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adding levels to Carpet parameter file
by Bernard Kelly 11 Oct '10

11 Oct '10

Hi all. I'm trying something very simple -- running the "qc0-mclachlan" parameter file (specifically, the version found in Cactus/par after checking out EinsteinToolkit -- the version in Cactus/repos/McLachlan/par seems almost identical). After getting rid of one thorn I can't check out anyway (LSUThorns/SummationByParts), the parfile seems to run OK. I've since modified it by switching to a full x-domain, removing the Pi-symmetry, and moving the punctures out a bit. That all seems to work. But now I'm getting stuck trying to modify it in a simple way -- enlarging the grid while adding refinement levels "on the outside". Diffing my new "bad" parfile with the old "good" one yields the differences below. I'm attaching the bad parfile here also. Can anyone tell me where I've gone wrong, please? Are there assumed parameter values never set in the test parfile? Thanks, Bernard P.S. The errors all seem to be from NaNChecker. Here's the first printed sample: WARNING level 1 in thorn NaNChecker processor 29 host borgh098.prv.cube (line 875 of /gpfsm/dnb31/bjkelly1/Cactus/configs/mcl/build/NaNChecker/NaNCheck.c): -> There were 35 NaN/Inf value(s) found in variable 'ML_BSSN::phi' (NaNmask bitfield 0) ---------- results of diffing "good" (<) and "bad" (>) parfiles ----------------- 47c47 < Carpet::max_refinement_levels = 10 --- > Carpet::max_refinement_levels = 11 99,100c99,100 < CoordBase::xmin = -120.00 < CoordBase::ymin = -120.00 --- > CoordBase::xmin = -240.00 > CoordBase::ymin = -240.00 102,107c102,107 < CoordBase::xmax = +120.00 < CoordBase::ymax = +120.00 < CoordBase::zmax = +120.00 < CoordBase::dx = 2.00 < CoordBase::dy = 2.00 < CoordBase::dz = 2.00 --- > CoordBase::xmax = +240.00 > CoordBase::ymax = +240.00 > CoordBase::zmax = +240.00 > CoordBase::dx = 4.00 > CoordBase::dy = 4.00 > CoordBase::dz = 4.00 170c170 < CarpetRegrid2::num_levels_1 = 7 --- > CarpetRegrid2::num_levels_1 = 8 172,177c172,178 < CarpetRegrid2::radius_1[ 1] = 64.0 < CarpetRegrid2::radius_1[ 2] = 16.0 < CarpetRegrid2::radius_1[ 3] = 8.0 < CarpetRegrid2::radius_1[ 4] = 4.0 < CarpetRegrid2::radius_1[ 5] = 2.0 < CarpetRegrid2::radius_1[ 6] = 1.0 --- > CarpetRegrid2::radius_1[ 1] = 128.0 > CarpetRegrid2::radius_1[ 2] = 64.0 > CarpetRegrid2::radius_1[ 3] = 16.0 > CarpetRegrid2::radius_1[ 4] = 8.0 > CarpetRegrid2::radius_1[ 5] = 4.0 > CarpetRegrid2::radius_1[ 6] = 2.0 > CarpetRegrid2::radius_1[ 7] = 1.0 180c181 < CarpetRegrid2::num_levels_2 = 7 --- > CarpetRegrid2::num_levels_2 = 8 182,187c183,189 < CarpetRegrid2::radius_2[ 1] = 64.0 < CarpetRegrid2::radius_2[ 2] = 16.0 < CarpetRegrid2::radius_2[ 3] = 8.0 < CarpetRegrid2::radius_2[ 4] = 4.0 < CarpetRegrid2::radius_2[ 5] = 2.0 < CarpetRegrid2::radius_2[ 6] = 1.0 --- > CarpetRegrid2::radius_2[ 1] = 128.0 > CarpetRegrid2::radius_2[ 2] = 64.0 > CarpetRegrid2::radius_2[ 3] = 16.0 > CarpetRegrid2::radius_2[ 4] = 8.0 > CarpetRegrid2::radius_2[ 5] = 4.0 > CarpetRegrid2::radius_2[ 6] = 2.0 > CarpetRegrid2::radius_2[ 7] = 1.0 190c192 < CarpetRegrid2::num_levels_3 = 7 --- > CarpetRegrid2::num_levels_3 = 8 192,197c194,200 < CarpetRegrid2::radius_3[ 1] = 64.0 < CarpetRegrid2::radius_3[ 2] = 16.0 < CarpetRegrid2::radius_3[ 3] = 8.0 < CarpetRegrid2::radius_3[ 4] = 4.0 < CarpetRegrid2::radius_3[ 5] = 2.0 < CarpetRegrid2::radius_3[ 6] = 1.0 --- > CarpetRegrid2::radius_3[ 1] = 128.0 > CarpetRegrid2::radius_3[ 2] = 64.0 > CarpetRegrid2::radius_3[ 3] = 16.0 > CarpetRegrid2::radius_3[ 4] = 8.0 > CarpetRegrid2::radius_3[ 5] = 4.0 > CarpetRegrid2::radius_3[ 6] = 2.0 > CarpetRegrid2::radius_3[ 7] = 1.0 206c209 < Carpet::time_refinement_factors = "[1,1,2,4,8,16,32,64,128,256]" --- > Carpet::time_refinement_factors = "[1,1,1,2,4,8,16,32,64,128,256]" ---------------------------------------------------------------- -- ----------------------------------------------- Bernard J. Kelly NASA Goddard Space Flight Center, Code 663 8800 Greenbelt Road Greenbelt, MD 20771, U.S.A. phone: +1 (301) 286-7243 -----------------------------------------------

