Re: [petsc-users] Eigenvalues always converge to zero when using slepc4py-complex
The new builds are up. Jose added instructions in the SLEPc FAQ. Could you try again? Regards, On Mon, 4 Oct 2021 at 16:13 Yelyzaveta Velizhanina wrote: > I see. Thanks, much appreciated. > > > > Best regards, > > Yelyzaveta Velizhanina. > > > > *From: *Jose E. Roman > *Date: *Monday, 4 October 2021 at 15:10 > *To: *Yelyzaveta Velizhanina > *Cc: *petsc-users@mcs.anl.gov > *Subject: *Re: [petsc-users] Eigenvalues always converge to zero when > using slepc4py-complex > > Conda supports complex scalars for petsc4py. However, this is not > implemented in slepc4py. Lisandro is trying to get this fixed, so if no > issues arise this will be available in a couple of days, with > slepc4py-3.16.0. > > Jose > > > > El 3 oct 2021, a las 22:45, Yelyzaveta Velizhanina < > velizhani...@gmail.com> escribió: > > > > Dear all, > > > > I am having a problem to get EPS run properly with PETSc and SLEPc build > with scalar_value=complex. I am using petsc4py and slepc4py. Installed > everything, including PETSc and SLEPc, with conda. While real scalar value > build works well, when using the complex one, all the eigenvalues always > converge to 0 for any matrix and any solver. I’ve tried running examples > given in this repo https://github.com/myousefi2016/slepc4py as well - > same outcome, only zero eigenvalues. I am running MacOSX BigSur. > > > > Will appreciate any help, > > > > Best regards, > > Yelyzaveta Velizhanina. > -- Lisandro Dalcin Senior Research Scientist Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/
Re: [petsc-users] headsup: switch git default branch from 'master' to 'main'
May the force be with you, Satish. On Tue, 23 Feb 2021 at 20:19, Satish Balay via petsc-users < petsc-users@mcs.anl.gov> wrote: > All, > > This is a heads-up, we are to switch the default branch in petsc git > repo from 'master' to 'main' > > [Will plan to do the switch on friday the 26th] > > We've previously switched 'maint' branch to 'release' before 3.14 > release - and this change (to 'main') is the next step in this direction. > > Satish > > -- Lisandro Dalcin Senior Research Scientist Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/
Re: [petsc-users] Python version needed for internal scripts
On Wed, 14 Oct 2020 at 14:12, Lisandro Dalcin wrote: > Disclaimer: I'm not an Ubuntu user. Google and inform yourself. > Just in case... What I'm trying to say is that I do not know Ubuntu very well, much less its Py2 -> Py3 transition details, and then you should try to find a more authoritative source than my occasional comments about the proper way to do things. -- Lisandro Dalcin Senior Research Scientist Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/
Re: [petsc-users] Python version needed for internal scripts
On Wed, 14 Oct 2020 at 13:01, Nicolas Barral < nicolas.bar...@math.u-bordeaux.fr> wrote: > > 'python' is usually an alias for python2, so making it point at python3 > seems a bit dangerous. Yet, python2 was removed from recent Ubuntus and > maybe others, and if I have no python2 installed, and no 'python' alias, > I have to manually edit all the scripts. > > apt install python-is-python3 and you should get the alias python -> python3 in /usr/bin Disclaimer: I'm not an Ubuntu user. Google and inform yourself. -- Lisandro Dalcin Senior Research Scientist Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/
Re: [petsc-users] compiling PETSc using c++ compiler
On Wed, 7 Oct 2020 at 02:45, Sam Guo wrote: >I want to experiment c++ compiler to see if I can compile real and > complex versions to different symbols (I've created another thread for this > topic.) but it seems c++ compiler does not help and I still get same > symbols. > > Indeed, that is not going to make it. Or you have to change the definition of PETSC_EXTERN, such that it does not use `extern "C"`. Even with that, you may have trouble with EXTERN_C_BEGIN/END macros. -- Lisandro Dalcin Senior Research Scientist Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/
Re: [petsc-users] HDF5 and ParaView
On Mon, 13 Jul 2020 at 14:14, Mark Adams wrote: > >> >> I would probably move out of VTK files in favor of something else if I >> had a way to encode VTK's (the library, not the file format) high-order >> Lagrange elements. >> Actually, I'm toying with dumping files with PETSc's raw binary I/O with >> MPI, and writing a proper ParaView plugin in Python to read the data. >> > > I'd love a high order viewer too. > Well, ParaView can actually do it. You need to open a vtu file with high-order Lagrange elements, and then look for "Nonlinear subdivision level" in the GUI and bump it up. The main issue is that the algorithm is not "adaptive" and you may need to bump too much, then the thing becomes quite slow. Another one that does things very well is GLVis, although not with all the features of the ParaView/VisIt+VTK combo. Stefano put a lot of effort integrating GLVIs into PETSc, but maybe the integration with PetscFE and DMPlex may require some extra work. -- Lisandro Dalcin Research Scientist Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/
Re: [petsc-users] HDF5 and ParaView
On Fri, 10 Jul 2020 at 15:37, Matthew Knepley wrote: > > That is true. Do they also get rid of the single mesh and single timstep > requirements? HDF5+XDMF makes it much easier since > we can put multiple meshes and timesteps in one file. > Well, I use ParaView's *.pvd files for that, and I dump each timestep to its own *.vtu file in a folder to pack the files. But you still have a point, the format is indeed restricting. Why do you consider it so important to put multiple meshes and timesteps in one file? It is just that you hate to have so many files scattered around? Or something deeper? I do hate the fact that the VTK formats (either legacy or XML) do not allow you to dump a single mesh to be reused for multiple timestep. I would probably move out of VTK files in favor of something else if I had a way to encode VTK's (the library, not the file format) high-order Lagrange elements. Actually, I'm toying with dumping files with PETSc's raw binary I/O with MPI, and writing a proper ParaView plugin in Python to read the data. -- Lisandro Dalcin Research Scientist Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/
Re: [petsc-users] HDF5 and ParaView
On Thu, 9 Jul 2020 at 23:11, Matthew Knepley wrote: > On Thu, Jul 9, 2020 at 3:28 PM David Scott wrote: > >> Matt, >> >> I'll have a go at writing Xdmf files. >> >> Am I right in thinking that VTK files are written sequentially? >> > > Yes, it is a rightly despised format, suitable only for beggars and serial > jobs :) > > By "rightly despised format", I hope you are talking about the legacy VTK files (the traditional .vtk extension). The new XML formats with are quite easy to write in parallel with MPI/IO (at least *.vtu files, which is what I'm using). -- Lisandro Dalcin Research Scientist Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/
Re: [petsc-users] Terminating a process running petsc via petsc4py without mpi_abort
(1) You can use PETSc.Sys.pushErrorHandler("abort"), but it will not help
you. What you really need is to override PETSc's default signal handling
(2) While it is true that PETSc overrides the signal handler, you can
override it again from python after from petsc4py import PETSc.
For implementing (2), maybe you should try sending SIGINT and not SIGTERM,
such that you can do the following.
from petsc4py import PETSc
import signal
signal.signal(signal.SIGINT, signal.default_int_handler)
...
if __name__ == "__main__":
try:
main()
except KeyboardInterrupt: # Triggered if Ctrl+C or signaled with SIGINT
... # do cleanup if needed
Otherwise, you just need signal.signal(signal.SIGINT, signal.SIG_DFL)
PS: I'm not in favor of changing current PETSc's signal handling behavior.
This particular issue is fixable with two lines of Python code:
from signal import signal, SIGINT, SIG_DFL
signal(SIGINT, SIG_DFL)
On Thu, 4 Jun 2020 at 23:39, Hudson, Stephen Tobias P
wrote:
> Lisandro,
>
> I don't see an interface to set this through petsc4py. Is it possible?
>
> Thanks,
> Steve
> --
> *From:* Hudson, Stephen Tobias P
> *Sent:* Thursday, June 4, 2020 2:47 PM
> *To:* Balay, Satish
> *Cc:* petsc-users@mcs.anl.gov ; Lisandro Dalcin <
> dalc...@gmail.com>
> *Subject:* Re: Terminating a process running petsc via petsc4py without
> mpi_abort
>
> Sounds good. I will have a look at how to set this through petsc4py.
>
> Thanks
> Steve
> --
> *From:* Satish Balay
> *Sent:* Thursday, June 4, 2020 2:32 PM
> *To:* Hudson, Stephen Tobias P
> *Cc:* petsc-users@mcs.anl.gov ; Lisandro Dalcin <
> dalc...@gmail.com>
> *Subject:* Re: Terminating a process running petsc via petsc4py without
> mpi_abort
>
> I don't completely understand the issue here. How is sequential run
> different than parallel run?
>
> In both cases - a PetscErrorHandler is likely getting invoked. One can
> change this behavior with:
>
>
> https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscPushErrorHandler.html
>
> And there are a few default error handlers to choose
>
>
> PETSC_EXTERN PetscErrorCode PetscTraceBackErrorHandler(MPI_Comm,int,const
> char*,const char*,PetscErrorCode,PetscErrorType,const char*,void*);
> PETSC_EXTERN PetscErrorCode PetscIgnoreErrorHandler(MPI_Comm,int,const
> char*,const char*,PetscErrorCode,PetscErrorType,const char*,void*);
> PETSC_EXTERN PetscErrorCode
> PetscEmacsClientErrorHandler(MPI_Comm,int,const char*,const
> char*,PetscErrorCode,PetscErrorType,const char*,void*);
> PETSC_EXTERN PetscErrorCode PetscMPIAbortErrorHandler(MPI_Comm,int,const
> char*,const char*,PetscErrorCode,PetscErrorType,const char*,void*);
> PETSC_EXTERN PetscErrorCode PetscAbortErrorHandler(MPI_Comm,int,const
> char*,const char*,PetscErrorCode,PetscErrorType,const char*,void*);
> PETSC_EXTERN PetscErrorCode
> PetscAttachDebuggerErrorHandler(MPI_Comm,int,const char*,const
> char*,PetscErrorCode,PetscErrorType,const char*,void*);
> PETSC_EXTERN PetscErrorCode PetscReturnErrorHandler(MPI_Comm,int,const
> char*,const char*,PetscErrorCode,PetscErrorType,const char*,void*);
>
> Some of the are accessible via command line option. for ex:
> -on_error_abort or -on_error_mpiabort
>
> Or perhaps you want to completely disable error handler with:
> -no_signal_handler
>
> cc: petsc-users
>
> Satish
>
> On Thu, 4 Jun 2020, Hudson, Stephen Tobias P wrote:
>
> > Satish,
> >
> > We are having issues caused by MPI_abort getting called when we try to
> terminate a sub-process running petsc4py. Ideally we would always use a
> serial build of petsc/petsc4py in this mode, but many users will have a
> parallel build. We need to be able to send a terminate signal that just
> kills the process.
> >
> > Is there a way to turn off the mpi_abort?
> >
> > Thanks,
> >
> > Steve
> >
> >
>
>
--
Lisandro Dalcin
Research Scientist
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/
Re: [petsc-users] Resuming analysis by importing Trajectory Data from external source
On Sat, 9 May 2020 at 23:44, Mohammed Ashour wrote: > I'm using TSALPHA1, as in ierr = TSSetType(ts,TSALPHA1); CHKERRQ(ierr); > > Well, TSALPHA1 uses some vectors keeping intenal state, as you know, generalized-\alpha is not really a one-step method. That intenal state should be saved and loaded if you want to implement a truly correct checkpoint/restart. But PETSc does not currently provide access to this vector in its public API, so you will have to hack things around. IIRC, just saving and restoring the internal V1 vector is all what you need, maybe also set ts->steprestart to FALSE and properly set the ts->steps counter. Or you can just ignore these detail, and restart the easy way from just the saved solution, at the price of a very small "glitch" at the restart time. But note that this glitch just means that you temporarily change the scheme to reinitialize, and it is exactly the same thing the implementation does at the initial time to initialize the method (as you surely know, the method is also not trully self-starting). The restarting procesure as implemented in TSALPHA1 is not in the literature, it is of my own cooking but based on rather trivial relations performing two steps with dt/2 time step size, the fist of those inner steps using backward-Euler. -- Lisandro Dalcin Research Scientist Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/
Re: [petsc-users] Resuming analysis by importing Trajectory Data from external source
On Sat, 9 May 2020 at 22:48, Mohammed Ashour wrote: > Oh, thanks for the tip. > I can do that. Aside from the solution vector, step number, and time, are > there any hidden details in TS I need to dump that would be essential for > the next run? > > This really depends on the timestepper. What TS type are you using? -- Lisandro Dalcin Research Scientist Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/
Re: [petsc-users] [EXTERNAL] Re: Alternate mesh partitioners to METIS/ParMETIS
On Thu, 7 May 2020 at 17:53, Hammond, Glenn E via petsc-users < petsc-users@mcs.anl.gov> wrote: > Jed, > > We call MatMeshToCellGraph() to generate the dual matrix. This function > relies upon ParMETIS. Can you point me to a similar function that does not > require ParMETIS ( e.g. for PTScotch)? > > Maybe a starting point: DMPlexCreateFromCellList(comm, ..., ); PetscSectionCreate(comm, ); DMPlexGetPartitioner(dm, ); PetscPartitionerSetType(partitioner, PETSCPARTITIONERPTSCOTCH); PetscPartitionerDMPlexPartition(partitioner, dm, NULL, cellPartSection, ); One minor annoyance is that the first call will need the vertex coordinates. Matthew, any better way? -- Lisandro Dalcin Research Scientist Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/
Re: [petsc-users] PetscObjectCompose error
On Sun, 12 Apr 2020 at 01:50, Mark Adams wrote:
> I am trying to compose a ISColoring to a Mat. THe code works, I know JacP
> and iscoloring are valid Mat and ISColoring. I have this:
>
> ierr =
> ((PetscObject)JacP,"coloring",(PetscObject)iscoloring);CHKERRQ(ierr);
>
> But it says my ISColoring is not valid. Any suggestions?
>
>
ISColoring is not a PetscObject, you cannot compose it.
struct _n_ISColoring {
PetscIntrefct;
PetscIntn;/* number of colors */
IS *is; /* for each color indicates columns */
MPI_Commcomm;
ISColoringValue *colors; /* for each column indicates color */
PetscIntN;/* number of columns */
ISColoringType ctype;
PetscBool allocated;
};
I guess your best option for now is to store it in a
PetscContainer object with a destroy callback, and then compose the
container.
--
Lisandro Dalcin
Research Scientist
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/
Re: [petsc-users] How to set an initial guess for TS
On Fri, 3 Apr 2020 at 18:26, Fande Kong wrote:
> Hi All,
>
> TSSetSolution will set an initial condition for the current TSSolve().
> What should I do if I want to set an initial guess for the current solution
> that is different from the initial condition? The initial guess is
> supposed to be really close to the current solution, and then will
> accelerate my solver.
>
> In other words, TSSetSolution will set "U_{n-1}", and now we call TSSolve
> to figure out "U_{n}". If I know something about "U_{n}", and I want to set
> "\bar{U}_{n}" as the initial guess of "U_{n}" when computing "U_{n}".
