Users November 2011

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22 participants
34 discussions

Re: [Users] IRC
by Ian Hinder 14 Nov '11

14 Nov '11

On 11 Nov 2011, at 00:34, Barry Wardell wrote: > On Thu, Nov 10, 2011 at 9:07 PM, Ian Hinder <ian.hinder(a)aei.mpg.de> wrote: > My problem was that I didn't find an easy way to have it connect automatically - I was using Adium in Mac OS. Adium is a multi-protocol chat program, so some of the way it works doesn't fit very naturally with IRC, but I didn't want to run a separate program. > > In the past, the best IRC client I could find for OSX was Colloquy [http://http://colloquy.info/]. It's not perfect, but I remember it being quite good in the past.I know you would rather not run a separate IRC client, but Adium really isn't an ideal solution right now, so you might find it better using Colloquy. You can also then hide the chat window (Cmd+H) rather than minimizing it. I think I tried it in the past and found it confusing, but I'll try again! > It would be nice to have the channel joined and messages logged even if the chat window was closed, but this doesn't seem to be possible in the currently released version (http://trac.adium.im/ticket/12068). Until this is implemented, I plan to just minimize the window. > > For message logs, you can always just look at the logs on the Cactus website. > > Another thing which might be useful would be to have commit messages automatically posted to IRC whenever a commit is made. I think this happens already. -- Ian Hinder http://numrel.aei.mpg.de/people/hinder

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Meeting minutes
by Roland Haas 14 Nov '11

14 Nov '11

Hello all, present were: Roladn, Tanja, Frank, Yosef, Peter, Christian, Eloisa, Josh, Ian, Peter ET paper: * acknowledge Ed Seidel * try to convert supermongo plots to matplotlib * Roland: check that references display properly 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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Einstein Toolkit Meeting Reminder
by Frank Loeffler 14 Nov '11

14 Nov '11

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#. My agenda contains only one, very important item of today: the ET paper. By the time of the call we will have about two hours to a possible submission to the preprint archive. I've gone through the paper again, but there are a few remaining \todo{}s. Please work on those before the meeting; I will not be able to. Frank Loeffler

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restart with simfactory
by Tsatsin Petr 13 Nov '11

13 Nov '11

Hello, I'm trying to restart my simulation on queenbee using simfactory. I tried "./sim submit --from-restart-id ..." and I got "Simulation Factory: [log] Submitting: [log] Using restart id "0002" [log] Requested recovering from restart id "0" [log] Could not find checkpoint files in restart id "0000" Aborting.'' Inside my parameter file for this simulation I set up HDF5 check pointing in following way: "IO::out_dir = $parfile IOHDF5::checkpoint = "yes" IO::checkpoint_every = 100000 IO::checkpoint_file = $parfile IO::checkpoint_dir = $parfile IO::recover="auto" IO::recover_file = $parfile IO::recover_dir = $parfile" I checked that h5 check point files are actually inside the output-0000 directory. Any suggestions how can I restart the my simulation from HDF5 checkpoint with a simfactory? Thank you. -- Petr Tsatsin Graduate Student- Department of Physics Charles E. Schmidt College of Science Florida Atlantic University (561)-297-3386 ptsatin(a)fau.edu, ptsatsin(a)gmail.com

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init_3_timelevels on Latest stable ET
by Yosef Zlochower 11 Nov '11

11 Nov '11

Hi, If I use the carpet::init_3_timelevels=yes I get the following error WARNING level 0 in thorn CarpetLib processor 0 host quasar.ccrg.rit.edu (line 385 of /home/yosef/ET/Maxwell/Cactus/configs/lazev/build/CarpetLib/gdata.cc): -> Internal error: extrapolation in time. variable=ADMBASE::alp time=1280 times=[2560,4955,2395] WARNING level 0 in thorn CarpetLib processor 0 host quasar.ccrg.rit.edu (line 385 of /home/yosef/ET/Maxwell/Cactus/configs/lazev/build/CarpetLib/gdata.cc): -> Internal error: extrapolation in time. variable=ADMBASE::alp time=1280 times=[2560,4955,2395] This error message did not occur when I ran with the previous stable ET version. Here is a short parfile with no physics thorns that displays the problem. #============================================================================== ActiveThorns = "admbase boundary coordgauge time cartgrid3d CoordBase Slab LocalReduce Carpet CarpetInterp CarpetLib CarpetReduce CarpetSlab CarpetRegrid2 InitBase SymBase LoopControl GSL IOUtil MoL" # Grid mol::ode_method = "RK4" mol::mol_intermediate_steps = 4 mol::mol_num_scratch_levels = 1 CoordBase::domainsize = "minmax" CoordBase::xmin = -400 CoordBase::ymin = -400 CoordBase::zmin = -400 CoordBase::xmax = 400 CoordBase::ymax = 400 CoordBase::zmax = 400 CoordBase::spacing = "numcells" CoordBase::ncells_x = 20 CoordBase::ncells_y = 20 CoordBase::ncells_z = 20 CartGrid3D::type = "coordbase" CartGrid3D::domain = "full" CoordBase::boundary_size_x_lower = 1 CoordBase::boundary_size_y_lower = 1 CoordBase::boundary_size_z_lower = 1 CoordBase::boundary_size_x_upper = 1 CoordBase::boundary_size_y_upper = 1 CoordBase::boundary_size_z_upper = 1 driver::ghost_size = 4 #--------------------------------------------------------------------------- cactus::cctk_itlast = 2 time::dtfac = 0.25 Carpet::domain_from_coordbase = yes Carpet::prolongation_order_space = 5 Carpet::prolongation_order_time = 2 Carpet::max_refinement_levels = 9 Carpet::use_buffer_zones = yes Carpet::init_3_timelevels = "yes" CarpetRegrid2::regrid_every = 32 CarpetRegrid2::num_centres = 1 CarpetRegrid2::num_levels_1 = 6 CarpetRegrid2::position_x_1 = 0 CarpetRegrid2::position_y_1 = 0 CarpetRegrid2::position_z_1 = 0 CarpetRegrid2::radius_1[ 1] = 200 CarpetRegrid2::radius_1[ 2] = 100 CarpetRegrid2::radius_1[ 3] = 50 CarpetRegrid2::radius_1[ 4] = 25 CarpetRegrid2::radius_1[ 5] = 12.5 admbase::metric_type = "Physical" admbase::lapse_timelevels=3 admbase::shift_timelevels=3 admbase::metric_timelevels=3

