Users February 2017

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23 participants
33 discussions

Re: [Users] [ET Trac] [Einstein Toolkit] #1326: running loopcontrol on strange number of threads fails
by Erik Schnetter 11 Apr '19

11 Apr '19

Do you have a backtrace? -erik On Sunday, March 22, 2015, Einstein Toolkit < trac-noreply(a)einsteintoolkit.org> wrote: > #1326: running loopcontrol on strange number of threads fails > ------------------------------------+--------------------------------------- > Reporter: rhaas | Owner: > Type: defect | Status: new > Priority: minor | Milestone: > Component: EinsteinToolkit thorn | Version: > Resolution: | Keywords: LoopControl > ------------------------------------+--------------------------------------- > > Comment (by rhaas): > > This still happens even with current (Sun Mar 22 18:46:21 CET 2015) trunk, > though failure looks a bit different now: > {{{ > actus_sim: > /data/rhaas/postdoc/gr/ET_trunk/configs/sim/build/LoopControl/loopcontrol.cc:312: > T {anonymous}::divexact(T, T) [with T = int]: Assertion `i % j == 0' > failed > }}} > > -- > Ticket URL: <https://trac.einsteintoolkit.org/ticket/1326#comment:1> > Einstein Toolkit <http://einsteintoolkit.org> > The Einstein Toolkit > _______________________________________________ > Trac mailing list > Trac(a)einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/trac > -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/

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ET on KNL.
by Eloisa Bentivegna 03 Apr '17

03 Apr '17

Dear all, I was wondering if anybody is using the ET on the Knights Landing architecture, and what sort of performance one could expect to get. Admittedly without much optimization, I am measuring a performance per core which is almost two orders of magnitude smaller than that of a Broadwell Xeon. Does this sound wildly off? Eloisa

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QuasiLocalMeasures BH Spin
by Gwyneth Allwright 13 Mar '17

13 Mar '17

Hi All, I'm trying to reproduce the testbed BBH results in Etienne et al. 2009: https://arxiv.org/abs/0812.2245 I'd like to calculate the final Kerr black hole spin using the ratio of the polar and equatorial circumferences. QuasiLocalMeasures qlm_scalars gives several spin-related quantities: qlm_spin_guess qlm_spin qlm_npspin qlm_wsspin qlm_cvspin qlm_coordspinx, qlm_coordspiny and qlm_coordspinz. How are these related? Are any of them calculated using the Kerr formula? Also: what's the difference between qlm_polar_circumference_0 and qlm_polar_circumference_pi_2? Thanks, Gwyneth

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Re: [Users] [ET Trac] [Einstein Toolkit] #2008: NaNs when running static tov on >40 cores
by Erik Schnetter 08 Mar '17

