Users February 2011

users@lists.einsteintoolkit.org

19 participants
31 discussions

parameter files
by Babiuc-Hamilton, Maria 03 Mar '11

03 Mar '11

Hello, I am trying to run the configuration compiled with einsteintoolkit.th and the parameter files qc0-mclachlan.par, static_tov and ks-mclachlan.par, on 12 processors with OpenMPI, but I am getting those errors: qc0-mclachlan.par: WARNING level 0 in thorn CarpetInterp processor 6 host muci-train01.marshall.edu (line 1683 of /home/babiuc/Einstein_Tooklit/Cactus/configs/einsteintoolkit/build/CarpetInterp/interp.cc): -> Grid function "AHFINDERDIRECT::ahmask" has only 1 active time levels on refinement level 1; this is not enough for time interpolation cactus_ks-mclachlan: /home/babiuc/Einstein_Tooklit/Cactus/configs/einsteintoolkit/build/Carpet/helpers.cc:201: int Carpet::Abort(cGH*, int): Assertion `0' failed. [muci-train01:11103] *** Process received signal *** [muci-train01:11103] Signal: Aborted (6) static_tov: WARNING level 0 in thorn Bindings processor 3 host muci-train01.marshall.edu (line 5193 of /home/babiuc/Einstein_Tooklit/Cactus/configs/einsteintoolkit/build/CactusBindings/Functions/AliasedFunctions.c): -> The function EOS_Omni_GetHandle has not been provided by any thorn in your thornlist cactus_ks-mclachlan: /home/babiuc/Einstein_Tooklit/Cactus/configs/einsteintoolkit/build/Carpet/helpers.cc:201: int Carpet::Abort(cGH*, int): Assertion `0' failed. [muci-train01:11439] *** Process received signal *** [muci-train01:11439] Signal: Aborted (6) ks-mclachlan.par: WARNING level 1 in thorn CarpetReduce processor 1 host muci-train01.marshall.edu (line 1084 of /home/babiuc/Einstein_Tooklit/Cactus/configs/einsteintoolkit/build/CarpetReduce/reduce.cc): -> Grid function "CARPETREDUCE::weight" has only 1 time levels on refinement level 0; this is not enough for time interpolation The first two parameter files abort the run. The last one keeps the run going until it ends in NaN. Is there a simple fix for this? thank you, Maria

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Meetinq minutes
by Roland Haas 28 Feb '11

28 Feb '11

Present were: Roland, Frank, Tanja, Christian, Ian, Erik, Bruno, Peter ET paper: * Christian will work on the "Evolution methods" section * add statement about NSF support/grants and number of funded personnel in introduction spring ET workshop: * afternoon Tue April 26th - Friday April 29th (with Friday not being a full day) * at CalTech (NOT at GT) * Christian will send out an email with logistical information (for CalTech hotel rates) fall ET workshop: * suggested to hold in Atlanta, up for further discussion (date, location, topics, target audience) Einstein Toolkit: * remove EOS general code from GRHydro * remove GZ_Pach code from GRHydro * remove EOS general EOS thorns from ET in next release or at least the release after next 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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GRHydro simplifications
by Christian D. Ott 28 Feb '11

28 Feb '11

Hi All, in today's call, I would like to discuss the following proposed changes to GRHydro that are primarily for code simplification: * remove "General" EOS interface and just keep EOS_Omni as the single EOS interface supported by GRHydro * remove obsolete routine connecting GRHydro to the GZ Patch System. - Christian

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link problems
by Mohror, Kathryn 26 Feb '11

