[petsc-dev] building sphinx doc only

2023-06-15 Thread Blaise Bourdin
Hi, I am trying to figure out why the doc page for PetscOptionsHeadBegin https://petsc.org/release/manualpages/Sys/PetscOptionsHeadBegin/ is broken. Following the instructions at https://petsc.org/release/developers/documentation/#developing-petsc-documentation I do cd $PETSC_DIR/doc make

Re: [petsc-dev] PetscOptionsXXX, PetscOptionsGetXX, and PetscBag in Fortran

2023-05-16 Thread Blaise Bourdin
interface, so that code is all unnecessary plus a Fortran programmer would never use a GUI anyways :-)   https://gitlab.com/petsc/petsc/-/merge_requests/6473   Barry     On May 16, 2023, at 11:33 AM, Blaise Bourdin wrote: Hi, I am revisiting the way I handle

[petsc-dev] PetscOptionsXXX, PetscOptionsGetXX, and PetscBag in Fortran

2023-05-16 Thread Blaise Bourdin
Hi, I am revisiting the way I handle options my fortran fracture code. I see the following options: - use PetscGetXXX, with the caveat that as far as I can see options define this way do not show up when using -help - use PetscBags, which is what I do now. It is a bit convoluted and I am

Re: [petsc-dev] Regression bug in Merge branch 'knepley/feature-hybrid-mass' into 'main'

2023-04-21 Thread Blaise Bourdin
023 at 3:33 PM Blaise Bourdin <bour...@mcmaster.ca> wrote: Actually that was an easy fix… see MR !6352 On Apr 20, 2023, at 9:18 PM, Blaise Bourdin <bour...@mcmaster.ca> wrote: Hi, I just noticed that b6b5caf99979f50a7774afdccea5ca5661fc1203 Merge branch '

Re: [petsc-dev] Regression bug in Merge branch 'knepley/feature-hybrid-mass' into 'main'

2023-04-20 Thread Blaise Bourdin
Actually that was an easy fix… see MR !6352 On Apr 20, 2023, at 9:18 PM, Blaise Bourdin wrote: Hi, I just noticed that b6b5caf99979f50a7774afdccea5ca5661fc1203 Merge branch 'knepley/feature-hybrid-mass' into ‘main’ seems to have introduced a bug See the attached

[petsc-dev] Regression bug in Merge branch 'knepley/feature-hybrid-mass' into 'main'

2023-04-20 Thread Blaise Bourdin
Hi, I just noticed that b6b5caf99979f50a7774afdccea5ca5661fc1203 Merge branch 'knepley/feature-hybrid-mass' into ‘main’ seems to have introduced a bug See the attached example (a very simple update of src/dm/impls/plex/tests/ex98.c) When calling DMGetMatrix, I get the following

[petsc-dev] GMSH reader and vertex sets

2023-03-09 Thread Blaise Bourdin
Hi, I am encountering an issue with the GMSH reader which seems to ignore vertex sets. I am attaching a small c example, as well as two meshes, both contain cell, face, and vertex sets, but somehow the vertex sets are not read by the GMSH reader. I am particularly confused since the

Re: [petsc-dev] Fortran-auto-interfaces

2023-01-10 Thread Blaise Bourdin
tMat,tTao   ... instead of  subroutine TaoGetLMVMMatrix(a,b,z)   import tMat El 10 ene 2023, a las 20:40, Blaise Bourdin escribió: Hi Jose, I have created the type tTAO and PETSC_NULL_TAO what I need to figure out is how to get bfort to import tTAO in each auto

Re: [petsc-dev] Fortran-auto-interfaces

2023-01-10 Thread Blaise Bourdin
PETSC_FORTRAN_TYPE_INITIALIZE  end type tTao Jose El 10 ene 2023, a las 17:22, Blaise Bourdin escribió: Hi, I am trying to bring TAO fortran interfaces up to par with SNES. How is tao/f90-mod/ftn-auto-interfaces/petsctao.h90 generated? I would need to import tTAO and replace

[petsc-dev] Fortran-auto-interfaces

2023-01-10 Thread Blaise Bourdin
Hi, I am trying to bring TAO fortran interfaces up to par with SNES. How is tao/f90-mod/ftn-auto-interfaces/petsctao.h90 generated? I would need to import tTAO and replace the call to the “Tao” macro with TAO. Regards, Blaise — Canada Research Chair in Mathematical and Computational Aspects

Re: [petsc-dev] Manualpage TOC

2022-10-23 Thread Blaise Bourdin
o find the time to fix this page, properly organize and order the entries on that page. I did a rush job to convert to .rst for other reasons and have not had time to clean up the page. On Oct 20, 2022, at 2:57 PM, Blaise Bourdin <bour...@mcmaster.ca> wrote: Resurrecting thi