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ET paper call reminder
by Frank Loeffler 11 Nov '11

11 Nov '11

Hi, This is a reminder about the ET paper call, planned at 10am central US time. The info to call in is given below. Frank Each participant of the teleconference will call 578-4942 (225-578-4942 from off-campus or 866-573-0 359 toll free). They will hear: Welcome to Voice Plus Conferencing. Please enter your Conference ID. Press the # key when complete. Participants will press 338310# for Conference Line two. They will hear: Welcome to Voice Plus Conferencing. For conference chairperson services, press the # key. All other participants please wait. “All other participants” will wait on the line until the chairperson has ‘entered’ the teleconferenc e.

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IRC
by Frank Loeffler 11 Nov '11

11 Nov '11

Hi, Some of you probably know that there is an Einstein Toolkit / Cactus channel #cactus on irc.oftc.net (see [1]). It was used for some time [2], and I rather liked the idea. However, it has gone stale lately. What is the general feeling about it? Is it worth keeping? It is not much effort doing so, but it is not a good idea to advertise it on the web if it is so under-used. Frank [1] http://einsteintoolkit.org/community/support/ [2] https://svn.cactuscode.org/irc-logs/stats/stats.cgi

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output parameter format
by Luca Baiotti 09 Nov '11

09 Nov '11

Hello, the request for output of a variable in Carpet (CarpetIOBasic, CarpetIOScalar, CarpetIOASCII) can be done in a parfile as, e.g., IOASCII::out1D_vars = "THORN_NAME::VARIABLE_GROUP_NAME" or IOASCII::out1D_vars = "IMPLEMENTATION_NAME::VARIABLE_GROUP_NAME" or IOASCII::out1D_vars = "THORN_NAME::VARIABLE_NAME" or IOASCII::out1D_vars = "IMPLEMENTATION_NAME::VARIABLE_NAME" Any of the above should work (correct me if I am wrong), but I found an exception: When requesting output as IOASCII::out1D_vars = "TestOutput::testoutput" for a *public:* or *protected:* variable group of the type: CCTK_REAL testoutput[nvar] type=GF TimeLevels=1 Dim=3 { output } "" where nvar is an integer parameter and the thorn name is TestOutput and differs from the implementation name, Carpet complains that WARNING[L1,P0] (Cactus): CCTK_TraverseString: invalid group/variable name 'TestOutput::testoutput' in traversed string 'TestOutput::testoutput' WARNING level 0 in thorn IOUtil processor 0 host mbaiotti2-2.local (line 140 of /Users/baiotti/Cactus.fresh-checkout/arrangements/CactusBase/IOUtil/src/Utils.c): -> error while parsing parameter 'IOBasic::outInfo_vars' For *private:* arrays of variables it works. I attach an example thorn and parfile. Comments? Luca

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OpenMP now used by default in Simfactory
by Erik Schnetter 09 Nov '11

09 Nov '11

Dear Einstein Toolkit users Up until now, Simfactory did not use OpenMP by default. That is, even if a code was built with OpenMP, Simfactory would by default use only a single thread when submitting a job, and parallelise purely via MPI instead. This reflected the state of the thorns, as several key thorns could in the past not make efficient use of OpenMP. This has changed, and e.g. the recent release of the Einstein Toolkit contains efficient OpenMP-parallelised implementations of the BSSN and GR-MHD equations, and all other key thorns. To our knowledge, most people use OpenMP for most of their production runs. We therefore now proudly announce that we are enabling OpenMP in job submissions by default. Simfactory "knows" what a good number of OpenMP threads is for most machines. This number depends on the hardware architecture, and thus differs from machine to machine, and Simfactory will use that many threads by default. You can override this via the --num-threads=... option; using a single thread will effectively disable OpenMP. I assume that this "good" number of threads described in Simfactory may require some adjustment in some cases. Please report cases where you think that Simfactory is mis-behaving. -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/

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Re: [Users] [Commits] [svn:einsteintoolkit] incoming/PITTNullCode/SphericalHarmonicReconASCII/ (Rev. 57)
by Frank Loeffler 08 Nov '11

08 Nov '11

On Tue, Nov 08, 2011 at 12:03:20AM +0000, reisswig(a)tapir.caltech.edu wrote: > Modified: > /PITTNullCode/SphericalHarmonicReconASCII/ > configuration.ccl, param.ccl > /PITTNullCode/SphericalHarmonicReconASCII/src/ > sph_database.cc, sph_database.hh, startup.cc > > Log: > Add capability of hdf5. Would it make sense to think about updating the thorn name? Frank

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Users November 2011