>
>
IMHO, the only reliable solution would be to implement
SNESSet{Pre|Post}Solve(snes, {Pre|Post}Solve, ctx) to set callback routines
{Pre|Post}Solve(snes,b,x,ctx) allowing users to modify the solution vector
'x' in place (but no 'b', of course).
We already have that feature in KSP, why not SNES which is an inner loop in
TS ?
--
Lisandro Dalcin
Research Scientist
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/
Re: [petsc-users] Error Installing Petsc4Py
Please note that I have not released yet petsc4py-3.13, so pip install will
not work with latest PETSc release 3.13
On Thu, 2 Apr 2020 at 20:48, Satish Balay via petsc-users <
petsc-users@mcs.anl.gov> wrote:
> Which version of petsc and which version of petsc4py is this?
>
> Lisandro can help with pip issues.
>
> Just want to mention an alternate mode that you might want to try:
>
> --download-petsc4py option to petsc configure
>
> Satish
>
> On Thu, 2 Apr 2020, Kyle Michael Booker wrote:
>
> > Hello,
> >
> >
> > I've been trying to install petsc4py for the past several days and have
> had the following errors installing:
> >
> >
> > "Command "/usr/bin/python -u -c "import setuptools,
> tokenize;__file__='/tmp/pip-build-0eWEiE/petsc4py/setup.py';f=getattr(tokenize,
> 'open', open)(__file__);code=f.read().replace('\r\n',
> '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record
> /tmp/pip-oUZMRL-record/install-record.txt
> --single-version-externally-managed --compile --user --prefix=" failed with
> error code 1 in /tmp/pip-build-0eWEiE/petsc4py/"
> >
> >
> > I currently have petsc installed correctly as well as mpich, it is just
> getting petsc4py installed that I have problems with. Any help would be
> greatly appreciated.
> >
> >
> > Sincerely,
> >
> >
> > Kyle
> >
>
>
--
Lisandro Dalcin
Research Scientist
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/
Re: [petsc-users] [petsc4py] Assembly fails
On Fri, 27 Mar 2020 at 17:10, Matthew Knepley wrote:
> On Fri, Mar 27, 2020 at 3:31 AM Alejandro Aragon - 3ME <
> a.m.ara...@tudelft.nl> wrote:
>
>> Dear Matthew,
>>
>> Thanks for your email. I have attached the python code that reproduces
>> the following error in my computer:
>>
>
> I think I see the problem. There were changes in DM in order to support
> fields which only occupy part of the domain.
> Now you need to tell the DM about the fields before it builds a Section. I
> think in your code, you only need
>
> f = PetscContainer()
> f.setName("potential")
> dm.addField(field = f)
>
>
Except that petsc4py do not expose a Container class :-(
@Alejandro, PETSc 3.13 is about to be released. Once that is done, we have
a small windows to make a few enhancements in petsc4py before releasing the
matching petsc4py-3.13 that you can use to upgrade your code. Would that
work for you?
--
Lisandro Dalcin
Research Scientist
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/
Re: [petsc-users] [petsc4py] Assembly fails
On Wed, 25 Mar 2020 at 19:38, Matthew Knepley wrote: > > It looks like you have an inconsistent build, or a memory overwrite. Since > you are in Python, I suspect the former. Can you build > PETSc from scratch and try this? Does it work in serial? Can you send a > small code that reproduces this? > > Well, I think Alejandro installed PETSc/petsc4py via pip as per my instructions. Can you confirm, Alejandro? -- Lisandro Dalcin Research Scientist Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/
Re: [petsc-users] KSPComputeOperator in petsc4py
On Thu, 26 Dec 2019 at 21:36, Mark Cunningham < mark.cunning...@ariacoustics.com> wrote: > I have an application written in python and using petsc4py. I would like > to study the effects of different preconditioners on my eigenvalue spectrum > and thought to use KSPComputeOperator to obtain the preconditioned matrix. > This, apparently, is not disclosed through the petsc4py implementation. > Could you share the modifications you implemented? This way I could quickly add them to petsc4py to make them available in next release. > I found KSP.pyx, where I believe that the KSP object is defined, and added > a definition for the function but, after a pip install, > If you "cd" to the top level petsc4py source directory with your modifications, then you may need $ pip install --no-cache-dir . # note the final dot "." otherwise pip may just reinstall petsc4py from a previously built wheel file stored in the pip cache. -- Lisandro Dalcin Research Scientist Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/
Re: [petsc-users] RAW binary write
On Tue, 4 Dec 2018 at 19:53, Matthew Knepley wrote: > On Tue, Dec 4, 2018 at 11:11 AM Lisandro Dalcin via petsc-users < > petsc-users@mcs.anl.gov> wrote: > >> PetscByteSwap ? But be careful, you should (1) vec get array, byteswap, >> vec restore array, (2) view, (3) vec get array, byteswap, vec restore >> array. Of course, if you do not care about the final Vec contents, you can >> just omit step (3) and let it be, let it be... >> >> PS: Eventually, PETSc binary viewers should gain an API like >> PetscViewerBinarySetByteOrder(viewer, PETSC_LITTLE_ENDIAN) ... >> > > Note that this enables exactly what we wanted to avoid, namely binary > files that an incompatible with some installations. > > 1) As a confessed libertarian (not to be confused with liberal), IMHO, we should not prevent power users to do something if they explicitly ask for it. Maybe someone has to dump a binary file in little endian with no headers, so that some other crappy software that do not care about endianness can happily read the file and do something with it. Why would we not add the feature (at least if someone contributes it)? 2) The whole native binary I/O in PETSc is messy. 3) In an ideal word, every PETSc binary file should start with a header 8bitEndianFlag,sizeof(PetscInt),sizeof(PetscReal),sizeof(PetscScalar), And maybe readers should handle gracefully binary files produced by PETSc builds with different integer/real sizes. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] RAW binary write
Use PetscViewerBinarySetSkipHeader(viewer, PETSC_TRUE) before VecView().
On Thu, 29 Nov 2018 at 18:50, Sal Am via petsc-users <
petsc-users@mcs.anl.gov> wrote:
> Is there a way to write the solution from the system Ax=b in raw binary
> instead of PETSc binary format?
>
> Currently I am doing:
> ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,
> "../../python/petscpy/Vector_x_petsc.dat", FILE_MODE_WRITE,
> );CHKERRQ(ierr);
> ierr = VecView(x,viewer);CHKERRQ(ierr);CHKERRQ(ierr);
> ierr = PetscViewerDestroy();CHKERRQ(ierr);
>
> And then use PetscBinaryIO to read it back and save it using
> write('newformat', 'wb') to get to raw... however this approach is not good
> it seems as there are some troubles with little/big endian when using the
> resulting converted file on other systems for post-processing.
>
> Thanks,
>
--
Lisandro Dalcin
Research Scientist
Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/
4700 King Abdullah University of Science and Technology
al-Khawarizmi Bldg (Bldg 1), Office # 0109
Thuwal 23955-6900, Kingdom of Saudi Arabia
http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
Re: [petsc-users] Extending petsc4py
On Tue, 10 Jul 2018 at 20:17, Ingo Gaertner wrote: > Hello, > can I find somewhere an example how to wrap my own PETSc-based code so > that it can be used together with petsc4py? > > Let's assume I have a C function, which I want to access from python: > Vec createMyVec(); > > I have written a SWIG interface file to generate a python wrapper for this > function. The wrapper works, but I cannot use the return value as input for > mpi4py routines that expect a Vec, because mpi4py's Vec type is different > from the SWIG generated Vec type in my python wrapper. Any idea, how I can > create mpi4py-compatible types? > > If the mpi4py wrapping technique is described somewhere, this may help as > well, although some working example would be perfect. > > As a final remark, I'd like to keep my project decoupled from mpi4py. > Therefore, including my extensions in the build process of mpi4py is not > quite what I am looking for, although I could live with this as a > workaround if no other solution is possible. > (I am using petsc-3.9.1 built from source and mpi4py installed using pip > on Ubuntu 18.04.) > > Sorry, but I'm quite confused. Why are you talking about mpi4py? There is no "Vec" in mpi4py. The only type intersection between petsc4py and mpi4py is "Comm" for MPI communicators, in that case you should use the following to make the conversions: mpi4py_comm = petsc4py_comm.tompi4py() # mpi4py <-- petsc4py petsc4py_comm = PETSc.Comm(mpi4py_comm) # petsc4py <-- mpi4py About SWIG, are you using typemaps written by yourself, or the typemaps provided by petsc4py? Have you looked at "demo/wrap-swig" in petsc4py sources? -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] "snes_type test" is gone?
./example.exe -snes_test_jacobian -snes_type ksponly -ksp_type preonly -pc_type none -snes_convergence_test skip On Sat, 30 Jun 2018 at 01:06, Alexander Lindsay wrote: > > Is there a way to mimic the behavior of `-snes_type test` with new PETSc? > E.g. don't attempt to perform any solves? They're stupid but we have a bunch > of tests in MOOSE that are set-up only to test the Jacobian, and any attempts > to actually solve the system are disastrous. I can hack around this by doing > things like setting the convergence reason to `SNES_CONVERGED_ITS` and > similarly for ksp, making sure I use `-pc_type gamg` since there are missing > Jacobian diagonal entries, etc. but this doesn't seem ideal. > > Alex > > On Mon, Jun 4, 2018 at 4:26 PM, Kong, Fande wrote: >> >> Thanks, Hong, >> >> I see. It is better if "-snes_type test" did not exist at the first place. >> >> >> Fande, >> >> On Mon, Jun 4, 2018 at 4:01 PM, Zhang, Hong wrote: >>> >>> >>> >>> > On Jun 4, 2018, at 4:59 PM, Zhang, Hong wrote: >>> > >>> > -snes_type has been removed. We can just use -snes_test_jacobian instead. >>> > Note that the test is done every time the Jacobian is computed. >>> >>> It was meant to be "-snes_type test". >>> >>> > Hong (Mr.) >>> > >>> >> On Jun 4, 2018, at 3:27 PM, Kong, Fande wrote: >>> >> >>> >> Hi PETSc Team, >>> >> >>> >> I was wondering if "snes_type test" has been gone? Quite a few MOOSE >>> >> users use this option to test their Jacobian matrices. >>> >> >>> >> If it is gone, any reason? >>> >> >>> >> Fande, >>> > >>> >> > -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] MATIS and DMDA in petsc4py
On 26 April 2018 at 11:05, Loic Gouarin <loic.goua...@math.u-psud.fr> wrote: > The problem is solved with the new 3.9.0 release on conda-forge. > > Thanks Lisandro !! > Well, you are most welcome, but I don't remember doing anything in particular to get that fixed :-) -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] petsc4py: reuse setup for multiple solver calls?
On 6 April 2018 at 08:48, Robert Speck <r.sp...@fz-juelich.de> wrote: > Thank you for your answer! Please see below for comments/questions. > > On 05.04.18 12:53, Matthew Knepley wrote: >> On Thu, Apr 5, 2018 at 6:39 AM, Robert Speck <r.sp...@fz-juelich.de >> >> For nonlinear solves which stay the same size, you do nothing. > > "nothing" in terms of "nothing you can do" or "nothing you have to do"? > I would say "nothing you have to do". Nonlinear solvers work by just setting two callback routines to compute the residual and the Jacobian. The user-defined residual routine receives a vector you have to put values in, same for the Jacobian routine, you have to put values in the (already preallocated) matrix that is reused on each newton step, and on each successive solve. SNES will take care of everything else (in particular, updating the KSP linear solver, and refreshing the preconditioner, always trying to reuse already-preallocated internal data structures as much as possible). All what what I said for SNES applies to TS, in case you ever want to give it a chance. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] Transform scipy sparse to partioned, parallel petsc matrix in PETSc4py
On 11 February 2018 at 20:35, Jan Grießer <griesser@googlemail.com> wrote:
> Hey,
>
> i have a precomputed scipy sparse matrix for which I want to solve the
> eigenvalue problem for a matrix of size 35000x35000. I don´t really get how
> to parallelize this problem correctly.
> Similar to another
> thread(https://lists.mcs.anl.gov/mailman/htdig/petsc-users/2013-August/018501.html)
> I tried the following code:
>
>
>
> D = scipy.sparse.load_npz("sparse.npz")
>
> B = D.tocsr()
>
>
>
> # Construct the matrix Ds in parallel
>
> Ds = PETSc.Mat().create()
>
> Ds.setSizes(CSRmatrix.shape)
>
> Ds.assemble()
>
Use DS.setUp()
>
>
> # Fill the matrix
>
> rstart, rend = Ds.getOwnershipRange()
>
> csr = (
>
> B.indptr[rstart:rend+1] - B.indptr[rstart],
>
> B.indices[B.indptr[rstart]:B.indptr[rend]],
>
> B.data[B.indptr[rstart]:B.indptr[rend]]
>
> )
>
This looks just fine
>
>
> Ds = PETSc.Mat().createAIJ(size=CSRmatrix.shape, csr=csr)
>
> Ds.assemble()
>
I think you don't need to assemble here.
>
>
> # Solve the eigenvalue problem
>
> solve_eigensystem(Ds)
>
>
>
> This code works for 1 processor with mpiexec –n 1 python example.py, however
> for increasing number of processors it appears as if al processors try to
> solve the overall problem instead of splitting it into blocks and solve for
> a subset of eigenvalues and eigenvectors.
> Why is this the case or did I miss something?
>
I guess you are using `mpiexec` from a different MPI implementation
than the one you used to build PETSc and petsc4py.