Re: [petsc-dev] Manualpage TOC

2022-10-20 Thread Blaise Bourdin
Resurrecting this thread: I find information really hard to find in https://petsc.org/release/docs/manualpages/ now that the hierarchy has been flattened In addition, the section headings are inconsistent, and the word “Manual pages” do not provide any information but make rapidly scanning

[petsc-dev] Make checkbadSource error

2022-10-20 Thread Blaise Bourdin
Hi, I am trying to run make checkbadSource on a branch ahead of a trivial MR, but get the following error message: eduroam062-155:petsc-main $ make checkbadSource SHELL=bash fatal: cannot use Perl-compatible regexes when not compiled with USE_LIBPCRE fatal: cannot use Perl-compatible regexes

Re: [petsc-dev] Bug in DMPlexVecGetClosure/DMPlexVecRestoreClosure in Fortran

2022-09-06 Thread Blaise Bourdin
`start + 520 (lldb) c On Sep 5, 2022, at 11:34 AM, Blaise Bourdin <bour...@mcmaster.ca> wrote: All, I am running in a very strange issue with DMPlexVecGetClosure/DMPlexVecRestoreClosure in Fortran when passing a point such that the returned array should be of 0 size. T

[petsc-dev] Bug in DMPlexVecGetClosure/DMPlexVecRestoreClosure in Fortran

2022-09-05 Thread Blaise Bourdin
All, I am running in a very strange issue with DMPlexVecGetClosure/DMPlexVecRestoreClosure in Fortran when passing a point such that the returned array should be of 0 size. The typical use case is a vector associated with cell-based unknowns, and requesting the values on the closure

Re: [petsc-dev] PETSc janitorial work

2022-08-23 Thread Blaise Bourdin
On Tue, Aug 23, 2022 at 9:37 AM Blaise Bourdin <bour...@mcmaster.ca> wrote: All, I think that there is quite a bit of low-skills / time consuming work which is a poor use of the main developers’ time: syncing C / Fortran / python headers, improving the tests coverage, proof

[petsc-dev] PETSc janitorial work

2022-08-23 Thread Blaise Bourdin
All, I think that there is quite a bit of low-skills / time consuming work which is a poor use of the main developers’ time: syncing C / Fortran / python headers, improving the tests coverage, proofreading the manual and man pages, etc. I’d be more than happy to help organizing a virtual or

Re: [petsc-dev] Type mismatch warnings

2022-08-19 Thread Blaise Bourdin
h work? Satish On Fri, 19 Aug 2022, Blaise Bourdin wrote: Hi, Does anybody know if there is a magic gfortran flag to get rid of type mismatch warnings? These pop up when using PetscObjectSetName with two different petsc objects, for instance. Warning: Type mismatch between actual argument

[petsc-dev] Type mismatch warnings

2022-08-19 Thread Blaise Bourdin
Hi, Does anybody know if there is a magic gfortran flag to get rid of type mismatch warnings? These pop up when using PetscObjectSetName with two different petsc objects, for instance. Warning: Type mismatch between actual argument at (1) and actual argument at (2)

Re: [petsc-dev] tests coverage

2022-08-12 Thread Blaise Bourdin
peline' and click 'index_gcov.html' i.e: https://petsc.gitlab.io/-/petsc/-/jobs/2841119765/artifacts/arch-ci-analyze-pipeline/index_gcov.html Satish On Fri, 12 Aug 2022, Blaise Bourdin wrote: Hi, Is the source coverage analysis by the tests easily available? When submitting a MR,

[petsc-dev] tests coverage

2022-08-12 Thread Blaise Bourdin
Hi, Is the source coverage analysis by the tests easily available? When submitting a MR, I want to know if adding a test is necessary. Regards, Blaise — Tier 1 Canada Research Chair in Mathematical and Computational Aspects of Solid Mechanics Professor, Department of Mathematics &

[petsc-dev] How to update tests output

2022-08-08 Thread Blaise Bourdin
Silly question, but I can’t find the answer in my notes or on the petsc developer pages: How do I automatically update the output of a series of tests without running them all by hand, one at a time? Regards, Blaise — Tier 1 Canada Research Chair in Mathematical and Computational Aspects of

[petsc-dev] test failure in main

2022-07-29 Thread Blaise Bourdin
Hi, I am trying to get a bunch of small MR through the test system without success. Right now, it looks like even the main branch does not pass the tests: ./configure --CFLAGS='-Wimplicit-function-declaration -Wunused' --FFLAGS='-ffree-line-length-none -fallow-argument-mismatch -Wunused'

