Users July 2012

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18 participants
30 discussions

Einstein Toolkit Meeting Reminder
by Frank Loeffler 14 May '15

14 May '15

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: - Fall workshop - PLEASE let us know if you come [1]! - Hotel booking - Release planning - release date: Mon Oct 24 2011 - freeze date: Mon Sep 26 - the day of the call! - branch name: ET_2011_10 - List of release-concerning bugs [2] - ET paper: proposed "freeze" by Oct 3rd (Mon after this call) As always: feel free to add to this list. Frank Loeffler [1] https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Fall_2011#Fall_Einstei… [2] https://trac.einsteintoolkit.org/query?status=!closed&milestone=ET_2011_11&…

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Simulation domain volume and reduction weight sum differ
by Jakob Hansen 25 Sep '12

25 Sep '12

Hi, Using mercurial, I get this warning during simulations : INFO (CarpetReduce): Simulation domain volume: 170368000 INFO (CarpetReduce): Reduction weight sum: 170367999.880642 WARNING level 1 in thorn CarpetReduce processor 0 host tachyon2974 (line 120 of /home01/r632kgw/jakob/CactusP/arrangements/Carpet/CarpetReduce/src/mask_test.c): -> Simulation domain volume and reduction weight sum differ Simulations seem to run okay though. What is causing this warning and is it serious or can I just ignore it? Cheers, Jakob

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support_old_CalcTmunu_mechanism
by Frank Loeffler 23 Sep '12

23 Sep '12

Hi, Are there objections to change the default of TmunuBase::support_old_CalcTmunu_mechanism from "yes" to "no"? Frank

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CarpetLib: compile error with commstate.hh
by Scott Hawley 02 Aug '12

02 Aug '12

Hi, I just did a fresh checkout of the development version, and I'm still having trouble with the comstate.hh file. I'm using -std=gnu++0x. (It's the 4.3 version of the compiler, so gnu++0x should be appropriate; std=gnu++11 began with version 4.7). How might one fix this? Thanks. make SILENT=no ... COMPILING /nics/c/home/hawleys/Cactus/arrangements/Carpet/CarpetLib/src/commstate.cc current_wd=`pwd` ; cd /nics/c/home/hawleys/Cactus/configs/texmex/scratch ; g++ -LMPICH_IGNORE_CXX_SEEK -g -DCARPET_DEBUG -fopenmp -O2 -m64 -std=gnu++0x -g -O0 -O3 -fopenmp -c -o $current_wd/commstate.cc.o $current_wd/commstate.cc -I"/opt/mpt/3.4.2/xt/mpich2-gnu//include" -I"/nics/c/home/hawleys/Cactus/configs/texmex/scratch/external/GSL/include" -I"/nics/c/home/hawleys/Cactus/arrangements/Carpet/CarpetLib/src" -I"/nics/c/home/hawleys/Cactus/arrangements/Carpet/CarpetLib/src/include" -I"/nics/c/home/hawleys/Cactus/configs/texmex/config-data" -I"/nics/c/home/hawleys/Cactus/configs/texmex/bindings/include" -I"/nics/c/home/hawleys/Cactus/src/include" -I"/nics/c/home/hawleys/Cactus/arrangements" -I"/nics/c/home/hawleys/Cactus/configs/texmex/bindings/Configuration/Thorns " -I"/nics/c/home/hawleys/Cactus/configs/texmex/bindings/include/CarpetLib" -I"/opt/mpt/3.4.2/xt/mpich2-gnu//include" -I"/nics/c/home/hawleys/Cactus/configs/texmex/scratch/external/GSL/include" -I"/nics/c/home/hawleys/Cactus/arrangements/Carpet/CarpetLib/src" -I"/nics/c/home/hawleys/Cactus/arrangements/Carpet/CarpetLib/src/include" -I"/nics/c/home/hawleys/Cactus/configs/texmex/bindings/include/CarpetLib" -DCCODE /usr/include/c++/4.3/bits/stl_vector.h: In member function Œvoid std::vector<_Tp, _Alloc>::push_back(_Args&& ...) [with _Args = <anonymous enum>, _Tp = unsigned int, _Alloc = std::allocator<unsigned int>]¹: /nics/c/home/hawleys/Cactus/arrangements/Carpet/CarpetLib/src/commstate.hh: 126: instantiated from here /usr/include/c++/4.3/bits/stl_vector.h:703: error: no matching function for call to Œforward(<anonymous enum>&)¹ /nics/c/home/hawleys/Cactus/arrangements/Carpet/CarpetLib/src/commstate.hh: 126: instantiated from here /usr/include/c++/4.3/bits/stl_vector.h:708: error: no matching function for call to Œforward(<anonymous enum>&)¹ make[3]: *** [commstate.cc.o] Error 1 make[3]: Leaving directory `/nics/c/home/hawleys/Cactus/configs/texmex/build/CarpetLib' make[2]: *** [make.checked] Error 2 make[2]: Leaving directory `/nics/c/home/hawleys/Cactus/configs/texmex/build/CarpetLib' make[1]: *** [/nics/c/home/hawleys/Cactus/configs/texmex/lib/libthorn_CarpetLib.a] Error 2 make[1]: Leaving directory `/nics/c/home/hawleys/Cactus' make: *** [texmex] Error 2 % g++ --version g++ (SUSE Linux) 4.3.4 [gcc-4_3-branch revision 152973] Copyright (C) 2008 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