08 Mar '17

Regarding OpenMP: Cactus usually tries to optimize which treads run on which cores. If there are multiple independent processes running on a node, then Cactus must not do that, since this will slow down both applications a lot. In particular, must not set "CACTUS_SET_THREAD_BINDINGS=1" (not setting it or setting it to 0 is fine). As Ian mentioned, you can either build without OpenMP support, or choose to use a single thread at run time, both will work. At this time, it might be best to post your complete setup, i.e. all the options and scripts you are using to configure and build and submit and run, so that others can have a look and cross-check. Of course, all of this is independent of any nans you encounter. Those are still due to a bug. I don't think it makes much sense at this point to debug this -- instead, you will want to run a larger simulations. -erik On Thu, Feb 23, 2017 at 4:34 AM, Einstein Toolkit < trac-noreply(a)einsteintoolkit.org> wrote: > #2008: NaNs when running static tov on >40 cores > ------------------------------------+----------------------- > ---------------- > Reporter: allgwy001@… | Owner: knarf > Type: defect | Status: assigned > Priority: major | Milestone: > Component: Carpet | Version: ET_2016_05 > Resolution: | Keywords: > ------------------------------------+----------------------- > ---------------- > > Comment (by hinder): > > Replying to [comment:6 allgwy001@…]: > > Thank you very much for looking into it! > > > > We can't seem to disable OpenMP in the compile. However, it's > effectively disabled by means of OMP_NUM_THREADS=1. Since "OpenMP does not > play nicely with other software, especially in the hybridized domain of > combining OpenMPI and OpenMP, where multiple users share nodes", they are > not willing to enable it for me. > > I have never run on a system where multiple users share nodes; it doesn't > really fit very well with the sort of application that Cactus is. You > don't want to be worrying about whether other processes are competing with > you for memory, memory bandwidth, or cores. When you have exclusive > access to each node, OpenMP is usually a good idea. By the way: what sort > of interconnect do you have? Gigabit ethernet, or infiniband, or > something else? If users are sharing nodes, then I suspect that this > cluster is gigabit ethernet only, and you may be limited to small jobs, > since the performance of gigabit ethernet will quickly become your > bottleneck. What cluster are you using? From your email address, I'm > guessing that it is one of the ones at http://hpc.uct.ac.za? If so, or > you are using a similar scheduler, then you should be able to do this, as > in their documentation: > > NB3: If your software prefers to use all cores on a computer then make > sure that you reserve these cores. For example running on an 800 series > server which has 8 cores per server change the directive line in your > script as follows: > > #PBS -l nodes=1:ppn=8:series800 > > Once you are the exclusive user of a node, I don't see a problem with > enabling OpenMP. Also note: OpenMP is not something that needs to be > enabled by the system administrator; it is determined by your compilation > flags (on by default in the ET) and activated with OMP_NUM_THREADS. Is it > possible that there was a confusion, and the admins were talking about > hyperthreading instead, which is a very different thing, and which I agree > you probably don't want to have enabled (it would have to be enabled by > the admins)? > > > > > Excluding boundary points and symmetry points, I find 31 evolved points > in each spatial direction for the most refined region. That gives 29 791 > points in three dimensions. For each of the other four regions I find > 25 695 points; that's 132 571 in total. Does Carpet provide any output I > can use to verify this? > > Carpet provides a lot of output :) You may get something useful by > setting > > CarpetLib::output_bboxes = "yes" > > On the most refined region, making the approximation that the domain is > divided into N identical cubical regions, then for N = 40, you would have > 29791/40 = 745 ~ 9^3^, so about 9 evolved points in each direction. The > volume of ghost plus evolved points would be (9+3+3)^3^ = 15^3^, so the > number of ghost points is 15^3^ - 9^3^, and the ratio of ghost to evolved > points is (15^3^ - 9^3^)/9^3^ = (15/9)^3^ - 1 = 3.6. So you have 3.6 > times as many points being communicated as you have being evolved. > Especially if the interconnect is only gigabit ethernet, I'm not surprised > that the scaling flattens off by this point. Note that if you use OpenMP, > this ratio will be much smaller, because openmp threads communicate using > shared memory, not ghost zones. Essentially you will have fewer > processes, each with a larger cube, and multiple threads working on that > cube in shared memory. > > > My contact writes the following: "I fully understand the [comments about > the scalability]. However we see a similar decrement with > cctk_final_time=1000 [he initially tested with smaller times] and hence I > would assume a larger solution space. Unless your problem is what is > called embarrassingly parallel you will always be faced with a > communication issue." > > > > This is incorrect, right? My understanding is that the size of the > solution space should remain the same regardless of cctk_final_time. > > Yes - it looks like your contact doesn't know that the code is iterative, > and cctk_final_time simply counts the number of iterations. In order to > test with a larger problem size, you would need to reduce CoordBase::dx, > dy and dz, so that there is higher overall resolution, and hence more > points. I would expect the scalability to improve with larger problem > sizes. > > -- > Ticket URL: <https://trac.einsteintoolkit.org/ticket/2008#comment:7> > Einstein Toolkit <http://einsteintoolkit.org> > The Einstein Toolkit > _______________________________________________ > Trac mailing list > Trac(a)einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/trac > -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/

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meeting minutes for 2017-02-27
by Roland Haas 27 Feb '17