--
Lisandro Dalcin
Research Scientist
Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/
4700 King Abdullah University of Science and Technology
al-Khawarizmi Bldg (Bldg 1), Office # 0109
Thuwal 23955-6900, Kingdom of Saudi Arabia
http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
Re: [petsc-users] petsc4py f2py
Line 71 is likely wrong, too, you likely meant: do k=grd%zs,grd%ze On 18 January 2018 at 21:59, Lisandro Dalcin <dalc...@gmail.com> wrote: > On 18 January 2018 at 18:56, Aurelien Ponte <aurelien.po...@ifremer.fr> wrote: >> The code is found here: >> https://github.com/apatlpo/qgsolver/tree/fwrapping/qgsolver > > Your code is not valid Fortran, you cannot use brackets [] for > indexing in lines 80-90, you have to use parentheses (). > > -- > Lisandro Dalcin > > Research Scientist > Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) > Extreme Computing Research Center (ECRC) > King Abdullah University of Science and Technology (KAUST) > http://ecrc.kaust.edu.sa/ > > 4700 King Abdullah University of Science and Technology > al-Khawarizmi Bldg (Bldg 1), Office # 0109 > Thuwal 23955-6900, Kingdom of Saudi Arabia > http://www.kaust.edu.sa > > Office Phone: +966 12 808-0459 -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] petsc4py f2py
On 18 January 2018 at 18:56, Aurelien Ponte <aurelien.po...@ifremer.fr> wrote: > The code is found here: > https://github.com/apatlpo/qgsolver/tree/fwrapping/qgsolver Your code is not valid Fortran, you cannot use brackets [] for indexing in lines 80-90, you have to use parentheses (). -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] petsc4py, cython
In Cython code using C types from petsc4py, you should do: from petsc4py.PETSc cimport Vec, PetscVec from petsc4py.PETSc cimport Mat, PetscMat # etcetera now you can "cdef" either "PetscVec" (the low-level PETSc C type) and "Vec" (the higher-level petsc4py Python type) Or you can just from petsc4py.PETSc cimport * to get all definitions, or even from petsc4py cimport PETSc then use properly-namespaced definitions "PETSc.PetscVec" (C type) and "PETSc.Vec" (Python type). -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] Installing petsc4py
Dear Nicholas, The errors you reported where just outdated Fortran code and makefiles in demo/, these are just examples. I pushed a fix to the maint branch of the repository. BTW, do you know that conda-forge provides prebuilt packages for petsc and petsc4py? Just create a new conda environment, activate, and then "conda install -c conda-forge petsc4py" On 18 October 2017 at 07:23, Stegmeier, Nicholas <nicholas.stegme...@sdstate.edu> wrote: > Hello all, > > > I was hoping to get some advice on installing petsc4py. Hopefully this is an > appropriate question as it's my first time emailing the list. > > > I failed numerous times installing petsc4py on my personal laptop, so I > decided to use a virtual machine with Ubuntu to try installing from a clean > slate. > > > I followed the steps listed on this webpage: > https://gist.github.com/mrosemeier/088115b2e34f319b913a > > Install openmpi > Install anaconda-python > Install petsc > Install petsc4py > > > After doing all this, I entered the petsc4py/demo folder and used make to > see if all the tests passed. But several of the tests promptly failed. Below > are some of the errors I received, but I also attached the full error > output. Maybe I have forgotten to assign some environment variable? > > Thank you, > Nicholas Stegmeier > > inside .bashrc: > export LD_LIBRARY_PATH=/home/nick/local/openmpi-1.10.5/lib:$LD_LIBRARY_PATH > export PATH=/home/nick/local/openmpi-1.10.5/bin:$PATH > export PATH="/home/nick/local/anaconda2/bin:$PATH" > export PETSC_DIR=/home/nick/local/petsc.git > export PETSC_ARCH=arch-python-linux-i686 > > nick@nick-VirtualBox:~/local/petsc.git/bin$ echo $PATH > /home/nick/local/anaconda2/bin:/home/nick/local/openmpi-1.10.5/bin:/home/nick/local/anaconda2/bin:/home/nick/local/openmpi-1.10.5/bin:/home/nick/bin:/home/nick/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin > > nick@nick-VirtualBox:~/local/petsc.git/bin$ echo $PATH > /home/nick/local/anaconda2/bin:/home/nick/local/openmpi-1.10.5/bin:/home/nick/local/anaconda2/bin:/home/nick/local/openmpi-1.10.5/bin:/home/nick/bin:/home/nick/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin > > sample error output: > > make -f makefile.petsc \ > PETSC_DIR=/home/nick/local/petsc.git > PETSC_ARCH=arch-python-linux-i686 > make[2]: Entering directory '/home/nick/local/petsc4py.git/demo/perftest' > cApp.f90 > make[2]: c: Command not found > makefile.petsc:15: recipe for target 'driver.exe' failed > make[2]: [driver.exe] Error 127 (ignored) > /home/nick/local/openmpi-1.10.5/bin/mpicc -c -Wall -Wwrite-strings > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > -fvisibility=hidden -g -O -I/home/nick/local/petsc.git/include > -I/home/nick/local/petsc.git/arch-python-linux-i686/include > `pwd`/driver.c > /home/nick/local/openmpi-1.10.5/bin/mpicc -Wall -Wwrite-strings > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > -fvisibility=hidden -g -O -o driver.exe > -Wl,-rpath,/home/nick/local/petsc.git/arch-python-linux-i686/lib > -L/home/nick/local/petsc.git/arch-python-linux-i686/lib -lpetsc -llapack > -lblas -lm -ldl driver.o App.o > gcc: error: App.o: No such file or directory > makefile.petsc:15: recipe for target 'driver.exe' failed > make[2]: [driver.exe] Error 1 (ignored) > > ... > > ./Bratu2D.F90:20:0: > > #include "petsc/finclude/petscdef.h" > ^ > Fatal Error: petsc/finclude/petscdef.h: No such file or directory > compilation terminated. > ./Bratu2D.F90:20:0: > > #include "petsc/finclude/petscdef.h" > ^ > Fatal Error: petsc/finclude/petscdef.h: No such file or directory > compilation terminated. > error: Command "/usr/bin/gfortran -Wall -g -fno-second-underscore > -DF2PY_REPORT_ON_ARRAY_COPY=1 > -I/home/nick/local/petsc.git/arch-python-linux-i686/include > -I/home/nick/local/petsc.git/include > -I/home/nick/local/anaconda2/lib/python2.7/site-packages/petsc4py/include > -I. -Ibuild/src.linux-i686-2.7/. > -I/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include > -I/home/nick/local/anaconda2/include/python2.7 -c -c ./Bratu2D.F90 -o > build/temp.linux-i686-2.7/Bratu2D.o -Jbuild/temp.linux-i686-2.7/ > -Ibuild/temp.linux-i686-2.7/" failed with exit status 1 > makefile:20: recipe for target 'Bratu2D.so' failed > make[1]: *** [Bratu2D.so] Error 1 > make[1]: Leaving directory '/home/nick/local/petsc4py.git/demo/wrap-f2py' > makefile:3: recipe for target 'all' failed > make: [all] Error 2 (ignored) > > > Thank you, > Nicholas Stegmeier -- Lisandro Dalcin Resea
Re: [petsc-users] Trouble installing petsc4py in Anaconda environment
PETSC_DIR:
> /home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/petsc
> PETSC_ARCH:
> version: 3.8.0 release
> integer-size: 32-bit
> scalar-type: real
> precision:double
> language: CONLY
> compiler: /vendor/sgi/mpt/2.14r19/bin/mpicc
> linker: /vendor/sgi/mpt/2.14r19/bin/mpicc
> building 'PETSc' extension
> creating build/temp.linux-x86_64-2.7
> creating build/temp.linux-x86_64-2.7/src
> /vendor/sgi/mpt/2.14r19/bin/mpicc -pthread -B
> /home/login/anaconda2/envs/myenv/compiler_compat -fPIC -Wall -Wwrite-strings
> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -g -O -fPIC
> -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
> -DPETSC_DIR=/home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/petsc
> -I/home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/petsc/include
> -Isrc/include
> -I/home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/numpy/core/include
> -I/home/login/anaconda2/envs/myenv/include/python2.7 -c src/PETSc.c -o
> build/temp.linux-x86_64-2.7/src/PETSc.o
> In file included from
> /home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1788:0,
> from
> /home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
> from
> /home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
> from src/include/petsc4py/numpy.h:11,
> from src/petsc4py.PETSc.c:519,
> from src/PETSc.c:3:
>
> /home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
> warning: #warning "Using deprecated NumPy API, disable it by " "#defining
> NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
> #warning "Using deprecated NumPy API, disable it by " \
> ^
> /vendor/sgi/mpt/2.14r19/bin/mpicc -pthread -B
> /home/login/anaconda2/envs/myenv/compiler_compat -fPIC -Wall -Wwrite-strings
> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -g -O -fPIC
> -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
> -DPETSC_DIR=/home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/petsc
> -I/home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/petsc/include
> -Isrc/include
> -I/home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/numpy/core/include
> -I/home/login/anaconda2/envs/myenv/include/python2.7 -c src/libpetsc4py.c -o
> build/temp.linux-x86_64-2.7/src/libpetsc4py.o
> /vendor/sgi/mpt/2.14r19/bin/mpicc -pthread -B
> /home/login/anaconda2/envs/myenv/compiler_compat -fPIC -Wall -Wwrite-strings
> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -g -O gcc
> -pthread -shared -B /home/login/anaconda2/envs/myenv/compiler_compat
> -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
> -L/home/login/anaconda2/envs/myenv/lib
> -Wl,-rpath=/home/login/anaconda2/envs/myenv/lib -Wl,--no-as-needed
> -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/src/PETSc.o
> build/temp.linux-x86_64-2.7/src/libpetsc4py.o
> -L/home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/petsc/lib
> -L/home/login/anaconda2/envs/myenv/lib
> -Wl,-rpath,/home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/petsc/lib
> -Wl,-rpath,/home/login/anaconda2/envs/myenv/lib -lpetsc -lpython2.7 -o
> build/lib.linux-x86_64-2.7/petsc4py/lib/PETSc.so
> gcc: error: gcc: No such file or directory
> error: command '/vendor/sgi/mpt/2.14r19/bin/mpicc' failed with exit
> status 1
>
>
> Command "/home/login/anaconda2/envs/myenv/bin/python -u -c "import
> setuptools,
> tokenize;__file__='/tmp/pip-build-v6lDIk/petsc4py/setup.py';f=getattr(tokenize,
> 'open', open)(__file__);code=f.read().replace('\r\n',
> '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record
> /tmp/pip-d6NYW8-record/install-record.txt
> --single-version-externally-managed --compile" failed with error code 1 in
> /tmp/pip-build-v6lDIk/petsc4py/
>
>
> --
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>
> Bill Jones w.t.jo...@nasa.gov
> Mail Stop 128 Computational AeroSciences Branch
> 15 Langley Boulevard Research Directorate
> NASA Langley Research Center Building 1268, Room 1044
> Hampton, VA 23681-2199 Phone +1 757 864-5318
> Fax +1 757 864-8816
> http://fun3d.larc.nasa.gov
--
Lisandro Dalcin
Research Scientist
Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/
4700 King Abdullah University of Science and Technology
al-Khawarizmi Bldg (Bldg 1), Office # 0109
Thuwal 23955-6900, Kingdom of Saudi Arabia
http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
Re: [petsc-users] [PETSc] How to read a Vector and Matrix from an ASCII file into PETSc?
On 11 September 2017 at 19:21, Ryan Morley <ryantmorley7...@gmail.com> wrote: > Dear all, > > I am working on a program in Petsc that will read a vector and matrix from > an ASCII file and store it into a vector and matrix object in Petsc so I can > eventually solve. It needs to be an ASCII file because I will be outputting > the vector and matrix to an ASCII file from code in Delphi. > Would it be OK to use an intermediate program to read the ASCII output and dump in PETSc binary format? That would be rather trivial to do with a Python script. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] TS for explicit equations
On 6 July 2017 at 17:10, Alejandro D Otero <aot...@fi.uba.ar> wrote: > > # Set rhs function > ts.setRHSFunction(self.evalRHSFunction, self.g) > (where evalRHSFunction has the form f(self, ts, t, Vort, f)) > Please double check that the RHS function "outputs" the result in the passed-in vector "f", my guess is that you are just returning a new vector that is eventually ignored. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] petsc4py and python's logging module
On 29 May 2017 at 19:17, David Nolte <dno...@dim.uchile.cl> wrote:
> Dear all,
>
> is it possible to use python's logging module
> (https://docs.python.org/2/howto/logging.html) to handle PETSc output in
> python, such as the residuals during a KSP/SNES solve?
> I log my solver's activity to a file using the logging module, it would
> be great to include the PETSc output aswell.
>
Not sure if this is what you really want, but you could...
1) Use {ksp|snes}.setConvergenceHistory() before solve, then
{ksp|snes}.getConvergenceHistory() after solve, you will get arrays
with the residual history, then you can do whatever you want with
them.
2) Implement a KSP/SNES monitor in a Python function and call
{ksp|snes}.setMonitor(), then you can use python's logging inside your
monitor function.
--
Lisandro Dalcin
Research Scientist
Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/
4700 King Abdullah University of Science and Technology
al-Khawarizmi Bldg (Bldg 1), Office # 0109
Thuwal 23955-6900, Kingdom of Saudi Arabia
http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
Re: [petsc-users] petsc4py bool type
On 25 April 2017 at 19:48, Garth N. Wells <gn...@cam.ac.uk> wrote: > I'm seeing some behaviour with bool types in petsc4py that I didn't > expect. In the Python interface, returned Booleans have type ' 'int'>', where I expected them to have type ' '. Below > program illustrates issue. Seems to be related to bint in cython. Am I > doing something wrong? Wow! Yes, you are right, this seems like a regression in Cython. In the past, a cast used to coerce values to the Python `bool` type. Damn, these casts are everywhere, it might take a while to fix all the code, unless I can find a hacky way to workaround the issue. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] petsc4py & GPU
On 20 April 2017 at 17:09, Damian Kaliszan <dam...@man.poznan.pl> wrote:
> Thank you for reply:) Sorry for maybe stupid question in the scope of
> setting petsc(4py) options.
> Should the following calls (somewhere before creating matrix & vectors):
>
> PETSc.Options().setValue("ksp_view", "")
> PETSc.Options().setValue("log_view", "")
>
Unfortunately, no. There are a few options (-log_view ?) that you should
set before calling PetscInitialize() (which happens automatically at import
time), otherwise things do not work as expected. To pass things from the
command line and set them before PetscInitialize() the usual idiom is:
import sys, petsc4py
petsc4py.init(sys.argv)
from petsc4py import PETSc
--
Lisandro Dalcin
Research Scientist
Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/
4700 King Abdullah University of Science and Technology
al-Khawarizmi Bldg (Bldg 1), Office # 0109
Thuwal 23955-6900, Kingdom of Saudi Arabia
http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
Re: [petsc-users] how to use petsc4py with mpi subcommunicators?
On 11 April 2017 at 17:31, Rodrigo Felicio <rodrigo.feli...@iongeo.com> wrote: > Thanks, Jed, but using color == 0 lead to the same error msg. Is there no > way to set PETSc.COMM_WORLD to a subcomm instead of MPI.COMM_WORLD in > python? > > You can do it, but it is a bit tricky, and related to the fact that PETSC_COMM_WORLD has to be set to subcomm before calling PetscInitialize(), which happens automatically the first time Python executes "from petsc4py import PETSc". The way to do it would be the following: import sys, petsc4py petsc4py.init(sys.argv, comm=subcomm) from petsc4py import PETSc -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] How to use f2py on a PETSc/SLEPc-based fortran code
On 22 March 2017 at 20:29, Barry Smith <bsm...@mcs.anl.gov> wrote: > > Lisandro, > > We've had a couple questions similar to this with f2py; is there a way > we could add to the PETSc/SLEPc makefile rules something to allow people to > trivially use f2py without having to make their own (often incorrect) > manual command lines? > >Thanks > > Barry, it is quite hard and hacky to get f2py working in the general case. I think the email from Gaetan in this thread proves my point. IMHO, it is easier to write a small Fortran source exposing the API to call using ISO_C_BINDINGS, then wrap that code with the more traditional C-based "static" tools (SWIG, Cython) or even "dynamically" with ctypes or cffi (which use dlopen'ing). -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] FFT using Petsc4py
On 27 September 2016 at 21:05, Amit Itagi <gcf...@gmail.com> wrote: > Hello, > > I am looking at the Petsc FFT interfaces. I was wondering if a parallel > FFT can be performed within a Petsc4Py code. If not, what would be the best > way to use the Petsc interfaces for FFT from Petsc4Py ? > > It should work out of the box by using mat.setType(Mat.Type.FFTW) before setup of your matrix. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] petsc4py with complex numbers?