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Introductory slides for SimFactory presentation
by Erik Schnetter 11 Oct '10

11 Oct '10

I attach a few introductory slides for Michael's SimFactory tutorial during the telecon later. I will also upload the slides to EVO. The main part of Michael's presentation will be broadcast over EVO (using screen sharing). -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/

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Problem while installing Visit Carpet plugin
by Sheler, Stephen Andrew 08 Oct '10

08 Oct '10

Hello, I am an undergraduate student at Marshall University doing research with Dr. Maria Babiuc-Hamilton. I encountered a problem while configuring Mac OS X for Cactus. I followed the instructions on http://docs.einsteintoolkit.org/et-docs/ConfiguringMacOSX exactly and everything worked fine until I tried to install the Visit Carpet plugin. This error showed up: ./install:line10: cmake:command not found. Could you please help me with this? Thank you -Stephen Sheler

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Reminder weekly call, Monday Oct 11
by Frank Loeffler 08 Oct '10

08 Oct '10

Hi, Michael Thomas will present the usage of the new Simfactory[1] verison at the next weekly Einstein Toolkit telecon: Monday, Oct 11th, 10am central US time. Besides some slides, he will show it's usage live, using screen sharing over EVO[2]. It will be hard to follow this without using EVO, so please plan ahead if you are not familiar with EVO already, and install/test EVO on your machine before the meeting. Despite using EVO for the screen sharing, the regular phone line will be used for the audio, so no audio setup nor a camera will be required. As usual, find the instructions for the call on the ET web pages[3], as well as the direct link to the EVO booking. Frank Loeffler [1] http://www.simfactory.org [2] http://evo.caltech.edu/ [3] http://einsteintoolkit.org/info/support/

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[Fwd: Kerr ID]
by Scott Noble 07 Oct '10

07 Oct '10

I see that this has not been patched yet. Can someone please confirm the fix and patch the repo? thanks, scott n. -------- Original Message -------- Subject: Kerr ID Date: Mon, 07 Jun 2010 16:54:20 -0400 From: Scott Noble <scn(a)astro.rit.edu> To: users(a)einsteintoolkit.org Hello Users, I believe I found a minor typo in EinsteinInitialData/IDAnalyticBH/src/Kerr.c of the ET. Just a missing term in the denominator of the shift vector, so it will not likely affect many users. I have attached a patch. cheers, -- scott n.

