[Libmesh-devel] Nemesis Appending not working?

2019-05-22 Thread Cody Permann
So we have a user that wants to try to start using the "recover" capability in MOOSE to resume a long running simulation on the clusters. This particular simulation is very large and the user is using nemesis output. I was suprised to see that we don't have any nemesis appending tests in all of MOO

Re: [Libmesh-devel] isEvaluable on DOFs?

2016-12-02 Thread Cody Permann
rtain moving the optional construction and maintenance of that data structure to libMesh? Cody > On Thu, 1 Dec 2016, Cody Permann wrote: > > > I'm starting to use the new Elem::isEvaluable() method available in > libMesh. It seems like it would be handy to promote this method u

[Libmesh-devel] isEvaluable on DOFs?

2016-12-01 Thread Cody Permann
I'm starting to use the new Elem::isEvaluable() method available in libMesh. It seems like it would be handy to promote this method up to DofObject though so it could be used with Node. If I understand correctly, a node "should" be evaluable if it's attached to any element that's evaluable so this

Re: [Libmesh-devel] New redirect option in libMesh

2016-08-24 Thread Cody Permann
:08 PM John Peterson wrote: > On Wed, Aug 24, 2016 at 9:02 AM, Cody Permann > wrote: > >> I'd like to propose a new stream redirect/suppress option or perhaps just >> expand the existing option in libMesh. >> >> Motivation: >> Our regression te

[Libmesh-devel] New redirect option in libMesh

2016-08-24 Thread Cody Permann
I'd like to propose a new stream redirect/suppress option or perhaps just expand the existing option in libMesh. Motivation: Our regression testing system has long struggled with the proper way to handle interleaved output due to multiple processors triggering expected errors in application code a

Re: [Libmesh-devel] PDESoft 2016 Coding Days?

2016-04-07 Thread Cody Permann
I'm not on the PETSc list so thanks for sharing. I wouldn't mind seeing MOOSE represented at this conference too (along with libMesh). I'll chat with my management and see if we can get one of our guys out there. Cody On Thu, Apr 7, 2016 at 12:36 PM Paul T. Bauman wrote: > Everyone probably saw

Re: [Libmesh-devel] Horked Up Double-checked Lock

2016-03-30 Thread Cody Permann
We aren't building C++11 yet on the build boxes so I guess that's why it appears fine. Also, our users are still defaulting to C++03 so yeah, nobody would be hitting this bug except for devs and we don't exercise threading too often in our day to day work. On Wed, Mar 30, 2016 at 10:01 AM Derek Ga

Re: [Libmesh-devel] Rename Mesh Classes

2016-03-10 Thread Cody Permann
I'm an AdvancedUser. I went to College such and such. I think I should use AdvancedMesh! On Thu, Mar 10, 2016 at 12:31 PM John Peterson wrote: > On Thu, Mar 10, 2016 at 11:44 AM, Derek Gaston wrote: > >> I do really think the classes should be renamed. Coming from the outside >> I would totall

Re: [Libmesh-devel] Rename Mesh Classes

2016-03-10 Thread Cody Permann
ng to scale a mesh with a thousand elements to several dozen processors... I have this link bookmarked for that case: http://www.mcs.anl.gov/petsc/documentation/faq.html#slowerparallel We need the same thing for when to use one mesh type over the other. Cody On Thu, Mar 10, 2016 at 10:56 AM Co

Re: [Libmesh-devel] Rename Mesh Classes

2016-03-10 Thread Cody Permann
On Thu, Mar 10, 2016 at 10:07 AM Derek Gaston wrote: > Backwards compatibility is trivial... a typedef will work... > > lol... you've been watching too much Walking Dead! > > Any other suggestions? > > SerialMesh -> MemoryWastingMesh > +1 > ParallelMesh -> TimeWastingMesh > +1 > ? > > Those reall

Re: [Libmesh-devel] More Ghosting

2016-03-06 Thread Cody Permann
It may be worth asking what you are trying to do. ;) So far I've been able to figure out everything I've ever needed to do for this grain tracker with s single layer and a little more communication. On Sun, Mar 6, 2016 at 12:22 PM Derek Gaston wrote: > I have a need for arbitrary numbers of layer

Re: [Libmesh-devel] Intree Broken?

2016-02-23 Thread Cody Permann
Are you using the --disable-maintainer flag? I think that's all you need. On Tue, Feb 23, 2016 at 8:09 PM David Knezevic wrote: > On Tue, Feb 23, 2016 at 10:01 PM, Derek Gaston wrote: > >> I'm guessing that the latest rounds of updating automake related tools >> killed intree compiling. This is

[Libmesh-devel] Interesting Observation

2016-01-29 Thread Cody Permann
So I'm working on incorporating the new packed range methods into MOOSE for use in transferring raw byte strings containing user-defined state and ran into an issue that I wanted to share. As a start I've taken the example code that Roy created in the new packed_range unit tests, which is fairly cl

