Need help adding a new solver to the petsc library

Barry Smith bsmith at mcs.anl.gov
Fri Nov 21 10:32:35 CST 2008 

On Nov 21, 2008, at 10:23 AM, Xavier Lacoste wrote:

> Barry Smith a écrit :
>>
>> On Nov 21, 2008, at 8:05 AM, Xavier Lacoste wrote:
>>
>>> Hello,
>>>
>>> I have some new questions.
>>>
>>> I haded a MPIAIJ to CSC conversion routine.
>>
>>   There is no such beast, computing it is painful.
>>
>>   What we do for solvers that need it is to just pass the CSR  
>> version and then instead of doing a solve in the package we do
>> a transpose solve from the package.
> Ok, I'll try this, do you have an example of solver using CSC with  
> this method ?

    This is how we handle Superlu; see src/mat/impls/aij/seq/superlu

>
>>>
>>> I managed to run ex19 on the solver PaStiX like it is done for  
>>> mumps but my matrix must be badly constructed (PaStiX doesn't  
>>> succeed in computing  the solution withe the given problem...).
>>> Is there a way to dump the MPIAIJ matrix into a matrixmarket  
>>> format so that I can check what's wrong with the CSC built ?
>>
>>   No we don't have any matrix output to matrixmarket format.
>>
>>  Does the code run correctly on 1 process?
>>
> No, because I only implemented the mpiaij subclass, not the seqaij  
> one, I get an error when launchin on one processor, but I can run  
> the code on two, I just have numerical issues.

    You can create and use mpiaij matrices on one process so you  
should not "get an error when launchin on one processor,".

    NEVER EVER EVER EVER EVER try to debug a 2 process  case when you  
don't know if a 1 process case runs!  Make sure it runs
properly on one process first.