Are you sure you built petsc4py with a PETSc build with complex scalars? Whats the output of "print(PETSc.ScalarType)" ? On 26 September 2016 at 07:47, Aurelien Ponte <aurelien.po...@ifremer.fr> wrote: > Hi, > > I am trying to solve a linear problem whose operator has complex > coefficients via petsc4py > but keep running into the following error: > > File > "/Users/aponte/Current_projects/people/kraig_marine/wd_response/solver/set_L.py", > line 52, in set_L > L.setValueStencil(row, col, value) > File "PETSc/Mat.pyx", line 882, in petsc4py.PETSc.Mat.setValueStencil > (src/petsc4py.PETSc.c:124785) > File "PETSc/petscmat.pxi", line 1017, in petsc4py.PETSc.matsetvaluestencil > (src/petsc4py.PETSc.c:31469) > File "PETSc/arraynpy.pxi", line 140, in petsc4py.PETSc.iarray_s > (src/petsc4py.PETSc.c:8811) > File "PETSc/arraynpy.pxi", line 121, in petsc4py.PETSc.iarray > (src/petsc4py.PETSc.c:8542) > TypeError: can't convert complex to float > > The code looks like: > > for j in range(ys, ye): > for i in range(xs, xe): > row.index = (i, j, kx) > row.field = 0 > col.index = (i, j, kx) col.field=0 > L.setValueStencil(row, col, 1j) > > Any idea about what am I doing wrong? > > cheers > > aurelien > > > > -- > Aurélien Ponte > Tel: (+33) 2 98 22 40 73 > Fax: (+33) 2 98 22 44 96 > UMR 6523, IFREMER > ZI de la Pointe du Diable > CS 10070 > 29280 Plouzané > > -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] [petsc4py] a problem with computeRHSFunctionLinear interface?
On 21 August 2016 at 13:01, Francesco Caimmi <francesco.cai...@polimi.it> wrote: > I will also take the chance to ask a related question: in the original C > code, > lines 213 -214 read > ierr = TSGetSNES(ts,);CHKERRQ(ierr); > ierr=SNESSetJacobian(snes,NULL,NULL,SNESComputeJacobianDefault, > NULL);CHKERRQ(ierr); > > How do I translate the last line in Python? I was not able to find the > equivalent of SNESComputeJacobianDefault. > That one is not directly available, however you can pass -snes_fd in the command line, or alternatively opts = PETSc.Options() opts['snes_fd'] = 1 snes.setFromOptions() -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] [petsc4py] a problem with computeRHSFunctionLinear interface?
Dear Francesco, sorry for the late answer, I missed your email. You have to do it this way: ts.setRHSFunction(PETSc.TS.computeRHSFunctionLinear) ts.setRHSJacobian(PETSc.TS.computeRHSJacobianConstant, J=A, P=A) I.e, you have to set unbound methods, not instance methods as you did in your original code. Additionally, do not pass "args" nor "kargs". On 11 August 2016 at 10:36, Francesco Caimmi <francesco.cai...@polimi.it> wrote: > Dear all, > > I was trying to reproduce /ts/examples/tutorials/ex4.c in python to learn how > to use TS solvers; the example uses the function TSComputeRHSFunctionLinear. > However I get an error when running my code (attached in case you want to look > at it), when I call ts.solve. > > Here is the trace: > [fcaimmi@Wotan 2645] > ./ts_ex4.py > Solving a linear TS problem, number of processors = 1 > Timestep 0 : time = 0.0 2-norm error = 1.14956855594e-08 max norm error = 0 > Traceback (most recent call last): > File "./ts_ex4.py", line 473, in > main(m = m, debug = debug) > File "./ts_ex4.py", line 340, in main > ts.solve(u) > File "PETSc/TS.pyx", line 568, in petsc4py.PETSc.TS.solve > (src/petsc4py.PETSc.c:188927) > File "PETSc/petscts.pxi", line 221, in petsc4py.PETSc.TS_RHSFunction > (src/petsc4py.PETSc.c:35490) > File "PETSc/TS.pyx", line 189, in petsc4py.PETSc.TS.computeRHSFunctionLinear > (src/petsc4py.PETSc.c:181611) > TypeError: computeRHSFunctionLinear() takes exactly 3 positional arguments (5 > given) > > I cannot understand if there is a problem with my code or if the problem is in > computeRHSFunctionLinear interface. > > I checked https://bitbucket.org/petsc/petsc4py/ and the interface to > computeRHSFunctionLinear has three arguments, however I am not that much into > petsc4py to tell how it gets called. > > I am on Petsc Release Version 3.7.3 > > Thank you for your time. > > Best, > -- > Francesco Caimmi > > Laboratorio di Ingegneria dei Polimeri > http://www.chem.polimi.it/polyenglab/ > > Politecnico di Milano - Dipartimento di Chimica, > Materiali e Ingegneria Chimica “Giulio Natta” > > P.zza Leonardo da Vinci, 32 > I-20133 Milano > Tel. +39.02.2399.4711 > Fax +39.02.7063.8173 > > francesco.cai...@polimi.it > Skype: fmglcaimmi (please arrange meetings by e-mail) -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] petsc4py - Change default line search for SNES Newton Line Search
On 12 July 2016 at 16:37, Hensgens, Marius <marius.hensg...@rwth-aachen.de> wrote: > how can I change the used line search method after setting the SNES Type to > 'newtonls' using petsc4py ? > Right now, you can either use the command line or programatically insert an option in the database opts = PETSc.Options() opts['snes_linesearch_type'] = lstype ... snes.setFromOptions() > In the official PETSc documentation there is a function called > SNESLineSearchSetType, however in petsc4py I can't find an equivalent > function. The SNESLineSearch type and related routines are not wrapped yet. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] How to determine the type of SNESLineSearch?
PetscBool match;
ierr = PetscObjectTypeCompare((PetscObject)linesearch,
SNESLINESEARCHBASIC,);CHKERRQ(ierr);
if (!match) {
...
}
On 6 July 2016 at 00:07, Gautam Bisht <gbi...@lbl.gov> wrote:
> Hi PETSc,
>
> After SNESSolve converges, I want to perform few additional operations only
> when SNESLineSearchType is not SNESLINESEARCHBASIC. But, there is no
> SNESLineSearchGetType routine. Any idea on how I can determine the type of
> LineSearch set by a user using command line option?
>
> Thanks,
> -Gautam.
--
Lisandro Dalcin
Research Scientist
Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/
4700 King Abdullah University of Science and Technology
al-Khawarizmi Bldg (Bldg 1), Office # 0109
Thuwal 23955-6900, Kingdom of Saudi Arabia
http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
Re: [petsc-users] Petsc4py DMREDUNDANT or equivalent functionality
On 15 April 2016 at 20:17, Ben Fogelson <benfogel...@gmail.com> wrote: > As best I can tell, Petsc4py doesn't have a method like > DM().createRedundant()--perhaps it this DM just isn't implemented? Yes, that is the case. > Can > anyone recommend an alternate approach to getting the same functionality? I guess the best way to go would be to implement the missing DM. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] PETSc release soon, request for input on needed fixes or enhancements
On 27 February 2016 at 23:36, Barry Smith <bsm...@mcs.anl.gov> wrote: > We are planning the PETSc release 3.7 shortly. If you know of any bugs that > need to be fixed or enhancements added before the release please let us know. Barry, long time ago I reported a regression in PetIGA related to the new Vec assembly routines. I guess Jed didn't have a chance to look at it. Until that happens, I propose to not use the new routines as the default ones. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] petsc4py installation error with PETSc v 3.6.1
On 25 July 2015 at 00:12, Justin Chang jychan...@gmail.com wrote: ImportError: /usr/local/lib/python2.7/dist-packages/petsc4py/lib/arch-linux2-c-opt/PETSc.so: undefined symbol: DMShellSetCreateSubDM make: *** [unit_sequential] Error 1 You need to git pull in branch master of petsc-dev and rebuild. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] petsc4py Build Problem
On 23 June 2015 at 12:15, Mikhail Khodak mkho...@princeton.edu wrote: Thank you for reviewing this. The errors for the command 'pip2 install .' inside the petsc4py directory are attached, along with the configure/make logs for the PETSc build. Best, Mikhail Khodak Not sure what's going on. Do you have PETSC_DIR and PETSC_ARCH in your environment? Does it work if you just do python setup.py build ? -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] petsc4py Build Problem
Dear Mikhail, Satish helped me and we managed to get petsc4py working with static builds and Cygwin's Open MPI. Please git pull and try again. On 11 June 2015 at 14:13, Mikhail Khodak mkho...@princeton.edu wrote: I have attached the log files. I tried using Open MPI before but received the same result. I will try a static build later and otherwise will get a VM. Thanks for looking at this, Mikhail On Thu, Jun 11, 2015 at 10:48 AM, Satish Balay ba...@mcs.anl.gov wrote: Also - should mention: - cygwin has OpenMPI pacakged - so you could also try that. - most of my builds are static [so never tried dll builds] Satish On Thu, 11 Jun 2015, Satish Balay wrote: If you get errors when running basic petsc examples - send us the relavant petsc logs [configure.log, make.log, test.log etc..] Also - note that mpich is not supported on cygwin/windows [it generally works for us - when we try the --download-mpich build]. Unless you really need a cywin build/use of petsc4py - it might be easier to install a linux VM - and use PETSc/petsc4py on it. Satish On Thu, 11 Jun 2015, Mikhail Khodak wrote: I added these lines to the petsc4py test files (specifically test_comm.py) but the error remains the same. However, I have done the standard 'which mpiexec', 'which mpicc', 'which mpirun' and they are all in the same folder. In fact it is the only MPI installed. The reason I thought it might be a PETSc build problem is because one of the PETSc 'make test' tests (ex5f) fails with the same error, even though the 'make streams' test works fine with MPI processes. Thanks, Mikhail On Thu, Jun 11, 2015 at 4:21 AM, Matthew Knepley knep...@gmail.com wrote: On Thu, Jun 11, 2015 at 5:07 AM, Mikhail Khodak mkho...@princeton.edu wrote: Thank you for your help - the install seems to work, apart from routines requiring MPI, which fail due to the Attempting to use an MPI routine before initializing MPI error. This seems to be an error in the PETSc build itself. The MPI routines will not work until after import petsc4py, sys petsc4py.init(sys.argv) from petsc4py import PETSc If they fail after this, it is usually a mismatch between the mpiexec being used and the MPI libraries being linked. Thanks, Matt Thanks again, Mikhail Khodak On Mon, Jun 8, 2015 at 5:11 AM, Lisandro Dalcin dalc...@gmail.com wrote: On 8 June 2015 at 02:50, Mikhail Khodak mkho...@princeton.edu wrote: Hello, I am trying to build petsc4py-3.5.1 using Cygwin on 64-bit Windows 7. I have built PETSc 3.5.4 with shared and dynamic libraries using mpich2-1.2.1 and successfully ran the installation tests. I am using Python 2.7 and NumPy 1.9.2 and have installed mpi4py. However, when I attempt to install petsc4py (both with pip and distutils) I get a mpicc compiler error due to undefined references/symbols. I have attached the output of running pip install petsc petsc4py --allow-external petsc --allow-external petsc4py I've never ever built or test petsc4py under Cygwin. The errors you see are expected. Perhaps you can manually workaround the issues following the following steps: 1) Download the petsc4py tarball and unpack it. 2) Open the file src/libpetsc4py/libpetsc4py.h, add remove all occurences of DL_IMPORT, i.e, replace DL_IMPORT(XYZ) for just XYZ 3) Use pip again: pip install petsc pip install . The last line assumes your current working directory is the one having petsc4py's setup.py Finally, I do not guarantee this will work. I'm just guessing, petsc4py never explicitly supported Windows and/or Cygwin. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi
Re: [petsc-users] petsc4py Build Problem
On 8 June 2015 at 02:50, Mikhail Khodak mkho...@princeton.edu wrote: Hello, I am trying to build petsc4py-3.5.1 using Cygwin on 64-bit Windows 7. I have built PETSc 3.5.4 with shared and dynamic libraries using mpich2-1.2.1 and successfully ran the installation tests. I am using Python 2.7 and NumPy 1.9.2 and have installed mpi4py. However, when I attempt to install petsc4py (both with pip and distutils) I get a mpicc compiler error due to undefined references/symbols. I have attached the output of running pip install petsc petsc4py --allow-external petsc --allow-external petsc4py I've never ever built or test petsc4py under Cygwin. The errors you see are expected. Perhaps you can manually workaround the issues following the following steps: 1) Download the petsc4py tarball and unpack it. 2) Open the file src/libpetsc4py/libpetsc4py.h, add remove all occurences of DL_IMPORT, i.e, replace DL_IMPORT(XYZ) for just XYZ 3) Use pip again: pip install petsc pip install . The last line assumes your current working directory is the one having petsc4py's setup.py Finally, I do not guarantee this will work. I'm just guessing, petsc4py never explicitly supported Windows and/or Cygwin. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] Create identity IS
On 20 April 2015 at 14:35, Florian Lindner mailingli...@xgm.de wrote: Hello, I use an index set for a row mapping but don't want to use one for the column mapping. I try to create an idenitity index set to supply to ISLocalToGlobalMappingCreateIS and MatSetLocalToGlobalMapping: IS is; ISCreate(PETSC_COMM_WORLD, is); At this point the index set does not have the type set. ISSetIdentity(is); but I get an segmentation fault at the last line. Bad error checking, you should get an error saying that the type is not yet set. What is the best way to create an identity index set? I would use ISCreateStride(), and perhaps next ISToGeneral() if you really want a ISGENERAL type. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] TimeStepper norm problems. EMIL Please read this
On 16 April 2015 at 04:51, Emil Constantinescu emcon...@mcs.anl.gov wrote: On 3/24/15 5:31 AM, Lisandro Dalcin wrote: Emil, is there any chance you can try my code with your problem? I really need some feedback to push this to PETSc, otherwise Hi Lisandro - we checked ts_alpha_adapt and we tested it on a small system (mildly stiff van der Pol ODE). I enclosed a Figure generated by Debo that compares the error at the final time against ATOL - there alpha is the original one (with original adaptor). Original adaptor? Do you mean TSAlphaSetAdapt(ts,TSAlphaAdaptDefault,NULL)? In such a case, no surprises, TSAlphaAdaptDefault() is quite naive, it does not estimate the LTE, it is actually based in the change of the solution. Can you send/point me your code to take a look? For this problem your adaptor works better [ error should be close to ATOL]. So from my perspective, your adaptor works well. However, we need to keep the old too so that we have a one step adaptor available ... since alpha is a one step method. Sorry, I'm not following you. Generalized alpha is not truly a one-step method, because it retains Xdot from the previous time step. In the initial step, other codes out there assume that Xdot_prev=0. My alpha1 implementation has a trick for the initial time step (using the same ideas, i.e. a BD formula) to both estimate Xdot_prev and the error. However, this is at the cost of performing two nonlinear solves in the initial step (IOW, two internal timesteps with backward Euler and dt/2). Please note this trick should be valid for any second-order method, at least to estimate the initial LTE in the first step. BTW, Have you compared my -ts_type tsalpha1 -ts_alpha_adapt with PETSc's -ts_type cn -ts_theta adapt? -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] TimeStepper norm problems. EMIL Please read this
On 16 April 2015 at 16:44, Emil Constantinescu emcon...@mcs.anl.gov wrote:
On 4/16/15 2:13 AM, Lisandro Dalcin wrote:
On 16 April 2015 at 04:51, Emil Constantinescu emcon...@mcs.anl.gov
wrote:
On 3/24/15 5:31 AM, Lisandro Dalcin wrote:
Emil, is there any chance you can try my code with your problem? I
really need some feedback to push this to PETSc, otherwise
Hi Lisandro - we checked ts_alpha_adapt and we tested it on a small
system
(mildly stiff van der Pol ODE). I enclosed a Figure generated by Debo
that
compares the error at the final time against ATOL - there alpha is the
original one (with original adaptor).