Re: [Libmesh-devel] libMesh Performance Issue

2015-10-28 Thread Cody Permann
way to small to be of any real value, but we have ideas of making timing more useful: http://mooseframework.org/docs/timing/ If you make a PR, you should immediately see it NOT fail due to timeout. On Wed, Oct 28, 2015 at 11:47 AM Roy Stogner wrote: > > On Tue, 27 Oct 2015, Cody Perman

Re: [Libmesh-devel] libMesh Performance Issue

2015-10-27 Thread Cody Permann
on exactly how he's engineered it but if you just open up the mesh file for that test you'll see that one 3d block is completely in contact (actually penetrating) with another large 3d block meaning we have a lot of ghosting to do. Cody On Mon, Oct 26, 2015 at 3:12 PM Cody Permann wr

Re: [Libmesh-devel] libMesh Performance Issue

2015-10-26 Thread Cody Permann
> > On Mon, 26 Oct 2015, Cody Permann wrote: > > > I just pulled the latest libMesh head and saw a serious performance > penalty that I narrowed down to 445b1c3 with John's help. We've had this > test > > for several years and it's been relatively stable. It&#

[Libmesh-devel] libMesh Performance Issue

2015-10-26 Thread Cody Permann
I just pulled the latest libMesh head and saw a serious performance penalty that I narrowed down to 445b1c3 with John's help. We've had this test for several years and it's been relatively stable. It's two overlapping structured 3D grids, one slightly embedded inside of the other. We are testing fo

[Libmesh-devel] Garbage characters in Exodus string fields

2015-03-11 Thread Cody Permann
Has anyone using libMesh seen invalid characters in string files output in the Exodus files? I'm seeing strings like this in several of our output files (output is from "ncdump") name_glo_var = "integral\000\340\000\000\277\367\220\276\f\"\203\254\277\367\220\276\f\"b>" ; Clearly there is ga

[Libmesh-devel] Linguist enhancement

2014-10-17 Thread Cody Permann
Finally a little control... Both libMesh and MOOSE can benefit from this: https://github.com/github/linguist#overrides Sent from my evil iPad-- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/M

Re: [Libmesh-devel] Possible Valgrind issue

2014-07-08 Thread Cody Permann
John, just so you are up to speed Jason has reproduced this result on "rod", "cone" and "hpcbuild4" in addition to the original failure on "hpcbuild5", you just need to add that new flag so it's definitely popping up on multiple systems now. Roy's theory is interesting but I'm surprised that we ar

Re: [Libmesh-devel] Possible Valgrind issue

2014-07-08 Thread Cody Permann
compiler bug since I still can't see what is wrong with that method. That means that I have a workaround for running our Valgrind tests but since we only recently added that option, I can't easily find if or when that problem was introduced - yikes! Cody On Mon, Jul 7, 2014 at 1:41 PM, Co

Re: [Libmesh-devel] Possible Valgrind issue

2014-07-07 Thread Cody Permann
ue-id --disable-warnings --disable-cxx11 --enable-openmp --enable-shared --disable-static On Mon, Jul 7, 2014 at 11:59 AM, Cody Permann wrote: > Devs, > > We updated the MOOSE users to a new revision of libMesh last week and > picked up a Valgrind error in the process. John spent a g

[Libmesh-devel] Possible Valgrind issue

2014-07-07 Thread Cody Permann
Devs, We updated the MOOSE users to a new revision of libMesh last week and picked up a Valgrind error in the process. John spent a good portion of the day on Thursday just trying to reproduce it on one of our development Linux boxes without success. Towards the end of the day he finally logged in

Re: [Libmesh-devel] Compiler warnings

2013-12-09 Thread Cody Permann
I'll vote "for" on dbg/devel modes. At least until things are cleaned up. Cody On Sun, Dec 8, 2013 at 9:07 PM, Roy Stogner wrote: > > On Sun, 8 Dec 2013, Derek Gaston wrote: > > > I guess I'll vote against adding this to opt: but it's not a strong vote. > > My vote "for" isn't a strong vote, e

Re: [Libmesh-devel] intro_ex1 error?

2013-11-19 Thread Cody Permann
This is related to the bug Roy, John and I were discussing yesterday. Cody Sent from my iPhone > On Nov 19, 2013, at 7:52 AM, "Kirk, Benjamin (JSC-EG311)" > wrote: > > I'm getting a rash of these failures on HEAD: > > *** > * Running

Re: [Libmesh-devel] Warning after recent change in xdr?

