Trac August 2011

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[Einstein Toolkit] #528: Use "andnot" instruction when vectorising
by Einstein Toolkit 25 Sep '11

25 Sep '11

#528: Use "andnot" instruction when vectorising -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- Use the "andnot" instruction to reduce the number of different bit masks that are required. Using fewer different bit masks may require fewer registers to hold them, or fewer load instructions to access them, thus potentially improving performance. Do not scalarize ifpos when SSE 4.1 is not available; instead, use logical operations to create a bit mask. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/528> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #451: Implement "dd" tensor type in symmetry conditions
by Einstein Toolkit 25 Sep '11

25 Sep '11

#451: Implement "dd" tensor type in symmetry conditions -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- The attached patch implements the "dd" tensor type (a full 3x3 tensor without symmetries) in the rotating symmetries. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/451> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #540: Change case in internal auto-generated file
by Einstein Toolkit 25 Sep '11

25 Sep '11

#540: Change case in internal auto-generated file -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: optional | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- Cactus auto-generates header files from CCL files into the bindings/include directory. One of these files is called ${thorn}_arguments.h, which stands out because "a" is lower case. Other auto-generated files are called e.g. ${thorn}_Schedule.h with an upper case "S". I suggest to change "arguments" to upper case "Arguments". -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/540> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #479: speed up VisIt's CarpetHDF5 plugin, set 2d masks
by Einstein Toolkit 25 Sep '11

25 Sep '11

#479: speed up VisIt's CarpetHDF5 plugin, set 2d masks -------------------+-------------------------------------------------------- Reporter: rhaas | Type: enhancement Status: new | Priority: minor Milestone: | Component: Other Version: | Keywords: CarpetHDF5 -------------------+-------------------------------------------------------- Hello all, the attached patches (when all of them are applied to VisIt's CarpetHDF5 plugin) speed up opening (large) HDF5 output files in VisIt by about a factor of 8. The two main speedups are replacing a linear search when translating from the Cactus iteration cctk_iteration to timestep (index) number and (surprisingly enough) the parsing of the Cactus variable name out of the dataset name rather than the "name" attribute (but it falls back to reading the attribute if the parsing fails). The third speed improvement is only visible when more than one file are opened and plotted. VisIt seems to consider reading metadata a cheap operation and creates and destroys the metadata object (avtCarpet...) very often. The patch caches metadata when VisIt destroys the object. This speeds up plotting several frames (or using the timestep slider) considerably, but has the unfortunate side effect that one cannot fully close files anymore (re-loading still works though). I attach timing information to show the gains. Data files and a python script to use with visit -cli -s openfile.py are provided at http://www.numrel.org/~rhaas3/CarpetHDF5/ . The data files are about 20MB when compressed and about 2-4GB when decompressed (they are actual data from one of my simulations with all values set to zero). There are three data sets provided. "flat" is the direct output from the Cactus simulation. "grouped" contains datasets from each timestep in a group of their own (grouping is mostly useful when mergin hdf5 files which is unbearably slow otherwise). "unchunked" used a python script to merge the individual Carpet components into the CarpetRegrid2 boxes (or equivalent), which results in much faster load times and smaller files (but is itself a slow operation). Code and scripts to group and unchunk hdf5 data is not yet public. If there is interested and I can post those as well but they are not nicely coded at all. The last patch (actually the first two by number) changes the way CarpetHDF5 sets up the nesting of components for 2D data so that eg. contour plots work properly (no more duplicate lines from the coarse points under fine points). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/479> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #459: Autodetect sched_getaffinity
by Einstein Toolkit 25 Sep '11

25 Sep '11

#459: Autodetect sched_getaffinity -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- The attached patch autodetects whether sched_getaffinity is available. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/459> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #514: Regenerate code for WeylScal4
by Einstein Toolkit 25 Sep '11

25 Sep '11

#514: Regenerate code for WeylScal4 -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- We need to regenerate the code for WeylScal4 with the current version of Kranc. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/514> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #443: Output a stack backtrace on a fatal error in a simulation
by Einstein Toolkit 21 Sep '11

