Trac January 2014

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[Einstein Toolkit] #1530: GRHydro updates
by Einstein Toolkit 27 Jan '14

27 Jan '14

#1530: GRHydro updates -------------------------+-------------------------------------------------- Reporter: rhaas | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: Other | Version: development version Keywords: | -------------------------+-------------------------------------------------- A large number of GRHydro updates have accumulated. Attached please find them all as well as a required update to EOS_Omni. Patches to follow in a bit. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1530> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1529: Included clickable link to archived posting in users list emails
by Einstein Toolkit 26 Jan '14

26 Jan '14

#1529: Included clickable link to archived posting in users list emails -------------------------------------+-------------------------------------- Reporter: rhaas | Owner: Type: enhancement | Status: new Priority: optional | Milestone: Component: EinsteinToolkit website | Version: development version Keywords: | -------------------------------------+-------------------------------------- I find myself often wanting to cite an email on the user's list in eg track tickets and usually want to provide a url to the email in the mailing list archive for this. Right now this requires me to manually navigate to the mailman archive (http://lists.einsteintoolkit.org/pipermail/users/) click on the relevant year and month and find the posting in question based on its subject line and author. It would be very nice is the emails were tagged with a unique identifier that could then be used to retrieve it from the mailing list archive (and if this tag showed up eg in the footer that already contains the url of the listinfo page). One such identifier that may be available would be the message number (eg 003400 for http://lists.einsteintoolkit.org/pipermail/users/2014-January/003400.html). I have no idea how hard providing this would be though. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1529> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1117: Wrong CarpetIOASCII headers for complex 2D output.
by Einstein Toolkit 25 Jan '14

25 Jan '14

#1117: Wrong CarpetIOASCII headers for complex 2D output. ----------------------------------------+----------------------------------- Reporter: reisswig@… | Type: defect Status: new | Priority: minor Milestone: | Component: Other Version: | Keywords: ----------------------------------------+----------------------------------- I am outputting a 2d _complex_ array (called "extracted_vars") using 2d CarpetIOASCII output. Using the standard output format, the data starts at column 13. So the first array element "extracted_vars[0]" is at column 13. Now, since I have a complex array, the second element, "extracted_vars[1]", must be at column 15 (column 14 contains the imaginary part of element [0]). In older versions of Carpet, this was reported correctly in the header. In the current version, it is incorrect. The second element, "extracted_vars[1]" is reported to be in column 14 instead of 15. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1117> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #542: Remove thorn CactusArchive/ADM from thorn list
by Einstein Toolkit 25 Jan '14

25 Jan '14

#542: Remove thorn CactusArchive/ADM from thorn list -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: task | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- Remove thorn CactusArchive/ADM from thorn list. This thorn is outdated, and we should updated out test cases instead. It also takes a long time and a lot of memory to compile. If we want an ADM formulation (which is doubtful since we don't use it ourselves), we should implement one via Kranc. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/542> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #114: per-variable tolerances for Cactus testsuites
by Einstein Toolkit 24 Jan '14

24 Jan '14

#114: per-variable tolerances for Cactus testsuites -------------------------+-------------------------------------------------- Reporter: knarf | Owner: Type: enhancement | Status: new Priority: major | Milestone: ET_2011_06 Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- It would be nice to be able to specify per-variable testsuite tolerances in Cactus (per regexp for the name in the ideal case). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/114> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1527: simfactory run script for bluewaters does not use -d or -cc numa_node
by Einstein Toolkit 23 Jan '14

23 Jan '14

#1527: simfactory run script for bluewaters does not use -d or -cc numa_node ------------------------+--------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: SimFactory | Version: development version Keywords: | ------------------------+--------------------------------------------------- the aprun man page states that {{{ For OpenMP applications, use both the OMP_NUM_THREADS environment variable to specify the number of threads and the aprun -d option to specify the number of CPUs hosting the threads. ALPS creates -n pes instances of the executable, and the executable spawns OMP_NUM_THREADS-1 additional threads per PE. }}} {{{-cc numa_node}}} is used on kraken (also a Cray using AMD cores) and lets threads migrate within a socket rather than tying them to an individual core. These changes improve run speed of qc0-mclachlan from 14 M/hr to 17 M/hr. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1527> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1525: cannt use environment variables in non-stringy parameters
by Einstein Toolkit 23 Jan '14