26 Feb '11

Hi, I'm new at Einstein/Cactus and am having trouble at link time when following the tutorial instructions (https://docs.einsteintoolkit.org/et-docs/Tutorial_for_New_Users#Any_Problem…) I've gotten to the point where the output of: ./simfactory/sim build --optionlist=simfactory/optionlists/generic.cfg --thornlist=manifest/einsteintoolkit.th Says: Creating cactus_sim in /g/g23/mohror1/Einstein/Cactus/exe from ... (followed by lots of names of thorns) Then, I get a load of undefined reference errors, the first two of which are: /g/g23/mohror1/Einstein/Cactus/configs/sim/lib/libthorn_CactusBindings.a(EOSG_Polytrope_Functions.c.o): In function `CCTK_Wrapper_FtoC_EOS_GP_DPDIE': EOSG_Polytrope_Functions.c:(.text+0xe): undefined reference to `eos_gp_dpdie_' /g/g23/mohror1/Einstein/Cactus/configs/sim/lib/libthorn_CactusBindings.a(EOSG_Polytrope_Functions.c.o): In function `CCTK_Wrapper_FtoC_EOS_GP_IntEn': EOSG_Polytrope_Functions.c:(.text+0x2e): undefined reference to `eos_gp_inten_' In configs/sim/lib there is a libthorn_EOSG_Polytrope.a which I believe should contain these symbols. However, when I do an 'nm' of the library, the symbols are undefined: configs/sim/lib/libthorn_EOSG_Polytrope.a: EOS_GP_Setup.c.o: U CCTK_Warn U EOS_GP_Inverse_SetArray U EOS_GP_SetArray 0000000000000000 T EOS_GP_Startup U EOS_RegisterCall U Util_TableCreate U Util_TableSetInt U Util_TableSetString EOS_GP.c.o: 0000000000000000 T EOS_GP_Inverse_SetArray 00000000000000e0 T EOS_GP_SetArray U eos_gp_cs2_ U eos_gp_dpdie_ U eos_gp_dpdrho_ U eos_gp_inten_ U eos_gp_inv_cs2_ U eos_gp_inv_dpdie_ U eos_gp_inv_dpdrho_ U eos_gp_inv_inten_ U eos_gp_inv_rho_ U eos_gp_pressure_ Any ideas on what I'm doing wrong? (I'm using gcc/g++/gfortran on a Linux cluster) Thanks, -- Kathryn

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segfault with kerr initial data using IDAnalyticBH
by Yosef Zlochower 24 Feb '11

24 Feb '11

Hi, If initial_data=kerr and metric_type=physical, IDAnalyticBH writes to psi[x-z] and psi[x-z][x-z] (it tries to set these GFs to zero) even if no storage is allocated. The problem is with the code IDAnalyticBH_zero_CCTK_REAL_array(npoints, psix); etc.., which is only executed when the metric is physical. I was able to use the Kerr data with the following patch, but just deleting the offending lines should be sufficient. --- Kerr.c 2011-02-10 09:08:58.000000000 -0500 +++ /tmp/Kerr.c 2011-02-23 18:15:38.000000000 -0500 @@ -103,6 +103,10 @@ conformal_storage); /*NOTREACHED*/ } } + else + { + *conformal_state = 0; + } /* printf("npoints: %i\n",npoints); */ @@ -311,15 +315,22 @@ } IDAnalyticBH_zero_CCTK_REAL_array(npoints, gxz); IDAnalyticBH_zero_CCTK_REAL_array(npoints, gyz); - IDAnalyticBH_zero_CCTK_REAL_array(npoints, psix); - IDAnalyticBH_zero_CCTK_REAL_array(npoints, psiy); - IDAnalyticBH_zero_CCTK_REAL_array(npoints, psiz); - IDAnalyticBH_zero_CCTK_REAL_array(npoints, psixx); - IDAnalyticBH_zero_CCTK_REAL_array(npoints, psixy); - IDAnalyticBH_zero_CCTK_REAL_array(npoints, psixz); - IDAnalyticBH_zero_CCTK_REAL_array(npoints, psiyy); - IDAnalyticBH_zero_CCTK_REAL_array(npoints, psiyz); - IDAnalyticBH_zero_CCTK_REAL_array(npoints, psizz); + + if (psix && *conformal_state < 2) + { + IDAnalyticBH_zero_CCTK_REAL_array(npoints, psix); + IDAnalyticBH_zero_CCTK_REAL_array(npoints, psiy); + IDAnalyticBH_zero_CCTK_REAL_array(npoints, psiz); + } + if (psixx && *conformal_state < 3) + { + IDAnalyticBH_zero_CCTK_REAL_array(npoints, psixx); + IDAnalyticBH_zero_CCTK_REAL_array(npoints, psixy); + IDAnalyticBH_zero_CCTK_REAL_array(npoints, psixz); + IDAnalyticBH_zero_CCTK_REAL_array(npoints, psiyy); + IDAnalyticBH_zero_CCTK_REAL_array(npoints, psiyz); + IDAnalyticBH_zero_CCTK_REAL_array(npoints, psizz); + } } return;

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Output with carpet in more than 1 proc
by Francisco S. Guzman 24 Feb '11

24 Feb '11

Dear all, I just coded a simple wavetoy and have found that the output when using carpet (the number of time levels) depends on the number of processors used for both h5 or ascii. Am I doing something clearly worng and easily fixable? Bests, Francisco -- Francisco S. Guzman Murillo. Instituto de Fisica y Matematicas, Universidad Michoacana de San Nicolas de Hidalgo Phone: +52 (443) 322 3500 ext 4142 http://www.ifm.umich.mx/guzman/