2013-11-18 Thread Cody Permann
Go ahead - I'm at SC and probably won't be sitting here much longer... Plus I'm on an underpowered laptop. Thanks! Cody On Mon, Nov 18, 2013 at 5:03 PM, Roy Stogner wrote: > > On Mon, 18 Nov 2013, John Peterson wrote: > > > Not really sure what the context for the change originally was... > > F

Re: [Libmesh-devel] Output Memory Usage

2013-11-12 Thread Cody Permann
Here's a plot after applying John's "avoid serializing to all processes" patch: https://drive.google.com/file/d/0B8csupg5nQaaVVpOUFRHZ0FJX28/edit?usp=sharing Cody On Mon, Nov 11, 2013 at 4:30 PM, Derek Gaston wrote: > On Mon, Nov 11, 2013 at 5:23 PM, Cody Permann wr

Re: [Libmesh-devel] Output Memory Usage

2013-11-11 Thread Cody Permann
On Mon, Nov 11, 2013 at 3:51 PM, Derek Gaston wrote: > I've mentioned this a few times in passing - but now I have concrete > evidence: Outputting the solution takes a TON of memory... way more than it > should. This is something we've seen for a very long time - and it's one > of the main reaso

Re: [Libmesh-devel] Partition pictures

2013-11-07 Thread Cody Permann
t; definitely worse than others > > The metis stuff: wow! > > There are options that can get passed into the partitioner, and we are > leaving them as defaults. Probably worth playing with some of those… > > -Ben > > > > On Nov 7, 2013, at 3:34 PM, Cody Permann >

[Libmesh-devel] Partition pictures

2013-11-07 Thread Cody Permann
I'm seeing some less than optimal partitioning for several processor counts using both Metis and Hilbert SFC. Also from what I can tell, Morton SFC is completely broken. I realize that I'm splitting a small mesh among a lot of processors, but the behavior is still pretty bad. The following pictu

Re: [Libmesh-devel] XDA Node/Element Numbering

2013-11-07 Thread Cody Permann
On Thu, Nov 7, 2013 at 8:36 AM, Kirk, Benjamin (JSC-EG311) < benjamin.k...@nasa.gov> wrote: > On Nov 7, 2013, at 9:13 AM, Derek Gaston > wrote: > > > I understand what you're saying - but the current format is so very > close to what I actually currently need. If it had element and node ids in

Re: [Libmesh-devel] XDA Node/Element Numbering

2013-11-06 Thread Cody Permann
On Wed, Nov 6, 2013 at 6:36 PM, Kirk, Benjamin (JSC-EG311) < benjamin.k...@nasa.gov> wrote: > > On Nov 6, 2013, at 6:42 PM, "Kirk, Benjamin (JSC-EG311)" < > benjamin.k...@nasa.gov> > wrote: > > >> > >> Unfortunately this has thrown an enormous monkey wrench into my current > project (doing perfec

[Libmesh-devel] Existing XDA bug

2013-11-05 Thread Cody Permann
Developers, I found a bug in the existing (old) XDA format while trying to add one more feature yesterday. It turns out that if you create a mesh without any sidesets and write it in XDA format. You trip an assertion when reading that mesh back in. The problem is that there is short-circuit cod

Re: [Libmesh-devel] Metis memory usage

2013-11-01 Thread Cody Permann
John, Did you and David make any more headway on the "Judy Array" C++ wrappers? http://judy.sourceforge.net On Fri, Nov 1, 2013 at 1:54 PM, John Peterson wrote: > > > > On Fri, Nov 1, 2013 at 11:59 AM, John Peterson wrote: > >> >> >> >> On Fri, Nov 1, 2013 at 11:54 AM, Kirk, Benjamin (JSC-EG311

Re: [Libmesh-devel] Metis memory usage

2013-11-01 Thread Cody Permann
On Fri, Nov 1, 2013 at 1:28 PM, John Peterson wrote: > > > > On Fri, Nov 1, 2013 at 11:50 AM, Roy Stogner wrote: > >> >> On Fri, 1 Nov 2013, John Peterson wrote: >> >> unordered_map ends up somewhere between vector and map in terms of >>> memory usage. >>> >>> https://drive.google.com/file/**d/0

Re: [Libmesh-devel] Metis memory usage

2013-11-01 Thread Cody Permann
Oops! I'm sure the label on the left is supposed to be in Megabytes. I forgot to make that Kilobyte adjustment when I simplified the scaling logic yesterday. I'll fix that up and get it checked back in :-) Cody Sent from my iPhone On Nov 1, 2013, at 12:37 PM, John Peterson wrote: On Fri,

Re: [Libmesh-devel] Metis memory usage

2013-10-30 Thread Cody Permann
Wow, If this does indeed fix the issue, then I can think of a lot of memory hog areas in MOOSE that we might have to cleanup sooner rather than later. I hope the overhead of the tree doesn't dominate the value_type stored so much that it blows us up our total usage by 200%! On the other hand size

Re: [Libmesh-devel] [Libmesh-users] Fwd: Memory usage in 3D mesh generation

2013-10-30 Thread Cody Permann
On Wed, Oct 30, 2013 at 9:08 AM, Kirk, Benjamin (JSC-EG311) < benjamin.k...@nasa.gov> wrote: > On Oct 30, 2013, at 10:03 AM, Cody Permann > wrote: > > > Very interesting, we are all about making sensible default choices for > our users. We might make MOOSE default t

Re: [Libmesh-devel] [Libmesh-users] Fwd: Memory usage in 3D mesh generation

2013-10-30 Thread Cody Permann
Very interesting, we are all about making sensible default choices for our users. We might make MOOSE default to sfc_hilbert for meshes built with the internal generator. At least until we figure out how to make Metis/Parmetis work better. I can't even come close to getting this problem to run o

