Trac March 2014

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[Einstein Toolkit] #445: Make Carpet timers hierarchical
by Einstein Toolkit 25 Aug '14

25 Aug '14

#445: Make Carpet timers hierarchical -------------------------+-------------------------------------------------- Reporter: hinder | Owner: eschnett Type: enhancement | Status: new Priority: major | Milestone: Component: Carpet | Version: Keywords: | -------------------------+-------------------------------------------------- With the current flat structure of timers in Carpet, it is difficult to identify which timers are contained in which other timers, and hence to avoid double-counting when adding up the times. This series of patches modifies the timer infrastructure in Carpet to generate a tree of timers where the hierarchy reflects the call-graph of the program. This makes it much easier to interpret the timer output than with the previous flat structure, where it was not possible to see which timers "contained" which others. More implementation details are given at the top of TimerNode.hh. Note that the Timer source and header files have been renamed as CactusTimer and a new Timer file and object has been created. This is because the Timer object now only provides a wrapper around the Cactus timer mechanism which was contained in the old Timer object. New parameters output_initialise_timer_tree and output_timer_tree_every control output of a new "timer tree diagram" to standard output for the Initialise and Evolve timer trees respectively. These diagrams indicate: 1. the value of each timer; 2. the percentage of the given tree taken by each timer; 3. which timers are contained in which other timers; 4. any untimed code for any timer which takes more than 1% of the tree time. Making the timers hierarchical means that the ad-hoc methods used before to identify the hierarchy (such as naming the timer Evolve::Sync, for example, to indicate that the Sync timer was a child of the Evolve timer) are no longer necessary and have been removed. Additionally, the construction of timers in a "dynamic" manner is now handled automatically for all timers, so special-case code is no longer needed and has been removed. Additionally some previously-untimed parts of the code are now timed, and timer names have been made more consistent in some places. There is code in the patches to output the entire timer tree as an XML file, but it is not enabled. Ideally the timer tree printed to standard output would contain reductions across processes, but at the moment it contains only the timer from the current process. The attached "tree-example.txt" file shows an example of the timer tree that is printed for a simulation using the qc0-mclachlan parameter file from the Einstein Toolkit. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/445> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1409: cleanup Avec in HydroBase
by Einstein Toolkit 02 Jun '14

02 Jun '14

#1409: cleanup Avec in HydroBase -----------------------------------+---------------------------------------- Reporter: knarf | Owner: Type: task | Status: new Priority: major | Milestone: ET_2013_11 Component: EinsteinToolkit thorn | Version: development version Keywords: | -----------------------------------+---------------------------------------- As discussed at the dev-workshop in summer 2013, Avec shouldn't be defined in HydroBase, but move to the evolution thorn. In particular, the current dev-version of HydroBase contains (will in a few hours) contain two different versions of it, depending on where it is defined. The needs to be cleaned up before the next release. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1409> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1210: CarpetIOASCII should not write column names info each iteration
by Einstein Toolkit 01 Jun '14

01 Jun '14

#1210: CarpetIOASCII should not write column names info each iteration --------------------+------------------------------------------------------- Reporter: knarf | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: | --------------------+------------------------------------------------------- Currently, CarpetIOASCII writes the column names header each iteration, leading to bloated output - easily double the size of what should suffice. Once after file creation would be much better. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1210> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1399: add evolution method "stationary" to ADMBase
by Einstein Toolkit 27 May '14

27 May '14

#1399: add evolution method "stationary" to ADMBase -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: ADMBase | -----------------------------------+---------------------------------------- This method is similar to "static" in that it can be used for Cowling runs, it differs from "static" in that it schedules the initial data routine after any grid changes and does not apply boundary conditions or SYNC calls. It can thus be used if one can compute the required metric/shift/lapse easily in a pointwise manner and would like to have exact (non-prolongated) data in the buffer zones. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1399> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1548: stdout redirection in multithreading scenario
by Einstein Toolkit 22 May '14

22 May '14

#1548: stdout redirection in multithreading scenario ---------------------------------+------------------------------------------ Reporter: gzheng@… | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Cactus | Version: development version Keywords: stdout redirection | ---------------------------------+------------------------------------------ Current stdout redirection scheme implemented in CommandLine.c:CCTKi_CommandLineFinished() (which redirects stdout to a file or /dev/null based on myproc) does not work on multithreaded MPI (e.g AMPI), because it redirects all output (from all threads in a process). That is, all MPI ranks in a process will be mistakenly directly to one file, or if redirecting to /dev/null, there will be simply no output. It may be possible to implement a cctk_printf function, which checks myproc and manage the output for each thread. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1548> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1302: Reduce time spent in deciding not to do output.
by Einstein Toolkit 21 May '14

