__color__ ticket summary component version milestone type owner status created _changetime _description _reporter 4 6 Shock tube restart broken enzo defect somebody new 2007-04-23T19:10:37-0700 2007-04-23T19:10:37-0700 "Some sort of trouble with the boundary conditions file. Restart works for spherical infall. {{{ cable:~/Projects/lcatest/runs/R0014/AMRShockTubeRestart-serial rpwagner$ ~/Projects/Enzo/bin/enzo -r DD0000/data0000 MPI_Init: NumberOfProcessors = 1 ========================= Enzo SVN Branch svn://mngrid.ucsd.edu/Enzo/branches/rpwagner/Enzo Enzo SVN Revision 387 ========================= Output to Global Dir /Users/rpwagner/Projects/lcatest/runs/R0014/AMRShockTubeRestart-serial HDF5-DIAG: Error detected in HDF5 library version: 1.6.5 thread 0. Back trace follows. #000: H5D.c line 1146 in H5Dopen(): not found major(15): Dataset interface minor(48): Object not found #001: H5G.c line 2296 in H5G_find(): object not found major(10): Symbol table layer minor(48): Object not found #002: H5G.c line 1495 in H5G_namei(): component not found major(10): Symbol table layer minor(48): Object not found #003: H5Gstab.c line 164 in H5G_stab_find(): not found major(10): Symbol table layer minor(48): Object not found #004: H5Gnode.c line 975 in H5G_node_found(): not found major(10): Symbol table layer minor(48): Object not found HDF5_Grid_ReadGrid.C:315: failed assertion `dset_id != h5_error' [cable:03549] *** Process received signal *** [cable:03549] Signal: Abort trap (6) [cable:03549] Signal code: (0) [ 1] (kill + 0xc) [0x00000000, 0x900484cc] (F--) [ 2] (abort + 0x5c) [0xbfffd180, 0x9012e934] [ 3] (_ZN9__gnu_cxx18__exchange_and_addEPVii + 0x0) [0xbfffd1e0, 0x94bec0b0] [ 4] (ZN4grid8ReadGridEP7__sFILEbb:F(0,3) + 0xd74) [0xbfffd230, 0x00264b1c] [ 5] (Z17ReadDataHierarchyP7__sFILEP14HierarchyEntryiS2_:F(0,3) + 0x1ac) [0xbfffd960, 0x001a5fe4] [ 6] (Z11ReadAllDataPcP14HierarchyEntryR11TopGridDataP16ExternalBoundary:F(0,1) + 0x268) [0xbfffd9d0, 0x001a49ec] [ 7] (main:F(0,473) + 0x540) [0xbfffde30, 0x00003534] [ 8] (start:F(0,1) + 0x154) [0xbfffe560, 0x000027ec] [ 9] (start + 0x3c) [0xbfffe5c0, 0x00002694] [10] [0xbfffe600, 0x00000000] (-P-) [11] [0x00000000, 0xffffffffffffffff] (FP-) [cable:03549] *** End of error message *** Abort trap cable:~/Projects/lcatest/runs/R0014/AMRShockTubeRestart-serial rpwagner$ cd DD0000/ cable:~/Projects/lcatest/runs/R0014/AMRShockTubeRestart-serial/DD0000 rpwagner$ ls Enzo_Options data0000.boundary data0000.grid0001 perfdata_1.0 data0000 data0000.boundary.hdf data0000.hierarchy cable:~/Projects/lcatest/runs/R0014/AMRShockTubeRestart-serial/DD0000 rpwagner$ h5ls data0000.boundary.hdf BoundaryDimensionType.0 Dataset {6} BoundaryDimensionValue.0 Dataset {6} cable:~/Projects/lcatest/runs/R0014/AMRShockTubeRestart-serial/DD0000 rpwagner$ }}}" rpwagner 4 10 Remove hard-coded path from hierarchy file enzo enhancement somebody new 2007-05-14T10:36:17-0700 2007-05-14T10:36:17-0700 Requested by dcollins@physics.ucsd.edu jbordner 4 11 2 processors different than 1 enzo defect Anyone with patience. new 2007-06-04T10:48:27-0700 2007-06-04T10:48:57-0700 "Some runs give slightly different answers on 2 processors than 1. 