Re: [petsc-dev] Fortran binding for VecGetValuesSection

2022-06-29 Thread Blaise Bourdin
scCall(VecGetArray(v, ));  *values = [s->atlasOff[p]];  PetscCall(VecRestoreArray(v, )); Can you make a draft MR with what you've tried thus far? Blaise Bourdin <bour...@mcmaster.ca> writes: Hi, I’ve been trying to add a fortran90 binding for VecGetValuesSection, without success, and

[petsc-dev] Fortran binding for VecGetValuesSection

2022-06-14 Thread Blaise Bourdin
Hi, I’ve been trying to add a fortran90 binding for VecGetValuesSection, without success, and could not find any function with a similar prototype to learn from. Can anybody help? Regards, Blaise -- Professor, Department of Mathematics & Statistics Hamilton Hall room 409A, McMaster

[petsc-dev] Moar namespacing

2012-08-27 Thread Blaise Bourdin
actually, what is the meaning of is in fortran? I can't find it as a keyword in any of my 2003 ref, so it must be a 2008 or later thing. Blaise On Aug 27, 2012, at 3:40 PM, Matthew Knepley knepley at gmail.com wrote: That depends on what the meaning of IS is. Matt On Mon, Aug 27, 2012

[petsc-dev] Moar namespacing

2012-08-27 Thread Blaise Bourdin
On Aug 27, 2012, at 3:54 PM, Jed Brown jedbrown at mcs.anl.gov wrote: On Mon, Aug 27, 2012 at 3:48 PM, Blaise Bourdin bourdin at lsu.edu wrote: actually, what is the meaning of is in fortran? I can't find it as a keyword in any of my 2003 ref, so it must be a 2008 or later thing. See

[petsc-dev] Issues with DMComplexSetCone

2012-08-24 Thread Blaise Bourdin
I am attaching a debugged version. Blaise On Aug 24, 2012, at 3:30 PM, Matthew Knepley knepley at gmail.com wrote: On Fri, Aug 24, 2012 at 2:16 PM, Chris Eldred chris.eldred at gmail.com wrote: The following code snippet does not appear to be working: 1) I hate Fortran. A lot. It is not

[petsc-dev] TS fortran binding patch

2012-08-17 Thread Blaise Bourdin
Hi, The attached trivial patch adds fortran bindings for a few TS functions (TSGetIFunction, TSGetRHSFunction, TSGetIJAcobian, TSSetOptiosnPrefix, TSAppendOptionsPrefix). Can somebody push it to petsc-3.3 if it makes sense? Blaise -- next part -- A non-text attachment

[petsc-dev] YAML patch take 3

2012-08-17 Thread Blaise Bourdin
Hi, Here is a revised version of my YAML patch that eliminates the limit on the yaml file length. Is there any rational objection to pushing it to petsc-3.3 and petsc-dev? Blaise -- next part -- A non-text attachment was scrubbed... Name:

[petsc-dev] YAML patch take 3

2012-08-17 Thread Blaise Bourdin
PETSC_MAX_YAML_LEN 128000 Yike... it was supposed to be removed indeed. Blaise On Fri, Aug 17, 2012 at 1:52 PM, Blaise Bourdin bourdin at lsu.edu wrote: Hi, Here is a revised version of my YAML patch that eliminates the limit on the yaml file length. Is there any rational objection

[petsc-dev] YAML patch

2012-08-08 Thread Blaise Bourdin
in the function name? We put in _ in function names for private functions and generally user called public functions (like this) would not have that. Barry On Aug 7, 2012, at 9:29 AM, Blaise Bourdin bourdin at lsu.edu wrote: Hi, My YAML patch did not exactly raise much enthusiasm so I

[petsc-dev] YAML patch

2012-08-08 Thread Blaise Bourdin
On Aug 8, 2012, at 9:39 AM, Sean Farley sean at mcs.anl.gov wrote: The existing, but non working, function is called PetscOptionsInsertFile_YAML. I just kept its name without checking the petsc developer style guide. My mistake. The attached patch fixes this issue. There is a limit of

[petsc-dev] YAML patch

2012-08-07 Thread Blaise Bourdin
Hi, My YAML patch did not exactly raise much enthusiasm so I tried to clean it up a bit... The attached patch is another attempt at providing partial support for parsing YAML files: -options_file_yaml now works from C and fortran. It's logic was changed so that it does not require

[petsc-dev] proposed patch: YAML parser

2012-07-24 Thread Blaise Bourdin
Hi, After trying to get the current yaml parser in petsc to work, I finally gave up and rewrote a very basic one. It supports only a subset of the standard and lacks support or sequences and aliases , for instance (would that be JSON?). Would you consider applying this patch (yaml-1.patch) to

[petsc-dev] fortran binding for DMGetNamedGlobalVector and DMRestoreNamedGlobalVector

2012-07-19 Thread Blaise Bourdin
Hi, I am attaching a patch adding fortran bindings for DMGetNamedGlobalVector and DMRestoreNamedGlobalVector. I think I got the file names right, this time. Is it possible to push this patch to petsc-3.3 and petsc-dev? Blaise -- next part -- A non-text attachment was

[petsc-dev] where is type(Mat) defined?