Original adaptor? Do you mean
TSAlphaSetAdapt(ts,TSAlphaAdaptDefault,NULL)?
In such a case, no surprises, TSAlphaAdaptDefault() is quite naive, it
does not estimate the LTE, it is actually based in the change of the
solution.
Yups, that's the one;
I was the author of TSAlphaAdaptDefault (the whole TSALPHA, in fact).
I coded that beast out of desperation long time ago. This thing is
not even implemented withing the current TSAdapt framework!. I think
at least we should re-implement this beast within TSAdapt (I mean,
similar as in -ts_theta_adapt).
but that still needs to be available unless a better
one-step one is implemented.
I think you have that feeling simply because TSAlphaAdaptDefault()
seems to work, but if you look carefully at the code, it does not make
sense from the point of view of a LTE-based theory.
OK, Then let's define a poor's man one-step adapt that at least have
some sense. How would you implement adaptivity for backward Euler or
the midpoint rule? Something based exclusively in some l2/inf norm of
Xdot? IOW, we define LTE = X^{n+1} - X^n of O(\delta_t) and use the
usual formula with exponent order=1 ?
Note however that even estimating exactly LTE
is not a guarantee that the error will be within ATOL.
Well, ATOL is to keep the LTE under control, of course there are no
guarantees about the global error at the end step. That's what you
meant?
--
Lisandro Dalcin
Research Scientist
Computer, Electrical and Mathematical Sciences Engineering (CEMSE)
Numerical Porous Media Center (NumPor)
King Abdullah University of Science and Technology (KAUST)
http://numpor.kaust.edu.sa/
4700 King Abdullah University of Science and Technology
al-Khawarizmi Bldg (Bldg 1), Office # 4332
Thuwal 23955-6900, Kingdom of Saudi Arabia
http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
Re: [petsc-users] petsc4py and mumps (or other direct sparse solver)
On 15 April 2015 at 18:15, Hong hzh...@mcs.anl.gov wrote: Benoit : mumps options can be called from PETSc C-code as ierr = PetscOptionsInsertString(-mat_mumps_icntl_13 1 -mat_mumps_icntl_24 1 -mat_mumps_cntl_3 1e-12);CHKERRQ(ierr); or see petsc/src/ksp/ksp/examples/tutorials/ex52.c I do not know how to translate these calls into python API though. opts = PETSc.Options() # dict-like opts[mat_mumps_icntl_13] = 1 opts[mat_mumps_icntl_24] = 1 opts[mat_mumps_cntl_3] = 1e-12 Or also: opts = PETSc.Options() opts.prefixPush(mat_mumps_) opts[icntl_13] = 1 opts[icntl_24] = 1 opts[cntl_3] = 1e-12 opts.prefixPop() Or also: opts = PETSc.Options(mat_mumps_) opts[icntl_13] = 1 opts[icntl_24] = 1 opts[cntl_3] = 1e-12 -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] running Petsc programs without a connection.
On 26 March 2015 at 10:15, Sanjay Kharche sanjay.khar...@manchester.ac.uk wrote: Is there a way of configuring or otherwise to get Petsc programs to run when I do not have an internet connection? Make sure you have localhost defined in /etc/hosts, I'm had the same issue in Fedora with fresh installs. $ cat /etc/hosts 127.0.0.1 localhost localhost.localdomain localhost4 localhost4.localdomain4 kw2060 kw2060.kaust.edu.sa ::1 localhost localhost.localdomain localhost6 localhost6.localdomain6 -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] petsc4py: Passing command line switches
On 25 March 2015 at 18:34, Matthew Knepley knep...@gmail.com wrote: That file is obviously old and was removed. After installing petsc4py, you can do make docs in the top level source tree, and the docs/ directory will be populated. For this to work, you need sphinx and epydoc installed. Lisandro, are we generating documentation somewhere? Two places: + http://petsc4py.readthedocs.org/ - This does not contain the epydoc-generated API reference. I'm not sure if setting up readthedocs to use epydoc is ever possible. + https://pythonhosted.org/petsc4py/, - It is for the last release, not the in-development version. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] TimeStepper norm problems. EMIL Please read this
On 24 March 2015 at 01:34, Jed Brown j...@jedbrown.org wrote: Lisandro Dalcin dalc...@gmail.com writes: On 21 March 2015 at 17:32, Emil Constantinescu emcon...@mcs.anl.gov wrote: When -ts_theta_adapt is used, then it detects the instability as an error and reduces the step by a lot! wlte=1.24e+03 which means that the reduction should be severe but the controller tries 0.1*dt and that seems to pass but it jig-saws (take a look at the next attempted step), which means that it is likely unstable. I think -ts_theta_adapt is seriously broken, I cannot make sense of the way the error estimator is computed. This was Shri's implementation. TSEvaluateStep_Theta looks wrong to me, both using U as an input and assuming that Xdot is set. I don't even know what the intended math is for a first-order embedded estimate in midpoint (theta=0.5). Pease note that -ts_adapt_tetha errors for midpoint. You actually need -ts_theta_endpoint to use adaptivity. But it is there, in the endpoint version, that I cannot make sense of the implementation. The trapezoidal rule is second-order, thus the LTE is O(dt^3). The computed error estimator should be O(dt^2), but the current code seems to compute an estimator O(dt), and that's the root of all evil. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] TimeStepper norm problems. EMIL Please read this
On 24 March 2015 at 06:15, Emil Constantinescu emcon...@mcs.anl.gov wrote: On 3/23/15 4:44 AM, Lisandro Dalcin wrote: Lisandro, that's a neat idea. If you are basically moving in the multistep realm for error estimation with one-step methods, I'm wondering if no one ever did it. I could not find any reference. I think there are two considerations: 1. The equations need to be continuous (no restarting, no events) or they would have to reset the error estimator somehow. Indeed. My generalized-alpha code does not handle events at all. I'll take a look into this. About restarting (not sure if we are talking about the same thing), I have some code that is specific to generalized-alpha (In the initial time step, I solve twice with backward-Euler using dt/2 and dt) that let me properly initialize generalized-alpha and also compute an initial error estimator. 2. Backward differences are sensitive to time stepping changes; unlike one-step methods that can accommodate any step changes, B-D has strict limits for stability. While this does not play a crucial role (it is just the estimator); Of course, though my B-D is order 2, and as you said, it is the just for the estimator. if the time step varies wildly (can be easily constrained), it may create some problems with the estimator. Indeed, the default clipping 0.1,10 is usually too wide, I usually do -ts_adapt_basic_clip 0.5,2.0 Emil, is there any chance you can try my code with your problem? I really need some feedback to push this to PETSc, otherwise -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] TimeStepper norm problems. EMIL Please read this
On 24 March 2015 at 18:40, Emil Constantinescu emcon...@mcs.anl.gov wrote:
Of course, though my B-D is order 2, and as you said, it is the just
for the estimator.
if the time step varies wildly (can be easily constrained),
it may create some problems with the estimator.
Indeed, the default clipping 0.1,10 is usually too wide, I usually do
-ts_adapt_basic_clip 0.5,2.0
The limits are a bit more strict for BDF2, but that's for the worst case and
no filtering. So that looks good too.
I'm not sure I'm following you 100%. Please note I'm not using BDF2 in
the usual sense, what I do is to compute an A POSTERIORI error
estimator using a BD of order 2 to estimate LTE^{n+1} with the
solution vectors U^{n+1}, U^{n} and U^{n-1}, and this is AFTER
computing U^{n-1}.
--
Lisandro Dalcin
Research Scientist
Computer, Electrical and Mathematical Sciences Engineering (CEMSE)
Numerical Porous Media Center (NumPor)
King Abdullah University of Science and Technology (KAUST)
http://numpor.kaust.edu.sa/
4700 King Abdullah University of Science and Technology
al-Khawarizmi Bldg (Bldg 1), Office # 4332
Thuwal 23955-6900, Kingdom of Saudi Arabia
http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
Re: [petsc-users] TimeStepper norm problems. EMIL Please read this
On 21 March 2015 at 17:32, Emil Constantinescu emcon...@mcs.anl.gov wrote: When -ts_theta_adapt is used, then it detects the instability as an error and reduces the step by a lot! wlte=1.24e+03 which means that the reduction should be severe but the controller tries 0.1*dt and that seems to pass but it jig-saws (take a look at the next attempted step), which means that it is likely unstable. I think -ts_theta_adapt is seriously broken, I cannot make sense of the way the error estimator is computed. I have an alternative implementation of adaptivity in PetIGA in custom Generalized-Alpha implementation. The adaptivity is not based on embed-RK like for TSCN, but in storing a solution vector from the previous step then estimate the LTE with backward differences. BTW, this idea can be generalized to any second-order method at the cost of tracking an extra solution vector and a bunch of Vec operations. Emil, if you want to try my code to give it a try, it is very easy to integrate, you just need to copy a file to your sources (https://bitbucket.org/dalcinl/petiga/src/tip/src/tsalpha1.c) and add a TSRegister() call after PetscInitialize(). Then you pass in the command line -ts_type alpha1 -ts_alpha_adapt. You can also pass -ts_alpha_radius 0.5 to add some high-frequency dissipation (the default is 1.0, then the method is roughly equivalent to the midpoint rule). PS: I would like to put all this in PETSc, but before that, I need help from you guys to make sure this method really makes sense. The fact that this has worked very well for me in some problems is not enough. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] Memory leak in PetscRandom?
On 26 February 2015 at 01:09, Jed Brown j...@jedbrown.org wrote: Barry Smith bsm...@mcs.anl.gov writes: Thanks for the report. I ran the example with those options under Linux with valgrind and found no memory leaks, I cannot run valgrind on my Mac. When are you going to get a real operating system? In the mean time, several people have reported that this works: http://ranf.tl/2014/11/28/valgrind-on-mac-os-x-10-10-yosemite/ When is valgrind going to use a real VCS? ;-) -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] Libraries destination directory is non-standard
On 8 January 2015 at 23:32, Juan Luis Cano juanlu...@gmail.com wrote: Hello all, I am trying to build a conda package of PETSc 3.4 using its Python build system so anybody can install it in the Anaconda Python distribution. I need PETSc as a dependency for FEniCS. Nice to know! I was thinking about doing it myself. You may find interesting my mpich and openmpi packages (newer versions than the available in Anaconda) to depend on https://binstar.org/mpi4py, I still have to put the recipes in github repo. The problem is that the required shared libraries (also those corresponding to external packages such as UMFPACK) are installed in $PREFIX/lib/python2.7/site-packages/petsc/lib. The build process goes perfectly fine but when packaging this into a tarball these libs won't be found by any package as they are not in $PREFIX/lib. Here is the build script I am using: Are you using pip to create/build the conda recipes? I really advice against that. You should create a petsc package that is independent of a Python runtime (of course, you still need Python to run configure), this way you can install in the standard $PREFIX location. Why do you say things are installed in site-packages? Who is installing there FEniCS ? Please note/remember that conda is not only for Python stuff, but for any other Python-independent package that install under a $PREFIX tree. https://github.com/Juanlu001/conda-recipes/blob/juanlu001/fenics/petsc/build.sh * Please remember to add the md5 hash under the source section. * python should not be a runtime dependency of the petsc package I tried to change the destination using `--prefix` in PETSC_CONFIGURE_OPTIONS and after `setup.py install`, but neither worked. Changing LD_LIBRARY_PATH seems dangerous to me and creating symbolic links three levels higher seems dirty. If the python version changes, or lib64 is added somewhere, this will surely break... Does anybody have a suggestion on how to do this? Knowing the full stack of conda packages you depend on would help to figure out your issue. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] Changing TSAdapt
On 12 December 2014 at 01:44, Barry Smith bsm...@mcs.anl.gov wrote: Miguel, Thanks for reporting this, you have found a bug in our code. When we changed the adapt type we did not zero out the function pointers for the old basic adaptor hence they were improperly called when the object was finally destroyed at the end. I've attached a patch. Once you apply this simply run make gnumake in the PETSc root directory, recompile your code and run it again and it should successfully end. Barry Your patch also clears any user-specified adapt-ops-checkstage. Perhaps you should revert your commit and merge my PR instead? https://bitbucket.org/petsc/petsc/pull-request/228/fixes-for-ts-tsadapt-and-tsalpha/diff -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] Checkpointing / restart
On 9 December 2014 at 18:24, Carles Bona carlesb...@gmail.com wrote: TS type is alpha I'm working on a reimplementation of TSALPHA in PetIGA, https://bitbucket.org/dalcinl/petiga/src/default/src/tsalpha1.c . Eventually, I'll update the code in PETSc with this new implementation. This new implementation features some attempts to implement time-step adaptivity. Additionally, it implements a poor man's attempt to estimate a initial derivative without requiring users to setup and solve a problem involving the mass matrix. We can experiment in this code with some extra APIs to let users specify the initial derivative. What about TSAlphaSetSolution(ts,U,V) and TSAlphaGetSolution(ts,U,V), where U and V are the initial solution and derivative vectors? -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] PETSc/petsc4py error detection
On 26 August 2014 13:24, Nicola Creati ncre...@inogs.it wrote: Thank you, but PetscPopSignalHandler has not been wrapped in petsc4py. What about overriding the signal handler using Python's builtin signal module? -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] petsc4py getVecArray magic
On 23 August 2014 05:15, Gianluca Meneghello gianm...@gmail.com wrote: Dear all, I just discovered that x = da.getVecArray(X) does not return a numpy array but rather a _DMDA_Vec_array, which has (I guess) the great advantage of allowing for a starting index which is not zero. So x[87] makes sense even if the actual length of x is only 50. What I would like to do is to split the _DMDA_Vec_array x into multiple variables, e.g. x1,x2,x3 = x[:,0:12] , x[:,12:16], x[:,16:28] which, written in this way, returns x1,x2,x3 as numpy view() arrays starting from zero and of length equal to the length of the global X divided by the number of processors. The arrays x1,x2,x3 thus becomes unaccessible when using global indices. Using local indices does not look like a good idea because of the presence of ghost entries. I was wondering if there is any good way to address this situation besides not splitting x in x1,x2,x3. Sorry, but I'm not following you. -- Lisandro Dalcin Research Scientist Computer, Electrical and Mathematical Sciences Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Re: [petsc-users] MPI-IO
On 21 July 2014 13:50, Jed Brown j...@jedbrown.org wrote: Must have been prior to MPI-2.1. Shall we test for MPI_Pack_external and use MPI-IO by default if it's available? Be prepared to file tickets for MPICH and OpenMPI. Pack/unpack_external with MPI_DOUBLE never worked for me: https://bitbucket.org/mpi4py/mpi4py/src/master/test/test_pack.py#cl-105 -- Lisandro Dalcin --- CIMEC (UNL/CONICET) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1016) Tel/Fax: +54-342-4511169
Re: [petsc-users] Vector Operations
On 25 December 2013 11:43, 吕超 luc...@mail.iggcas.ac.cn wrote: So, I want to kown how can I get c = a.*b in Petsc. Can you help me? http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecPointwiseMult.html -- Lisandro Dalcin --- CIMEC (UNL/CONICET) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1016) Tel/Fax: +54-342-4511169
Re: [petsc-users] MatMPIBAIJSetPreallocationCSR i and j indices
On 29 September 2013 17:31, Barry Smith bsm...@mcs.anl.gov wrote: I forgot that MatSetValuesBlocked() takes row oriented input even within the blocks. So if we simply call MatSetOption(mat,MAT_ROW_ORIENTED,PETSC_FALSE) on the matrix after it is created then the storage should work as I originally planned. Barry I found this discussion values(bs,nblockcols,bs,nblockrows) very confusing. MatMPIBAIJSetPreallocationCSR() doesn't take a square block of values so I didn't see what you are talking about. You must be talking about each internal call to MatSetValuesBlocked_MPIBAIJ(B,1,row,ncols,icols,svals,INSERT_VALUES) where it puts in one block row of values with each call. Yes, that's what I was talking about. And yes, if you have column-oriented block values [e.g, in fotran you use an array VALUES(bs,bs,nnz) ] and use MatSetOption(), you are fine and MatMPIBAIJSetPreallocationCSR() will do the right thing. Otherwise (e.g, you are in C and use VALUES[nnz][bs][bs]), feeding MatMPIBAIJSetPreallocationCSR() with these values will not work. I guess we have to live with that. -- Lisandro Dalcin --- CIMEC (UNL/CONICET) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1016) Tel/Fax: +54-342-4511169
Re: [petsc-users] MatMPIBAIJSetPreallocationCSR i and j indices
On 27 September 2013 21:23, Barry Smith bsm...@mcs.anl.gov wrote: Just use MatCreateMPIBAIJWithArrays() saves thinking and work. BTW, Have you ever thought about how hard to use is this API if you want to provide the matrix values? How are users supposed to fill the values array for a matrix with bs1 ? This API is certainly not Fortran-friendly (and I think it not even C-friendly). Mateo had the CSR indices as well as the block values, but I recommended to use the CSR indices to perform proper matrix preallocation, then loop over cells and call MatSetValuesBlocked(). Otherwise, he would need to create an new intermediate array and fill it the right way for MatCreateMPIBAIJWithArrays() to work as expected. The root of the problem is how MatSetValuesBlocked() expects the array of values to be layout in memory. While I understand that the current convention make it compatible with MatSetValues(), I'm always wondering if a layout like values[nblockrows][nblockcols][bs][bs] would not be much more convenient for users. -- Lisandro Dalcin --- CIMEC (UNL/CONICET) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1016) Tel/Fax: +54-342-4511169
[petsc-users] petsc 3.4:
On 15 May 2013 16:54, Satish Balay balay at mcs.anl.gov wrote:
On Wed, 15 May 2013, Matteo Parsani wrote:
Hello Satish,
Lisandro has found that in the make file we have
include ././${PETSC_ARCH}/conf/petscvariables
we try to support too many ways of installing petsc [with prefix/
without prefix, with a defaut PETSC_ARCH, without PETSC_DIR set etc..]
