Trac September 2012

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[Einstein Toolkit] #918: Usage of appendix in both UsersGuide and ReferenceManual
by Einstein Toolkit 20 Oct '12

20 Oct '12

#918: Usage of appendix in both UsersGuide and ReferenceManual -------------------------+-------------------------------------------------- Reporter: knarf | Owner: Type: enhancement | Status: new Priority: minor | Milestone: ET_2012_11 Component: Cactus | Version: development version Keywords: | -------------------------+-------------------------------------------------- The usage of the appendix of the UsersGuide inside the ReferenceManual led to a lot of internal references being commented out. This probably happened when UsersGuide and ReferenceManual had been divided, but it means that currently a lot of useful information is missing. In #885 there is agreement that the best solution would be to have the appendix included only by one of the two documents, and to restore references as much as possible. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/918> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #990: Cacuts documentation describes staggering
by Einstein Toolkit 20 Oct '12

20 Oct '12

#990: Cacuts documentation describes staggering ---------------------------+------------------------------------------------ Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: Documentation | ---------------------------+------------------------------------------------ didn't we recently remove this? The docs are at: http://einsteintoolkit.org/documentation/UsersGuide/UsersGuidech9.html#x13-… It also still mentions cctk_lssh which was removed. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/990> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1021: Fortran example for CCTK_Equals in the reference guide has multiple issues
by Einstein Toolkit 20 Oct '12

20 Oct '12

#1021: Fortran example for CCTK_Equals in the reference guide has multiple issues ---------------------------+------------------------------------------------ Reporter: hinder | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: documentation | ---------------------------+------------------------------------------------ The example for CCTK_Equals in the reference guide (http://cactuscode.org/documentation/referencemanual/ReferenceManualch2.html…) has an errant semicolon and does not include the macro DECLARE_CCTK_FUNCTIONS which seems to be needed for CCTK_Equals to be used. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1021> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1081: Add index file support for sliced output to CarpetIOHDF5
by Einstein Toolkit 20 Oct '12

20 Oct '12

#1081: Add index file support for sliced output to CarpetIOHDF5 -------------------------+-------------------------------------------------- Reporter: hinder | Owner: eschnett Type: enhancement | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: | -------------------------+-------------------------------------------------- CarpetIOHDF5 has support for writing an "index" file alongside the normal HDF5 output files. This is an HDF5 file in which the datasets are present but contain no data. This index file is much faster to read than the full HDF5 file (due to locality of data in the index file and block reads on slow filesystems) and can significantly speed up analysis of the data. Index files are currently written for the "standard" (typically 3D) data in Output.cc, but are not written for the "sliced" data in OutputSlice.cc. Since visualisation of 2D data is very common, OutputSlice.cc should be modified to output index files as well. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1081> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1109: LoopControl::printstats should default to "no"
by Einstein Toolkit 19 Oct '12

19 Oct '12

#1109: LoopControl::printstats should default to "no" -------------------------+-------------------------------------------------- Reporter: hinder | Owner: eschnett Type: enhancement | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: | -------------------------+-------------------------------------------------- LoopControl::printstats should default to "no". The output is not important enough to show to the user unless they ask for it. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1109> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #928: openmp parallelization within Exact broken
by Einstein Toolkit 13 Oct '12

13 Oct '12

#928: openmp parallelization within Exact broken --------------------+------------------------------------------------------- Reporter: knarf | Owner: Type: defect | Status: new Priority: major | Milestone: ET_2012_05 Component: Other | Version: Keywords: | --------------------+------------------------------------------------------- Exact uses openmp for the loop over grid points. However, quite a few metrics (which get called pointwise) use static (saved) data. In all cases I have looked at this is only used to initialize some local variables with values from Cactus parameters - and only as long as a 'global' variable 'firstcall' is true. This variable is set to 'false' after the other variables had been initialized, which should be ok even when using multiple threads. However, the compiler can switch the two (and does according to the assembly output), leading to another thread 'seeing' first_call being false, but the global variables not being initialized yet. The right solution would be to remove these variables. They are not really necessary, because the Cactus parameters could directly be used. However, that patch would be quite large. A simple and quick workaround would be to remove the openmp parallelization for that loop, at least for the upcoming release. We have to do one of the two - or something else in case someone comes up with another idea. This is currently breaking several testsuites (sometimes). In case you want to see an example: look at de_Sitter.F77 and firstcall and arad. Thoughts? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/928> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #902: carpetioascii with compact_format writes wrong set of columns
by Einstein Toolkit 11 Oct '12

11 Oct '12

#902: carpetioascii with compact_format writes wrong set of columns ---------------------------+------------------------------------------------ Reporter: rhaas | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: carpetioascii | ---------------------------+------------------------------------------------ For 0d output (in my case systemstatistics data) I get: {{{ # SYSTEMSTATISTICS::PROCESS_MEMORY_MB (systemstatistics::process_memory_mb) # # column format: 1:it 2:ix 3:time 4:x 5:data # data columns: 5:maxrss_mb 6:majflt_mb 7:arena_mb 8:ordblks_mb 9:hblks_mb 10:hblkhd_mb 11:uordblks_mb 12:fordblks_mb 13:keepcost_mb 14:swap_used_mb 3840 0 5.76 4956 23 628 0 0 651 -1189 1818 17 0 4096 0 6.144 5100 23 726 0 0 651 -1188 1915 21 0 }}} Note that the headers claim 14 columns but counting them, there are only 13 columns. From the look of it the "x" column is absent (since 4956 makes sense for being MB of memory used and 5.76 is clearly the time) -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/902> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1107: New thorn ML_WaveToy_Test
by Einstein Toolkit 09 Oct '12

