dorsal team mailing list archive

[Andy Ray Terrel <andy.terrel@xxxxxxxxx>]

On Sat, Oct 9, 2010 at 8:46 AM, Andre Massing <massing@xxxxxxxxx> wrote:
>  Den 08.10.10 16.07, skrev Andy Ray Terrel:
>>
>> Andre, did you get any demo programs to work with the mpich2 port?
>>
>> I got an error that mpi_init wasn't called correctly again.  When I
>> disabled MPI but kept PETSc enabled, I get an error that a pointer is
>> freed before allocated (stack trace points at Global Parameters
>> KrylovSolver dying in the default Parameters copy constructor ... most
>> values were optimized away so I stopped digging).
>>
> Tested it out, my setup is:
> -macports mpich2 +gcc44, gcc44 is also now my standard compiler.
> -used petsccore.
>
> Everything compiled fine, but the demos failed in general :
>
> Sat Oct 09 15:23 andre@beluga:cpp 74>./poisson-demo
> Solving linear variational problem
>  Applying boundary conditions to linear system.
>  Solving linear system of size 1089 x 1089 (PETSc Krylov solver).
>  PETSc Krylov solver (gmres, ilu) converged in 39 iterations.
> Plotting u (a function), press 'q' to continue...
> Attempting to use an MPI routine before initializing MPICH
> *** Warning: Unable to plot.
>
> Same applies for the mixed poisson example.
> It seems somehow caused by the plot function, both examples run smoothly
> through
> when I comment it out. Maybe I have to recompile vtk5 with mpich2 now? It is
> really fun
> to dig into all these libraries, compilers etc. dependencies ..
>
> What can of failure did you experience? Does it work now on your machine?

So I got the same type of failure.  Although I didn't try commenting
out the plotting.  I probably won't have too much time for debugging
this as it takes so much time to futz with MacPorts.

-- Andy

>
>> Switching over to using all MacPorts system could be better but for
>> that super easy install the dmg would probably be easier to support.
>> I stopped using the Apple gcc because I wanted to use openmp for some
>> code.  Of course I'm accustom to fine tuning my builds of software so
>> unless there is a large need out there I wouldn't waste too many
>> cycles on it.
>>
> Yes, you are right. Then at some point I have to look at the cuda/nvida
> examples, whether then can easily adapted.
> But that's another story.
>
> --
> Andre
>
>> -- Andy
>>
>>
>>
>> On Fri, Oct 8, 2010 at 6:07 AM, Garth N. Wells<gnw20@xxxxxxxxx>  wrote:
>>>
>>> On 08/10/10 11:58, Anders Logg wrote:
>>>>
>>>> On Fri, Oct 08, 2010 at 10:10:02AM +0100, Garth N. Wells wrote:
>>>>>
>>>>> On 08/10/10 08:18, Anders Logg wrote:
>>>>>>
>>>>>> On Thu, Oct 07, 2010 at 04:29:05PM -0500, Andy Ray Terrel wrote:
>>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> I wanted to send in my unsuccessful account of installing FEniCS with
>>>>>>> Dorsal, hopefully there can be someone who benefits from this.
>>>>>>>
>>>>>>> My installation was attempted by updating mac ports and installing
>>>>>>> the
>>>>>>> list of ports requested by dorsal.
>>>>>>>
>>>>>>> The first problem I encountered was vtk-devel +python26 doesn't work
>>>>>>> for mac ports unless you are using the gcc originally installed by
>>>>>>> Apple (/usr/bin/g++-4.2).
>>>>>>>
>>>>>>> Second, petsc complained that fortran for mpi can't be used.  At this
>>>>>>> point I tried out the openmpi ports project but that caused many
>>>>>>> headaches later.  Perhaps setting --with-fortran=0 would be good
>>>>>>> here.
>>>>>>>
>>>>>>> Next, petsc could not link to metis correctly, turns out the octave
>>>>>>> port installed a older version of metis that was getting in the way.
>>>>>>>
>>>>>>> Finally, everything installs but when I run any demo, the demo runs
>>>>>>> then openmpi gives an error claiming 1) a system-required executable
>>>>>>> either could not be found and 2) mpi_init is called after finalize.
>>>>>>>  I
>>>>>>> couldn't figure out what is going on here as the mpi init and
>>>>>>> finalize
>>>>>>> should be set correctly by the subsystem manager.  The problem did
>>>>>>> not
>>>>>>> occur when running the Petsc demos.
>>>>>>>
>>>>>>> At this point I just installed everything by hand. Since Anders says
>>>>>>> things work, I wanted to make sure there was some knowledge of where
>>>>>>> things are breaking in the wild.  If you want me to try something
>>>>>>> different for testing let me know.
>>>>>>
>>>>>> Thanks for the report. It seems like most of the issues result from
>>>>>> using a different configuration than what Harish and I have been using
>>>>>> when testing (not using GCC from Apple etc). I'm not sure how to fix
>>>>>> this. It would require quite a bit more of work on the build scripts.
>>>>>>
>>>>>> One thing that might solve this issue is a mac bundle (.dmg) for the
>>>>>> whole FEniCS (which does not even require mac ports). It might not be
>>>>>> the best option for you if you want to control which GCC etc is used,
>>>>>> but it might help others.
>>>>>>
>>>>> Another thing that we've discussed is using MacPorts rather than the
>>>>> Apple supplied compilers and libs. If we use MacPorts for everything
>>>>> and have the configuration system check for MacPorts versions, we
>>>>> can be more confident in what's being used. Hopefully the PETSc
>>>>> Fortran issue would then go away too.
>>>>>
>>>>> Garth
>>>>
>>>> Yes, that's an option but it would require quite a bit of work and
>>>> Harish didn't think it was worth the effort.
>>>>
>>> It didn't seem to me that the work was the issue. My recollection is that
>>> Harish favoured using the systems libs over MacPorts.
>>>
>>> Garth
>>>
>>>> --
>>>> Anders
>>>
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>
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