2012-07-18 Thread Blaise Bourdin
Desc: not available URL: http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20120717/13a4804c/attachment.obj -- next part -- Barry On Jul 17, 2012, at 10:41 PM, Blaise Bourdin wrote: Hi, I am still trying to figure out how to add support for MatNullSpace

[petsc-dev] where is type(Mat) defined?

2012-07-18 Thread Blaise Bourdin
, Barry Smith wrote: Satish, Please apply this patch if it makes sense. Thanks Barry On Jul 17, 2012, at 11:25 PM, Blaise Bourdin wrote: On Jul 17, 2012, at 10:51 PM, Barry Smith wrote: If you are using Fortran modules (and being a FORTRAN lover you

[petsc-dev] MatNullSpace with fortran data types

2012-07-16 Thread Blaise Bourdin
Hi, I am having trouble with MatNullSPace in fortran with fortran data types enabled. I don't mind if MatNullSpace is not a f90 data type, but right now, neither the old style MatNullSpace nsp nor the more f90-ish type(MatNullSpace) nsp seem to work. galerkin:PetscF90

[petsc-dev] patch: fortran binding for PetscOptionsView

2012-07-13 Thread Blaise Bourdin
Hi, Here is a trivial patch that adds fortran binding for PetscOptionsView. Is it possible to apply it to petsc-3.3 and petsc-dev? Blaise -- next part -- A non-text attachment was scrubbed... Name: PetscOptionsViewFortranBinding.patch Type: application/octet-stream Size:

[petsc-dev] second patch for DMDAVecGetArrayF90

2012-07-06 Thread Blaise Bourdin
Hi, I have added the creation, destruction and accessor functions for 4d vectors in F90. The accessor was missing and needed for DMDAVecGetArrayF90 with a 3d DMDA and 1 dof. As far as I can test, ex11f90 in DM should now completely work with the intel compilers. Some of the functions are

[petsc-dev] [petsc-users] Getting 2d array with updated ghost values from DM global vector

2012-07-02 Thread Blaise Bourdin
Hi, There appears to be a bug in DMDAVecRestoreArrayF90. It is probably only triggered when the intel compilers. gfortran and intel seem to have very different internal implementations of fortran90 allocatable arrays. Developers, can you check if the attached patch makes sense? It will not

[petsc-dev] Getting from and to IS from a VecScatter

2012-06-21 Thread Blaise Bourdin
On Jun 21, 2012, at 7:42 AM, Matthew Knepley wrote: On Wed, Jun 20, 2012 at 8:40 PM, Blaise Bourdin bourdin at lsu.edu wrote: Hi, I want to change the way I handle boundary conditions in my finite elements code: Right now, I skip the rows and columns during the matrices assembly, using

[petsc-dev] PetscLogView vs. -log_summary

2012-06-21 Thread Blaise Bourdin
Hi, PetscLogView does not display the same amount of information as running with -log_summary. In the summary of stages section, the former contains only information on the main stage while the later contains much more. Add the following block at the end of src/snes/examples/tutorials/ex1.c,

[petsc-dev] PetscLogView vs. -log_summary

2012-06-21 Thread Blaise Bourdin
On Jun 21, 2012, at 2:55 PM, Matthew Knepley wrote: On Thu, Jun 21, 2012 at 1:11 PM, Blaise Bourdin bourdin at math.lsu.edu wrote: Hi, PetscLogView does not display the same amount of information as running with -log_summary. In the summary of stages section, the former contains only

[petsc-dev] PetscLogView vs. -log_summary

2012-06-21 Thread Blaise Bourdin
On Jun 21, 2012, at 3:40 PM, Matthew Knepley wrote: On Thu, Jun 21, 2012 at 2:08 PM, Blaise Bourdin bourdin at lsu.edu wrote: On Jun 21, 2012, at 2:55 PM, Matthew Knepley wrote: On Thu, Jun 21, 2012 at 1:11 PM, Blaise Bourdin bourdin at math.lsu.edu wrote: Hi, PetscLogView does

[petsc-dev] Getting from and to IS from a VecScatter

2012-06-20 Thread Blaise Bourdin
Hi, I need to reconstruct the IS that were used to build a VecScatter between a local and a global Vec.