Re: [Libmesh-devel] [Libmesh-users] Fwd: Memory usage in 3D mesh generation

2013-10-30 Thread Cody Permann
On Tue, Oct 29, 2013 at 3:17 PM, Kirk, Benjamin (JSC-EG311) < benjamin.k...@nasa.gov> wrote: > If forced to choose one of those options for a cube, though, I'd suggest > the SFC option. > > -Ben > > Thanks Ben! I wasn't even aware of that Partitioner. I just tried it on my very large 3D cube d

[Libmesh-devel] USNCCM13

2013-07-17 Thread Cody Permann
I'm going to the Computational Mechanics conference in Raleigh, NC next week. Are any of the libMesh developers going? Cody -- See everything from the browser to the database with AppDynamics Get end-to-end visibility wit

Re: [Libmesh-devel] Potential Centroid-Partitioner Bug

2013-07-09 Thread Cody Permann
9, 2013, at 12:40 PM, Cody Permann wrote: > > > While I'm on the subject of partitioners, does anyone know of a way to > make the Metis partitioner less sporadic in moving the partitions around? > With each time step of this PF simulation, the set of elements owned by a >

[Libmesh-devel] Potential Centroid-Partitioner Bug

2013-07-09 Thread Cody Permann
I'm running a phase-field simulation with adaptivity and decided to use the centroid partitioner instead of the default partitioner (Metis for serial mesh?) for reasons I'll explain in a moment. Unfortunately, I'm triggering a segfault, but so far it's been rather difficult to hit. I've run the s

Re: [Libmesh-devel] Pthread Periodic Boundary Issue

2013-07-08 Thread Cody Permann
Sent from my iPhone On Jul 8, 2013, at 9:28 PM, Roy Stogner wrote: > > On Mon, 8 Jul 2013, Derek Gaston wrote: > >> It appears that something is wrong in there (or we're missing a lock >> somewhere). Here is what happens in optimized mode: >> PeriodicBoundaries point locator object returned NUL

[Libmesh-devel] Need extra data in XDA

2013-06-27 Thread Cody Permann
Gentlemen, We need to get the named entities on the mesh saved to the XDA format for the purpose of restart. There are only three maps in mesh_base.h and boundary_info.h (shown below) that need to be written and read through the XDA reader/writer. I was going to put this in a long time ago, but J

Re: [Libmesh-devel] 0.9.2

2013-06-13 Thread Cody Permann
Any update as to where 0.9.2 is at? Cody -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ Libmesh-devel mailing li

[Libmesh-devel] Mesh Partitioning and Stitching

2013-06-05 Thread Cody Permann
I have a question about the whole mesh bootstrap procedure as I track down an issue that Derek and I bumped into when tiling and stitching meshes a few weeks back. We are starting to grow utilities to programmatically build meshes for our simulations on the fly out of several primitives like build

Re: [Libmesh-devel] libMesh 0.9.0 Release Candidate 1

2013-04-23 Thread Cody Permann
So are there any more outstanding issues for the 0.9.1 release? Just trying to get an idea of when it'll be available. We are going to deploy this version to our users instead of wherever HEAD is at. Thanks, Cody On Mon, Apr 22, 2013 at 8:53 AM, Cody Permann wrote: > Roy, > >

Re: [Libmesh-devel] libMesh 0.9.0 Release Candidate 1

2013-04-22 Thread Cody Permann
Roy, RC1 passed all of our tests in MOOSE. Thanks, Cody On Fri, Apr 19, 2013 at 4:54 PM, Roy Stogner wrote: > > Release candidate 1 of libMesh version 0.9.1 is now available: > http://sourceforge.net/projects/libmesh/files/libmesh/libmesh-0.9.1-rc1/ > > Testing before we make a 0.9.1 final rel

[Libmesh-devel] Simple question

2013-04-12 Thread Cody Permann
I just noticed that FE::get_normals(), get_tangents() and other related methods in that class return vectors of "Points". Any desire to change these return types to VectorValue types? Just curious, Cody -- Precog is a nex

Re: [Libmesh-devel] Automatically git fetch github pull requests

2013-04-08 Thread Cody Permann
Sent from my evil iPad On Apr 8, 2013, at 8:14 PM, Jed Brown wrote: > Cody Permann writes: > >> Ah close - looks like I need 'git pull --prune'! > > I guess I don't know what you're looking for. You want to prune the > remote tracking branch wh

Re: [Libmesh-devel] Automatically git fetch github pull requests

2013-04-08 Thread Cody Permann
On Mon, Apr 8, 2013 at 7:54 PM, Jed Brown wrote: > Cody Permann writes: > > > Nice! Now I just need to figure out how to filter out closed requests. > My > > "git branch -av" command is a mess now :) > > Are you looking for 'git fetch --prune&#

