- petsc-dev - mailman3.cels.anl.gov

Re: tracking petsc
by Satish Balay 03 Nov '05

03 Nov '05

On Thu, 3 Nov 2005, Matthew Knepley wrote: > Simon Burton <simon(a)arrowtheory.com> writes: > > > On Thu, 03 Nov 2005 17:49:46 -0600 > > Matthew Knepley <knepley(a)mcs.anl.gov> wrote: > > > >> > >> Simon Burton <simon(a)arrowtheory.com> writes: > >> > >> This was patched in 2.3.0, but maybe you have an unpatched version. It is > >> easy to check. The symbol comes from > > > > We have been tracking your bitkeeper repository. I don't know if this is > > sane or not because we want to release something (in a few weeks) > > and that basically means it is up to us to somehow stabilize PETSc, > > or at least "bless" some particular version of PETSc. > > > > No, that doesn't sound right either: fixes that you guys make will go into > > the bk repository, so... I guess what I am asking is, are we just insane to > > try and do this ? Or, is it possible to maybe branch your repository so > > we can stabilize PETSc for some kind of beta release ? > > This is our preference. Why? It is jsut as stable as tarballs because you can > clone to any particular revision, BUT its more flexible because you can easily > pull any fixes or upgrades. Unless we are moving away from making any more releases - we should make a release for this.. It would be a bit difficult to manage patches for 2 relases but this might be better than folks having different dev-snapshots [and we trying to keep track of these bugreports].. > > > Sounds like we just need to make it clear that petsc is on the move > > and that you guys are completely responsive to bug reports, etc. > > > > We are going to build a "petsc doesn't work" FAQ, but, gee i wish your email > > list (petsc-maint) was archived somewhere... > > The DOE really frowns on this I believe. We discuss a lot of DOE internal stuff > on it. However, it there were an archived list to Cc, we could talk about doing that. We can have publically archived mailing lists for eg: http://www-unix.mcs.anl.gov/web-mail-archive/lists/mpich-discuss/threads.ht… But currently petsc-dev list archives are available only locally. And petsc-maint is a 'bug-tracker' - not a mailing list. The archives of this are also available locally only. I'm checking if we can upgrade to a better bug tracker - with both public/private entries [like bugzilla]. But.... Satish > > > If you start getting 10 more support queires a day can you handle that ? > > What about 50 ? Maybe I can also act as a gateway, if I tell our users to come to > > me first. > > Well, we get anywhere from 50-200 per day, so I think we can probably handle some more. In > my experience there are a lot up front with a new community,but it rapidly tails off. > > Matt >

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more inlining ?
by Barry Smith 03 Nov '05

03 Nov '05

Should we inline VecSetValues, MatSetValues, and friends? Barry

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Re: tracking petsc
by Matthew Knepley 03 Nov '05

03 Nov '05

Simon Burton <simon(a)arrowtheory.com> writes: > On Thu, 03 Nov 2005 17:49:46 -0600 > Matthew Knepley <knepley(a)mcs.anl.gov> wrote: > >> >> Simon Burton <simon(a)arrowtheory.com> writes: >> >> This was patched in 2.3.0, but maybe you have an unpatched version. It is >> easy to check. The symbol comes from > > We have been tracking your bitkeeper repository. I don't know if this is > sane or not because we want to release something (in a few weeks) > and that basically means it is up to us to somehow stabilize PETSc, > or at least "bless" some particular version of PETSc. > > No, that doesn't sound right either: fixes that you guys make will go into > the bk repository, so... I guess what I am asking is, are we just insane to > try and do this ? Or, is it possible to maybe branch your repository so > we can stabilize PETSc for some kind of beta release ? This is our preference. Why? It is jsut as stable as tarballs because you can clone to any particular revision, BUT its more flexible because you can easily pull any fixes or upgrades. > Sounds like we just need to make it clear that petsc is on the move > and that you guys are completely responsive to bug reports, etc. > > We are going to build a "petsc doesn't work" FAQ, but, gee i wish your email > list (petsc-maint) was archived somewhere... The DOE really frowns on this I believe. We discuss a lot of DOE internal stuff on it. However, it there were an archived list to Cc, we could talk about doing that. > If you start getting 10 more support queires a day can you handle that ? > What about 50 ? Maybe I can also act as a gateway, if I tell our users to come to > me first. Well, we get anywhere from 50-200 per day, so I think we can probably handle some more. In my experience there are a lot up front with a new community,but it rapidly tails off. Matt -- "Failure has a thousand explanations. Success doesn't need one" -- Sir Alec Guiness

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tracking petsc
by Simon Burton 03 Nov '05