64 cubed turbulence, 6 timesteps, with PPM and PPM-L. Errors on the order of 1e-5 Hacking out driving (by return SUCCESS at the top of AddRandomForcing): PPM-L works just fine, PPM still gives errors Not big errors, but it's annoying." dcollins 4 15 Memory leaks enzo defect anyone new 2007-10-16T17:21:42-0700 2007-10-16T17:25:47-0700 "The following were detected as memory leaks by the {{{MemoryScape}}} tool: {{{CosmologySimulationInitialize.C:231}}} {{{ReadParameterFile.C:499}}} {{{CosmologyReadParameters.C:29}}} {{{FastSib_MPICH_EvolveLevelRoutinesOptimized.C:800}}} {{{LevelHierarchy_AddLevel.C:38}}} " jbordner 3 25 add wiki docs on file format schema documentation Enzo v1.5 documentation feature request mturk new 2008-05-30T14:32:19-0700 2008-09-07T22:00:55-0700 please add doc on enzo file format schema. Wiki page is FileFormatSchema. bwoshea 4 37 Restart on different number of processors enzo task somebody new 2008-08-08T14:22:44-0700 2008-08-08T14:22:44-0700 (re)implement support for restarting Enzo with an increased processor count. jbordner 3 38 Analysis Tools - Projections enzo devel svn task rpwagner assigned 2008-08-26T10:03:55-0700 2008-09-05T12:26:55-0700 "== TODO == Roll projection tool into trunk. == Analysis Tools for Trunk == This is one of a list of analysis tools that need be merged into the devel trunk." rpwagner 3 39 Analysis Tools - Extractions enzo devel svn task rpwagner assigned 2008-08-26T10:04:45-0700 2008-09-05T12:27:03-0700 "== TODO == Build parallel extraction tool. == Analysis Tools for Trunk == This is one of a list of analysis tools that need be merged or built for the devel trunk." rpwagner 3 40 Analysis Tools - Directory Articulation enzo devel svn task rpwagner assigned 2008-08-26T10:05:49-0700 2008-09-05T12:27:12-0700 "== TODO == Add directory articulation to inline analysis tools. == Analysis Tools for Trunk == This is one of a list of analysis tools that need be merged into the devel trunk." rpwagner 3 41 Analysis Tools - Restart Correctly enzo devel svn bug rpwagner assigned 2008-08-26T10:06:56-0700 2008-09-05T12:26:48-0700 "== TODO == Make sure the inline analysis tools don't reset when restarting. == Analysis Tools for Trunk == This is one of a list of analysis tools that need be merged into the devel trunk." rpwagner 4 42 build system optimization flags enzo devel svn Enzo 1.5 Code Development task jbordner new 2008-08-26T14:00:47-0700 2008-08-26T14:00:47-0700 "The current build system requires that all four of the C, C++, Fortran and Fortran90 compilers accept the identical optimization flags, due to the use of Makefile definitions MACH_OPT_WARN, MACH_OPT_DEBUG, MACH_OPT_HIGH and MACH_OPT_AGGRESSIVE. For many compilers, these options are not the same when calling the C/C++ and F77/F90 compilers (e.g. icc and ifort, gcc and g95, etc.). I suggest that we update these flags to be language-specific. Since the build system already allows for different C, C++, F, F90 and LD executables, we should have the full set of MACH_OPT_{C,CXX,F,F90,LD}_{WARN,DEBUG,HIGH,AGGRESSIVE} definitions, where the appropriate ones are selected as usual according to the optimization level. " dreynolds 3 47 Write wiki tutorial on adding new baryon fields documentation 1.5 Enzo v1.5 documentation task dcollins new 2008-09-04T13:23:01-0700 2008-09-04T13:23:01-0700 Please modify [wiki:Tutorials/HowToAddNewBaryonField] to explain to users how to add a new baryon field. Include files that need to be modified, what to add, what should not be touched, etc. bwoshea 3 49 Create wiki documentation on file format schema documentation 1.5 Enzo v1.5 documentation task mturk new 2008-09-04T13:25:28-0700 2008-09-04T13:34:58-0700 Create wiki documentation describing Enzo's file format schema. Current page is FileFormatSchema. 