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HDF5 output with cell-centered grid
by Vassilios Mewes 16 Jan '13

16 Jan '13

sorry for the messages before, hopefully the mail is now small enough, but i thought that adding a plot might explain better what i mean.. Hello all, i recently read the Reisswig et al. 2012 paper and started trying to switch to cell-centered grid in order to be able to use the LSUThorns/Refluxing thorn. i am trying to simulate BH+torus systems and due to the size of the torus its hard to have it contained within a refinement level, so i thought that using a cell-centered grid in order to use refluxing might improve results.. i however run into problems getting the hdf5 output of 3D grid frundtions to work... using the static_tov_cc_rf.par file from the Refluxing trunk, i get weird output in the mesh at the reflection boundaries (the par file uses octant mode).. i am using the following parameters for CarpetIOHDF5: IOHDF5::out_every = 256 IOHDF5::one_file_per_group = no IOHDF5::output_symmetry_points = no IOHDF5::out3D_ghosts = no IOHDF5::output_ghost_points = no IOHDF5::out3D_outer_ghosts = no IOHDF5::output_boundary_points = no IOHDF5::output_buffer_points = no IOHDF5::compression_level = 9 IOHDF5::use_checksums = yes IOHDF5::out_vars = " HydroBase::rho HydroBase::press HydroBase::eps HydroBase::vel ADMBase::lapse ADMBase::metric ADMBase::curv GRHydro::scon " the simulations seems to work fine, so is the carpetiohdf5 thorn not suitable for cell-centered output? another effect (that might be output related) is that the different refinement levels are shifted (i'll attach a file showing this in the TOV from the par file (i added extra refinement levels to illustrate the effect) as well as a plot of the density in the torus)... are the specific parameters for cell-centered hdf5 output or other thorns that could take care of that? best wishes, Vassili

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Einstein Toolkit Meeting
by Frank Loeffler 13 Jan '13

13 Jan '13

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CactusExamples
by Erik Schnetter 12 Jan '13

12 Jan '13

Last Monday we briefly discussed whether to add thorns from CactusExamples to the Einstein Toolkit. I looked at the thorns, and I suggest to add the following two thorns to the EinsteinToolkit, after possibly minor cleanups: IDWaveMoL WaveMoL There may be other thorns worth adding; I didn't check them. -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/

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Meeting Minutes
by Tanja Bode 07 Jan '13

07 Jan '13

Present: Frank, Steve, Eloisa, Ian, Tanja, Erik, Josh, Bruno (did I miss anyone?) Minutes: * Reminder: Loni allocation changed from loni_cactus07 to loni_cactus08 See meeting announcement and emails to lists. * Parameter files: Small representative parameter files are requested. These should not necessarily be confinable to a workstation, but should not require many SUs. There is a growing list at http://einsteintoolkit.org/about/gallery . We should include typical simulated systems, with typical parameters. That is, simulations should include standard analysis thorns and output choices. These should also show the typical yet diverse practices, e.g. of handling output directories and checkpointing files. We can adapt parameter files from the ET paper, but only some fit the above requirements. We need to clean these up, update them, and include details on resources required (memory, runtime, & thornlist). We should also expand the list from the ET paper to include more example systems to show what the ET is capable of. * CactusExamples: Currently part of the Cactus release but not the ET. https://trac.einsteintoolkit.org/ticket/809 Erik will look at these one by one to see whether the demonstrated methods are ones we wish to push others to use. Somebody else will need to review. * TmunuBase: Default of support_old_CalcTmunu_mechanism is currently "yes". Frank will change the default to "no" after call in development since it slows down simulations. Removing support completely would break BSSN_MoL among others, so this will be discussed later. * Compiler Warnings: Please look at the compiler warnings and fix. Still of order 1000 lines of warnings with Frank's compiler flag settings. See the following graphic for current flag status: http://www.cct.lsu.edu/~knarf/ET_stats/warnings.png Cheers, Tanja

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Einstein Toolkit Meeting
by Frank Loeffler 07 Jan '13