27 Feb '17

Present: Roland, Vassilios, Christian, Erik, Yosef provide overriding con2prim for GRHydro: * presented the two competing implementation: ** using aliased functions which lets GRHydro control exactly when con2prim is called and guarantees that only one is present in a run ** using a schedule group is more Cactus like, GRHydro controls where con2prim is called by scheduling the group on its own, there is however no way to strictly guarantee that only one con2prim thorn is active * currently the first approach is used in production and the second (scheduled group) approach has a test implementation * will go ahead and implement the group method and check how well it works in production. Consider using hydrobase::evoution_method type parameter to advertise/select which con2prim is to be used. This is "Cactus like" but often not ahered to eg by the initial data thorns that use a similar mechanism. * the idea is to have problem adapted con2prim routines that are independent on GRHydro so that one can update GRHydro independently * do not want to use parameters and many different routines in GRHydro to keep the code small comet file corruption: * CarpetIOASCII output files can contain corrupted lines of output in the middle of a component * happens only on the scratch file system, not on $HOME and only for more than 1 MPI ranks * happens for both the current release version of ET (ET_PayonGaposhkin 2016_11) as well as old (years old) versions of Carpet * workaound is to force flushing after each line by using std::eol instead of "\n". This may be slow since flushing can be a very slow operation (milliseconds if it flushes all the way to the physical disk) * a workaround may be to write output into a string stream first then dump its rdbuf() to file * will engage SDSC support to see if they have suggestions on how to avoid this issue without having to first write to a local file, then copy to scratch once the run finishes Yours, Roland -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://keys.gnupg.net.

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Einstein Toolkit Meeting Reminder
by Roland Haas 27 Feb '17

27 Feb '17

Hi Please consider joining the weekly Einstein Toolkit phone call at 9:30 am US central time on Mondays. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/community/support/ We use a Google hangout, using this https://hangouts.google.com/call/yhqwnfyq4jakffiqetzwdyoxzqe URL if it is still functioning on Monday otherwise I will announce a new one on this list about 15 minutes before the meeting. Due to Mardi Gras (and Fastnacht or your local equivalent) we may have reduced attendance. Topics to cover (please reply on the mailing list to suggest extra ones): * status of ET on comet * testsuite status * (summer) student projects involving the ET Roland Haas -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://keys.gnupg.net. _______________________________________________ Users mailing list Users(a)einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users

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web-development session postponed
by Frank Loeffler 24 Feb '17

24 Feb '17

Hi everyone, I am sorry, but I am unable to host the web-development session today. Quite likely I'll re-schedule it some time next week. Frank

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Is "sudo ln -sf libmpichcxx.so libmpicxx.so" safe?
by 赵志超 23 Feb '17

23 Feb '17

Dear all, I am using Scientific Linux 7, and I get an error when I try to building the toolkit: " /usr/bin/ld: cannot find -lmpicxx /usr/bin/ld: cannot find -lmpi " It seems that the library libmpi is missed, but I have installed mpich and mpich-devel and mpich-autoload. And there exist "libmpichcxx.so" and "libmpich.so". So I try to run this command "sudo ln -sf libmpichcxx.so libmpicxx.so" and "sudo ln -sf libmpich.so libmpi.so" and the build has done. I want to know if this operation safe? Will it have some harmful effect on the result of EinsteinToolkit?

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adding inner refinement levels with Carpet
by Miguel Zilhão 22 Feb '17

22 Feb '17

hi all, i was wondering whether there is a way to add inner refinement levels with CarpetRegrid2 (or CarpetRegrid) as a simulation progresses. let's say that i have some configuration that collapses to a black hole, and i want to keep resolving accurately the inner region. is there some way for me to tell CarpetRegrid to add inner levels whenever a certain condition is fulfilled, ie, enough time elapses, or some grid quantity (like the lapse) grows beyond a certain value? thanks, Miguel

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Thorn documentation on homepage
by Jens Mahlmann 22 Feb '17

22 Feb '17

Dear all, I have been trying to access the thorn documentation on the homepage this morning. I keep receiving "Not found" prompts. Sorry to use this channel - however, I did not find a webmaster on the homepage for direct contact. Thank you so much and my best! Jens

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Users February 2017