3 50 Write wiki tutorial on how to add new refinement criteria documentation 1.5 Enzo v1.5 documentation task mturk new 2008-09-04T13:26:56-0700 2008-09-04T13:26:56-0700 "Write a wiki tutorial on how to add new refinement critiera. Current page is [wiki:Tutorials/AddingRefinementCriteria]. Please mention files that you have to add, files to modify (including headers), and where added files need to be called. " bwoshea 3 54 Merge Evolve Routines enzo devel svn task dcollins new 2008-09-05T12:16:36-0700 2008-09-05T12:16:36-0700 "Merge *Evolve* into single files per function. " rpwagner 3 55 Merge Write & Read Routines enzo devel svn task rpwagner assigned 2008-09-05T12:18:43-0700 2008-09-05T12:21:11-0700 "Merge *Write* *Read* routines/files into one file per functionality. == Note to self: == * Pass grid hid_t pointer to open group or open file. * Split hierarchy info writing out to new file, make it easier to add HDF5 hierarchy file. == Note to others == This is for things are called from ReadAllData, or WriteAllData, not movies or other formats." rpwagner 3 59 Update flowchart to reflect v1.5 documentation task dcollins new 2008-09-10T10:41:35-0700 2008-09-10T10:41:35-0700 "Source pointers and line anchors in flowchart. Sed on most references #L[\d]{0,3} goes to @tag#L(\1) " dcollins 3 61 yt build instructions documentation task mturk new 2008-09-16T06:31:43-0700 2008-09-16T06:31:43-0700 I'm working on a new script to install YT from within the source distribution. This information needs to be added to an appropriate place in the Enzo Wiki, too. mturk 4 62 Enzo needs to be quieter enzo devel svn feature request somebody new 2008-09-17T14:59:00-0700 2008-09-17T23:30:21-0700 "Enzo currently spews an excessive amount out information to stderr and stdout, for things that are purely informational. This should be minimized, by wrapping statements in conditionals, like {{{ if(MyProcessorNumber == ROOT_PROCESSOR && debug) printf(""My FORTRAN style debugging information\n""); }}} By default, I think some top grid cycle info, and data output notification is sufficient. Error messages should be the only thing using stderr. " rpwagner 4 68 Move all constants to phys_constants.h enzo devel svn feature request somebody new 2008-09-23T21:30:03-0700 2008-09-23T21:30:03-0700 "{{{M_PI}}} has been in standard math headers for a while (along with other convenient numbers). We should get in the habit of defining the constants in one place (i.e., [browser:public/trunk/src/enzo/phys_constants.h phys_constants.h]), and being consistent. {{{ rpwagner@cable:~/Projects/analysis_merge/src/enzo$ grep '3\.14' *C Grid_AddExternalAcceleration.C: float Pi = 3.14159, accel; Grid_CollapseTestInitializeGrid.C: pi = 3.14159, mh = 1.67e-24, kboltz = 1.381e-16; Grid_FlagCellsToBeRefinedByJeansLength.C: FLOAT JLSquared = (double(3.14159*1.38e-16/6.67e-8)/ Grid_FlagCellsToBeRefinedByJeansLength.C: JLSquared = double(4.0*3.14159*3.14159)/GravitationalConstant; //AK Grid_PrepareGreensFunction.C: float GravConst, pi = 3.14159; Grid_PreparePeriodicGreensFunction.C: const float twopi = 2.0*3.14159; Grid_SetMinimumSupport.C: const float pi = 