[petsc-dev] Getting from and to IS from a VecScatter

2012-06-20 Thread Blaise Bourdin
, 2012, at 6:19 PM, Blaise Bourdin wrote: Hi, I need to reconstruct the IS that were used to build a VecScatter between a local and a global Vec. From what I see in VecScatterView_MPI (vpscat.c:13), it looks like I can get the indices from from-local.vslots[i],to-local.vslots[i], i=0

[petsc-dev] error reading binary file

2012-06-12 Thread Blaise Bourdin
try deleting the .info file Blaise On Jun 12, 2012, at 11:45 AM, Mark F. Adams wrote: I'm getting this error when I try to read a matrix/vector with block size 3: ~/Desktop/GAMG./ex10 -f0 binaryoutput-sym [0]PETSC ERROR: - Error Message

[petsc-dev] Problem with VecLoad and .info files

2012-06-10 Thread Blaise Bourdin
-vecload_block_size 3 Very good point. That fixes the problem. and for existing files, I can always delete the .info file. I need to switch to the built-in binary vtk viewer anyway... Blaise On Sun, Jun 10, 2012 at 8:37 AM, Blaise Bourdin bourdin at lsu.edu wrote: Hi, I think I found another bug

[petsc-dev] Fwd: [petsc-maint #119133] petsc-dev configure crash

2012-06-06 Thread Blaise Bourdin
On Wed, Jun 6, 2012 at 2:49 PM, Barry Smith bsmith at mcs.anl.gov wrote: A) make buildsystem a subrepo (svn external for those familiar with svn) There have already been many discussions on petsc-dev about how hg subrepos suck and don't satisfy all our needs. I think our needs are

[petsc-dev] misleading error message in VecWAXPY

2012-06-05 Thread Blaise Bourdin
Hi, It looks like when VecWAXPY is called with alpha=Nan, PetscValidLogicalCollectiveScalar causes the message Scalar value must be same on all processes, argument # 2 to be printed. This is a bit misleading, and confusing when running on only 1 processor. Is this something worth fixing?

[petsc-dev] What needs to be done before a release?

2012-06-03 Thread Blaise Bourdin
On Jun 1, 2012, at 6:35 PM, Barry Smith wrote: On Jun 1, 2012, at 1:34 PM, Blaise Bourdin wrote: On Jun 1, 2012, at 12:47 PM, Barry Smith wrote: On Jun 1, 2012, at 12:37 PM, Blaise Bourdin wrote: What compiler is this? I don't have access to any solaris box, and have pretty bad

[petsc-dev] What needs to be done before a release?

2012-06-01 Thread Blaise Bourdin
On Jun 1, 2012, at 11:44 AM, Satish Balay wrote: Ok - nightly builds on opensolaris has the following error. character(kind=c_char),pointer :: nullc = null() Character(kind=C_char,len=99),Dimension(:),Pointer::list1 /export/home/petsc/soft/mpich2-1.2.1p1/bin/mpif90

[petsc-dev] What needs to be done before a release?

2012-06-01 Thread Blaise Bourdin
On Jun 1, 2012, at 12:47 PM, Barry Smith wrote: On Jun 1, 2012, at 12:37 PM, Blaise Bourdin wrote: What compiler is this? I don't have access to any solaris box, and have pretty bad memories of sun's fortran compilers. My understanding of the C interoperability

[petsc-dev] What needs to be done before a release?

2012-06-01 Thread Blaise Bourdin
On Jun 1, 2012, at 2:23 PM, Jed Brown wrote: On Fri, Jun 1, 2012 at 1:34 PM, Blaise Bourdin bourdin at lsu.edu wrote: Apologies, will do next time. That would also have helped me realize that I had pushed to my own clone, not petsc-3.3 or petsc-dev repository... I am attaching the patch I

[petsc-dev] What needs to be done before a release?

2012-06-01 Thread Blaise Bourdin
Hm - we do have explicit interfaces - for ex: VecGetArrayF90() does not work without it.. Touch?... So where should the interfaces for PetscOptionsGetEnum and PetscBagRegisterEnum go? Blaise -- Department of Mathematics and Center for Computation Technology Louisiana State University,

[petsc-dev] What needs to be done before a release?

2012-05-31 Thread Blaise Bourdin
Hi, Is this a real or potential issue? C interoperability has been implemented in all compilers I know of for a while. In 2007, cray, gfortran, g95, intel and NAG already supported this functionality. http://dx.doi.org/10.1145/1243413.1243414 The current version is at

[petsc-dev] What needs to be done before a release?