09 Oct '12

#1107: New thorn ML_WaveToy_Test -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- I propose to add a new thorn ML_WaveToy_Test to the Einstein Toolkit. This thorn exists in the McLachlan arrangement and complements the auto- generated McLachlan/ML_WaveToy with test cases. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1107> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #946: Undefined symbol ___emutls_get_address
by Einstein Toolkit 09 Oct '12

09 Oct '12

#946: Undefined symbol ___emutls_get_address ------------------------+--------------------------------------------------- Reporter: hinder | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: SimFactory | Version: Keywords: | ------------------------+--------------------------------------------------- When I try to compile on Mac OS using the SimFactory optionlist macos- fink-gcc.cfg (https://svn.cct.lsu.edu/repos/numrel/simfactory2/trunk/mdb/optionlists /macos-fink-gcc.cfg), I get the following error at link time: {{{ ld: warning: alignment lost in merging tentative definition _tmunubaserest_ ld: warning: alignment lost in merging tentative definition _admmacrosrest_ ld: warning: alignment lost in merging tentative definition _staticconformalrest_ Undefined symbols: "___emutls_get_address", referenced from: __ZN4dist25collect_total_num_threadsEv.omp_fn.0 in libthorn_CarpetLib.a(dist.cc.o) dist::collect_total_num_threads() in libthorn_CarpetLib.a(dist.cc.o) Carpet::SetupGH(tFleshConfig*, int, _cGH*) in libthorn_Carpet.a(SetupGH.cc.o) ld: symbol(s) not found collect2: ld returned 1 exit status make[1]: *** [/Users/ian/Cactus/Kerrness/exe/cactus_sim] Error 1 make: *** [sim] Error 2 }}} I don't know if the "alignment lost" warnings are related to the fatal error. This seems to be some issue related to OpenMP. The problem appeared fairly recently, as I have been able to compile older versions of the ET with no problem, and this option list has not been changed. I am reporting this against SimFactory because the problem does not happen with other option lists in the machine database, but I suspect that the issue arose due to a change in Carpet (maybe related to affinity?). From some Google searching, this symbol is part of GCC's thread-local storage emulation for Mac OS. Some people have had this problem when mixing object files compiled by different versions of GCC. I am using GCC 4.4.4 from Fink: {{{ > g++-4 --version g++-4 (GCC) 4.4.4 }}} This page, http://stackoverflow.com/questions/7885246/what-is-the-emutls- get-address-symbol, says {{{ Using thread local storage (e.g. OpenMP ThreadPrivate variables) on Darwin requires manually linking to TLS emutls, via either -lgcc_s.so.1 or -lgcc_eh }}} There is also a suggestion to upgrade the version of GCC, which I am trying now. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/946> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1054: Formaline can enter into an infinite loop if git-lock.pl cannot create its lock directory
by Einstein Toolkit 09 Oct '12

09 Oct '12

#1054: Formaline can enter into an infinite loop if git-lock.pl cannot create its lock directory -------------------+-------------------------------------------------------- Reporter: rhaas | Type: defect Status: new | Priority: minor Milestone: | Component: EinsteinToolkit thorn Version: | Keywords: Formaline -------------------+-------------------------------------------------------- if for some reason the source base directory returned by git-get- localdir.pl is not accessible (eg. since one has uses an invalid or empty (simfactory) defs.local.ini) then the loop in line 35 of git-lock.pl: {{{ 32 my $waittime = 0.01; 33 my $maxwaittime = 10; 34 print "Attempting to obtain $lockdir cwd = ".getcwd()." GIT_DIR=$git_dir\n"; 35 while (! (mkdir $lockdir)) { 36 # Wait some time 37 my $unit = $waittime==1 ? "second" : "seconds"; 38 print "Git repository is busy; waiting $waittime $unit...\n"; 39 system "sleep '$waittime'"; 40 # Back off exponentially 41 $waittime *= 2; 42 $waittime = 1 if $waittime>1 && $waittime<2; 43 $waittime = $maxwaittime if $waittime > $maxwaittime; 44 } }}} never quits and without SILENT=no the make system also does not output the "Git repository busy" messages it seems. Possible remedies would seem to either introduce a timeout after which Formaline gives up and does not push into the source code repository (with a loud warning at the end) or to ensure that the print statement's output appears on screen. It might also be useful to add an option to Formaline to not rely on simfactory. Right now without simfactory it will fail at some later point in the build process (since it cannot call simfactory/bin/sim whoami) or might use the wrong local source path (if simfactory is downloaded but not properly set up). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1054> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac September 2012