3.14159; Grid_TestGravityCheckResults.C: float r, fanalytic, fradial, ftang, pi = 3.14159; Grid_TestGravityInitializeGrid.C: float phi, r, theta, pi = 3.14159; Grid_TestGravitySphereInitializeGrid.C: float phi, r, theta, pi = 3.14159; Grid_TestOrbitInitializeGrid.C: VelocityUnits = 1, TimeUnits = 1, MassUnits = 1, pi = 3.1415926; Grid_ZeldovichPancakeInitializeGrid.C: const float Pi = 3.14159; PrepareIsolatedGreensFunction.C: float GravConst, pi = 3.14159; RotatingCylinderInitialize.C: float Pi = 3.14159; SedovBlastInitialize.C: float Pi = 3.14159; SetDefaultGlobalValues.C: const float Pi = 3.14159; SupernovaRestartInitialize.C: (4.0/3.0*3.14159*POW(EjectaRadius, 3)); rpwagner@cable:~/Projects/analysis_merge/src/enzo$ }}}" rpwagner 4 71 Incorrect HD cooling rate in the low density limit enzo devel svn bug bwoshea new 2008-10-07T03:34:07-0700 2008-10-07T09:24:14-0700 " The expression given in Galli & Palla (1998) for the low density HD cooling rate is incorrect: it includes cooling from the 0->1 and 1->2 collisional transitions, but in the low density limit this should actually be 0->1 and 0->2. (NB Daniele Galli has confirmed to me that this is a mistake in the original paper). The attached patch for calc_rates.src corrects this problem. The revised rate gives roughly 25-30% less cooling at temperatures between 100 and 200 K. " sglover 3 74 problems with building enzo enzo task somebody new 2008-11-03T07:42:40-0800 2008-11-03T07:42:40-0800 "I've encountered two problems with building enzo on a Linux PC: (1) should be trivial to fix: upon compiling wall_clock.c wall_clock.c(19): error: argument of type ""void *"" is incompatible with parameter of type ""timezone *"" gettimeofday(×tr, Tzp); (2) after commenting out that line, compilation succeeds for all files; but linking yields many undefined references (out.compile attached); might be related to the machine-specific configuration (attached file Make.mach.astrowue) " wschmidt 3 76 Restarting from Old Enzo Datasets enzo devel svn task Whoever has a minute. new 2008-11-10T12:36:36-0800 2008-11-10T12:36:36-0800 "Ensure Enzo1.5 can restart from old datasets with zero hassle from the user. Things I've found so far: 1. Task = ? line in hierarchy: a. Check for the lines existence. a. If it isn't there, set some reasonable default (probably round-robin over grids) 1. Make sure this works with old Packed formats." dcollins 4 77 Better referencing documentation 1.5 Enzo Web Site task sskory new 2008-11-21T14:54:22-0800 2008-12-10T09:56:00-0800 "There are some references in the wiki pages to papers that are incomplete (like Joe & Dave 1999) which aren't enough to know what it is. This needs to be fixed. I may do this eventually as much as I can, but I felt that it was important enough to make a ticket about it. I'm assigning it to myself but the rest of ya'll can feel free to fix this." sskory 4 78 pseudo-fields and the FieldTypeIsDensity macro enzo 1.5 Enzo 1.5 Code Development task somebody new 2009-01-08T14:49:21-0800 2009-03-25T17:00:48-0700 "In the conversion to Enzo 1.5, a number of additional field types were added to typedefs.h (pseudo-fields). Immediately following their definition is an existing macro, FieldTypeIsDensity, that returns TRUE or FALSE depending on whether the argument is a density field or not. This macro is now incorrect, given the newly-defined fields. My