Re: [Libmesh-devel] Automatically git fetch github pull requests

2013-04-08 Thread Cody Permann
Nice! Now I just need to figure out how to filter out closed requests. My "git branch -av" command is a mess now :) Cody On Mon, Apr 8, 2013 at 5:00 PM, Derek Gaston wrote: > Very cool! Nice tip! > > Derek > > > On Mon, Apr 8, 2013 at 4:55 PM, Roy Stogner wrote: > >> >> I may be the last to

[Libmesh-devel] Examples can't be compiled in "oprof" mode

2013-04-06 Thread Cody Permann
I just noticed that the installed Make.common file is missing the logic for setting the METHOD appropriately for oprof when compiling the examples. Should be a quick fix. Cody -- Minimize network downtime and maximize tea

Re: [Libmesh-devel] Broadcasting boundary/subdomain names

2013-04-05 Thread Cody Permann
Alright gents, I'm finally getting back to this task. We kinda need this now since we are running large jobs quite regularly and reading the mesh on every processor is not making our I/O system happy. I know that Derek had just stopped using "boundary names" so that we could just revert back to t

Re: [Libmesh-devel] [Libmesh-users] Has anyone tripped this error?

2013-04-02 Thread Cody Permann
On Tue, Apr 2, 2013 at 4:42 PM, Kirk, Benjamin (JSC-EG311) < benjamin.kir...@nasa.gov> wrote: > On Apr 2, 2013, at 5:22 PM, Cody Permann wrote: > > > > > RemoteElem should be being created from LibMeshInit (see the > Singleton::create() call and related bits in remote_

Re: [Libmesh-devel] one step short of beautify...

2013-04-02 Thread Cody Permann
On Tue, Apr 2, 2013 at 4:19 PM, Kirk, Benjamin (JSC-EG311) < benjamin.kir...@nasa.gov> wrote: > You've got that as a git hook? > > Not quite - we just have that little one-liner hanging around on our "tips" page for developers to run to clean stuff up. Our svn-hook is basically the same thing (i.

Re: [Libmesh-devel] [Libmesh-users] Has anyone tripped this error?

2013-04-02 Thread Cody Permann
On Tue, Apr 2, 2013 at 3:22 PM, Cody Permann wrote: > Trying this now... > Cody > > > > On Tue, Apr 2, 2013 at 3:17 PM, Kirk, Benjamin (JSC-EG311) < > benjamin.kir...@nasa.gov> wrote: > >> On Apr 2, 2013, at 4:12 PM, "Kirk, Benjamin (JSC-EG3

Re: [Libmesh-devel] [Libmesh-users] Has anyone tripped this error?

2013-04-02 Thread Cody Permann
Trying this now... Cody On Tue, Apr 2, 2013 at 3:17 PM, Kirk, Benjamin (JSC-EG311) < benjamin.kir...@nasa.gov> wrote: > On Apr 2, 2013, at 4:12 PM, "Kirk, Benjamin (JSC-EG311)" < > benjamin.kir...@nasa.gov> wrote: > > > RemoteElem should be being created from LibMeshInit (see the > Singleton::cr

Re: [Libmesh-devel] one step short of beautify...

2013-04-02 Thread Cody Permann
Haha - it seems like we've done whitespace cleanup before and it's already a mess again! Perhaps you should seriously consider taking the more draconian approach like we have and rejecting all commits containing whitespace! There's nothing funnier then watching Derek prepare a huge patch for MOOS

Re: [Libmesh-devel] exodusII_int.h

2013-04-01 Thread Cody Permann
Hmm - I like that idea! Should we make it an option since 99% of our users don't need it? Cody On Mon, Apr 1, 2013 at 10:29 AM, Kirk, Benjamin (JSC-EG311) < benjamin.kir...@nasa.gov> wrote: > On Apr 1, 2013, at 11:20 AM, John Peterson wrote: > > > I think there is probably a sanctioned manner

Re: [Libmesh-devel] exodusII_int.h

2013-04-01 Thread Cody Permann
: > On Apr 1, 2013, at 9:53 AM, Cody Permann wrote: > > > We have a user that is using exo_jack.c (part of the FORTRAN bindings > for exodus) but we are missing a header file in the installed version of > libmesh. I haven't really dug around but is there a reason that we a

[Libmesh-devel] exodusII_int.h

2013-04-01 Thread Cody Permann
We have a user that is using exo_jack.c (part of the FORTRAN bindings for exodus) but we are missing a header file in the installed version of libmesh. I haven't really dug around but is there a reason that we aren't adding exodusII_int.h to the installed include directory? Thanks, Cody -

Re: [Libmesh-devel] Compilation Error with Intel Compiler

2013-03-22 Thread Cody Permann
Sent from my iPhone On Mar 22, 2013, at 9:10 AM, Robert wrote: > Hello, > > I am trying to build current master git version of libMesh with the Intel C++ > Compiler (icpc (ICC) 11.0 20081105) > > CXX src/partitioning/libmesh_dbg_la-centroid_partitioner.lo > ../src/src/partitioning/centroid

Re: [Libmesh-devel] [Libmesh-users] Hanging Job (down in PETSc?)