23 Jan '14

#1525: cannt use environment variables in non-stringy parameters --------------------+------------------------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: development version Keywords: | --------------------+------------------------------------------------------- the attached parfile, when run with {{{ TERMINATE_NEXT=no RUNTIME=12 TERMINATE=never RUNTITLE=test ~/data/postdoc/gr/Zelmani/exe/cactus_null env.par }}} produces an error {{{ WARNING level 0 in thorn Cactus processor 0 host horizon.tapir.caltech.edu (line 1 of env): -> Invalid assignment: Attempting to set a variable of type REAL with (STRING)"12" }}} preventing any number-valued parameter to be passed into the simulation via environment variables. In my case I wanted to use the runtime that I computed based on the information available in a qsub script (ie without using simfactory), which is useful to eg run several short Cactus runs in a single qsub script. It would be useful if (as in eg awk for data read from files) environment variables are considered to be "numeric strings" which can be converted to numbers if required. Boolean, string type parameters and keyword type parameters work fine. This is a regression compared to the old parser which did to the env expansion before the parsing stage so would allow env variables everywhere (though I think only on the RHS and not on the LHS of a parameter setting). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1525> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1524: Configure Script Processing Bug
by Einstein Toolkit 22 Jan '14

22 Jan '14

#1524: Configure Script Processing Bug ---------------------+------------------------------------------------------ Reporter: sbrandt | Owner: Type: defect | Status: new Priority: minor | Milestone: Cactus_4.3.0 Component: Cactus | Version: development version Keywords: | ---------------------+------------------------------------------------------ I was working on modifying the java code compiled during the Chemora project, and discovered that a syntax error in the java source file resulted in an infinite number of blank lines being sent to standard output. I traced the problem down to the fact that certain loops in ConfigScriptParser.pl don't check for end of file. The attached patch fixes that, and unifies some replicated code. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1524> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1526: CactusTest/TestArray outputs unitialized data for gf4d
by Einstein Toolkit 22 Jan '14

22 Jan '14

#1526: CactusTest/TestArray outputs unitialized data for gf4d -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: CactusTest | -----------------------------------+---------------------------------------- the current test arrays in CactusTest/TestArrays does not initialize the 4d array that it outputs. The data in the test output files apparently ended up being zero in the past but gives me poison on my machine right now. The attached patch adds the required code to fill in the 4d array the same way that the 0d-3d arrays are filled in. Passes the tests if I copy the 3d output files onto the 4d ones. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1526> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1519: Parameter parser leaks memory
by Einstein Toolkit 17 Jan '14

17 Jan '14

#1519: Parameter parser leaks memory --------------------+------------------------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: development version Keywords: | --------------------+------------------------------------------------------- The function cctk_PirahaParser in src/piraha/Call.cc wraps each argument to its set_function (points to CCTKi_SetParameter) in a strdup (with the exception of ActiveThorns). This leads to a memory leak since CTKi_SetParameter does not free() them. To test, run a minimal parfile {{{ Cactus::cctk_itlast = 42 }}} with an executable from an empty thornlist through valgrind: {{{ valgrind --log-file=valgrind.log --leak-check=full --tool=memcheck cactus_null answer.par }}} and you will find eg {{{ ==27121== 20 bytes in 1 blocks are definitely lost in loss record 297 of 1,362 ==27121== at 0x4C2935B: malloc (vg_replace_malloc.c:270) ==27121== by 0x6249D91: strdup (strdup.c:42) ==27121== by 0x43D1C1: cctk_PirahaParser (Call.cc:875) ==27121== by 0x419855: CCTKi_ProcessParameterDatabase (ProcessParameterDatabase.c:158) ==27121== by 0x416760: CCTKi_InitialiseCactus (InitialiseCactus.c:101) ==27121== by 0x415FFD: main (flesh.cc:64) }}} The attached patch fixes this. There is still some memory leakage (couple hundred bytes that seem to be due to the flesh and persist even when the old parser is reactivated). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1519> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac January 2014