question is this: will that cause a problem? The FieldTypeIsDensity macro is used throughout the AMR handling of parent/child interfaces, so I would be somewhat concerned that any 'pseudo-field' (or for that matter a new emissivity field -- Geoffrey), would be treated incorrectly." dreynolds 3 88 Protostellar Collapse is broken documentation bug bwoshea new 2009-12-11T08:58:54-0800 2009-12-11T08:58:54-0800 The protostellar collapse problem is currently broken. Allocation of the temperature field fails on flagging method 6. Additionally, even with Jeans on, the test problem fails in the hydro method. mturk 2 90 Bug in week-of-code: CreateSUBlingList.C:[135|137] enzo 2.0 bug dcollins assigned 2010-04-12T16:47:59-0700 2010-04-13T11:07:13-0700 "Crashes or hangs at new[] or delete[], which indicates corruption of the dynamic memory heap. Affects the following problems: * SedovBlastAMR * ImplosionAMR {{{ #0 __lll_lock_wait () at ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:136 #1 0x00007f89673e0295 in _L_lock_949 () from /lib/libpthread.so.0 #2 0x00007f89673e00b8 in __pthread_mutex_lock (mutex=0x7f89684c0d00) at pthread_mutex_lock.c:61 #3 0x00007f896823836e in free () from /usr/lib/liblam.so.4 #4 0x00007f8968ea028e in H5MM_xfree () from /usr/lib/libhdf5-1.6.6.so.0 #5 0x00007f8968e9fb90 in H5I_destroy_group () from /usr/lib/libhdf5-1.6.6.so.0 #6 0x00007f8968e53acf in H5D_term_interface () from /usr/lib/libhdf5-1.6.6.so.0 #7 0x00007f8968e426a5 in H5_term_library () from /usr/lib/libhdf5-1.6.6.so.0 #8 0x00007f89670a0c12 in __run_exit_handlers (status=1) at exit.c:78 #9 *__GI_exit (status=1) at exit.c:100 #10 0x00007f89681e3ee9 in _cio_bail () from /usr/lib/liblam.so.4 #11 0x00007f8968233407 in ?? () from /usr/lib/liblam.so.4 #12 #13 0x00007f8968239bbb in _int_malloc () from /usr/lib/liblam.so.4 #14 0x00007f896823afcf in malloc () from /usr/lib/liblam.so.4 #15 0x00007f8967b5564d in operator new(unsigned long) () from /usr/lib/libstdc++.so.6 #16 0x00007f8967b55769 in operator new[](unsigned long) () from /usr/lib/libstdc++.so.6 #17 0x0000000000466adb in CreateSUBlingList (MetaData=0x7fff7186db40, LevelArray=0x7fff7186de50, level=1, SiblingList=0x514d880, SUBlingList=0x7fff7186cf28) at CreateSUBlingList.C:135 #18 0x000000000047e9cf in EvolveLevel (MetaData=0x7fff7186db40, LevelArray=0x7fff7186de50, level=1, dtLevelAbove=7.8791696844059342e-05, Exterior=0x7fff7186d2f0) at EvolveLevel.C:581 #19 0x000000000047e866 in EvolveLevel (MetaData=0x7fff7186db40, LevelArray=0x7fff7186de50, level=0, dtLevelAbove=7.8791696844059342e-05, Exterior=0x7fff7186d2f0) at EvolveLevel.C:545 #20 0x0000000000475201 in EvolveHierarchy (TopGrid=..., MetaData=..., Exterior=0x7fff7186d2f0, LevelArray=0x7fff7186de50, Initialdt=0) at EvolveHierarchy.C:455 #21 0x000000000040c196 in main (argc=3, argv=0x7fff7186e488) at enzo.C:631 }}} " jbordner 3 93 Bug in week-of-code: NohProblem3DAMR generates 'Too Many Shearing Boundaries' exception at CheckShearingBoundaryConsistency.C:36 enzo 2.0 bug sskillman assigned 2010-04-12T17:06:39-0700 2010-04-13T07:53:09-0700 "{{{ Caught fatal exception: 'Too Many Shearing Boundaries' at CheckShearingBoundaryConsistency.C:36 Backtrace: BT symbol: ./enzo [0x41014e] BT symbol: ./enzo [0x426024] BT symbol: ./enzo [0x62dce6] BT symbol: ./enzo [0x5a3066] BT symbol: ./enzo [0x40bfff] BT symbol: /lib/libc.so.6(__libc_start_main+0xfd) [0x7ff25dab2abd] BT