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hdf5 output for testsuites
by Yosef Zlochower 01 Aug '12

01 Aug '12

I was thinking about how to generate better testsuite for the CCE code, in particular, SphericalHarmonicDecomp thorn. The code generates an hdf5 file with coefficients for a Chebyshev/spherical harmonic expansions of the metric functions. Ideally, I would like to test that this hdf5 has the correct data. I could have the thorn also produce ascii output, but it seems to be a stronger test to examine the hdf5 file itself. Would it be possible to do this as an extension to the testsuite mechanism? It seems like the h5diff (with the -d or -p option) program could be used for the comparison itself. -- Dr. Yosef Zlochower Center for Computational Relativity and Gravitation Assistant Professor School of Mathematical Sciences Rochester Institute of Technology 85 Lomb Memorial Drive Rochester, NY 14623 Office:74-2067 Phone: +1 585-475-6103 yosef(a)astro.rit.edu CONFIDENTIALITY NOTE: The information transmitted, including attachments, is intended only for the person(s) or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and destroy any copies of this information.

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Error to write PittNull during checkpointing
by Jakob Hansen 30 Jul '12

30 Jul '12

Hi, I'm experimenting a bit with using the PittNull / SphericalHarmonicDecomp thorn but I've been experiencing a few errors in writing to its output metric_obs_0_Decomp.h5 file. On some occations it seems that this output file cannot be opened and hence leaving gaps in the data file. This always occurs when carpet is doing checkpoininting. Everything else runs well, though, and the simulations finishes fine. However, when trying to fftwfilter the metric_obs_0_Decomp.h5 file, I notice the missing data points. I've checked system logs and there seem to be no hardware failure. Also, as far as I can see, I'm not overusing memory allocation either. Anyone else experienced similar issues? Here follows output from error file : ----------------------------------------------------------------------------------------- HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5F.c line 1509 in H5Fopen(): unable to open file major: File accessability minor: Unable to open file #001: H5F.c line 1300 in H5F_open(): unable to read superblock major: File accessability minor: Read failed #002: H5Fsuper.c line 324 in H5F_super_read(): unable to load superblock major: Object cache minor: Unable to protect metadata #003: H5AC.c line 1597 in H5AC_protect(): H5C_protect() failed. major: Object cache minor: Unable to protect metadata #004: H5C.c line 3333 in H5C_protect(): can't load entry major: Object cache minor: Unable to load metadata into cache #005: H5C.c line 8177 in H5C_load_entry(): unable to load entry major: Object cache minor: Unable to load metadata into cache #006: H5Fsuper_cache.c line 469 in H5F_sblock_load(): truncated file major: File accessability minor: File has been truncated HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5Gdeprec.c line 214 in H5Gcreate1(): not a location major: Invalid arguments to routine minor: Inappropriate type #001: H5Gloc.c line 253 in H5G_loc(): invalid object ID major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5Adeprec.c line 153 in H5Acreate1(): not a location major: Invalid arguments to routine minor: Inappropriate type #001: H5Gloc.c line 253 in H5G_loc(): invalid object ID major: Invalid arguments to routine minor: Bad value [etc. etc. etc. ...... ] ------------------------------------------- Cheers, Jakob

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Einstein Toolkit Meeting Reminder
by Roland Haas 29 Jul '12

29 Jul '12

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differences in results between two versions of ET
by Yosef Zlochower 27 Jul '12