07 Jan '13

Hi Please consider joining the weekly Einstein Toolkit phone call at 10 am US central time on Mondays. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/community/support/ I short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. There was not a lot of activity over the holidays, as expected. The server svn.cactuscode.org has a new ssl certificate because the old expired; you might (but actually shouldn't) need to accept that in your clients. The LONI Cactus allocation loni_cactus07 expired end of last year. We got a new allocation loni_cactus08 approved. Simfactory defaults have been changed (do svn update), but users might need to adapt local changes. Also, please note that this allocation is meant for infrastructure development and testing, not for production runs (it is also not so large to support that). Having said that - please use it whenever you do development or testing on LONI and acknowledge it whenever you have used it for a publication, even if only used during the early phase for code development. On the agenda for this meeting is: - http://einsteintoolkit.org/about/gallery Please create example parameter files. I volunteer to start working on the long-term evolution of a single, stable neutron star. Others are needed. We should be able to get this up before the next release, and this will also help ourselves with events like new-user workshops. - CactusExamples into the ET? This arrangement was part of the last Cactus release. There is a ticket [1] about including it in the ET as well, so we need to decide. - TmunuBase::support_old_CalcTmunu_mechanism = no The default for this setting is currently "yes", but this is _really_ slow and not needed for ET thorns. There is a ticket [2] about changing the default for the next release (so, now in trunk) and removing it after the next release (in the fall). We need to decide about both; about the change of default now and about the removal (in fall) at latest before the release in spring to be able to warn users. - We are still working on reducing the number of compiler warnings. This of course depends on your compiler and compiler flags, but most of them aught to be fixed in any case. There is a ticket [3] about this, and a daily overview can be seen at [4]. Any help is appreciated. As always - feel free to bring up any issue related to the ET in any form. This agenda is not meant to be extended if needed. Frank Löffler [1] https://trac.einsteintoolkit.org/ticket/809 [2] https://trac.einsteintoolkit.org/ticket/1105 [3] https://trac.einsteintoolkit.org/ticket/1174 [4] http://www.cct.lsu.edu/~knarf/ET_stats/warnings.png

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Einstein Toolkit Meeting Reminder
by Roland Haas 06 Jan '13

06 Jan '13

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Loni allocation loni_cactus07/8
by Frank Loeffler 04 Jan '13

04 Jan '13

Hi, It is time to update the name of the Cactus LONI allocation from loni_cactus07 to loni_cactus08. Updating simfactory should bring in the new name as default but if you specified it by hand at some place you need to update it there now. loni_cactus07 is now expired and has been replaced by loni_cactus08. Please note that, like loni_cactus07, also loni_cactus08 is meant for Cactus development and testing - not for production runs. We have 250kSU for 2013. To update simfactory, change into its installation directory (e.g. Cactus/simfactory) and issue 'svn update'. thanks, Frank Loeffler

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Re: [Users] [Commits] [svn:einsteintoolkit] Multipole/trunk/ (Rev. 88)
by Ian Hinder 04 Jan '13

04 Jan '13

On 4 Jan 2013, at 23:09, Ian Hinder <ian.hinder(a)aei.mpg.de> wrote: > > On 4 Jan 2013, at 20:52, Frank Loeffler <knarf(a)cct.lsu.edu> wrote: > >> On Fri, Jan 04, 2013 at 06:20:23PM +0100, Ian Hinder wrote: >>>> Does that work with the parser in utils/Scripts/Parse_READMES.pl? >>> >>> I doubt it. The README predates that script. >> >> I don't care which format we end up with, but there should only be one >> format for these READMEs. Maybe it is time to change (and parsing that >> should be relatively easy), but right now most READMEs follow the format >> that script understands. >> >> Which tools can parse the format of the Multipole README? > > e.g. http://docutils.sourceforge.net/rst.html, http://docs.python.org/devguide/documenting.html, etc > > If we want to recommend a format, then it should be documented at https://docs.einsteintoolkit.org/et-docs/Einstein_Toolkit_standards. If starting from scratch now, I would use an existing format which was supported by external tools. Since most thorns I assume follow the original format however, that is the most sensible one to use in the short term. Feel free to convert the Multipole README file. > > How reliable is machine-parsing of that format? My motivation in experimenting with the restructured text format was to have something which could be rendered nicely on a web page and was also easily human-readable. -- Ian Hinder http://numrel.aei.mpg.de/people/hinder

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Re: [Users] [Commits] [svn:einsteintoolkit] Multipole/trunk/ (Rev. 88)
by Frank Loeffler 04 Jan '13

04 Jan '13

On Fri, Jan 04, 2013 at 09:16:01AM +0000, ian.hinder(a)aei.mpg.de wrote: > User: hinder > Date: 2013/01/04 03:16 AM > > Added: > /trunk/ > README > > Log: > Add README > > The format of the README is slightly different to the other READMEs in > the Einstein Toolkit. It is in reStructuredText format, a markdown > format which can be easily converted to HTML. This was a test to see > how well this would work. Does that work with the parser in utils/Scripts/Parse_READMES.pl? Frank

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position at RIT
by Frank Loeffler 27 Dec '12

27 Dec '12

Hi, Folks at RIT would like to draw attention to the following tenure track opening: http://hyperspace.aei.mpg.de/2012/12/18/tenure-track-faculty-position-in-co… Frank Löffler

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