Users January 2021

users@lists.einsteintoolkit.org

21 participants
31 discussions

Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 18 Jan '21

18 Jan '21

Please update the Wiki with agenda items for Thursday's meeting. Thanks! https://docs.einsteintoolkit.org/et-docs/meeting_agenda --The Maintainers

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Seeking a postdoc
by Evan Patrick O'Connor 18 Jan '21

18 Jan '21

Hi ET users, I'm seeking a postdoc to join my group for work on core-collapse supernova simulations and black hole formation in Stockholm (for full details see the ad linked below; due date: Jan 31). I'm particularly interested in candidates with a numerical relativity background so it is likely some members of this list may find this relevant. If you have any questions, feel free to contact me. Also, feel free to forward the opportunity to anyone you may think is interested. https://jobregister.aas.org/ad/40b7c88c Evan

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Kelvin-Helmholtz instability .par file
by Miquel Miravet 15 Jan '21

15 Jan '21

Hello everyone, I am trying to run a 2D box simulation in order to develop a Kelvin-Helmholtz instability, but I cannot find any .par file for that. Does anyone have a .par file to run this simulation? Thanks so much, Miquel. #################################################### Miquel Miravet Tenés, Ph.D. student Dept. Astronomia i Astrofísica Universitat de València C/ Dr. Moliner 50, E46100 Burjassot, València Spain Phone: + 34 963543081 email: Miquel.Miravet(a)uv.es ####################################################

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Out-Dated Code Version Error
by KARIMA SHAHZAD 14 Jan '21

14 Jan '21

Hello, There is a spinning single BH evolution example inside (Cactus Cactus/par/arXiv-1111.3344/kerr/by-a0.7.par) which is using the code version 2010. I am trying to simulate it using the newest version of the ETK with the only changes of refinement levels (reduced to 3) in the parameter file. It is giving some warnings and suggestions to change the out-dated parameters ( LapseAdvectionCoeff, ShiftAdvectionCoeff) along with the boundary condition to set as usual (what it means?). I also tried using the suggested parameters, but the data output is not as expected (incomplete output data), probably because of these out-dated parameters (?), the output and the error files are attached. I am asking if there are any alternatives (solutions) to these parameters, or should I prefer using the old ETK version, 2010? In the latter case, I am again encountering the download error, pasted below. Likewise, I want to get around this issue as well. I assume this email contains multi issues, but they are co-related, sorry to put them in one post. ./GetComponents --parallel https://bitbucket.org/einsteintoolkit/manifest/raw/ET_2010_06/einsteintoolk…<http://einsteintoolkit.th/> Note: I have tried without using the "--parallel option" as well, but the same error persists. Error: No definition for ET_RELEASE found in input file or ENV. --------------------------------------------------------------------------- CalledProcessError Traceback (most recent call last) <ipython-input-26-9fa64924ebf0> in <module> ----> 1 get_ipython().run_cell_magic('bash', '', './GetComponents https://bitbucket.org/einsteintoolkit/manifest/raw/ET_2010_06/einsteintoolk…'<https://bitbucket.org/einsteintoolkit/manifest/raw/ET_2010_06/einsteintoolk…'>) ~/.local/lib/python3.8/site-packages/IPython/core/interactiveshell.py in run_cell_magic(self, magic_name, line, cell) 2369 with self.builtin_trap: 2370 args = (magic_arg_s, cell) -> 2371 result = fn(*args, **kwargs) 2372 return result 2373 ~/.local/lib/python3.8/site-packages/IPython/core/magics/script.py in named_script_magic(line, cell) 140 else: 141 line = script --> 142 return self.shebang(line, cell) 143 144 # write a basic docstring: <decorator-gen-110> in shebang(self, line, cell) ~/.local/lib/python3.8/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k) 185 # but it's overkill for just that one bit of state. 186 def magic_deco(arg): --> 187 call = lambda f, *a, **k: f(*a, **k) 188 189 if callable(arg): ~/.local/lib/python3.8/site-packages/IPython/core/magics/script.py in shebang(self, line, cell) 243 sys.stderr.flush() 244 if args.raise_error and p.returncode!=0: --> 245 raise CalledProcessError(p.returncode, cell, output=out, stderr=err) 246 247 def _run_script(self, p, cell, to_close): CalledProcessError: Command 'b'./GetComponents https://bitbucket.org/einsteintoolkit/manifest/raw/ET_2010_06/einsteintoolk…''<https://bitbucket.org/einsteintoolkit/manifest/raw/ET_2010_06/einsteintoolk…''> returned non-zero exit status 25. Any kind of assistance would highly be appreciated and worthwhile. Thank you Best, Karima S

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Einstein Toolkit Telecon Minutes: Dec 10, 2020
by Zach Etienne 14 Jan '21