And we need this line for users who forget to set PETSC_ARCH in a
non-prefix build. [to pick up a defaut PETSC_ARCH]
Satish, I think all what is needed is to fix a little the test_build
target. Basically, test if the file under PETSC_ARCH exists, otherwise
use PETSC_DIR/include/petscconf.h . Perhpas I'm missing something, but
this should be near to work.
--
Lisandro Dalcin
---
CIMEC (INTEC/CONICET-UNL)
Predio CONICET-Santa Fe
Colectora RN 168 Km 472, Paraje El Pozo
3000 Santa Fe, Argentina
Tel: +54-342-4511594 (ext 1011)
Tel/Fax: +54-342-4511169
[petsc-users] petsc 3.4:
On 15 May 2013 17:12, Satish Balay balay at mcs.anl.gov wrote:
On Wed, 15 May 2013, Lisandro Dalcin wrote:
On 15 May 2013 16:54, Satish Balay balay at mcs.anl.gov wrote:
On Wed, 15 May 2013, Matteo Parsani wrote:
Hello Satish,
Lisandro has found that in the make file we have
include ././${PETSC_ARCH}/conf/petscvariables
we try to support too many ways of installing petsc [with prefix/
without prefix, with a defaut PETSC_ARCH, without PETSC_DIR set etc..]
And we need this line for users who forget to set PETSC_ARCH in a
non-prefix build. [to pick up a defaut PETSC_ARCH]
Satish, I think all what is needed is to fix a little the test_build
target. Basically, test if the file under PETSC_ARCH exists, otherwise
use PETSC_DIR/include/petscconf.h . Perhpas I'm missing something, but
this should be near to work.
We've avoided using gnu make extensions - so there is no usage of 'if'
directives in petsc makefiles. [and we've used include directive as
alternative]
I was not clear enough. I'm talking about a shell if, something like
if [-f ${PETSC_DIR}/${PETSC_ARCH}/include/petscconf.h]; then \
egrep ...
else
egrep
fi
--
Lisandro Dalcin
---
CIMEC (INTEC/CONICET-UNL)
Predio CONICET-Santa Fe
Colectora RN 168 Km 472, Paraje El Pozo
3000 Santa Fe, Argentina
Tel: +54-342-4511594 (ext 1011)
Tel/Fax: +54-342-4511169
[petsc-users] Is there any counterpart of TSSetMatrices in petsc4py?
On 15 August 2012 14:13, Xin Zhao sean.null at gmail.com wrote: Dear all, What I need is just to solve a very easy linear ODE. u_t = Au A is sparse and constant. But I didn't find a counterpart of TSSetMatrices in petsc4py for this. It is strange because petsc4py can handle much harder problems. TSSetMatrices() is no longer supported in petsc-3.3. You have to rewrite your problem in implicit nonlinear form, and ask TS to solve a linear problem. You still have to code your IFunction and IJacobian in Python, use the PETSc C implementations TSComputeIFunctionLinear() and TSComputeIJacobianConstant() and translate to Python. -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] Getting 0 for both start and end with MatGetOwnershipRange()
On 9 May 2012 20:01, Daniel Christian Weflen Daniel.Weflen at colorado.edu wrote: I have the following code: ??? Mat H; ??? PetscInt mat_size=x_npts*y_npts; ??? ierr=MatCreate(PETSC_COMM_WORLD,H);CHKERRQ(ierr); ierr=MatSetSizes(H,PETSC_DECIDE,PETSC_DECIDE,mat_size,mat_size);CHKERRQ(ierr); ??? ierr=MatSetType(H,MATSEQMAIJ);CHKERRQ(ierr); ??? PetscInt* nonzeros; ??? PetscInt start_row,end_row,row_index; ??? MatGetOwnershipRange(H,start_row,end_row); When I check the values of start_row and end_row right after calling MatGetOwnershipRange, both are 0. What am I doing wrong here? Am I calling MatCreate(), MatSetSizes() and MatSetType() in the wrong order? Call MatSetUp() after MatSetType(). -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] petsc4py and numpy
On 8 May 2012 12:04, Matthew Knepley knepley at gmail.com wrote: On Tue, May 8, 2012 at 11:00 AM, Christian Staudt christian.staudt at ira.uka.de wrote: Matthew Knepley?knepley at gmail.com?wrote: a) Is there an easy and efficient way to convert a numpy.ndarray to a PETSc.Vec or PETSc.Mat (and vice-versa)? ?(A PETSc.Vec.getArray() returns a numpy.ndarray, though I have found no such method for PETSc.Mat yet. ) If you are using dense matrices (MATDENSE) then MatGetArray() works. I don't think this is implemented in petsc4py: At least, there's no method PETSc.Mat.getArray() If you ask Lisandro for it, he will put it in. Matt, I've never put that in just because I'm not sure how to make it general. PETSc have many different matrix formats, and MatGetArray() call is like a hack, where you can get very different things (the 1D values of an AIJ matrix, the 2D values of a dense matrix in Fortran order). What about MPIAIJ, what should I return to users? Can you suggest some approach or API to implement this (I mean, how to get arrays for the various matrix types)? -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] petsc4py and numpy
On 8 May 2012 12:25, Matthew Knepley knepley at gmail.com wrote: On Tue, May 8, 2012 at 11:15 AM, Lisandro Dalcin dalcinl at gmail.com wrote: On 8 May 2012 12:04, Matthew Knepley knepley at gmail.com wrote: On Tue, May 8, 2012 at 11:00 AM, Christian Staudt christian.staudt at ira.uka.de wrote: Matthew Knepley?knepley at gmail.com?wrote: a) Is there an easy and efficient way to convert a numpy.ndarray to a PETSc.Vec or PETSc.Mat (and vice-versa)? ?(A PETSc.Vec.getArray() returns a numpy.ndarray, though I have found no such method for PETSc.Mat yet. ) If you are using dense matrices (MATDENSE) then MatGetArray() works. I don't think this is implemented in petsc4py: At least, there's no method PETSc.Mat.getArray() If you ask Lisandro for it, he will put it in. Matt, I've never put that in just because I'm not sure how to make it general. PETSc have many different matrix formats, and MatGetArray() call is like a hack, where you can get very different things (the 1D values of an AIJ matrix, the 2D values of a dense matrix in Fortran order). What about MPIAIJ, what should I return to users? Can you suggest some approach or API to implement this (I mean, how to get arrays for the various matrix types)? I think the whole point is that you should not do it. However, that has never stopped us from giving users what they ask for. We are not int he business of reforming computing practices, which is why we have MatGetArray(). I would make a wrapper that failed unless the type was MATDENSE. Yea, that's really easy. However, Is there anything better for AIJ matrices? Right now, we have mat.getValuesCSR()... it works by calling MatGetRow() row by row twice (first pass to count and allocate, next to get values and copy to NumPy arrays). -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] Petsc CMake conf
On 14 April 2012 01:19, Jed Brown jedbrown at mcs.anl.gov wrote:
On Fri, Apr 13, 2012 at 17:17, Mohammad Mirzadeh mirzadeh at gmail.com
wrote:
Hi,
Are there any cmake conf file that I can include in my CMakeLists.txt that
would automatically detect include/lib directory for my petsc installation?
Right now I'm doing this manually and was wondering if its possibel to
automate it.
https://github.com/jedbrown/cmake-modules/blob/master/FindPETSc.cmake
Jed, have you considered adding this to petsc-dev, removing all the
checks for old PETSc releases? Or perhaps better, how about dumping
an autogenerated PETSc.cmake in
$PETSC_DIR/$PETSC_ARCH/conf/PETSc.cmake, or perhaps other name,
defining all the stuff end users need. For example, I'm using the code
below in a codebase I'm working on (note that at the end I'm loading
PETScConfig.cmake), but this is not robust, it does not handle builds
with separate libraries. If PETSc provides all these variables, then I
could simply include (${PETSC_DIR}/${PETSC_ARCH}/conf/PETSc.cmake),
and you can make your FindPETSc.cmake much simpler (at least for the
upcoming version of PETSc)
find_path (PETSC_DIR include/petsc.h HINTS ENV PETSC_DIR DOC PETSc
Directory)
set (PETSC_ARCH $ENV{PETSC_ARCH})
find_path (PETSC_INCLUDE_DIR petsc.h HINTS ${PETSC_DIR}
PATH_SUFFIXES include NO_DEFAULT_PATH)
find_path (PETSC_INCLUDE_CONF petscconf.h HINTS ${PETSC_DIR}
PATH_SUFFIXES ${PETSC_ARCH}/include NO_DEFAULT_PATH)
mark_as_advanced (PETSC_INCLUDE_DIR PETSC_INCLUDE_CONF)
set (PETSC_INCLUDES ${PETSC_INCLUDE_CONF} ${PETSC_INCLUDE_DIR} CACHE
PATH PETSc include paths FORCE)
set (PETSC_DEFINITIONS -D__INSDIR__= CACHE STRING PETSc
preprocesor definitions FORCE)
find_path (PETSC_LIB_DIR NAMES HINTS ${PETSC_DIR} PATH_SUFFIXES
${PETSC_ARCH}/lib NO_DEFAULT_PATH)
find_library (PETSC_LIBRARY NAMES petsc HINTS ${PETSC_LIB_DIR}
NO_DEFAULT_PATH)
set (PETSC_LIBRARIES ${PETSC_LIBRARY} CACHE FILEPATH PETSc library FORCE)
include (${PETSC_DIR}/${PETSC_ARCH}/conf/PETScConfig.cmake)
--
Lisandro Dalcin
---
CIMEC (INTEC/CONICET-UNL)
Predio CONICET-Santa Fe
Colectora RN 168 Km 472, Paraje El Pozo
3000 Santa Fe, Argentina
Tel: +54-342-4511594 (ext 1011)
Tel/Fax: +54-342-4511169
[petsc-users] petsc4py KSP Question
On 7 March 2012 02:22, Gaetan Kenway kenway at utias.utoronto.ca wrote:
Hello
I'm in the process of using petsc4py to solve a large multidisciplinary,
non-linear system and its adjoint. I have the non-linear solution with
snes() working correctly and I'm now doing the linear solution.
For the non-linear solve, I create the snes and set my user context as
follows:
? ?# Create SNES Object
? ASContext = ASNKSolver(self) # Context to hold data
? snes = PETSc.SNES().createPython(ASContext, comm=self.gcomm)
? snes.setFunction(ASContext.formFunction, resVec)
For the linear part, I'm a little confused. I currently have
? ? # Create Python Context and KSP Object
? ? KSPContext = AdjointKSPSolver(self) # Context to hold data
? ? ksp = PETSc.KSP().createPython(KSPContext, comm=self.gcomm)
What I'm not sure of is how to specify the operator for the KSP solver in
the KSPContext object. Is this possible? Is there something like def apply()
you must do?
The petsc4py poisson2d.py example, first creates a Mat, then sets a context
for that, and then uses ksp.setOperators() to use that matrix. Is this the
only way to do it? If, so, what is the use of
the??PETSc.KSP().createPython() command?
Unless you want to implement a custom KSP/SNES in Python, you should
just use KSP/SNES.create(). KSP/SNES.createPython() is a rather
advanced feature, it is not obvious at all how to use them, there are
no demos nor documentation about it (however, there is some code in
test/test_{ksp|snes}_py.py ).
