Trac April 2012

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[Einstein Toolkit] #695: Don't buffer output from configuration scripts
by Einstein Toolkit 15 Nov '12

15 Nov '12

#695: Don't buffer output from configuration scripts ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | ----------------------+----------------------------------------------------- Output from configuration scripts is buffered, and is only output after the script has finished. This is inconvenient for long-running scripts. Instead, the output should be shown right away. This buffering is done in file lib/sbin/ConfigScriptParser.pl, which uses Perl backquotes `` to collect all of the script's output. Instead, Cactus should use a pipe to read the script's output line-by-line, and process it immediately. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/695> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #163: Assertion `tl>=0 and tl<timelevels' failed error
by Einstein Toolkit 13 Nov '12

13 Nov '12

#163: Assertion `tl>=0 and tl<timelevels' failed error ------------------------------------+--------------------------------------- Reporter: azebrowski@… | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: Carpet | Version: Keywords: | ------------------------------------+--------------------------------------- I'm currently running a Cactus simulation based off the ET mclachlan parameter file. I have some custom thorns which force checkpointing every iteration, and then write new parameter files. The new parameter files are used to run specific functions from the host simulation ("spawning"), but I'm having some problems resuming simulations. Currently, I get this error when resuming: INFO (Carpet): GF: rhs: 818k active, 1440k owned (+76%), 1896k total (+32%), 328 steps/time cactus_sim: /home/azebrowski/Cactus/arrangements/Carpet/CarpetLib/src/th.hh:79: double th::get_time(int, int, int) const: Assertion `tl>=0 and tl<timelevels' failed. [cyder:32759] *** Process received signal *** [cyder:32759] Signal: Aborted (6) I'm guessing there's a parameter I'm not setting properly in my child simulation, could anyone give me a pointer to where I should be looking? I looked for things relating to timelevels in the host/spawned parameter files, but didn't see anything that stood out. My parameter files used and full output are attached to this email, with the disclaimer that I modified the spawned parameter file to run every function instead of skipping some in an attempt to bypass any problems that could be caused by skipping some Carpet function on accident. I've made a bzipped tarball containing the checkpointed data from the simulation. It contains several parameter files. The parameter file of interest here is spawn.par, as it doesn't use any of my custom code but still causes Cactus to abort with an error. I left the other parameter files in on the off chance that I might need to refer to them later. Here is the source parameter file, which creates the spawned simulation: http://www.cct.lsu.edu/~azebrowski/ml-ahfinder-spawn.par Here is the spawned simulation's parameter file: http://www.cct.lsu.edu/~azebrowski/spawn.par Here is the full checkpointed data and another copy of the spawned parameter file: http://www.cct.lsu.edu/~azebrowski/data.tar.bz2 Other information: I ran the simulation using OpenMP with 12 cores to generate the checkpointed data. I've also tried MPI, but that didn't seem to make a difference. Thornlist: http://www.cct.lsu.edu/~azebrowski/ThornList gcc: azebrowski@cyder:~/Cactus$ gcc -v Using built-in specs. Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.4.3-4ubuntu5' --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable- shared --enable-multiarch --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4 --program-suffix=-4.4 --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-plugin --enable-objc-gc --disable-werror --with-arch-32=i486 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu Thread model: posix gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5) Fortran is gfortran-4.4 I'm using the Mercurial version of Carpet, and the ET development thorns. If you need more information, please let me know. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/163> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #434: Keep track of masked-out volume in CarpetMask
by Einstein Toolkit 08 Nov '12

08 Nov '12

#434: Keep track of masked-out volume in CarpetMask -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: eschnett Type: enhancement | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: | -------------------------+-------------------------------------------------- Keep track of the volume that is masked out by CarpetMask, and take this volume into account when checking in CarpetReduce that the integral over the simulation domain equals the domain volume. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/434> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #663: thornlists within Cactus should get cleaned up
by Einstein Toolkit 01 Nov '12

01 Nov '12

#663: thornlists within Cactus should get cleaned up -------------------------+-------------------------------------------------- Reporter: knarf | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: development version Keywords: | -------------------------+-------------------------------------------------- Most of the thornlists in https://svn.cactuscode.org/Utilities/trunk/Thornlist* are out of date, and should get cleaned up. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/663> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #361: delta_time when setting up ID with explicit time dependence
by Einstein Toolkit 28 Oct '12