    Barry

>
>
>>
>>>
>>>
>>> Second question, in the petsc-dev/config/PETSc/packages/Scotch.py  
>>> I wrote, do I have a way to check if libz.a is present, so that I  
>>> can decide if I compile with -DCOMMON_FILE_COMPRESS_GZ and -lz ?  
>>> (libz.a requirement is depending of an optional feature of  
>>> Scotch...)
>>
>>  In your PaStiX.py you can add something like
>>    if self.libraries.add('-lz','function_in_library'):
>>      self.addDefine('HAVE_WHAT_YOU_WANT_STRINGH',1)
> Ok, thanks I'll try this
>
> XL.
>>
>>  Barry
>>
>>
>>>
>>>
>>> thanks,
>>>
>>> XL.
>>>
>>>
>>> Barry Smith a écrit :
>>>>
>>>>    Take a look at, for example, MatGetFactor_MPIAIJ_mumps (in src/ 
>>>> mat/impls/aij/mpi/mumps)
>>>> you will need to create one for pastix and then take a look at  
>>>> MatCreate_MPIAIJ and see
>>>> how the mumps function is registered, you will need to register  
>>>> in the same way.
>>>>
>>>>   Barry
>>>>
>>>>
>>>>
>>>> On Nov 7, 2008, at 10:07 AM, Xavier Lacoste wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I'm still working on adding PaStiX into PETSc.
>>>>>
>>>>> I managed to pass the configure and "make all test" steps.
>>>>> (./config/configure.py -with-scotch=1 -download-scotch=ifneeded - 
>>>>> with-pastix -download-pastix=ifneeded )
>>>>>
>>>>>
>>>>> Here are the modification I made on petsc-dev version  
>>>>> 12911:0e70d56474b2
>>>>>
>>>>> http://dept-info.labri.fr/~lacoste/petsc/adding_pastix_12911_0e70d56474b2.patch
>>>>>
>>>>> - I added PaStiX.py package
>>>>> - I modified Scotch.py package to use last version
>>>>> - I modified partition/impls/scotch.c so that it compiles (it  
>>>>> would not work in the current state)
>>>>> - I had aij/mpi/pastix/pastix.c file to make an interface to  
>>>>> pastix.
>>>>> - I tried to use example 19 with pastix, like it is done with  
>>>>> mumps but pastix solver is not found :
>>>>>
>>>>> http://dept-info.labri.fr/~lacoste/petsc/error_log
>>>>>
>>>>> Now, I have to know how to tell petsc it has a new solver  
>>>>> implementing mpiaij.
>>>>>
>>>>> How can I do that ?
>>>>>
>>>>> After that I should be able to test if my implementation of  
>>>>> mpiaij matrix is working or not.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> XL.
>>>>>
>>>>>
>>>>>
>>>>> Barry Smith a écrit :
>>>>>>
>>>>>> Please send your $PETSC_ARCH/conf/configure.log and $PETSC_ARCH/ 
>>>>>> conf/make.log to petsc-maint at mcs.anl.gov (not to this email  
>>>>>> address)
>>>>>> and we'll take a look.  Also send your modified Scotch.py file.
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>>
>>>>>> Barry
>>>>>>
>>>>>> On Nov 3, 2008, at 10:45 AM, Xavier Lacoste wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> I want to add the solver PaStiX (https://gforge.inria.fr/projects/pastix/ 
>>>>>>> ) to the PETSc library.
>>>>>>> I Check-outed the last hg version of PETSc and started adding  
>>>>>>> my PaStiX.py script, based on MUMPS one, in petsc-dev/config/ 
>>>>>>> PETSc/packages/ .
>>>>>>> I modified first Scotch.py wich wasn't updated because PaStiX  
>>>>>>> needs Scotch.
>>>>>>>
>>>>>>> My problem is that I couldn't succed in configuring PETSCc  
>>>>>>> with "--with-pastix=1 etc." because i don't know how to say  
>>>>>>> PETSc that PaStiX needs the "-L/Scotch/dir -lscotch etc."
>>>>>>>
>>>>>>> I have the setupDependencies :
>>>>>>>
>>>>>>>
>>>>>>> def setupDependencies(self, framework):
>>>>>>> PETSc.package.Package.setupDependencies(self, framework)
>>>>>>> self.mpi        = framework.require('config.packages.MPI',self)
>>>>>>> self.blasLapack =  
>>>>>>> framework.require('config.packages.BlasLapack',self)
>>>>>>> self.scotch     =  
>>>>>>> framework.require('PETSc.packages.Scotch',self)
>>>>>>> self.deps       = [self.mpi,self.blasLapack,self.scotch]
>>>>>>> return
>>>>>>>
>>>>>>> But it didn't helped, the -L/scotchdir/lib is still missing...
>>>>>>>
>>>>>>> > Executing: mpicc  -o conftest    -g  conftest.o  -Wl,-rpath,/ 
>>>>>>> home/xl/pastix/lib -L/home/xl/pastix/lib -lpastix -lpthread - 
>>>>>>> lscotch -llapack -lblas *
>>>>>>> > -L/usr/lib/gcc/i486-linux-gnu/4.3.2 -L/lib -ldl -lgcc_s - 
>>>>>>> lgfortranbegin -lgfortran -lm -L/usr/lib/gcc/i486-linux-gnu/ 
>>>>>>> 4.3.2 -L/usr/lib/gcc/i486-linux-gnu
>>>>>>> > -L/usr/lib/gcc/i486-linux-gnu/4.3.2 -L/usr/lib/gcc/i486- 
>>>>>>> linux-gnu -L/usr/lib/gcc/i486-linux-gnu/4.3.2 -L/usr/lib/gcc/ 
>>>>>>> i486-linux-gnu
>>>>>>> > -L/usr/lib/gcc/i486-linux-gnu/4.3.2 -L/lib -L/lib -lm -L/usr/ 
>>>>>>> lib/gcc/i486-linux-gnu/4.3.2 -L/usr/lib/gcc/i486-linux-gnu/ 
>>>>>>> 4.3.2 -L/lib -ldl -lgcc_s -ldl
>>>>>>> > sh:
>>>>>>> > Possible ERROR while running linker: /usr/bin/ld: cannot  
>>>>>>> find -lscotch
>>>>>>>
>>>>>>> Hope i'm on the good Mailing list for this kind of questions.
>>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>> XL.
>>>>>>> PaStiX team, INRIA-Bordeaux-Sud-Ouest, France.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

More information about the petsc-dev mailing list