Please take a look at the demo/bratu2d and demo/bratu3d about how to
setup a SNES solver. For KSP, take a look at
demo/kspsolve/petsc-mat.py and demo/kspsolve/petsc-ksp.py
--
Lisandro Dalcin
---
CIMEC (INTEC/CONICET-UNL)
Predio CONICET-Santa Fe
Colectora RN 168 Km 472, Paraje El Pozo
3000 Santa Fe, Argentina
Tel: +54-342-4511594 (ext 1011)
Tel/Fax: +54-342-4511169
[petsc-users] invalid object classid 0 between PETSc and SLEPc
On 28 December 2011 01:16, Geoffrey Irving irving at naml.us wrote: Hello, I've installed PETSc 3.2 and SLEPc 3.2 on Mac OS 10.7 through MacPorts 2.0.3. ?PETSc works fine by itself, but SLEPc fails on the initial EPSCreate call. ?The error follows. This is presumably a MacPorts misconfiguration issue, but thought I'd check here first to see if anyone has seen this before in a similar situation. ?Only static libraries exist, so as far as I know the suggested explanation doesn't apply. ?The conf directory is at http://naml.us/~irving/random/petsc-conf.tar.gz if it helps. Just in case, please run: $ otool -L ./your_executable Do you have any other PETSc/SLEPc build lying around? -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] petsc4py: PetSc is no longer initialised when calling C Function from Cython
On 20 October 2011 19:34, Jeff Wiens jeffrey.k.wiens at gmail.com wrote: Thanks for your help. It saved me a LOT of time. Jeff BTW, have you ever used SWIG? If the functions you need to wrap are simple (let say, any PetscObject subtype and scalar paramenters) you can get your wrappers with less code to write on your side. -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] petsc4py: PetSc is no longer initialised when calling C Function from Cython
On 20 October 2011 17:05, Jeff Wiens jeffrey.k.wiens at gmail.com wrote: The problem seems to be that PetSc is no longer initialised when you call a C function. If I initialise PETSc from C, the program works. However, if I don't call init() from C, the program won't use the python PetSc. Mmm... I bet you built PETSc with static libraries. There is not (easyportable) way to mix petsc4py and other C codes when using static libraries. Please build PETSc with shared libraries. Eventually, I would like to Initialise PETSc and construct my PETSc vectors in python and then have my C code perform operations on them. Again, this yet another test problem. Have you seen the demo/wrap-cython example in petsc4py sources? -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] petsc4py: PetSc is no longer initialised when calling C Function from Cython
On 20 October 2011 19:34, Jeff Wiens jeffrey.k.wiens at gmail.com wrote: Lisandro, the shared library was the problem. I seem to have everything working by including the --with-shared and --with-dynamic options in my PetSc 3.1 configuration. The --with-dynamic stuff should not be required, and I think it's better if you remove it. Note, I had to make significant modifications to your setup.py file for your cython demo to work (on my installation). Expected I have attached my setup.py file, which is based on code I found in PyClaw. The main differences is overloading: ? ? ? ? build_src.build_src.generate_a_pyrex_source = generate_a_cython_source and including the following directories: ? ?INCLUDE_DIRS +=[/PATH/To/openmpi/1.4.3/include] ? ?INCLUDE_DIRS += [/PATH/To/hdf5/1.8.5-patch1/include] Thanks for your help. It saved me a LOT of time. Jeff I'll take a look at your setup.py, thanks! -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] Naturally ordered to DA vector copy
On 20 July 2011 01:34, khalid ashraf khalid_eee at yahoo.com wrote: Hello, In my application, I need to do both Finite element(FEM) and Finite Difference(FD) computations. I am doing the FD using the DA and FEM using natural numbering(x changes fastest, then y then z). My question is what would be the fastest way to copy the FEM vectors to the FD vectors. Looks like DAGetAO may provide a mapping between DA vector layout and natural layout. Since I am not very familiar with programming using AO, just wanted to ask if there is a more efficient/easier way to copy from the naturally ordered vector to the DA vector before delving into AO. If I have to use AO, could you please redirect me to some related example. Thanks in advance. Khalid DMDAGlobalToNaturalBegin/End and DMDANaturalToGlobalBegin/End -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] PETSc recommended visualization packages
On 14 July 2011 16:22, Ethan Coon ecoon at lanl.gov wrote: Attached patch takes Lisandro's matio.py and puts it in a PetscBinaryRead.py that reads a binary with (potentially) multiple Petsc objects, deciphers the contents of the file from the header, and returns numpy objects. ?It's basically the same as the PetscBinaryRead.m I've tested this on Vecs, but not Mats or ISs, and I haven't thoroughly tested degenerate cases. ?Will do some testing, but I wanted Lisandro to take a look at it as well... 1) readMatDense() is wrong. The I,J,V arrays are the CSR structure, not the COO (coordinate) format, Then you cannot simply: for i,j,v in zip(I,J,V): mat[i,j] = v I think you have to: for row, rstart in enumerate(I): rend = I[row+1] mat[row, J[rstart:rend]] = V[rstart:rend] 2) It would be nice to provie a 'scipy' Mat format returning a 'scipy.sparse.csr_matrix' instance. A possible implementation would be: def readMatSciPy(fh): (M, N), (I, J, V) = readMatSparse(fh) from scipy.sparse import csr_matrix return csr_matrix((V, J, I), shape=(M, N)) -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] PETSc recommended visualization packages
On 14 July 2011 18:33, Ethan Coon ecoon at lanl.gov wrote: On Thu, 2011-07-14 at 17:47 -0300, Lisandro Dalcin wrote: 1) readMatDense() is wrong. The I,J,V arrays are the CSR structure, not the COO (coordinate) format, Then you cannot simply: Ok, thanks, I wasn't sure of which format you were using, Well, PETSc's AIJ matrices are CSR in memory (but not in disk, binary files store row counts instead of row pointers) 2) It would be nice to provie a 'scipy' Mat format returning a 'scipy.sparse.csr_matrix' instance. A possible implementation would be: Agreed, I considered doing that as the default for sparse, but wasn't sure what others would want. ?Providing both makes sense. Note however that this would require a SciPy installation. PS: Sorry for not being more helpful and contributing actual code, but I'm really busy. -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] PETSc recommended visualization packages
On 6 July 2011 11:41, Ethan Coon ecoon at lanl.gov wrote: Both Paraview and Visit generally make ugly axes/colorbars/keys/etc. ?In my opinion they both look fine for presentations and my own viewing, but are not really acceptable for publication-quality. ?For things run on a reasonably-sized problem, matplotlib (using either h5py to read hdf5, pyvtk to read vtk, or petsc4py to read PETSc's binary format) makes publishable plots. Using petsc4py for reading PETSc binary formats is overkill. All this can be done with just NumPy. Should PETSc ship some Python code to read IS's, Vec's, Mat's in binary format? Can any of you suggest an appropriate location in the source tree? -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] PETSc recommended visualization packages
On 5 July 2011 12:53, Brad Aagaard baagaard at usgs.gov wrote: Hi, I agree with Blaise's assessment of ParaView. It is good for quick and dirty visualization, but its scripting interface is very limited. MayaVi provides a GUI along with high-level API access to VTK data structures through Python. One can update/modify the data values through the API without ever writing VTK compatible files. I read my data from HDF5 files using PyTables and create VTK data objects using the API. A similar mechanism could be used for data stored using SQLite. I think some Linux and Mac packaging systems include MayaVi; I usually build from source. I recently added support (requires petsc4py, of course) for -ksp|snes|ts_monitor_python filename.py:function|class. Perhaps you can find this useful for live monitoring of simulations. -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] Question for time dependent problems
On 5 July 2011 17:35, Barry Smith bsmith at mcs.anl.gov wrote: Beginning of a time step (1st implicit stage of RK scheme): 1. Use MatZeroEntries on the preconditioner ?Do not call MatZeroEntries on a freshly created matrix (that destroys the preallocation pattern) so skip the MatZeroEntries the first time. What do you mean? The OP said that the nonzero structure was set at problem set up. -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] petsc4py DA with dof1 confusion
On 4 July 2011 14:25, Matthew Emmett memmett at unc.edu wrote:
Hi everyone,
I am trying to use petsc4py in a fairly straight forward finite volume
shallow-water code (the PDE has three unknowns). I have a structured
grid and am using a DA to communicate ghost cells. ?When I use dof=1,
everything works as I would expect. ?However, when I try to use dof=3,
I am confused by the results. ?I have probably mis-understood
something -- any suggestions would be appreciated.
For example (see attached script), first I create the DA ('dof' and
'width' are defined):
?da = PETSc.DA().create(dim=2, sizes=[8, 8], dof=dof,
? ? ? ? ? ? ? ? ? ? ? ? boundary_type='periodic',
? ? ? ? ? ? ? ? ? ? ? ? stencil_width=width,
? ? ? ? ? ? ? ? ? ? ? ? stencil_type='box')
Next, I create global and local vectors:
?gvec = da.createGlobalVec()
?lvec = da.createLocalVector()
Then, put something into the local vectors, and scatter:
?with da.getVecArray(lvec) as va:
? ?if dof == 1:
? ? ?va.array[width:-width,width:-width] = MPI.COMM_WORLD.rank+1
? ?else:
? ? ?va.array[width:-width,width:-width,0] = MPI.COMM_WORLD.rank+1
?da.localToGlobal(lvec, gvec)
Finally, get the local vector again and print:
?da.globalToLocal(gvec, lvec)
?with da.getVecArray(lvec) as va:
? ?if dof == 1:
? ? ?print va.array[:,:]
? ?else:
? ? ?print va.array[:,:,0]
With 'dof=1' I get the following on the second processor:
[[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]]
With 'dof=3' I get the following on the second processor:
[[ 0. ?0. ?0. ?0. ?0. ?0.]
?[ 0. ?0. ?0. ?0. ?2. ?0.]
?[ 0. ?0. ?0. ?0. ?2. ?0.]
?[ 0. ?0. ?0. ?2. ?2. ?0.]
?[ 0. ?0. ?0. ?2. ?2. ?0.]
?[ 0. ?0. ?0. ?2. ?2. ?0.]
?[ 0. ?0. ?0. ?2. ?2. ?0.]
?[ 0. ?0. ?0. ?2. ?2. ?2.]
?[ 0. ?0. ?0. ?2. ?2. ?2.]
?[ 0. ?0. ?0. ?0. ?0. ?2.]]
I was expecting to see the same as the 'dof=1' case, since I am
setting (and printing) va.array[:,:,0].
Again, any suggestions would be appreciated. ?Thanks,
Matt
PS, thanks to the developers of PETSc and petsc4py for all your hard
work. ?I had the pleasure of meeting Jed and Matt at KAUST recently.
Mmm, it seems that this functionality is broken for the case of
boundary_type='periodic'. I'll take a look.
--
Lisandro Dalcin
---
CIMEC (INTEC/CONICET-UNL)
Predio CONICET-Santa Fe
Colectora RN 168 Km 472, Paraje El Pozo
3000 Santa Fe, Argentina
Tel: +54-342-4511594 (ext 1011)
Tel/Fax: +54-342-4511169
[petsc-users] petsc4py DA with dof1 confusion
On 4 July 2011 15:17, Lisandro Dalcin dalcinl at gmail.com wrote:
On 4 July 2011 14:25, Matthew Emmett memmett at unc.edu wrote:
Hi everyone,
I am trying to use petsc4py in a fairly straight forward finite volume
shallow-water code (the PDE has three unknowns). I have a structured
grid and am using a DA to communicate ghost cells. ?When I use dof=1,
everything works as I would expect. ?However, when I try to use dof=3,
I am confused by the results. ?I have probably mis-understood
something -- any suggestions would be appreciated.
For example (see attached script), first I create the DA ('dof' and
'width' are defined):
?da = PETSc.DA().create(dim=2, sizes=[8, 8], dof=dof,
? ? ? ? ? ? ? ? ? ? ? ? boundary_type='periodic',
? ? ? ? ? ? ? ? ? ? ? ? stencil_width=width,
? ? ? ? ? ? ? ? ? ? ? ? stencil_type='box')
Next, I create global and local vectors:
?gvec = da.createGlobalVec()
?lvec = da.createLocalVector()
Then, put something into the local vectors, and scatter:
?with da.getVecArray(lvec) as va:
? ?if dof == 1:
? ? ?va.array[width:-width,width:-width] = MPI.COMM_WORLD.rank+1
? ?else:
? ? ?va.array[width:-width,width:-width,0] = MPI.COMM_WORLD.rank+1
?da.localToGlobal(lvec, gvec)
Finally, get the local vector again and print:
?da.globalToLocal(gvec, lvec)
?with da.getVecArray(lvec) as va:
? ?if dof == 1:
? ? ?print va.array[:,:]
? ?else:
? ? ?print va.array[:,:,0]
With 'dof=1' I get the following on the second processor:
[[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]
?[ 1. ?2. ?2. ?2. ?2. ?1.]]
With 'dof=3' I get the following on the second processor:
[[ 0. ?0. ?0. ?0. ?0. ?0.]
?[ 0. ?0. ?0. ?0. ?2. ?0.]
?[ 0. ?0. ?0. ?0. ?2. ?0.]
?[ 0. ?0. ?0. ?2. ?2. ?0.]
?[ 0. ?0. ?0. ?2. ?2. ?0.]
?[ 0. ?0. ?0. ?2. ?2. ?0.]
?[ 0. ?0. ?0. ?2. ?2. ?0.]
?[ 0. ?0. ?0. ?2. ?2. ?2.]
?[ 0. ?0. ?0. ?2. ?2. ?2.]
?[ 0. ?0. ?0. ?0. ?0. ?2.]]
I was expecting to see the same as the 'dof=1' case, since I am
setting (and printing) va.array[:,:,0].
Again, any suggestions would be appreciated. ?Thanks,
Matt
PS, thanks to the developers of PETSc and petsc4py for all your hard
work. ?I had the pleasure of meeting Jed and Matt at KAUST recently.
Mmm, it seems that this functionality is broken for the case of
boundary_type='periodic'. I'll take a look.
No, sorry... It has nothing to do with periodicity... It is actually a
C/Fortran ordering issue I need to fix...
In Fortran 90, it seems you index a DA Vec array as A[dof,x,y,z]... ,
However, I think that for Python we should follow a more C-ish
indexing A[x,y,z,dof]. Or we could do it like PETSc in C, that is
A[z,y,x,dof] (wich is the transpose of the Fortran way) but it is
counter-intuitive to C (and likely Python) programmers ...
What do others think about this?