21 May '14

#1302: Reduce time spent in deciding not to do output. --------------------------------------+------------------------------------- Reporter: diener | Owner: eschnett Type: enhancement | Status: new Priority: major | Milestone: Component: Carpet | Version: development version Keywords: performance optimization | --------------------------------------+------------------------------------- I noticed, during some scaling tests, that for my code a significant amount of time was spent by CarpetIOASCII, even though I only had it activated and didn't actually request any output. The reason is that in order to figure out whether to do output or not, there is a loop over all grid variables and a routine (TimeToOutput) is called. In this routine there is a check if the out_dir and out_vars parameters have been steered and if so update some internal data structures. It should be sufficient to do this before entering the loop over grid variables. The same issue is present in CarpetIOScalar and CarpetIOHDF5. The attached patches for CarpetIOASCII, CarpetIOScalar and CarpetIOHDF5 moves this check outside of the loop over grid variables and in addition bypasses the loop completely if the out_vars parameter string is the empty string. Note that the code where I noticed this problem uses large vectors of 1D grid arrays, and it turns out that Cactus counts each vector element as a distinct grid variables and the length of the loop over grid variables in my case was close to 100.000, which might explain why nobody has noticed this before. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1302> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1554: Want to define constants in parameter files
by Einstein Toolkit 21 May '14

21 May '14

#1554: Want to define constants in parameter files -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: Cactus | Version: development version Keywords: | -------------------------+-------------------------------------------------- I would like to define constants in parameter files, such as: {{{ $rho = 1 grid::dx = 1.0/$rho IOASCII::out_every = 10*$rho }}} The expansion of expressions is already implemented, but is limited to parameters. Being able to define constants would be very cool. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1554> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1468: Building a configuration with just the MPI thorn fails
by Einstein Toolkit 20 May '14

20 May '14

#1468: Building a configuration with just the MPI thorn fails ----------------------+----------------------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: optional | Milestone: Component: Cactus | Version: development version Keywords: | ----------------------+----------------------------------------------------- If I build a Cactus configuration with a thornlist containing just the MPI thorn (i.e no driver or any other thorns), the compilation fails with {{{ COMPILING /Users/ian/Cactus/EinsteinToolkit/src/comm/CactusDefaultComm.c In file included from /Users/ian/Cactus/EinsteinToolkit/configs/mpitest/build/Cactus/comm/CactusDefaultComm.c:33: /opt/local/include/openmpi/mpi.h:367: error: wrong number of arguments specified for ‘__deprecated__’ attribute }}} Building the flesh without the MPI thorn works OK. This is on Mac OS with MPI from MacPorts. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1468> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1207: Einstein toolkit sites with invalid security certificates
by Einstein Toolkit 19 May '14

19 May '14

#1207: Einstein toolkit sites with invalid security certificates -------------------------------------+-------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit website | Version: Keywords: | -------------------------------------+-------------------------------------- https://einsteintoolkit.org exists but has an invalid security certificate (http://www.sslshopper.com/ssl-checker.html#hostname=einsteintoolkit.org). I don't think we need SSL/TLS on this server. It should either be disabled or a valid certificate used. The same applies to https://cactuscode.org (http://www.sslshopper.com/ssl- checker.html#hostname=cactuscode.org). Note that Frank's page (http://www.cct.lsu.edu/~knarf/cgi-bin/monitor.cgi) reports these certificates as self-signed; they are also expired. Self- signed certificates on public websites are bad: they encourage people to click through the warnings. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1207> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1546: LoopControl commit e0ddb732 contains Fortran 2003 code
by Einstein Toolkit 19 May '14

19 May '14

#1546: LoopControl commit e0ddb732 contains Fortran 2003 code --------------------+------------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: Carpet | Version: development version Keywords: | --------------------+------------------------------------------------------- commit e0ddb732 "LoopControl: Rewrite" from Wed Jan 16 14:46:17 2013 -0500 introduces Fortran 2003 features (namely {{{bind(C)}}} in loopcontrol_types.F90. This fails to compile with gfortran 4.1.2 (the default gfortran on RH 5 machines, which are still around). David Radice stumbled oppon this. We had 2003 code in Carpet before, in ticket #670. At that point we modified the code to compile with gfortran 4.1.2 and removed the advanced features. Since gfortran 4.1.2 is by now 4 years old and none of our production option lists show the problem, I think we are finally ready to use some F2003 features in the code. We should then document this in the release notes, either for Cactus if we want to make this choice system wide or only for the ET/Carpet if we want to support running eg PUGH with only F90 around. We already require C99 in the Cactus flesh. Possibly we should take this discussion to cactus-devel. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1546> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac March 2014