27 Jul '12

While trying to understand why the results from a BBH run differed when using the 2011_05 and 2011_10 version of ET I noticed that the two versions gave different results on every other point of the buffer region (in a 2 level run) on the 2nd time level. I reran the test using McLachlan and I found a similar behavior, but for fewer points (here, only 3, rather than 8) and only the innermost points. diff -w -u ~/ET/Old/Cactus/test/mc/gxx.x.asc ~/ET/Develop/Cactus/test/mc | grep "^[+-]2" -2 0 0 0 0 26 8 8 0.1 1.8 0 0 5.86163790879802 +2 0 0 0 0 26 8 8 0.1 1.8 0 0 5.86163790879801 -2 0 1 0 0 26 8 8 0.1 1.8 0 0 5.86163790879802 +2 0 1 0 0 26 8 8 0.1 1.8 0 0 5.86163790879801 -2 0 1 0 0 59 8 8 0.1 5.1 0 0 2.06954055131151 +2 0 1 0 0 59 8 8 0.1 5.1 0 0 2.06940807802512 -2 0 1 0 0 61 8 8 0.1 5.3 0 0 2.01672019300839 +2 0 1 0 0 61 8 8 0.1 5.3 0 0 2.01674238678588 -2 0 1 0 0 63 8 8 0.1 5.5 0 0 1.96875965038995 +2 0 1 0 0 63 8 8 0.1 5.5 0 0 1.96875664800624 One of the major differences between these two versions of ET is the switch from the git to hg version of carpet. Here is the full parfile that I used. #============================================================================== ActiveThorns = "admanalysis admbase admcoupling admmacros coordgauge spacemask StaticConformal boundary time cartgrid3d ioutil iobasic nanchecker CoordBase aeilocalinterp Slab SphericalSurface LocalReduce MoL Carpet CarpetInterp CarpetIOASCII CarpetLib CarpetReduce CarpetSlab CarpetRegrid2 SphericalSurface CarpetIOHDF5 CarpetIOScalar InitBase SymBase LoopControl GSL ReflectionSymmetry" ActiveThorns = "TimerReport" TimerReport::out_every = 512 TimerReport::out_filename = "TimerReport" Carpet::output_timers_every = 512 #------------------------------------------------------------------------------ # Run parameters #------------------------------------------------------------------------------ # Grid mol::ode_method = "RK4" mol::mol_intermediate_steps = 4 mol::mol_num_scratch_levels = 1 CoordBase::domainsize = "minmax" CoordBase::xmin = 0 CoordBase::ymin = 0 CoordBase::zmin = 0 CoordBase::xmax = 10 CoordBase::ymax = 10 CoordBase::zmax = 10 CoordBase::spacing = "numcells" CoordBase::ncells_x = 50 CoordBase::ncells_y = 50 CoordBase::ncells_z = 50 CartGrid3D::type = "coordbase" CartGrid3D::domain = "full" CartGrid3D::bitant_plane = "xy" CartGrid3D::avoid_originx = no CartGrid3D::avoid_originy = no CartGrid3D::avoid_originz = no CoordBase::boundary_size_x_lower = 4 CoordBase::boundary_size_y_lower = 4 CoordBase::boundary_size_z_lower = 4 CoordBase::boundary_shiftout_x_lower = 1 CoordBase::boundary_shiftout_y_lower = 1 CoordBase::boundary_shiftout_z_lower = 1 CoordBase::boundary_size_x_upper = 4 CoordBase::boundary_size_y_upper = 4 CoordBase::boundary_size_z_upper = 4 ReflectionSymmetry::reflection_x = yes ReflectionSymmetry::reflection_y = yes ReflectionSymmetry::reflection_z = yes ReflectionSymmetry::avoid_origin_x = no ReflectionSymmetry::avoid_origin_y = no ReflectionSymmetry::avoid_origin_z = no driver::ghost_size = 4 #--------------------------------------------------------------------------- cactus::cctk_itlast = 16 time::dtfac = .5 Carpet::domain_from_coordbase = yes Carpet::prolongation_order_space = 5 Carpet::prolongation_order_time = 2 Carpet::max_refinement_levels = 2 Carpet::use_buffer_zones = yes Carpet::verbose = no Carpet::schedule_barriers = no Carpet::veryverbose = no CarpetLib::output_bboxes = no CarpetLib::check_bboxes = no CarpetLib::interleave_communications = yes CarpetLib::combine_sends = yes #Carpet::time_refinement_factors = "[1,1,1,1,2,2,4,8,16,32,64]" Carpet::init_3_timelevels = "no" Carpet::init_each_timelevel = "no" Carpet::init_fill_timelevels = "yes" Carpet::enable_all_storage = no Carpet::regrid_during_recovery = no ActiveThorns="CarpetRegrid2" CarpetRegrid2::regrid_every = 16 CarpetRegrid2::num_centres = 1 CarpetRegrid2::num_levels_1 = 2 CarpetRegrid2::radius_1[ 1] = 5 # MODEL ActiveThorns="IDAnalyticBH" ADMBase::initial_data="bl_bh" IDAnalyticBH::bl_nbh = 2 IDAnalyticBH::bl_x0_1 = 1.01001 IDAnalyticBH::bl_y0_1 = 1.01001 IDAnalyticBH::bl_x0_2 = -1.01001 IDAnalyticBH::bl_y0_2 = -1.01001 initbase::initial_data_setup_method = init_some_levels admbase::metric_type = "Physical" #staticconformal::conformal_storage = "factor+derivs+2nd derivs" #--- numerics ActiveThorns = "ML_BSSN ML_BSSN_Helper TmunuBase GenericFD" ADMBase::evolution_method = "ML_BSSN" ADMBase::lapse_evolution_method = "ML_BSSN" ADMBase::shift_evolution_method = "ML_BSSN" ML_BSSN::timelevels = 3 ML_BSSN::harmonicN = 1 # 1+log ML_BSSN::harmonicF = 2.0 # 1+log ML_BSSN::ShiftGammaCoeff = 0.75 ML_BSSN::BetaDriver = 1.0 ML_BSSN::LapseAdvectionCoeff = 1 ML_BSSN::ShiftAdvectionCoeff = 1 ML_BSSN::my_boundary_condition = "Minkowski" ML_BSSN::ML_log_confac_bound = "none" ML_BSSN::ML_metric_bound = "none" ML_BSSN::ML_Gamma_bound = "none" ML_BSSN::ML_trace_curv_bound = "none" ML_BSSN::ML_curv_bound = "none" ML_BSSN::ML_lapse_bound = "none" ML_BSSN::ML_dtlapse_bound = "none" ML_BSSN::ML_shift_bound = "none" ML_BSSN::ML_dtshift_bound = "none" admbase::initial_lapse = "one" ADMBase::initial_shift = "zero" ADMBase::initial_dtlapse = "zero" ADMBase::initial_dtshift = "zero" #------------------------------------------------------------------------------ # Output #------------------------------------------------------------------------------ IO::out_dir = $parfile IO::out_fileinfo = "none" CarpetIOASCII::out1D_every = 1 CarpetIOASCII::out1D_vars = "admbase::alp admbase::metric admbase::curv admbase::shift " CarpetIOASCII::out1D_d=no