2013-02-26 Thread Cody Permann
Cody On Thu, Jan 24, 2013 at 8:25 AM, Cody Permann wrote: > > > > On Thu, Jan 24, 2013 at 8:00 AM, Dmitry Karpeev wrote: > >> >> >> On Wed, Jan 23, 2013 at 9:41 PM, Cody Permann wrote: >> >>> On Wed, Jan 23, 2013 at 11:05 AM, Kirk, Benjamin (JSC-EG3

Re: [Libmesh-devel] Broadcasting boundary/subdomain names

2013-02-13 Thread Cody Permann
On Wed, Feb 13, 2013 at 1:27 PM, Roy Stogner wrote: > > On Wed, 13 Feb 2013, Cody Permann wrote: > > So I'd be happy to work on this unless someone else wants to >> volunteer. Clearly we'll need a pack this data up since the strings >> will be variable length

[Libmesh-devel] Broadcasting boundary/subdomain names

2013-02-13 Thread Cody Permann
One of the things (maybe the only thing) that we are missing when broadcasting the mesh are the boundary/subdomain names which are stored in boundary_info. Namely these two guys: std::map _ss_id_to_name; std::map _ns_id_to_name; I have only myself to blame since I originally added these data stru

Re: [Libmesh-devel] Fwd: Build Error

2013-02-12 Thread Cody Permann
On Tue, Feb 12, 2013 at 1:23 PM, Kirk, Benjamin (JSC-EG311) < benjamin.kir...@nasa.gov> wrote: > > On Feb 12, 2013, at 2:13 PM, Cody Permann wrote: > > > We have a number of tests that have started failing that use several > hundred subdomains. I haven't dived int

Re: [Libmesh-devel] Fwd: Build Error

2013-02-12 Thread Cody Permann
Here's another "new" error when using the new contribs: Exodus Library Error: [ex_put_block] Error: failed to define number of nodes/entity for element block 507 in file id 131072 [-41] netcdf constraint NC_MAX_DIMS exceeded Error writing element block. Stack frames: 14 0: 0 libmesh_dbg.0.dyli

Re: [Libmesh-devel] build*/contrib/bin/libmesh-config misses include paths in build directory

2013-02-09 Thread Cody Permann
Sent from my iPhone On Feb 9, 2013, at 7:56 PM, Derek Gaston wrote: On Sat, Feb 9, 2013 at 11:53 AM, Kirk, Benjamin (JSC-EG311) < benjamin.kir...@nasa.gov> wrote: > Yeah Derek, I'm in winter park this weekend. > Nice! We should put together a libMesh conference / ski weekend sometime ;-) >

Re: [Libmesh-devel] PROP: Prefer Rebase Over Pull

2013-02-05 Thread Cody Permann
On Mon, Feb 4, 2013 at 9:58 PM, Derek Gaston wrote: > Yes, I just made up that acronym, but I like it. ;-) > > I thought I would bring this discussion (that some of us were having on my > recent Pull Request) to the list. > > If you haven't been following the GitHub conversation... I made an > o

Re: [Libmesh-devel] nemesis regression tests

2013-02-04 Thread Cody Permann
Sent from my iPhone On Feb 4, 2013, at 5:45 PM, "Kirk, Benjamin (JSC-EG311)" wrote: > > On Feb 4, 2013, at 4:33 PM, John Peterson wrote: > >> We have one that is enabled if you build libmesh with ParallelMesh support, >> and it appears to be "green" right now. >> >> I admit I have not been bui

[Libmesh-devel] build_extrusion

2013-01-29 Thread Cody Permann
So I'm finally getting around to replacing our mesh extruder class with the libMesh implementation. It's always nice to delete duplicate code :) In switching things over, I noticed that there were two things that our extruder class does that the implementation in libMesh does not. The first is t

Re: [Libmesh-devel] Our GetPot now supports include directives

2013-01-23 Thread Cody Permann
On Wed, Jan 23, 2013 at 4:27 PM, Roy Stogner wrote: > > Hm... I'd be tempted to add this to our contrib/, after I think about > a few small worries: > > It's not header-only, whereas I'd like to keep getpot.h header-only > for use in non-libMesh projects, so I'd have to add some more "here's > wha

Re: [Libmesh-devel] Should GetPot throw an error when it can't open a file?