03 Nov '05

On Thu, 03 Nov 2005 17:49:46 -0600 Matthew Knepley <knepley(a)mcs.anl.gov> wrote: > > Simon Burton <simon(a)arrowtheory.com> writes: > > This was patched in 2.3.0, but maybe you have an unpatched version. It is > easy to check. The symbol comes from We have been tracking your bitkeeper repository. I don't know if this is sane or not because we want to release something (in a few weeks) and that basically means it is up to us to somehow stabilize PETSc, or at least "bless" some particular version of PETSc. No, that doesn't sound right either: fixes that you guys make will go into the bk repository, so... I guess what I am asking is, are we just insane to try and do this ? Or, is it possible to maybe branch your repository so we can stabilize PETSc for some kind of beta release ? Sounds like we just need to make it clear that petsc is on the move and that you guys are completely responsive to bug reports, etc. We are going to build a "petsc doesn't work" FAQ, but, gee i wish your email list (petsc-maint) was archived somewhere... If you start getting 10 more support queires a day can you handle that ? What about 50 ? Maybe I can also act as a gateway, if I tell our users to come to me first. Simon. -- Simon Burton, B.Sc. Licensed PO Box 8066 ANU Canberra 2601 Australia Ph. 61 02 6249 6940 http://arrowtheory.com

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couple small API changes to petsc-dev
by Barry Smith 28 Oct '05

28 Oct '05

PetscViewerFileType merged into PetscFileMode PetscViewerASCIISetFilename/Type() changed to PetscViewerFileSetName/Mode() to match what is used for Binary viewer PetscBinaryOpen() now takes PetscFileMode as argument instead of int Matt, This will mess up your python bindings. Dinesh and Satish, The viewers for netcdf and hdf5 have not been tested with this change and probably won't compile. They need to be in a nightly build. Barry

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MIT Lincoln Researchers Release pMatlab (fwd)
by Barry Smith 14 Oct '05

14 Oct '05

MIT Lincoln Researchers Release pMatlab HPCwire M489132 October 14, 2005 For years, users of high performance computing users have struggled with difficult low-level message passing programming environments to exploit parallel computers. MIT Lincoln Laboratory researchers Jeremy Kepner, Nadya Travinin, Albert Reuther and Hahn Kim -- under the sponsorship of the Department of Defense's High Performance Computing Modernization Program, the Defense Advanced Research Projects Administration and the Air Force -- have been leading an effort to bring MATLAB -- a common high-level language used in technical computing -- into the HPC world. The first stage of this effort was the development of the MatlabMPI library (<http://www.ll.mit.edu/MatlabMPI>), which now has thousands of users. More recently, this team has developed the pMatlab library (<http://www.ll.mit.edu/pMatlab>), which brings the benefits of Parallel Global Array Semantics (PGAS) to the Matlab community. Currently, PGAS is mostly found in specialized HPC languages, such as UPC, Co-Array Fortran and Titanium, as well as numerous C++ libraries (e.g. POOMA, GA++, and ||VSIPL++). pMatlab allows users to describe how to break up their problems on a parallel computer using extremely compact and natural array semantics that are intuitive to most scientists and engineers. pMatlab allows users to write vastly more complex parallel codes with a lot less work. For example, pMatlab implementations of the HPCChallenge benchmark suite (http://www.HPCChallenge.org <http://www.hpcchallenge.org/>) were between two and 60 times smaller while delivering comparable performance. Most importantly, novice users can convert serial Matlab programs to parallel programs in an average of less than two hours. According to Lincoln Laboratory's Grid Computing lead Albert Reuther, "We have over 80 pMatlab users at Lincoln. We have never seen a MatlabMPI user go back after they have tried pMatlab." One example of the impact of pMatlab was a recent flight test where pMatlab was used to quickly process research sensor data on a 28-processor blade cluster on a Boeing 707 aircraft. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.1 (Cygwin) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFDT8uOmWA2y7s1YXMRAg0UAJ0Ywtvcncf84X2Gfg7hurnWTZ6BMwCgoFFf 3mwzWHvzmxmiesxUEEYaYFk= =TlNf -----END PGP SIGNATURE-----

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petsc-dev change
by Barry Smith 13 Oct '05

13 Oct '05

I have finally made this change. pcimpl.h has been moved from src/ksp/pc/pcimpl.h to include/private/pcimpl.h (thus "make install" will preserve it). Anyone using pcimpl.h with petsc-dev will need to make the change in their source code. Barry On Mon, 4 Jul 2005, Johan Jansson wrote: > Hi! > > We've implemented a PetSc preconditioner in DOLFIN, but it seems the > preconditioner implementation API (pcimpl.h) isn't a public API > (i.e. user code cannot see it). We've solved this by copying pcimpl.h > into DOLFIN, but this is not a good solution. Could you consider > making the preconditioner implementation API public? > > The reason the preconditioner is implemented in DOLFIN and not in > PetSc is because the preconditioner depends on DOLFIN. The idea is to > solve a nonlinear system in a time-stepping method for ODEs by > Newton's method with a Krylov solver preconditioned with a fixed-point > solver. The fixed-point solver is part of DOLFIN. There are likely > other such applications of externally implemented preconditioners. > > Thank you, > Johan > >

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Re: [PETSC #13286] Make pcimpl.h a public API
by Barry Smith 13 Oct '05

