Users October 2010

users@lists.einsteintoolkit.org

15 participants
33 discussions

Fwd: Problems when opening Visit
by Erik Schnetter 16 Oct '10

16 Oct '10

Stephen There are two slightly different Cactus output formats, depending on which driver you are using, PUGH or Carpet. The VisIt Cactus reader works with Carpet, which is what we use for production runs. The WaveToy demo may be using PUGH as driver, and these files may then not be readable. Which driver did you use? You can see in the parameter file which thorns are activated, and you are probably activating either PUGH or Carpet. VisIt is not very clever about detecting file formats. It may become confused and assume that this is a Pixie file, even though it is actually a Cactus file. -erik On Fri, Oct 15, 2010 at 2:27 PM, Sheler, Stephen Andrew <sheler1(a)live.marshall.edu> wrote: > Hello, > I have a question concerning the opening of Visit and trying to visualize > the wave toy demo there. I am following the instructions on configuring Mac > OS X for Cactus. After compiling HDF5, I opened Visit and ran the file > phi.h5 and this warning was shown... > If this is not a Pixie file, you can manually select the correct file format > reader when opening the file, set the correct reader as a preferred plugin, > disable the Pixie plugin, or request that the developers of the Pixie plugin > add code to distinguish your file from one of theirs. > how do set the correct reader? > one more thing, if I ignore the warning i can visualize but i have the > following error > HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0: > #000: H5G.c line 397 in H5Gopen2(): unable to open group > major: Symbol table > minor: Can't open object > > I would appreciate your help with these problems, > Stephen Sheler > _______________________________________________ > Users mailing list > Users(a)einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users > > -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/

1 0

Problems when opening Visit
by Sheler, Stephen Andrew 15 Oct '10

15 Oct '10

Hello, I have a question concerning the opening of Visit and trying to visualize the wave toy demo there. I am following the instructions on configuring Mac OS X for Cactus. After compiling HDF5, I opened Visit and ran the file phi.h5 and this warning was shown... If this is not a Pixie file, you can manually select the correct file format reader when opening the file, set the correct reader as a preferred plugin, disable the Pixie plugin, or request that the developers of the Pixie plugin add code to distinguish your file from one of theirs. how do set the correct reader? one more thing, if I ignore the warning i can visualize but i have the following error HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0: #000: H5G.c line 397 in H5Gopen2(): unable to open group major: Symbol table minor: Can't open object I would appreciate your help with these problems, Stephen Sheler

1 0

simulationfactory issue?
by Richard O'Shaughnessy 15 Oct '10

15 Oct '10

Helloall, After a seemingly successful compile, I tried a simple single-cpu run (using generic.sh submission) on my cluster head node. I believe this installation is the release version; the only changes have been to the optionlist and udb.pm. A similar configuration works on other machines (i.e, my laptop, albeit with svn rather than release versions), but for some reason not here. It's not creating the simulations directory at all. Thoughts? --- command-line [oshaughn@hydra Cactus]$ ./simfactory/sim create-submit static_tov --parfile=par/static_tov.par --procs=1 --walltime=8:0:0 Simulation Factory: Configuration name(s) not specified -- using default configuration "sim" Uncaught exception from user code: Configuration "sim" contains no executable at ./simfactory/sim line 5216. at ./simfactory/sim line 5216 main::get_executable() called at ./simfactory/sim line 1883 main::command_create('static_tov') called at ./simfactory/sim line 2955 main::command_create_submit('static_tov') called at ./simfactory/sim line 452 ---- udb.pm # What you will refer to the machine as in simfactory commands set_option 'hydra', 'nickname', 'hydra'; set_option 'hydra', 'hostname', 'hydra.phys.uwm.edu'; set_option 'hydra', 'aliaspattern', '^hydra(\.phys\.uwm\.edu)?$'; set_option 'hydra', 'user', 'oshaughn'; set_option 'hydra', 'sourcebasedir', '/home/oshaughn/Numerical/EinsteinToolkit'; set_option 'hydra', 'basedir', '/home/oshaughn/Numerical/simulations'; set_option 'hydra', 'optionlist', 'hydra.cfg'; Richard O'Shaughnessy oshaughn(a)gravity.phys.uwm.edu 462 Physics Building Phone: 414 229 6674 Center for Gravitation and Cosmology University of Wisconsin, Milwaukee 53211

2 1

Question: odd compilation failure
by Richard O'Shaughnessy 15 Oct '10

15 Oct '10

Hello, While setting up a local cluster, I've run into a problem I just don't understand when compiling. It seems that the compiler's not finding <math.h>! (for one program, at least) To this point, the compilation procedure has proceeded without trouble; I've successfully compiled on other machines. Thoughts? Thanks, -Richard PS: for reference, the compilation is below [oshaughn@hydra Cactus]$ ./simfactory/sim build --thornlist=manifest/einsteintoolkit.th --optionlist=simfactory/optionlists/hydra.cfg </cut> Checking status of thorn LoopControl ________________________________________________________________________ Preprocessing /home/oshaughn/Numerical/EinsteinToolkit/Cactus/arrangements/Carpet/LoopControl/src/wavetoy-loopcontrol.c Compiling /home/oshaughn/Numerical/EinsteinToolkit/Cactus/arrangements/Carpet/LoopControl/src/wavetoy-loopcontrol.c /home/oshaughn/Numerical/EinsteinToolkit/Cactus/arrangements/Carpet/LoopControl/src/wavetoy-loopcontrol.c: In function 'lc_demo': /home/oshaughn/Numerical/EinsteinToolkit/Cactus/arrangements/Carpet/LoopControl/src/wavetoy-loopcontrol.c:183: error: 'M_PI' undeclared (first use in this function) /home/oshaughn/Numerical/EinsteinToolkit/Cactus/arrangements/Carpet/LoopControl/src/wavetoy-loopcontrol.c:183: error: (Each undeclared identifier is reported only once /home/oshaughn/Numerical/EinsteinToolkit/Cactus/arrangements/Carpet/LoopControl/src/wavetoy-loopcontrol.c:183: error: for each function it appears in.) Richard O'Shaughnessy oshaughn(a)gravity.phys.uwm.edu 462 Physics Building Phone: 414 229 6674 Center for Gravitation and Cosmology University of Wisconsin, Milwaukee 53211

2 4

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 -----------------------------------------------

2 3

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/

1 0

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

2 1

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/

1 0

[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.

4 6

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/

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

Users October 2010