2013-01-23 Thread Cody Permann
On Wed, Jan 23, 2013 at 1:09 PM, Roy Stogner wrote: > > I'm making some changes to our fork of GetPot at the moment, most of > which are backwards compatible, but one of which might not be: > > I just noticed that when you try to get a GetPot object to parse a > non-existent file, it doesn't give

[Libmesh-devel] --enable-fpe

2013-01-14 Thread Cody Permann
Roy, It appears that the enableFPE() function is currently hidden from the outside world. I noticed that it can be triggered with a handy command line option but it would be nice if we could call it from within our framework. Would you mind if I adjust the interface to make it so? Thanks, Cody

Re: [Libmesh-devel] Regular Expressions

2013-01-10 Thread Cody Permann
On Fri, Jan 4, 2013 at 10:05 AM, Kirk, Benjamin (JSC-EG311) < benjamin.kir...@nasa.gov> wrote: > On Jan 4, 2013, at 11:00 AM, Cody Permann wrote: > > > Yes a very decent idea, however would we attempt to distribute > boost::regex with libMesh? I haven't looked a

Re: [Libmesh-devel] Regular Expressions

2013-01-04 Thread Cody Permann
On Fri, Jan 4, 2013 at 9:51 AM, Kirk, Benjamin (JSC-EG311) < benjamin.kir...@nasa.gov> wrote: > On Jan 4, 2013, at 10:41 AM, Cody Permann wrote: > > > Bottom line: Do any of you have any experience with how widespread and > reliable the standard regex library is on a wi

[Libmesh-devel] Regular Expressions

2013-01-04 Thread Cody Permann
I wanted to poll the libMesh developers for ideas on using regular expressions in a libMesh derived code (i.e. MOOSE). I realize that regular expressions are about as far away from FE as you can get but the library contains so many other handy configure detection routines for things like threads a

Re: [Libmesh-devel] Compile error in libmesh automake branch

2012-11-07 Thread Cody Permann
Sent from my iPhone On Nov 7, 2012, at 4:04 PM, "Paul T. Bauman" wrote: On Wed, Nov 7, 2012 at 4:50 PM, Paul T. Bauman wrote: > On Wed, Nov 7, 2012 at 4:40 PM, John Peterson wrote: > > >> .) On the automake branch, I still get the (system-level) segfaults with >> my hand-built compilers. >>

Re: [Libmesh-devel] OS X Compilers

2012-10-31 Thread Cody Permann
Ben, Are you able to run all of the libMesh examples (automake branch) with GNU GCC on your mac? I've been chatting with Paul and he mentioned that misc_ex6 seg faults (which we have confirmed here), but we are also seeing a similar problem with adjoints_ex1. These problems aren't unique to the

Re: [Libmesh-devel] Parallel::broadcast(std::vector) ??

2012-10-30 Thread Cody Permann
On Tue, Oct 30, 2012 at 6:06 AM, Kirk, Benjamin (JSC-EG311) < benjamin.kir...@nasa.gov> wrote: > A simple but less elegant solution would be to pack two contiguous arrays > - one of the string lengths in an integer vector and another of all the > strings concatenated into a vector and broadcast bo

Re: [Libmesh-devel] OS X Compilers

2012-10-29 Thread Cody Permann
On Mon, Oct 29, 2012 at 9:51 AM, Kirk, Benjamin (JSC-EG311) < benjamin.kir...@nasa.gov> wrote: > > On Oct 22, 2012, at 11:05 AM, Cody Permann wrote: > > > > > I like the "include both, selectable at configure-time" option best, > > if it's not to

Re: [Libmesh-devel] Next release

2012-10-25 Thread Cody Permann
Ah, yes my mistake. I didn't mean Makefile, but I think you all figured out what I meant. Just wanted to maintain old behavior as much as possible from the user perspective. I don't particularly have any strong opinions on exactly how we generate those files (something akin to our current bootstr

Re: [Libmesh-devel] Next release

2012-10-25 Thread Cody Permann
On Oct 25, 2012, at 4:10 PM, Roy Stogner wrote: > > On Thu, 25 Oct 2012, Kirk, Benjamin (JSC-EG311) wrote: > >> Im thrilled with all the recent trunk activity, and I've got some >> major changes id like to implement soon, but first - anything >> outstanding before we create a new release? > > If

Re: [Libmesh-devel] Compiler Fiasco Upate

2012-10-25 Thread Cody Permann
! > > > > On Oct 22, 2012, at 4:00 PM, "Cody Permann" wrote: > > > > On Mon, Oct 22, 2012 at 4:50 PM, Paul T. Bauman wrote: > >> Sorry I haven't been able to be more helpful in reproducing the errors. >> Is the pretty much settled at this poi

Re: [Libmesh-devel] Compiler Fiasco Upate

2012-10-24 Thread Cody Permann
Alright, My fparser patch is now in HEAD. --with-fparser=release (default) --with-fparser=devel --with-fparser=none Hopefully this will satisfy all :) Cody On Wed, Oct 24, 2012 at 11:02 AM, Roy Stogner wrote: > > On Wed, 24 Oct 2012, Derek Gaston wrote: > > > Between license incompatibility an

Re: [Libmesh-devel] Compiler Fiasco Upate

2012-10-24 Thread Cody Permann
Looks good - please commit Cody On Wed, Oct 24, 2012 at 8:10 AM, Cody Permann wrote: > I'll check it out and let you know. > > > On Wed, Oct 24, 2012 at 7:37 AM, Paul T. Bauman wrote: > >> On Tue, Oct 23, 2012 at 10:20 PM, Paul T. Bauman wrote: >> >>>