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[yates@cct.lsu.edu: Re: [Allcct] storage problems]
by Frank Loeffler 25 Jul '12

25 Jul '12

Hi, LSUThorns and LSUDevelopment might be affected by this hardware failure at LSU. Frank ----- Forwarded message from Adam Yates <yates(a)cct.lsu.edu> ----- Date: Wed, 25 Jul 2012 15:02:56 -0500 From: Adam Yates <yates(a)cct.lsu.edu> To: allcct(a)cct.lsu.edu Subject: Re: [Allcct] storage problems User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:13.0) Gecko/20120615 Thunderbird/13.0.1 List-Id: <allcct.cct.lsu.edu> Content-Type: text/plain; charset="us-ascii" Hi everyone, here is a brief update: We've sustained a failed controller in our storage solution from HP. This has not caused any data loss as far as we can tell. We are having a new controller shipped to us and it will be installed tomorrow morning. After that we should be back to production with our systems. Again, service on affected systems will be spotty at best. Please contact the helpdesk if you need specific files and we will do our best to provide them to you. In the next week or so we will also be performing a firmware upgrade on the storage to bring it up to the most current version. I will send out more information on this maintenance as the time draws near. Thanks! Adam On 07/25/2012 11:54 AM, Adam Yates wrote: > Hi everyone; > We are having some hardware failures with our central storage solution. > Some services may be intermittently available throughout the day as we > get the problems resolved. The services that are currently affected: > > web > subversion > nfs / samba (office drive) > compilers > shared software (matlab,comsol,tecplot,etc.) > > I will send out another update when we have some more information > from our vendor. > > Thanks! > Adam > -- Adam Yates Systems Administrator -- Research Infrastructure Center for Computation and Technology 231 Johnston Hall, Baton Rouge, LA 70803 W: 225.578.8235 C: 225.663.0218 <yates(a)cct.lsu.edu> _______________________________________________ Allcct mailing list Allcct(a)cct.lsu.edu https://mail.cct.lsu.edu/mailman/listinfo/allcct ----- End forwarded message -----

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schedule option LOCAL
by Petr Tsatsin 24 Jul '12

24 Jul '12

Hello, I scheduled some subroutines for my initial data thorn inside the "HydroBase_Initial" with option LOCAL, but then I realized that cctk_delta_space give me the delta space for the coarsest grid. I expected to get resolution of the "local" grids. Is that a bug or I misunderstood meaning of option LOCAL? -- Petr Tsatsin Graduate Student - Department of Physics Charles E. Schmidt College of Science Florida Atlantic University (561)-297-3386 cell: 561-692-2040 ptsatin(a)fau.edu, ptsatsin(a)gmail.com

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