--
Lisandro Dalcin
---
CIMEC (INTEC/CONICET-UNL)
Predio CONICET-Santa Fe
Colectora RN 168 Km 472, Paraje El Pozo
3000 Santa Fe, Argentina
Tel: +54-342-4511594 (ext 1011)
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[petsc-users] petsc4py DA with dof1 confusion
On 4 July 2011 16:19, Matthew Emmett memmett at unc.edu wrote: On Mon, Jul 4, 2011 at 2:52 PM, Lisandro Dalcin dalcinl at gmail.com wrote: No, sorry... It has nothing to do with periodicity... It is actually a C/Fortran ordering issue I need to fix... Ah, I see. ?Thanks for looking into this so quickly. ?Let me know if there is anything I can do on my end to help. ?I will poke around the code for petsc4py, but you obviously know it better than I do. In Fortran 90, it seems you index a DA Vec array as A[dof,x,y,z]... , However, I think that for Python we should follow a more C-ish indexing A[x,y,z,dof]. Or we could do it like PETSc in C, that is A[z,y,x,dof] (wich is the transpose of the Fortran way) but it is counter-intuitive to C (and likely Python) programmers ... What do others think about this? I think A[x,y,z,dof] is probably the most intuitive for Python. OK. I pushed a fix solving the issue. As a consequence, the underlying NumPy array do have a mixed ordering (no C nor Fortran) where the latest dim varies fastest, then first, second, third. So, you have to be very careful about accessing the underlying array (I mean, doing va.array[...] in your previous code), I would recomend you against that, and code like this instead: with da.getVecArray(lvec) as va: if dof == 1: va[:,:] = rank+1 else: va[:,:,0] = rank+1 da.localToGlobal(lvec, gvec) da.globalToLocal(gvec, lvec) with da.getVecArray(lvec) as va: if dof == 1: print va[:,:] else: print va[:,:,0] -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] Flexiable AIJ matrix for nonzeros -- hash table version
2011/5/9 Gong Ding gdiso at ustc.edu: Hi I created a flexible AIJ matrix type ?named as FAIJ. It has an extra hash table for nonzero which do not have pre-allocated position. And the buffered values in hash table will be flushed to AIJ array at MatAssemblyEnd. Both sequential and parallel version have been implemented and tested. Great!! Have you thought about extending regular AIJ matrices to use a hash table on first assembly (perhaps activated with an option) and switch back to regular assembly for the next assemblies? I'm assuming here that calls to MatSetValues() fill the hash table even if values are zero. The test results show that for middle size problem ? matrix size around 1M, FAIJ without any pre-allocation still pretty fast. The shortcoming is memory overkill exists. Fortunately, modern computers have larger and larger memory. ?User with FAIJ matrix only needs to provide approximate nonzero pattern or even skip this step. How did you wrote your hash table? What are the keys and values? Are you using a hash table per row? Or it is actuallyan (i,j)-a hash table? However, direct solvers such as mumps and superlu_dist will crash. This is caused by type compare functions, i.e.: ierr = PetscTypeCompare((PetscObject)A,MATMPIAIJ,isAIJ);CHKERRQ(ierr); FAIJ matrix is derived from AIJ, but it has its own type name, i.e. MATMPIFAIJ. The above function will assign isAIJ false. That's the reason I think that adding this feature to regular AIJ matrices could be better. Is there any function like ?PetscBaseType? exist? ?FAIJ matrix can hold its type name as well as its base type name. I hope FAIJ can be accepted by petsc 3.2. Thanks. I think Satish pushed something related to this a few days ago... -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] Building with MKL 10.3
On 14 March 2011 20:48, Barry Smith bsmith at mcs.anl.gov wrote: ?Eric, ? With the current PETSc design that uses one MPI process per core I am not sure that it makes sense to use multi-threaded MKL since the processes are already using all the cores. I could be wrong. ? Barry Well, I think that PETSc should support sequential codes using multi-threaded blas-lapack and perhaps some OpenMP. Moreover, perhaps we could get some little speedup in MatMult for these kinds of users/applications. -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] Using PETSc from MATLAB code, experimental
On 13 January 2011 08:38, Michel Cancelliere fernandez858 at gmail.com wrote: Hi Barry, is Matlab under Windows with petsc-cygwin supported? Unlikely, we would need to build PETSc as a DLL... If anyone can manage to do that, then Barry's work should work out of the box. Or perhaps PETSc do build as a DLL under cygwin? Thanks, Michel On Sun, Dec 26, 2010 at 5:17 AM, Barry Smith bsmith at mcs.anl.gov wrote: ?PETSc users, ? It is now possible to write MATLAB programs (sequential) that use PETSc KSP, SNES, and TS solvers directly in MATLAB. The code is still experimental and incomplete. But if you are interested in trying it out, get the development release of PETSc http://www.mcs.anl.gov/petsc/petsc-as/developers/index.html join the development mailing list petsc-dev http://www.mcs.anl.gov/petsc/petsc-as/miscellaneous/mailing-lists.html, read bin/matlab/classes/PetscInitialize.m, configure and make PETSc and join the fun. We are definitely in need of more developers for this code. ? Barry -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] petsc rpath
Perhaps you should add a --with-rpath option to ./configure ? For reference, MPICH2 did that (=1.3), I believe the idea was to make the life of distro packagers easier. On 24 November 2010 15:28, Jens-Malte Gottfried jmgottfried at web.de wrote: Thanks a lot Satish, your patch did the job :-) Am 24.11.2010 17:19, schrieb Satish Balay: On Wed, 24 Nov 2010, Satish Balay wrote: B1;2601;0cOn Wed, 24 Nov 2010, Jed Brown wrote: On Wed, Nov 24, 2010 at 16:26, Jens-Malte Gottfried jmgottfried at web.dewrote: I am trying to write a gentoo ebuild for petsc (my current work is already in the science overlay). Is there any possibility to disable writing the RPATH of the to-be-generated libpetsc.so? Currently, the library is built fine but RPATH is set to /usr/lib64:/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4:/usr/x86_64-pc-linux-gnu/lib which is not neccessary. Before trying to patch the build system, perhaps there is a simple configure option which I did not find. The standard build system does not provide an easy way to do this. ?If you are using petsc-dev, you use CMake (configure as usual, but then run make from $PETSC_DIR/$PETSC_ARCH instead of from $PETSC_DIR). ?The CMake build files default to setting RPATH, but it is easy to set the cache variables to disable RPATH. Some of the above comes from 'gfortran -v' - which checkFortranLibraries() etc do.. For such known systems with known compatibility libraries [ and each language compiler can find each others libs] you can use: [for c++ build] I meant c build.. -with-clib-autodetect=0 -with-fortranlib-autodetect=0 LIBS=-lgfortran [for c++ build] -with-clib-autodetect=0 -with-cxxlib-autodetect=0 -with-fortranlib-autodetect=0 LIBS='-lstdc++ -lgfortran' Wrt -rpath for -lpetsc, perhaps commenting out the following line in config/BuildSystem/config/setCompilers.py is sufficient: ? ? self.executeTest(self.checkSharedLinkerPaths) Actually you need '-L' there - so the following change will remove -rpath asterix:/home/balay/tmp/petsc-dist-test/config/BuildSystemhg diff diff -r 5fac76781491 config/setCompilers.py --- a/config/setCompilers.py ? ?Mon Sep 20 16:15:14 2010 -0500 +++ b/config/setCompilers.py ? ?Wed Nov 24 10:12:46 2010 -0600 @@ -1188,7 +1188,7 @@ ? ? ? ?self.pushLanguage(language) ? ? ? ?# test '-R' before '-rpath' as sun compilers [c,fortran] don't give proper errors with wrong options. ? ? ? ?if not Configure.isDarwin(): - ? ? ? ?testFlags = ['-Wl,-rpath,', '-R','-rpath ' , '-Wl,-R,'] + ? ? ? ?testFlags = [] ? ? ? ?else: ? ? ? ? ?testFlags = [] ? ? ? ?# test '-R' before '-Wl,-rpath' for SUN compilers [as cc on linux accepts -Wl,-rpath, but ?f90 CC do not. asterix:/home/balay/tmp/petsc-dist-test/config/BuildSystem Satish -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] access da local vector data array in petsc4py
On 12 October 2010 05:21, Amal Alghamdi amal.ghamdi at kaust.edu.sa wrote: Dear All, I have a question regarding petsc4py. I'd like to access the data array in a local vector generated from a one-dimension da, which has dof = 1. I used ?q = localVec.getArray(). However, q shape now does not take into account dof which is one in my example. I always need to reshape q to match the intended dof. Is there a way to do that automatically? Thank you very much. Amal Almost all functions and methods in petsc4py treat arrays as linear data, I mean, unidimensional arrays. As Vec.getArray() knows nothing about the DA, there is no way to get the DA shape. Note that recently I've added DA.getVecArray() to provide some support for global indexing, this new thing is not finished, I want to improve interoperability with regular numpy arrays, the functionality you want could be added there. Other possibility would be to add a method to Vec, let say Vec.getArrayBlock(), that return an array reshaped to (n/bs, bs) where n is the local vec size and bs is the block size (should equal ndof for Vec's originating from DA). What do you think? In the mean time, you could use an utility function like the one below: def get_array_block(vec): n = vec.getLocalSize() bs = vec.getBlockSize() a = numpy.asarray(vec) a.shape = (n//bs, bs) return a -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] petsc4py
2010/9/29 ??? ??? kutuzovnp at gmail.com: Where can i get it? I've tried this one -- http://code.google.com/p/petsc4py/source/browse/demo/ode/rober.py This is from branch release-1.1, a new release 1.1.2 is planned for the weekend. As you can see from the output at the very end, SNES is using matrix free. Note that I've not changed he code code, just passed -snes_mf What petsc4py and PETSc versions are you using? [dalcinl at trantor petsc4py-release-1.1]$ python demo/ode/rober.py -ts_view -snes_mf TS Object: type: theta Theta=0.5 Extrapolation=no maximum steps=100 maximum time=1e+30 total number of nonlinear solver iterations=203 total number of linear solver iterations=311 SNES Object: type: ls line search variant: SNESLineSearchCubic alpha=0.0001, maxstep=1e+08, minlambda=1e-12 maximum iterations=50, maximum function evaluations=1 tolerances: relative=1e-08, absolute=1e-50, solution=1e-08 total number of linear solver iterations=3 total number of function evaluations=8 KSP Object: type: gmres GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement GMRES: happy breakdown tolerance 1e-30 maximum iterations=1, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=1 left preconditioning using PRECONDITIONED norm type for convergence test PC Object: type: none linear system matrix = precond matrix: Matrix Object: type=mffd, rows=3, cols=3 matrix-free approximation: err=1e-07 (relative error in function evaluation) Using wp compute h routine Computes normA Does not compute normU -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] petsc4py, plotting DA and writing to file
On 27 September 2010 13:33, Barry Smith bsmith at mcs.anl.gov wrote: ?Lisandro ? ?In C he could do VecView(vec,PETSC_VIEWER_DRAW_WORLD); can he not do the equivalent in Python? What syntax would he use? viewer = PETSc.Viewer.DRAW(globalvec.comm) globalvec.view(viewer) # or viewer(globalvec) Perhaps the 2d bratu python example could demonstrate this since it is simple and there is no monkeying with copying to one process etc. Well, that example does not even use a DA, the plot is going to be a bit ugly. ? Barry On Sep 27, 2010, at 11:27 AM, Lisandro Dalcin wrote: On 27 September 2010 13:12, Amal Alghamdi amal.ghamdi at kaust.edu.sa wrote: Dear All, I'm using the DA structure in petsc4py. I'd like to know please what is the right way to: plot the DA vector (the global vector). write the global vector to a file. Is that each process writes or draws its own part? or I should communicate all the data to one process? or none of these?!! Thank you very much Amal Use a PETSc.Viewer().createBinary() to save the global vector. Each process will save its own part. In order to plot it, I think you should use numpy.fromfile() to load the data, and then plot the array. Other way would be to use a PETSc.Scatter.toZero() to get the data at process 0, and then plot it scatter, seqvec = PETSc.Scatter.toZero(globalvec) im = PETSc.InsertMode.INSERT_VALUES sm = PETSc.ScatterMode.FORWARD scatter.scatter(globalvec, seqvec, im, sm) if globalvec.comm.rank == 0: ? ?plot(seqvec.array) -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169 -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] petsc4py, plotting DA and writing to file
On 27 September 2010 14:02, Barry Smith bsmith at mcs.anl.gov wrote: On Sep 27, 2010, at 11:47 AM, Lisandro Dalcin wrote: On 27 September 2010 13:33, Barry Smith bsmith at mcs.anl.gov wrote: ?Lisandro ? ?In C he could do VecView(vec,PETSC_VIEWER_DRAW_WORLD); can he not do the equivalent in Python? What syntax would he use? viewer = PETSc.Viewer.DRAW(globalvec.comm) globalvec.view(viewer) # or viewer(globalvec) Perhaps the 2d bratu python example could demonstrate this since it is simple and there is no monkeying with copying to one process etc. Well, that example does not even use a DA, the plot is going to be a bit ugly. ?Sorry. Barry I could add a poisson2d implemented with DA and working in parallel. ? Barry On Sep 27, 2010, at 11:27 AM, Lisandro Dalcin wrote: On 27 September 2010 13:12, Amal Alghamdi amal.ghamdi at kaust.edu.sa wrote: Dear All, I'm using the DA structure in petsc4py. I'd like to know please what is the right way to: plot the DA vector (the global vector). write the global vector to a file. Is that each process writes or draws its own part? or I should communicate all the data to one process? or none of these?!! Thank you very much Amal Use a PETSc.Viewer().createBinary() to save the global vector. Each process will save its own part. In order to plot it, I think you should use numpy.fromfile() to load the data, and then plot the array. Other way would be to use a PETSc.Scatter.toZero() to get the data at process 0, and then plot it scatter, seqvec = PETSc.Scatter.toZero(globalvec) im = PETSc.InsertMode.INSERT_VALUES sm = PETSc.ScatterMode.FORWARD scatter.scatter(globalvec, seqvec, im, sm) if globalvec.comm.rank == 0: ? ?plot(seqvec.array) -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169 -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169 -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] petsc4py, plotting DA and writing to file
On 27 September 2010 13:54, Jed Brown jed at 59a2.org wrote: On Mon, Sep 27, 2010 at 18:47, Lisandro Dalcin dalcinl at gmail.com wrote: viewer = PETSc.Viewer.DRAW(globalvec.comm) globalvec.view(viewer) # or viewer(globalvec) What do you think about having a top-level matplotlib viewer? Yes, we could have it, and a VisIt plugin, and a ParaView one, and what about Mayavi, and put here your preferred viewer... This could go to a separate petsc4py.plotting module (I prefer to not contaminate the petsc4py.PETSc namespace with stuff that is not pure-PETSc) ?Ideally it would have an option to drop you into an interactive python session after the initial view. Could you elaborate? I know this brings up the multiple dispatch problem, since the viewer would naturally be distributed with petsc4p, but then you don't get to modify the case statement in VecView_XX. Sorry, now I'm confused. Are you suggesting this for petsc4py, or core PETSc? -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
[petsc-users] petsc4py, plotting DA and writing to file
On 27 September 2010 14:34, Amal Alghamdi amal.ghamdi at kaust.edu.sa wrote: Thank you very much everybody for the prompt help. Amal I've just pushed a new demo: matrix-free Poisson 2D http://code.google.com/p/petsc4py/source/browse/demo/poisson2d/poisson2d.py At the very end you have: draw = PETSc.Viewer.DRAW(x.comm) OptDB['draw_pause'] = 1 draw(x) Additionally, I've updated other demos. Take a look here for matplotlib usage gathering values to processor 0: http://code.google.com/p/petsc4py/source/browse/demo/bratu3d/bratu3d.py (note that this demo is 3D, I'm plotting the solution at plane Z=0.5) -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169
