli" <address@hidden>
>> Cc: "Octave Help" <address@hidden>
>> Subject: Re: problem building geometry package, Ubuntu 14.04
>> On Thu, Jun 5, 2014 at 4:37 PM, Robin Urselli <address@hidden>
>> wrote:
>>> Dear all,
>>>
>>> I am having some trouble installing the geometry package in Octave 3.8.1
>>> under Linux Ubuntu 14.04.
>>> In addition to the warnings, I get the following error:
>>>
>>>>> pkg install -forge geometry
>>> warning: addpath: //home/robin/octave/geom2d: No such file or directory
>>> warning: addpath: //home/robin/octave/io: No such file or directory
>>> warning: addpath: //home/robin/octave/polygons2d: No such file or
>>> directory
>>> warning: addpath: //home/robin/octave/shape2d: No such file or directory
>>> warning: addpath: //home/robin/octave/octclip: No such file or directory
>>> warning: addpath: //home/robin/octave/graphs: No such file or directory
>>> warning: addpath: //home/robin/octave/geom3d: No such file or directory
>>> warning: addpath: //home/robin/octave/meshes3d: No such file or directory
>>> warning: addpath: //home/robin/octave/polynomialCurves2d: No such file or
>>> directory
>>>
>>>
>>> /home/robin/octave/geometry-1.7.0/x86_64-unknown-linux-gnu-api-v49+/_oc_polybool.oct:
>>> failed to load:
>>>
>>>
>>> /home/robin/octave/geometry-1.7.0/x86_64-unknown-linux-gnu-api-v49+/_oc_polybool.oct:
>>> undefined symbol: GOMP_parallel_start
>>> error: called from 'doc_cache_create>create_cache' in file
>>> /usr/local/share/octave/3.8.1/m/help/doc_cache_create.m near line 101,
>>> column 18
>>> error: called from:
>>> error: /usr/local/share/octave/3.8.1/m/pkg/private/install.m at line 241,
>>> column 5
>>> error: /usr/local/share/octave/3.8.1/m/pkg/pkg.m at line 394, column 9
>>>
>>> Octave was installed by compiling the source code. I had to link the LLVM
>>> library by hand, otherwise the make process would have complained. In
>>> particular I had run config as follows:
>>>
>>> ./configure --enable-openmp
>>>
>>>
>>> LLVM_CONFIG=~/Downloads/clang+llvm-3.2-x86_64-linux-ubuntu-12.04/bin/llvm-config
>>>
>>> We have used the --enable-openmp option as it was suggested i some forum
>>> to
>>> solve the probem, but it did not really help.
>>>
>>> Version of gcc:
>>> gcc version 4.8.2 (Ubuntu 4.8.2-19ubuntu1)
>>>
>>> Any help would be greatly appreciated.
>>> Thanks a lot
>>>
>>> robin
>>>
>>> _______________________________________________
>>> Help-octave mailing list
>>> address@hidden
>>> https://lists.gnu.org/mailman/listinfo/help-octave
>>>
>>
>> Hi Robin,
>>
>> Welcome to the mailing list.
>> As a quick check. Can you try to install the dev version of the
>> geometry package?
>> You can get the tar.gz from here
>> http://users.elis.ugent.be/~jcarbaja/misc/geometry-1.7.0.tar.gz
>>
>> To install it, go to the folder where you downloaded the file and run
>> octave. Once in the octave prompt run
>>
>> pkg install geometry-1.7.0.tar.gz
>>
>> Probably you will still get the warnings. The package installs and
>> works fine, I just got to fix the warning...
>> If it compiles we will need to make a new release of geometry.
>
> Hi Robin,
> Please keep the Octave mailing list in CC when communicating about
> Octave issues.
>
> Ok, then the problem might be another one (damn mpi!). Try the following:
> Option a) Ubuntu 14.04 has a rather updated version of octave 3.8 if I
> am not wrong. You can just install from apt-get.
> Option b) If you want to compile from sources then
> Recompile octave with configuration minimum flags. For example in
> ubuntu 14.04 I compile with the following commands
>
> ./configure
> CPPFLAGS=-I/usr/include/mpi make -j8
>
> As you see nothing extra except telling make where to find mpi (check
> if that is your path). Also the -j options tell make to compile using
> y 8 cores, adjust to your hardware
> With this configuration I have no problem with the dev version of
> geomtry package (now without warning anymore).
>
> If you really need JIT, then I can't help, cause I haven't managed to
> get it to compile in Ubuntu 14.04.
>
> Does this help?

Robin,

I hope it works on your real machine as well. I took the solution from
Mike Miller and Carlo in this post
http://octave.1599824.n4.nabble.com/mpi-h-vs-hdf5-h-td4662703.html

Just a small remark. Due to the way the mails in th emailing list are
stored (as in the link there) we prefer to do bottom-posting. Try to
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Thanks