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Fwd: Meeting minutes
by Erik Schnetter 04 Oct '10

04 Oct '10

On Mon, Oct 4, 2010 at 7:12 PM, Roland Haas <roland.haas(a)physics.gatech.edu> wrote: > Meeting minutes: > > Citation policy: > > * Erik will send an email to the user mailing list and to the authors > mentioned in the README files of contributed thorns, asking for which > paper should.must be cited to use the thorn > * eventually we will collect this information in a form that can be > parsed in one of the thorn description files Did we already describe the citation policy on the web or wiki pages? I couldn't find it. There is a general statement "The Einstein Toolkit citation guidelines are designed to appropriately credit individuals who have made intellectual contributions to the toolkit in designing the algorithms and software implementations that contribute substantially to provision of an effective framework." but nothing at the level of detail we discussed recently. -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/

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Meeting minutes
by Roland Haas 04 Oct '10

04 Oct '10

Meeting minutes: Present were: Tanja, Roland, Bruno, Erik, Ian, Yosef, Manuella Citation policy: * Erik will send an email to the user mailing list and to the authors mentioned in the README files of contributed thorns, asking for which paper should.must be cited to use the thorn * eventually we will collect this information in a form that can be parsed in one of the thorn description files MHD: * the development copy at RIT has been committed to the repository * done are HLLE, PPM, TVD, ENO * still missing are more in-depth tests, divergence cleaning, Con2Prim_polytype Carpet Mercurial: * please test refluxing * error in reduction operation has been fixed * it should now be ready for beta-testing Einstein Toolkit release: * will likely have the next ET release in the week "right after the SEASAPS meeting (the week of October 25), and still before Supercomputing" New modules: * NoMPI: minimal set of MPI stub routines * GetComponents moved to GitHub, we will need to decide whether to use GitHub or distribute our own branch/copy in subversion User support: * Erik, Frank and Eloisa have started weekly Cactus support hotlines using Evo, scheduled Wednesdays 9:00am Central Time (Evo meeting: "Cactus"), http://evo.caltech.edu/evoNext/koala.jnlp?meeting=eleBevvsvIa8avaeIl We will have a presentation on simfactory during the next phone conference. Yours, Roland -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://keys.gnupg.net.

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Meeting Reminder
by Erik Schnetter 04 Oct '10

04 Oct '10

This is a brief reminder about our regular EinsteinToolkit phone call later today at 10:00 CDT. I apologise for the late notice. Instructions for joining the call are at <http://einsteintoolkit.org/info/support/>. -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/

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Meeting minutes
by Roland Haas 02 Oct '10

02 Oct '10

Meeting minutes: Present were: Tanja, ROland ,Frank, Gabrielle, Scoot, Joshua, Yosef, Eloisa, Erik, Bruno Carpet workshop recap: * refluxing is implemented (for multiple processors) but needs more testing in production sized runs ** it requires Carpet support as well as an external refluxing thorn ** refluxing adds constraints to how the grid is laid out that have to be enforced by the regridding thorn ** CarpetRegrid2 adheres to these constraints ** it now works on multiple processors * MHD is largely implemented, implemented are HLL, Con2Prim, Prim2COn, PPM, still needed is Con2Prim_Polytype. It passes simple shocktube tests but requires more testing. * the unused grid points mask is implemented but it turns out it is only non-empty if the grids are very large * we know what to do to support higher numbers of refinement levels, but implementing it requires carefully going through the code * the code to not output 3d buffer zones is written but not well tested, it will be committed to the Mercurial version * I/O ** Nirvana (N5) library has been written and provides a high level interface to I/O similar to Werner Bengers F5 format ** ADIOS 2.0 has been made public, and now supports AMR, so it might be a useful backend for N5 ** Christian Reiswig has added code to create subdirectories for the output files to avoid having tens of thousands of files in a single directory * Ian Hinder has written a timer class and a Mathematica notebook to visualize the output of the class Citation policy: * thorn authors are free to specify which citations they would like to see, the Toolkit does not mandate any particular requirements (or lack of) * files listing both the compulsory and recommended citations will be part of the Einstein Toolkit checkout (possibly auto-generated form the thorn sources) We will have a presentation on simfactory during the next (or soon after) phone conference. Yours, Roland -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://keys.gnupg.net.

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New parallel HDF5 API proposed
by Erik Schnetter 29 Sep '10

29 Sep '10

The HDF5 groups is apparently contemplating adding a new high-level API for "HPC HDF5", based on parallel HDF5. I find the idea intriguing, as it would move much code that we have currently written in Carpet (and that we will have to write to address the "slow recovery" issue) into HDF5. In particular, recovering would consist essentially of a single call to H5HPCdataset_read_mult_all(), which would read multiple datasets from multiple processes. -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/

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