14 Jan '21

Present: Zach, Steve, Roland, Peter, David Bradley, Maria, Ken Sible, Leo Werneck, Liu Haoyang, Miguel Gracia, Sam Cupp, Bill Gabella, Yosef - *SPEC benchmark*: Steve reports no progress, but says we should do it. Roland wrote a to-do list for this task: https://bitbucket.org/einsteintoolkit/tickets/issues/2470 . Some details regarding this to-do list were discussed. - *Webserver issues*: einsteintoolkit.org was down for ~70 hours (including Dec 5-6 weekend). - Roland: was it a glitch or something systemic? - Steve: glitch. Machine hosting virtual webserver went down -- just needed LSU CCT support to reboot machine. Will work with Roland & Peter to ensure there's more redundancy in the future. After ticket, machine was back within an hour. - Bill: cactuscode.org has problems redirecting to new github.io page. Roland: Only sometimes, and not with Chrome. Firefox indeed doesn't redirect unless www.cactuscode.org is used. Roland: *Always* use *www.cactuscode.org <http://www.cactuscode.org>* - *Updates for next release*: - POWER: Used for waveform extraction on Scri+ -- Maria & Zach are interested in this code. Roland is improving interface, etc. - GRHydro con2prim updates -- Roland: A number of improvements have been reported from various groups. - selfforce1D updates -- Peter: new features are in progress, depending on progress might be a candidate for inclusion - Canuda updates -- Roland has been in touch with authors, privately. - *Unanswered mailing list queries*: One MPI query (failure) discussed, will need more details to help. Peter said he'd send an email. - *Tickets*: - #2335 ( https://bitbucket.org/einsteintoolkit/tickets/issues/2335/switch-simfactory… ) Steve: Patch makes SimFactory compatible with Python3. Pull request ready for review. Bill said he'd test it out. Roland has started to review. - Roland: other tickets ready for review, nothing super urgent at the moment. - *NRPy+ LaTeX parser update*: Ken Sible reports ability to now parse another of the BSSN equations. \gamma and \phi (using W variable) can now be parsed. Continued robustness improvements. Hope to have remaining equations parsed within the week. Bill asked for a progress report on parsing non-tensorial expressions, like those in PN expressions. Ken: we're very close to being ready to parse those expressions. - *Tabulated EOS with single TOV star*: Some discussion on whether this has been done with GRHydro. Roland pointed out a TOVHot code that may be on stellarcollapse.org ( https://svn.einsteintoolkit.org/incoming/TOVSolverHot/); Miguel: RNS thorn may have a parfile with tabEOS as well, could try out (HydroRNSID: test/RNS_a2.par). - *Jan 7 meeting*: Minute taker: Bill. Chair: Maria -Zach * * * Prof. Zachariah Etienne Physics & Astronomy Dept. West Virginia University http://astro.phys.wvu.edu/zetienne/ http://blackholesathome.net <https://blackholesathome.net>

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Re: [Users] cores and threads
by David N Bradley 14 Jan '21

14 Jan '21

Your message appeared before I could send my own. This could explain some things I was not aware of. Hope I did not disrupt the meeting, as usual my audio had an echo. I usually copy vara.hamradio.net.ini to generic.ini and proceed. On 1/14/21 10:09 AM, Roland Haas wrote: > Hello David, > > since "hyperthreads" is an Intel concept AMD does not always use it > (plus there are flavors of the same concept eg on AMD's Bulldozer CPUs > there are 4 floating point units for 8 integer units, where we tend > to sometimes see benefits going to all 8 integer cores or at least > will do so on clusters since even a 5% speed increase "for free" is > worth it). > > Anyhow, if you can provide the output of lscpu on your system that will > explain things. > > Simfactory uses the "Core(s) per socket" and "Socket(s)" values to > compute the number of physical cores and hence the number of threads it > allows. The hyperthreads (or equivalent) would be "Thread(s) per core". > > Note that Wikipedia: > > https://en.wikipedia.org/wiki/List_of_AMD_FX_microprocessors#Bulldozer_Core… > > does list your processors as 4 cores and 8 threads. > > I don't have access to your CPU but eg on a the Blue Waters login nodes > (Instanbul/Bulldozer, AMD Opteron(TM) Processor 6276) the output is: > > Architecture: x86_64 > CPU op-mode(s): 32-bit, 64-bit > Byte Order: Little Endian > CPU(s): 64 > On-line CPU(s) list: 0-63 > Thread(s) per core: 2 > Core(s) per socket: 8 > Socket(s): 4 > NUMA node(s): 8 > Vendor ID: AuthenticAMD > CPU family: 21 > Model: 1 > Model name: AMD Opteron(TM) Processor 6276 > > Yours, > Roland >

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Announcing a new Python package for post-processing simulation data: kuibit
by Gabriele Bozzola 14 Jan '21