symbol: ./enzo [0x40b599] terminate called after throwing an instance of 'EnzoFatalException' MPI_Init: NumberOfProcessors = 1 Initialdt in ReadParameterFile = 0.000000e+00 }}} " jbordner 3 96 Bug in week-of-code: CollapseTest has no stopping criteria enzo 2.0 bug britton new 2010-04-12T17:14:29-0700 2010-04-12T20:56:18-0700 "Stopping criteria are commented out: {{{ % grep Stop CollapseTest.enzo #StopTime = 0.0002 #StopCycle = 4 }}}" jbordner 4 97 Bug in week-of-code: Driving Turbulence (presumably in ether /src/enzo/hydro_rk/Turbulence_Generator.C or /src/enzo/hydro_rkGrid_TurbulenceInitializeGrid.C enzo devel svn bug somebody new 2010-04-13T16:45:33-0700 2010-04-13T16:45:33-0700 When running DrivenTurbulence3D.enzo (now updated to problemtype = 106) the Turbulence seems to be driven to remain around Mach 6 even if in Parameter file it is set to Mach = 10 or Mach = 15. Initial decaying Turbulence is correct but decays to ~ 6 and then remains there! eharperclark 3 100 1DHydroShockTubes: fatal exception at hydro_rk/HydroSweepX.C:126 enzo 2.0 bug somebody new 2010-04-21T11:26:01-0700 2010-04-21T11:26:01-0700 "Single-processor [http://client65-77.sdsc.edu/~bordner/lcatest-woc-default-1/runs/R1349/1DHydroShockTubes/index.html lcatest run] on Linux platform of 1DHydroShockTubes generates a fatal exception after the initial timestep. Output with trace: {{{ Caught fatal exception: '' at hydro_rk/HydroSweepX.C:126 Backtrace: BT symbol: ./enzo(_ZN18EnzoFatalExceptionC1EPKcS1_i+0x3a) [0x43958c] BT symbol: ./enzo(_Z11HydroSweepXPPdS0_PxS1_S0_dx+0xb21) [0x71af79] BT symbol: ./enzo(_ZN4grid7Hydro3DEPPdS1_dPP6fluxesxdx+0x3bc) [0x70af84] BT symbol: ./enzo(_ZN4grid19RungeKutta2_1stStepEPP6fluxesxxP16ExternalBoundary+0x842) [0x70da46] BT symbol: ./enzo(_Z15EvolveLevel_RK2P11TopGridDataPP19LevelHierarchyEntryxdP16ExternalBoundaryd+0x9d3) [0x6fd8c7] BT symbol: ./enzo(_Z15EvolveHierarchyR14HierarchyEntryR11TopGridDataP16ExternalBoundaryPP19LevelHierarchyEntryd+0x100d) [0x49f255] BT symbol: ./enzo(main+0xb42) [0x434c46] BT symbol: /lib/libc.so.6(__libc_start_main+0xfd) [0x7f7886f0ac4d] BT symbol: ./enzo() [0x434049] Failure reported on processor 0 }}}" jbordner 3 102 fatal exception in Group_WriteGrid enzo 2.0 bug somebody reopened 2010-04-21T11:41:31-0700 2010-04-22T13:36:20-0700 "lcatest runs of the following test problems crash in various ways in Group_WriteGrid (links to output) * [http://client65-77.sdsc.edu/~bordner/lcatest-yoc-default-1/runs/R1337/HD-Sedov-Taylor-BlastWave/4.output HD-Sedov-Taylor-BlastWave] * [http://client65-77.sdsc.edu/~bordner/lcatest-yoc-default-1/runs/R1337/MHD2DBlastWave/4.output MHD2DBlastWave] FIXED IN changeset 1337: * [http://client65-77.sdsc.edu/~bordner/lcatest-yoc-default-1/runs/R1332/RampedKelvinHelmholtz2D/4.output RampedKelvinHelmholtz2D] * [http://client65-77.sdsc.edu/~bordner/lcatest-yoc-default-1/runs/R1332/HDMHD2DCheckOddEvenCouplingOfRiemannSolver/4.output HDMHD2DCheckOddEvenCouplingOfRiemannSolver]" jbordner 4 106 Append show-diff to output files enzo 2.0 feature request sskillman assigned 2010-05-11T16:18:58-0700 2010-05-11T16:32:46-0700 It would be nice to have the show-diff output along with the show-flags/config/version in the datadump.configure file. It would probably be best to put in a .source_diff file so that it doesn't overwhelm the .configure file. sskillman