2012-05-30 Thread Blaise Bourdin
Fantastic! Thanks you so much, Blaise On May 30, 2012, at 10:04 PM, Barry Smith wrote: Blaise, I have pushed PetscOptionsGetEnum() and PetscBagRegisterEnum() for f90 to petsc-dev tests are in src/sys/examples/tutorials Barry On May 29, 2012, at 3:29 AM, Blaise Bourdin

[petsc-dev] What needs to be done before a release?

2012-05-29 Thread Blaise Bourdin
the C_NULL_CHAR)? The alternative would be to modify PetscBagRegisterEnum, in order to store the content of list instead of just a reference, which may not be something you want to do right now. Blaise Barry On May 27, 2012, at 10:16 AM, Blaise Bourdin wrote: Barry, If I

[petsc-dev] What needs to be done before a release?

2012-05-27 Thread Blaise Bourdin
needs to be done before a release? Blaise If you provide a fortran function to convert an array of Fortran strings to an array of C strings and tell us how to delete the result then we'll provide a PetscOptionsGetEnum() for Fortran. Barry On May 2, 2012, at 12:02 PM, Blaise Bourdin

[petsc-dev] fortran questions

2012-05-16 Thread Blaise Bourdin
Hi, I am trying to have a look at the fortran modules code. - the petsc and petscdef modules are defined in src/ts/f90-mod/petsctsmod.F would it make more sense to move them to src/f90-mod/petscmod.F - Is there a valid reason for not including petscdef.h in the module petsc? - I would like to

[petsc-dev] fortran questions

2012-05-16 Thread Blaise Bourdin
On May 16, 2012, at 11:48 AM, Satish Balay wrote: On Wed, 16 May 2012, Satish Balay wrote: On Wed, 16 May 2012, Blaise Bourdin wrote: Hi, I am trying to have a look at the fortran modules code. - the petsc and petscdef modules are defined in src/ts/f90-mod/petsctsmod.F would it make

[petsc-dev] What needs to be done before a release?

2012-05-02 Thread Blaise Bourdin
Barry, Also, fortran wrappers over PetscOptionsEnum and PetscBagRegisterEnum would be nice. I understand that it is a bit tricky since it involves passing fortran arrays of strings. Yup. We'd be willing to support these from FORTRAN but someone else has to do the dirty work of

[petsc-dev] What needs to be done before a release?

2012-04-30 Thread Blaise Bourdin
Hi, I know I suggested it before and the idea did not get much traction, but it would be _really_ nice to add Real and Integer arrays to PetscBag. The idea is _not_ to add full fields in a bag. Instead, I would like to be able to pass material properties as command line arguments in a concise

[petsc-dev] Weird interaction between VecDuplicate and VecSetBlockSize

2012-03-30 Thread Blaise Bourdin
not mention that the Vecs share anything. Perhaps it should. On a different topic, is there a way to generate the xdmf description with the hdf5 viewer? Blaise On Mar 30, 2012 9:02 AM, Blaise Bourdin bourdin at lsu.edu wrote: Hi, I am trying to make use of the more advanced features

[petsc-dev] PetscOptionsInsertFile_YAML

2012-01-19 Thread Blaise Bourdin
0x00010540cb75 in PetscOptionsInsertFile_YAML (comm=1140850688, file=0x10527bf4f options.yml, require=PETSC_TRUE) at yamlimpls.c:763 #5 0x00010527bd48 in main (argc=2, argv=0x7fff64e798e8) at TestOptionsC.c:20 On Thu, Jan 19, 2012 at 10:12, Blaise Bourdin bourdin at lsu.edu wrote

[petsc-dev] PetscOptionsInsertFile_YAML

2012-01-18 Thread Blaise Bourdin
On Jan 18, 2012, at 11:28 AM, Sean Farley wrote: I sound the function PetscOptionsInsertFile_YAML in src/sys/yaml/yamplimpls.c but I can't get even a simple example to work. Instead, I get a segfault in PetscOptionsInsertFile_YAML Is it supposed to work or is it part of some unfinished

[petsc-dev] Is gamg in petsc 3.2?

2012-01-06 Thread Blaise Bourdin
Hi, I see that some of the examples using gamg are in petsc 3.2, but I can't figure out how to run them: galerkin:tutorials bourdin$ ./ex54 [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Unknown type. Check for miss-spelling or missing

[petsc-dev] Is gamg in petsc 3.2?