21 Sep '11

#443: Output a stack backtrace on a fatal error in a simulation -------------------------+-------------------------------------------------- Reporter: hinder | Owner: eschnett Type: enhancement | Status: new Priority: major | Milestone: Component: Carpet | Version: Keywords: | -------------------------+-------------------------------------------------- When a Cactus simulation aborts with a signal, it is often difficult to determine which part of the code led to the problem. The attached patch registers a signal handler on Carpet startup for signals 11 and 6 (segmentation fault and abort, e.g. from assert()) which outputs a stack backtrace from each process to a file, including demangling symbol names. It uses some low-level and possibly unofficial APIs, and is likely not completely portable. However, I have tested it on Mac OS (gcc) and Linux (intel) and it works in those places. Part of this code was contributed by Justin Luitjens at the Carpet developers' workshop in summer 2010. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/443> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #482: GetComponents chokes on thorn list using DOS EOL characters in !DEFINEs
by Einstein Toolkit 21 Sep '11

21 Sep '11

#482: GetComponents chokes on thorn list using DOS EOL characters in !DEFINEs ---------------------------+------------------------------------------------ Reporter: rhaas | Owner: rhaas Type: defect | Status: new Priority: major | Milestone: Component: GetComponents | Version: Keywords: | ---------------------------+------------------------------------------------ the attached file uses DOS EOL conventions (ie. \r\n instead of the Unix typical \n) gives error messages: {{{ [rhaas3@phys44230 rhaas3]$ ./GetComponents --root dos --parallel cactus.th Unsuccessful stat on filename containing newline at ./GetComponents line 663. Unsuccessful stat on filename containing newline at ./GetComponents line 663. ----------------------------------------------------------------- Checking out module: Cactus from repository: http://svn.cactuscode.org/flesh/trunk into: dos as: . ----------------------------------------------------------------- Checking out module: CactusBase/Boundary from repository: http://svn.cactuscode.org/arrangements/CactusBase/Boundary/trunk into: dos/arrangements : No such file or directoryments Warning: Could not checkout module CactusBase/Boundary <some more of the same> ----------------------------------------------------------------- 1 components checked out. 0 components updated. Unable to process CactusBase/Boundary Unable to process CactusBase/CartGrid3D Unable to process CactusBase/CoordBase Unable to process CactusBase/InitBase Unable to process CactusBase/IOUtil Unable to process CactusBase/SymBase Unable to process CactusBase/Time Unable to process CactusNumerical/MoL Unable to process CactusBase/LocalInterp Unable to process CactusUtils/NaNChecker Unable to process CactusNumerical/Periodic Unable to process CactusUtils/Formaline Unable to process CactusNumerical/Slab Summary of Warnings: Could not checkout module CactusBase/Boundary Could not checkout module CactusBase/CartGrid3D Could not checkout module CactusBase/CoordBase Could not checkout module CactusBase/InitBase Could not checkout module CactusBase/IOUtil Could not checkout module CactusBase/SymBase Could not checkout module CactusBase/Time Could not checkout module CactusNumerical/MoL Could not checkout module CactusBase/LocalInterp Could not checkout module CactusUtils/NaNChecker Could not checkout module CactusNumerical/Periodic Could not checkout module CactusUtils/Formaline Could not checkout module CactusNumerical/Slab Time Elapsed: 0 minutes, 8 seconds }}} This is due to a \r which becomes part of the ARRANGEMENTS !DEFINE. A simple solution might be for GetComponents to remove whitespace from end of input lines via a: {{{ diff --git a/GetComponents b/GetComponents index 133487e..5e801f3 100755 --- a/GetComponents +++ b/GetComponents @@ -305,6 +305,9 @@ sub parse_list { my @lines = <$COMPONENT_LIST>; close($COMPONENT_LIST); + # convert CRNL and CR to newline (for lists generated by windows and macs) + map s/(\r\n|\r)/\n/gm, @lines; + # handle includes my $i = -1; foreach my $line (@lines) { }}} Note that his renders the CRtoNL regex on $file below useless (I am also not sure to what extent we need $orig_file to have the native EOL character). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/482> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #259: Update PETSc to 3.1p7
by Einstein Toolkit 20 Sep '11

20 Sep '11

#259: Update PETSc to 3.1p7 -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- The current version of 3.1p5, the difference are probably only small bug fixes. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/259> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #537: Formaline: Use bzip2 or xz if available to compress thorn source code
by Einstein Toolkit 18 Sep '11

18 Sep '11

#537: Formaline: Use bzip2 or xz if available to compress thorn source code -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- Formaline Could use bzip2 or xz if available to compress thorn source code; this would reduce the size of the tarballs by up to a factor of 2. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/537> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac August 2011