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Re: [Users] [Commits] [svn:einsteintoolkit] HydroBase/trunk/ (Rev. 38)
by Bruno Coutinho Mundim 21 Feb '11

21 Feb '11

Hi Christian: > File [modified]: interface.ccl > Delta lines: +2 -0 > =================================================================== > --- trunk/interface.ccl 2011-02-21 15:49:06 UTC (rev 37) > +++ trunk/interface.ccl 2011-02-21 17:14:39 UTC (rev 38) > @@ -35,6 +35,8 @@ > > CCTK_REAL vel[3] type = GF Timelevels = 3 tags='ProlongationParameter="HydroBase::prolongation_type" tensortypealias="U" interpolator="matter"' "velocity v^i" > > +CCTK_REAL w_lorentz type = GF Timelevels = 3 tags='ProlongationParameter="HydroBase::prolongation_type" tensortypealias="U" interpolator="matter"' "Lorentz Factor" > + > CCTK_REAL Y_e type = GF Timelevels = 3 tags='ProlongationParameter="HydroBase::prolongation_type" tensortypealias="Scalar" interpolator="matter"' "Electron Fraction" Shouldn't we have tensortypealias="Scalar" tensorweight=+1.0 instead of tensortypealias="U" for the Lorentz factor? Cheers, Bruno.

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Cactus compilation issue
by Steven R. Brandt 21 Feb '11

21 Feb '11

I'm attempting to compile Einsteintoolkit on my laptop. I have gcc/g++/gfortran. The config looks like this: CPP = gcc FPP = gfortran CC = gcc CXX = g++ F77 = gfortran F90 = gfortran CPPFLAGS = -DMPICH_IGNORE_CXX_SEEK -DKRANC_DIFF_FUNCTIONS FPPFLAGS = -traditional # no -msse3 CFLAGS = -g3 -m128bit-long-double -march=native -std=gnu99 CXXFLAGS = -g3 -m128bit-long-double -march=native -std=gnu++0x F77FLAGS = -g3 -m128bit-long-double -march=native -fcray-pointer -ffixed-line-length-none F90FLAGS = -g3 -m128bit-long-double -march=native -fcray-pointer -ffixed-line-length-none LDFLAGS = My compiler gives a slew of errors, starting with this one. Checking status of thorn TwoPunctures ________________________________________________________________________ /home/sbrandt/Cactus/arrangements/LSUThorns/SummationByParts/src/Poisoning.F90:9.26: REAL*8 diss_fraction(3)&&REAL*8 epsdis&&REAL*8 h_scaling(3)&&REAL*8 poiso What's going wrong? How can I fix it? Cheers, Steve 1

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Meetinq minutes
by Roland Haas 21 Feb '11

21 Feb '11

Present were: Frank, Tanja, Roland, Peter, Ian, Eloisa, Bruno, Erik, Josh, Christian HydroBase: * include w_lorentz as a grid function in HydroBase ET paper: * update references to use ET bibtex file (Peter, Frank, anyone else is welcome!) * add section on (Cactus) component structure/component interface (Erik) * Kranc section is finished (Ian) * ID data will be looked at during the next week (Josh), will likely have go over the 1/2 page limit * Evolution methods (Christian) * two level approach: ** produce a first "text only" paper that will be a CCT technical report and also posted to the arXive ** send to interested parties (LRR, Computational Science & Discovery) to ascertain if there is interest in a longer more detailed version (50-60 pages) showing basic equations, numerical implementation ** long version would be core reference for ET, would need more substance (more test cases) *** http://iopscience.iop.org/1749-4699/1/1/015005, http://arxiv.org/abs/0804.1394 *** http://iopscience.iop.org/1749-4699/1/1/015003 * add stellar core collapse to sample results spring ET workshop: * afternoon Mon April 25th - morning Wed April 27th * GT will find possible hotel venues 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 Frank Loeffler 21 Feb '11

21 Feb '11

Hi, This is a reminder about our usual Monday Einstein Toolkit phone call at 10 am US central time. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/info/support/ Some points of tomorrows discussion will be: - ET paper plans - ET workshops http://doodle.com/ayigys5kv7zzyxna -> looks like Apr Mon 25 - Wed 27? - "Poll" Visualization of simulation results https://docs.einsteintoolkit.org/et-docs/Visualization_of_simulation_results Connected to this, Ian Hinder will give an EVO-presentation on the mathematica scripts he uses. The EVO meeting is called "Einstein Toolkit weekly" and the link to it should be http://evo.caltech.edu/evoNext/koala.jnlp?meeting=eIe9esvvv8anaiatII We will use the phone line for audio, not evo. Evo will only be used for the slides/presentations. Frank Löffler

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Users February 2011