14 Jan '21

Hello, I developed a new package to analyze Einstein Toolkit simulations, kuibit [0,1]. kuibit is a Python3.6+ code that I built from scratch following the same design (and in various instances, implementation details too) of Wolfgang Kastaun's PostCactus. kuibit provides high-level data types to easily work with grid functions, time and frequency series, gravitational waves, and so on. It also has readers to effortlessly access simulation data with full support for HDF5 and ASCII output (1D, 2D, 3D grid data, scalar data, reductions, horizon data, ...). You can find a reasonably comprehensive list of features in the documentation [2] or a high-level summary in the frontpage of the docs [3]. One of the main reasons I wrote this code is for other people to use it. Our group (University of Arizona) is a young one and we don't have any sophisticated toolchain to analyze simulation data. Without suitable tools, post-processing simulations can be a daunting task for those that are new to the Einstein Toolkit. Given that I want other people to use kuibit, I made the effort to make the code user and developer-friendly. For users, there is documentation [4] with examples and small tutorials. Also, the package is on PyPI so it can be easily installed and updated. For developers, the entire codebase has unit tests and continuous integration [5], there are extensive comments, and the style of the code is rather verbose to help developers understand what is going on. The continuous integration also lints the code, performs static analysis, and generates the documentation, reducing the maintenance costs. kuibit takes care of all the low-level details need to deal with simulation data, so it greatly lowers the entry barrier in using the Einstein Toolkit. I believe that this, along with the care I put in making the code accessible to other developers, makes kuibit a good candidate for inclusion in the Einstein Toolkit. The main problem with kuibit is that it is a new code: regardless of all the tests I wrote, there will be bugs, unergonomic interfaces, and performance issues. kuibit needs to be tested with several real-world projects and cross-checked with other codes. I am happy to give a short introduction to kuibit during a weekly call if there's interest. In the meantime, the code is available here: https://github.com/Sbozzolo/kuibit Best regards, Gabriele Bozzola [0] https://github.com/Sbozzolo/kuibit [1] https://github.com/Sbozzolo/kuibit#what-is-a-kuibit [2] https://sbozzolo.github.io/kuibit/features.html [3] https://sbozzolo.github.io/kuibit/#summary-of-features [4] https://sbozzolo.github.io/kuibit/ [5] https://github.com/Sbozzolo/kuibit/actions

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Re: [Users] A problem met in downloading
by Roland Haas 14 Jan '21

14 Jan '21

Hello Jimmy, please use the users(a)einsteintoolkit.org list to respond. A quick Google search does find a couple of hits but nothing that really looks exactly like this. I am afraid I cannot reproduce the issue. You are running Ubuntu 18.04 LTS curl version 7.47.0, are you? Can you access https://raw.githubusercontent.com/gridaphobe/CRL/ET_2020_11/GetComponents in your browser? Could it be some sort of proxy or firewall issue? Can you include the screen output of curl -v https://raw.githubusercontent.com/gridaphobe/CRL/ET_2020_11/GetComponents >/dev/null 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://pgp.mit.edu .

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Makefile:260: recipe for target 'sim' failed: error in building Einstein Toolkit
by Abhishek Chattaraj 14 Jan '21

14 Jan '21

Hi, I am trying to build Einstein Toolkit on my laptop with Ubuntu 18.04, i5 8th Gen using the instructions on the git page: https://github.com/nds-org/jupyter-et/blob/master/CactusTutorial.ipynb While building the toolkit using ./simfactory/bin/sim build -j<N> --thornlist ../einsteintoolkit.th, where I used N=2, I get the following error: ------------------------------------------------------ There were 3 errors during execution of the CST These must be corrected before compilation can proceed ------------------------------------------------------ ------------------------------------------------------ Warnings were generated during execution of the CST ------------------------------------------------------ CST error in /home/abhishek/Cactus/lib/sbin/CST (at 322) -> Missing thorn ExternalLibraries/BLAS CST error 2: -> Thorn 'LAPACK' requires the capability 'BLAS'. Please add a thorn that provides 'BLAS' to your ThornList or remove 'LAPACK' from it ! CST error 3: -> Thorn 'LORENE' requires the capability 'BLAS'. Please add a thorn that provides 'BLAS' to your ThornList or remove 'LORENE' from it ! ------------------------------------------------------ /home/abhishek/Cactus/lib/make/make.configuration:212: recipe for target '/home/abhishek/Cactus/configs/sim/config-data/make.thornlist' failed make[1]: *** [/home/abhishek/Cactus/configs/sim/config-data/make.thornlist] Error 1 Makefile:260: recipe for target 'sim' failed make: *** [sim] Error 2 Can anyone please provide some insight on how to proceed from here to solve this? Thanks! Abhishek -- Abhishek Chattaraj Department Of Physics Indian Institute Of Technology Madras Chennai 600036 India

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A problem met in downloading
by bekicat0326 14 Jan '21

14 Jan '21

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Users January 2021