Trac June 2012

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[Einstein Toolkit] #632: Changegroup hook failed when pushing to Carpet repository
by Einstein Toolkit 22 Oct '12

22 Oct '12

#632: Changegroup hook failed when pushing to Carpet repository --------------------+------------------------------------------------------- Reporter: hinder | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: | --------------------+------------------------------------------------------- When I push to the Carpet repository, I get the following message: {{{ remote: error: changegroup.cia hook failed: http://cia.vc returned an error: queued. }}} The push succeeds. What is the cause of this error? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/632> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #359: Add MDB entry for Pandora at LSU
by Einstein Toolkit 22 Oct '12

22 Oct '12

#359: Add MDB entry for Pandora at LSU ------------------------+--------------------------------------------------- Reporter: eschnett | Owner: mthomas Type: task | Status: new Priority: major | Milestone: Component: SimFactory | Version: Keywords: | ------------------------+--------------------------------------------------- -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/359> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #412: Split Appendices
by Einstein Toolkit 22 Oct '12

22 Oct '12

#412: Split Appendices -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- Currently, the appendices of the users' guide are repeated into the reference manual. This is somewhat confusing, and causes problems because the appendices cannot easily reference other sections (e.g. "see page 15" doesn't make sense since one doesn't know in which document this will be read). I suggest to split the appendices and have some of them in the users' guide while moving others into the reference manual, so that each appendix is included in only one document -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/412> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #704: Carpet complains about lack of mpi after ExternalLibraries/OpenMPI is built
by Einstein Toolkit 20 Oct '12

20 Oct '12

#704: Carpet complains about lack of mpi after ExternalLibraries/OpenMPI is built ---------------------+------------------------------------------------------ Reporter: bmundim | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: | ---------------------+------------------------------------------------------ I was able to compile ExternalLibraries/OpenMPI successfully, but the Cactus compilation stops afterwards with the message: /home/bruno/tmp/einstein_dev_maxwell/Cactus/arrangements/Carpet/CarpetLib/src/make.configuration.defn:5: *** Configuration error: The Carpet thorns require MPI. Please configure with MPI, or remove the Carpet thorns from the ThornList.. Stop. make: *** [einstein] Error 2 I indicated in my configuration file the following options: OPENMPI_DIR = BUILD OPENMPI_INSTALL_DIR = /home/bruno/local/gcc4.6.1/openmpi-1.5.4 I have then tried to indicate in my config file these extra options after the library was built (and the rest of Cactus compilation stopped): OPENMPI_DIR = /home/bruno/local/gcc4.6.1/openmpi-1.5.4 OPENMPI_INC_DIRS = /home/bruno/local/gcc4.6.1/openmpi-1.5.4/include OPENMPI_LIB_DIRS = /home/bruno/local/gcc4.6.1/openmpi-1.5.4/lib The config-info file does reflect these choices afterwards, and apparently the flag indicating the presence of mpi library, HAVE_MPI, was set correctly at ~/Cactus/configs/einstein/bindings/Configuration/Capabilities: grep -i have_mpi * cctki_MPI.h:#define HAVE_MPI 1 make.MPI.defn:HAVE_MPI = 1 however since I didn't use the old mechanism to tell Cactus about MPI, the ~/Cactus/configs/einstein/config-data/make.extra.defn doesn't have anything indicating the presence of mpi library there. It seems to me a compilation order issue. Somehow HAVE_MPI definition is coming after Carpet compilation, triggering this error then. Does anyone have any idea where I should look at in order to fix this problem? Thanks, Bruno. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/704> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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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] #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] #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] #720: check at runtime that all REQUIREd and OPTIONAL thorns and capabilities are active
by Einstein Toolkit 19 Sep '12

19 Sep '12

#720: check at runtime that all REQUIREd and OPTIONAL thorns and capabilities are active -------------------------+-------------------------------------------------- Reporter: rhaas | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- This is an offshot of a discussion on the Cactus developers mailing list: http://cactuscode.org/pipermail/developers/2011-November/006258.html On 6 Jan 2012 12:54:13 -0500 eschnett said: > What is currently missing is the mechanism that checks that all thorns > providing required capabilities are activated. If they are not, code > in inactive thorns is called -- this is fine as long as no Cactus > infrastructure is used (parameters, scheduled routines, grid > functions, etc.). > > Yes, we should implement the respective checks; yes, we should > automatically activate thorns required for capabilities (and maybe > some others as well?); yes, we should then output this thorn list to > the screen (done anyway) and into a file. > > By the way, Cactus already determines which thorns need to be > activated automatically as a service to the user in the error message > that complains about missing thorns. The idea seems to be to document all thorns whose code is executed in the parameter file. Ian's original need might be served by an "OPTIONAL" statement in configuration.ccl (http://einsteintoolkit.org/documentation/UsersGuide/UsersGuidech12.html#x17…) and some #ifdefs, maybe. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/720> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #929: GRHydro_test_tov_ppm_ML fails intermittently
by Einstein Toolkit 19 Sep '12

19 Sep '12

#929: GRHydro_test_tov_ppm_ML fails intermittently -----------------------------------+---------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: GRHydro | -----------------------------------+---------------------------------------- The test GRHydro_test_tov_ppm_ML sometimes fails on Datura. This seems to be nondeterministic. The most recent occurrence of this (http://git.barrywardell.net/EinsteinToolkitTestResults.git/blob/0fed62edfcc…) is due to differences in the constraints and vel[0]_norm1.xg very close to the tolerance. This does not happen every time. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/929> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac June 2012