28 Oct '12

#361: delta_time when setting up ID with explicit time dependence ------------------------------------------+--------------------------------- Reporter: eloisa.bentivegna@… | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: Carpet | Version: ET_2010_11 Keywords: | ------------------------------------------+--------------------------------- In CallInitial, delta_time is used to calculate the time corresponding to the different timelevels (line 399 of Carpet/src/Initialise.cc). At this stage, though, delta_time is always equal to 1, leading to potentially very separated initial-data slices when using init_each_timelevel and an initial-data thorn that uses cctk_time explicitly. Should cctkGH->cctk_delta_time be used here instead? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/361> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #323: GetComponents overwrites thorn list
by Einstein Toolkit 25 Oct '12

25 Oct '12

#323: GetComponents overwrites thorn list ---------------------------+------------------------------------------------ Reporter: eschnett | Owner: eric9 Type: defect | Status: new Priority: critical | Milestone: Component: GetComponents | Version: Keywords: | ---------------------------+------------------------------------------------ I specified a thorn list located in the main Cactus directory. GetComponents overwrote this thorn list with its own thorn list (the one it generates automatically). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/323> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #631: Documentation fails to build
by Einstein Toolkit 25 Oct '12

25 Oct '12

#631: Documentation fails to build ---------------------+------------------------------------------------------ Reporter: hinder | Owner: Type: defect | Status: new Priority: blocker | Milestone: Component: Cactus | Version: Keywords: | ---------------------+------------------------------------------------------ With the current ET, I cannot build the documentation: [ianhin@login-damiana EinsteinToolkit]$ make AllDoc Creating user documentation UsersGuide.pdf Running pdflatex.... ! Argument of \CA@getsvndate has an extra }. ! Paragraph ended before \CA@getsvndate was complete. ! Argument of \CA@getsvndate has an extra }. ! Paragraph ended before \CA@getsvndate was complete. ! Paragraph ended before \@parse@version was complete. ! Missing number, treated as zero. ! Missing = inserted for \ifnum. ! Missing number, treated as zero. ! LaTeX Error: Missing \begin{document}. ! Undefined control sequence. Problem in . See doc/UsersGuide/LATEX_MESSAGES. make: *** [UsersGuide] Error 1 I am attaching LATEX_MESSAGES. I have tried this both on damiana and on my laptop. I consider this a blocker issue which could delay the release. We must have working documentation. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/631> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #831: Cactus FAQ is out of date
by Einstein Toolkit 24 Oct '12

24 Oct '12

#831: Cactus FAQ is out of date ----------------------------+----------------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: major | Milestone: ET_2012_05 Component: Cactus website | Version: Keywords: | ----------------------------+----------------------------------------------- The FAQ at http://cactuscode.org/documentation/faq is ancient and some of its content is irrelevant now. It would be nice for this to be revised before the next release. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/831> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #797: N13CarpetRegrid211snap_coarseE does not hold after being enforced in cell centering
by Einstein Toolkit 23 Oct '12

23 Oct '12

#797: N13CarpetRegrid211snap_coarseE does not hold after being enforced in cell centering --------------------+------------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: Carpet | Version: Keywords: | --------------------+------------------------------------------------------- I have a run (on Caltech's shc and on lonestar) which runs fine for about 300M or so and then fails with a property enforcement error inside of CarpetRegrid. Attached please find stdout with Carpet::veryverbose=yes, CarpetRegrid2::veryverbose=yes as well as the parameter file. It takes about 1hr to reproduce this starting from the checkpoints on shc. Most of this time is IO (the checkpoint is iteration 133120 failure occurs at preregrid in iteration 133185). Turning off cell centering makes the error go away. Turning on refluxing makes the run fails (much) earlier with a boxes not contained error (re- running this on shc right now, the XSEDE clusters are just too slow). In case you have access to shc (or zwicky) and would look at the actual output files, the path is: /panfs/ds06/sxs/rhaas/cactus/simulations/noreflux/output-0003 -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/797> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #517: archive CactusExternal
by Einstein Toolkit 23 Oct '12

23 Oct '12

#517: archive CactusExternal -------------------------+-------------------------------------------------- Reporter: knarf | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- We should move the CactusExternal thorns to archive. They cause trouble and confusion where they are right now. This should happen for the next Cactus release. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/517> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac April 2012