13 Oct '05

I have finally made this change. pcimpl.h has been moved from src/ksp/pc/pcimpl.h to include/private/pcimpl.h (thus "make install" will preserve it). Anyone using pcimpl.h with petsc-dev will need to make the change in their source code. Barry On Mon, 4 Jul 2005, Johan Jansson wrote: > Hi! > > We've implemented a PetSc preconditioner in DOLFIN, but it seems the > preconditioner implementation API (pcimpl.h) isn't a public API > (i.e. user code cannot see it). We've solved this by copying pcimpl.h > into DOLFIN, but this is not a good solution. Could you consider > making the preconditioner implementation API public? > > The reason the preconditioner is implemented in DOLFIN and not in > PetSc is because the preconditioner depends on DOLFIN. The idea is to > solve a nonlinear system in a time-stepping method for ODEs by > Newton's method with a Krylov solver preconditioned with a fixed-point > solver. The fixed-point solver is part of DOLFIN. There are likely > other such applications of externally implemented preconditioners. > > Thank you, > Johan > >

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make_lineal.py
by S V N Vishwanathan 28 Sep '05

28 Sep '05

Hi! If you check out the latest Numerix repository, under externalpackages/petsc you will find make_lineal.py which essentially is your make.py with minor tweaks to build our python wrappers into $PETSC_DIR/lib/$PETSC_ARCH/pypetsc We would ideally like to run this file from within our root directory i.e. use $LINEAL_DIR but the hardcoded dependencies built into the PETSc configure prevent us from doing this. We can submit patches to PETSc configure if give us specific pointers on how to go around doing this. Alternatively, if you make changes, we are willing to be perfect gunieapigs :) vishy ----- Allen's Axiom: When all else fails, read the instructions.

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Re: BuildSystem question
by S V N Vishwanathan 26 Sep '05

26 Sep '05

Hi! >> Ideally, I would like to use your BuildSystem to hack up a quick build >> for Numerix. Then as we add and integrate more tools in, I would work on >> making it fancier. Matt> Cool, we can do that. Step one in that direction would be for me to adapt make.py in $PETSC_DIR to build our shared libraries. I have made some effort in this direction (see attachment). But when I run it I get the following error: [dhcp-215-103]:~/Repositories/numerix % export PYTHONPATH=~/Repositories/numerix/externalpackages/petsc/python/BuildSystem:~/Repositories/numerix/externalpackages/petsc/python/PETSc:$PYTHONPATH [dhcp-215-103]:~/Repositories/numerix % python make.py Tue 09:09 Traceback (most recent call last): File "make.py", line 82, in ? Make().run() File "/Users/vishy/Repositories/numerix/externalpackages/petsc/python/BuildSystem/maker.py", line 213, in run self.executeSection(self.configure, self.builder) File "/Users/vishy/Repositories/numerix/externalpackages/petsc/python/BuildSystem/maker.py", line 207, in executeSection return section(*args) File "make.py", line 46, in configure framework = maker.BasicMake.configure(self, builder) File "/Users/vishy/Repositories/numerix/externalpackages/petsc/python/BuildSystem/maker.py", line 291, in configure framework = Make.configure(self, builder) File "/Users/vishy/Repositories/numerix/externalpackages/petsc/python/BuildSystem/maker.py", line 149, in configure if not self.setupConfigure(self.framework): File "make.py", line 36, in setupConfigure maker.BasicMake.setupConfigure(self, framework) File "/Users/vishy/Repositories/numerix/externalpackages/petsc/python/BuildSystem/maker.py", line 283, in setupConfigure Make.setupConfigure(self, framework) File "/Users/vishy/Repositories/numerix/externalpackages/petsc/python/BuildSystem/maker.py", line 136, in setupConfigure self.configureObj.setupPackageDependencies(framework) File "/Users/vishy/Repositories/numerix/externalpackages/petsc/python/PETSc/petsc.py", line 88, in setupPackageDependencies framework.addPackageDependency(petscConf, confPath) File "/Users/vishy/Repositories/numerix/externalpackages/petsc/python/BuildSystem/config/framework.py", line 297, in addPackageDependency self.childGraph.replaceVertex(self.require(child.__module__, None), child) File "/Users/vishy/Repositories/numerix/externalpackages/petsc/python/BuildSystem/config/framework.py", line 255, in require config = self.getChild(moduleName, keywordArgs) File "/Users/vishy/Repositories/numerix/externalpackages/petsc/python/BuildSystem/config/framework.py", line 235, in getChild config.setupDependencies(self) File "/Users/vishy/Repositories/numerix/externalpackages/petsc/python/PETSc/Configure.py", line 40, in setupDependencies for utility in os.listdir(os.path.join('python', 'PETSc', d)): OSError: [Errno 2] No such file or directory: 'python/PETSc/utilities' You can also find the latest version checked into SVN. vishy ----- Parting is such sweet sorrow. -William Shakespeare

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