Re: [Libmesh-devel] Compiler Fiasco Upate

2012-10-24 Thread Cody Permann
I'll check it out and let you know. On Wed, Oct 24, 2012 at 7:37 AM, Paul T. Bauman wrote: > On Tue, Oct 23, 2012 at 10:20 PM, Paul T. Bauman wrote: > >> Actually, check that. That patch was not the right way to do this. Will >> post an updated version soon. Instead of just checking if we're on

Re: [Libmesh-devel] Compiler Fiasco Upate

2012-10-23 Thread Cody Permann
I vote that we stop the license war. I plan to satisfy all requirements with my fparser patch tomorrow. :-) cheers Sent from my iPhone On Oct 23, 2012, at 5:43 PM, Derek Gaston wrote: On Tue, Oct 23, 2012 at 5:21 PM, Roy Stogner wrote: > > The whole reason the GPL was created was to protect p

Re: [Libmesh-devel] Nemesis regressions?

2012-10-23 Thread Cody Permann
Works great - thanks! On Tue, Oct 23, 2012 at 1:44 PM, Cody Permann wrote: > Great - I'll give it a shot! > > > On Tue, Oct 23, 2012 at 1:41 PM, Roy Stogner wrote: > >> >> On Fri, 14 Sep 2012, Cody Permann wrote: >> >> Well, it turns out that

Re: [Libmesh-devel] Nemesis regressions?

2012-10-23 Thread Cody Permann
Great - I'll give it a shot! On Tue, Oct 23, 2012 at 1:41 PM, Roy Stogner wrote: > > On Fri, 14 Sep 2012, Cody Permann wrote: > > Well, it turns out that this issue is rather difficult to find, but >> super easy to replicate! I'm using introduction_ex1 to locate t

Re: [Libmesh-devel] Compiler Fiasco Upate

2012-10-23 Thread Cody Permann
-- Forwarded message -- From: Roy Stogner Date: Tue, Oct 23, 2012 at 1:00 PM Subject: Re: [Libmesh-devel] Compiler Fiasco Upate To: Derek Gaston Cc: Cody Permann , libmesh-devel@lists.sourceforge.net On Tue, 23 Oct 2012, Derek Gaston wrote: _We_ don't have to distribute

Re: [Libmesh-devel] Compiler Fiasco Upate

2012-10-23 Thread Cody Permann
On Tue, Oct 23, 2012 at 11:08 AM, Roy Stogner wrote: > > On Tue, 23 Oct 2012, Cody Permann wrote: > > So I just sent the patch to John and he wasn't very crazy about the >> whole direction as he reviewed my patch. I made the arbitrary >> decision to turn off

Re: [Libmesh-devel] Compiler Fiasco Upate

2012-10-23 Thread Cody Permann
; benjamin.kir...@nasa.gov> wrote: > That error is eerily familiar to what I get on OSX when I use boost.unit > in my app code. No resolution yet, but definitely let me know if you figure > it out! > > > > On Oct 22, 2012, at 4:00 PM, "Cody Permann" wrote: > >

Re: [Libmesh-devel] Compiler Fiasco Upate

2012-10-22 Thread Cody Permann
7;m receiving (pointer being freed was not allocated) was one of the errors I saw repeatedly with the fparser stuff. Still investigating... Thanks, Cody > > Isn't the retina display bad ass? > > > On Fri, Oct 19, 2012 at 10:32 AM, Cody Permann wrote: > >> >> >

Re: [Libmesh-devel] OS X Compilers

2012-10-22 Thread Cody Permann
On Mon, Oct 22, 2012 at 9:08 AM, Roy Stogner wrote: > > On Mon, 22 Oct 2012, Kirk, Benjamin (JSC-EG311) wrote: > > To be clear, 4.5 is a proper release. >> >> The issue is they distribute two packages - the peon version >> consisting of two files (which we propose we move to) and the >> developer

Re: [Libmesh-devel] OS X Compilers

2012-10-22 Thread Cody Permann
'll give 4.5 a shot. > What happens when you run > > ./bootstrap > ./contrib/bin/buildall.sh? > Let me try it now and I"ll let you know. Cody > > -Ben > > > > On Oct 20, 2012, at 9:30 AM, "Cody Permann" wrote: > > > >

Re: [Libmesh-devel] OS X Compilers

2012-10-22 Thread Cody Permann
On Sat, Oct 20, 2012 at 9:56 AM, Kirk, Benjamin (JSC-EG311) < benjamin.kir...@nasa.gov> wrote: > >> > >> I'll double check with the latest port of everything, although I do > think a lot of this is self imposed - why don't we use the released fparser > package? > >> > >> The development version us

Re: [Libmesh-devel] OS X Compilers

2012-10-20 Thread Cody Permann
t; -Ben > > > > On Oct 20, 2012, at 9:30 AM, "Cody Permann" wrote: > > > > On Wed, Oct 3, 2012 at 7:34 AM, Kirk, Benjamin (JSC-EG311) < > benjamin.kir...@nasa.gov> wrote: > >> >> Thought I'd follow up here. I've been working in libM

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