2012-01-06 Thread Blaise Bourdin
Cool, thanks. Blaise On Jan 6, 2012, at 9:19 AM, Jed Brown wrote: On Fri, Jan 6, 2012 at 09:05, Blaise Bourdin bourdin at lsu.edu wrote: Has gamg made its way into 3.2? If so, is there a magic trick to use it? $ head -3 ~/petsc-3.2/src/ksp/pc/impls/gamg/makefile #requirespackage

[petsc-dev] fortran modules and datatypes

2012-01-04 Thread Blaise Bourdin
Hi, Sorry for the potential double post. I posted from the wrong account. I am looking at many fortran90 examples which will only compile without fortran datatypes, like src/vec/is/examples/tutorial/ex1f90.F Is there a preprocessor variable indicating if petsc is compiled with fortran

[petsc-dev] XXXGetContext() in Fortran

2011-11-08 Thread Blaise Bourdin
On Nov 8, 2011, at 8:57 PM, Jed Brown wrote: We have bindings for this, but I can't find a way to make it work. I can pass a context into a function, but I can't get one back out with a subroutine call. F90 pointers are grotesque creatures that don't seem to be up to this task either, at

[petsc-dev] Problem mixing sieve and TS

2011-10-27 Thread Blaise Bourdin
On Wed, Oct 26, 2011 at 12:45, Blaise Bourdin bourdin at lsu.edu wrote: Any suggestion? FWIW, in this test, both the IJacobian matrix and RHS Vector are constant, but this will not be the case once in the future. Something else bugging me is that the Jacobian function does not seem

[petsc-dev] fortran binding for TSConvergedReason

2011-10-27 Thread Blaise Bourdin
Hi, Thanks for all the help in tracking our issue with TS... I think that there is a small problem with the auto binding for TSGetConvergedReason (both dev and 3.2). I added a call to TSGetConvergedReason after the TSSolve in ex22f.F and get the following result: (gdb) cont Continuing.

[petsc-dev] fortran binding for TSConvergedReason

2011-10-27 Thread Blaise Bourdin
Satish On Thu, 27 Oct 2011, Blaise Bourdin wrote: Hi, Thanks for all the help in tracking our issue with TS... I think that there is a small problem with the auto binding for TSGetConvergedReason (both dev and 3.2). I added a call to TSGetConvergedReason after the TSSolve in ex22f.F

[petsc-dev] fortran binding for TSConvergedReason

2011-10-27 Thread Blaise Bourdin
wrote: I just updated the tarball with an entry for TSGetConvergedReason [hence the rebuild request] Satish On Thu, 27 Oct 2011, Blaise Bourdin wrote: Satish, This is a brand new petsc configured and installed today using sowing 1.1.16c Blaise On Oct 27, 2011, at 2:57 PM

[petsc-dev] fortran binding for TSConvergedReason

2011-10-27 Thread Blaise Bourdin
:/home/balay/hg-repo/petsc-release-3.2 On Thu, 27 Oct 2011, Blaise Bourdin wrote: after deleting externalpackages/sow*, updating petsc and BuildSystem, reconfiguring, deleting src/ts/interface/ftn-auto/tsf.c, regenerating the fortran bindings, then rebuilding, I still get the same error

[petsc-dev] fortran binding for TSConvergedReason

2011-10-27 Thread Blaise Bourdin
It works, great. Any chance these changes will make their way in 3.2? Blaise On Oct 27, 2011, at 4:04 PM, Jed Brown wrote: On Thu, Oct 27, 2011 at 15:00, Blaise Bourdin bourdin at lsu.edu wrote: OK, so this time, I deleted externalpackages/sow* externalpackages/_d_sow* , $PETSC_ARCH

[petsc-dev] Problem mixing sieve and TS

2011-10-26 Thread Blaise Bourdin
Hi, We are slowly progressing in our attempt to use TS to solve evolution problems with our Sieve-based f90 unstructured element code, but are having a small problem. When we pass a DMMesh object to TSSetDM, we get the following error in TSSetup: [0]PETSC ERROR: DMCreateGlobalVector_Mesh()

[petsc-dev] undefined reference to `petscstack'

2011-06-28 Thread Blaise Bourdin
Hi, On a freshly pulled / reconfigured / rebuild version of petsc-dev, I get the following link error whenever I try to compile any example: /share/apps/mvapich2-1.6-ib-intel11.1/bin/mpicxx -lstdc++ -wd1572 -O3 -axSSE4.2 -Kc++ -o ex10 ex10.o

[petsc-dev] undefined reference to `petscstack'

2011-06-28 Thread Blaise Bourdin
with something optimized. 'petscstack' is only defined for debug builds. Matt On Tue, Jun 28, 2011 at 4:17 AM, Blaise Bourdin bourdin at lsu.edu wrote: Hi, On a freshly pulled / reconfigured / rebuild version of petsc-dev, I get the following link error whenever I try to compile any example

[petsc-dev] Fix for long-standing bug in DMMeshRestoreCoordinatesF90 and DMMeshRestoreElementsF90

2011-06-08 Thread Blaise Bourdin
Hi, After poking a bit, I found out the bug causing a segfault in the above-mentioned functions. It seems that gfortran will gladly nullify a bogus pointer, whereas ifort can be a bit pickier, hence the bug coming up only with intel compilers. Can you check that the following patch makes

[petsc-dev] preparing for a PETSc release

2011-05-10 Thread Blaise Bourdin
Barry, is there any way I can reproduce the bugs without going through all that crap? Let me see if I can build a Mesh from an exo file in C, and save it in a binary file, once MeshLoad is fixed, we can replicate the other bugs from there. Ok, let's try that. I am attaching 2

[petsc-dev] preparing for a PETSc release

2011-05-09 Thread Blaise Bourdin
Hi, There are still a bunch a sieve-related open issues (I realize that I email the tickets to petsc-maint and not petsc-dev) introduced when Mesh, DA and DM were consolidated, and after the XXXDestroy calling sequence was altered: - DMMeshView writes a text file, even when instructed to use a

[petsc-dev] preparing for a PETSc release

2011-05-09 Thread Blaise Bourdin
On May 9, 2011, at 4:03 PM, Jed Brown wrote: On Mon, May 9, 2011 at 22:53, Blaise Bourdin bourdin at lsu.edu wrote: How feasible would it be to mark all non-namespace names as deprecated until the next release but offer preprocessor macros in the meantime? This would buy everybody some

[petsc-dev] preparing for a PETSc release

2011-05-09 Thread Blaise Bourdin
On May 9, 2011, at 9:01 PM, Barry Smith wrote: On May 9, 2011, at 3:53 PM, Blaise Bourdin wrote: There are still a bunch a sieve-related open issues (I realize that I email the tickets to petsc-maint and not petsc-dev) introduced when Mesh, DA and DM were consolidated, and after

[petsc-dev] JSON library

2011-03-14 Thread Blaise Bourdin
On Mar 14, 2011, at 4:04 PM, Jed Brown wrote: I want to reiterate a statement I made a while back that any alternative input format really needs to support references. This is a good reason to prefer Yaml over JSON. Yaml is a superset of JSON, but offers a more readily human-readable

[petsc-dev] Recent changeset confuses the heck of intel compilers

2011-02-24 Thread Blaise Bourdin
Hi, Changeset f301815fc494cb333d15c0cefabf71a0988a0321 (rev 18363) seems to confuse the intel compilers (I tested 11.1 on linux x86_64 and mac OS X). After updating past this point, I get tons of warnings like drawv.c(397): warning #187: use of = where == may have been intended ierr =

[petsc-dev] Recent changeset confuses the heck of intel compilers

2011-02-24 Thread Blaise Bourdin
Jed, It's still not happy... Blaise On Feb 24, 2011, at 4:36 PM, Jed Brown wrote: On Thu, Feb 24, 2011 at 23:25, Blaise Bourdin bourdin at lsu.edu wrote: Changeset f301815fc494cb333d15c0cefabf71a0988a0321 (rev 18363) seems to confuse the intel compilers (I tested 11.1 on linux x86_64

[petsc-dev] Fortran 2003 enum

2010-12-08 Thread Blaise Bourdin
Hi, On Tue, Dec 7, 2010 at 20:05, Barry Smith bsmith at mcs.anl.gov wrote: In fact many of the Fortran manual bindings come from string issues. Why has this not been automated? I don't know the bfort source, but is it somehow fundamentally hard? It is not fundamentally hard, just a

[petsc-dev] Fortran 2003 enum

2010-12-07 Thread Blaise Bourdin
On Dec 7, 2010, at 11:34 AM, Jed Brown wrote: On Tue, Dec 7, 2010 at 18:24, Matthew Knepley knepley at gmail.com wrote: It is present and mandated to be interoperable with C enums. Blaise pointed this out to me. Do any compilers at MCS support this? Gfortran got it in version 4.1, I

[petsc-dev] PetscCheck__FUNCT__ and PETSC_FUNCTION_NAME

2010-10-07 Thread Blaise Bourdin
Hi, As of changeset 16818, it looks like PetscFunctionBegin checks for consistency of PETSC_FUNCTION_NAME (which is set in $PETSC_ARCH/include/petscconf.h to __func__ ) and __FUNCT__, which is user set This is a problem when __FUNCT__ as been set purposely (or not) to not match __func__ Tao,

[petsc-dev] [petsc4py] PETSc.Viewer().createHDF5 wipes out existing files

2010-09-09 Thread Blaise Bourdin
Hi, I am trying to do HDF5 IO in petsc4py. I noticed that when I create a viewer using PETSc.Viewer().createHDF5(inputfile,comm= PETSc.COMM_WORLD) the file outputfile is wiped out and replaced with a empty hdf5 container, which is bad since I am trying to read forrm it... Unsurprisingly, I