Users September 2019

users@lists.einsteintoolkit.org

21 participants
39 discussions

Fwd: Failed installation
by Haas, Roland 30 Sep '19

30 Sep '19

Begin forwarded message: Date: Mon, 30 Sep 2019 14:44:44 +0200 From: Villani <mattia.villani(a)uniurb.it> To: "Haas, Roland" <rhaas(a)illinois.edu> Subject: Re: [Users] Failed installation The comman lbd release --all says: No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 16.04.6 LTS Release: 16.04 Codename: xenial The University uses G-Mail so I cannot do anything about that. Il 30/09/19 14:37, Haas, Roland ha scritto: > Hello Villani, > >> svn --version says: >> >> svn, version 1.10.6 (r1863367) > Ok so at least subversion is installed. > >> the long command says that everything is installed and updated. > Did you also run the two commands > > ./GetComponents --update ./einsteintoolkit.th &>GetComponents.log > > and > > svn info https://github.com/einsteintoolkit/ExternalLibraries-GSL.git &>svn.log > > producing the two files GetComponents.log and svn.log . > > Could you please send me to two output files GetComponents.log and > svn.log? > > I have seen failures of this sort for svn (really openssl) versions that > were too old since github will not accept any ssl connections from > servers that are to using at least tls v 1.2. However your svn version > seems sufficiently new that I would expect it to be linked against a > new enough version of OpenSSL. > > Can you let me know what version of Linux / OSX / Whatnot you are > running? > > On Linux you can try and use the command "lsb_release --all". > >> I am encountering some problem emailing you: i have been trying for >> almost a week now and always got the message: >> >> 554 5.7.1 Service unavailable; Client host [209.85.221.47] blocked >> using dnsbl.sorbs.net; Currently Sending Spam See: >> http://www.sorbs.net/lookup.shtml?209.85.221.47 >> >> as a response. > There is not much that I can do about this as this is a University wide > spam filter. The IP address that is banned (209.85.221.47) seems to > belong to Google (mail-wr1-f47.google.com). Are you trying to use > Google to send emails? I would rather use your "regular" University > account (and email server) which does not seem to be blocked. Sending > emails just to users(a)einsteintoolkit.org is enough though, there is no > actual need to CC me on it. > > I will forward your blocked email message to the admins here as I would > have hoped that GMail was not blocked since quite a number of US > Universities actually run their (student) emails using Google's > services. > > 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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Fwd: Failed installation
by Haas, Roland 30 Sep '19

30 Sep '19

Begin forwarded message: Date: Mon, 30 Sep 2019 15:20:30 +0200 From: Villani <mattia.villani(a)uniurb.it> To: "Haas, Roland" <rhaas(a)illinois.edu> Subject: Re: [Users] Failed installation which svn says: /usr/local/bin/svn Il 30/09/19 15:19, Haas, Roland ha scritto: > Hello Villani, > > I think you are getting this error: > > https://serverfault.com/questions/522646/svn-e170000-unrecognized-url-schem… > > ie your subversion command was built without https support. Which is > indeed what the output of your svn --version command confirms (since it > only lists ra_snv and ra_local but not ra_serf). > > This is highly unusual for subversion installed via apt-get. > > Did you perhaps compile your own? Can you check that "which svn" > reports /usr/bin/svn? > > Yours, > Roland > >> Here. Now the files should be attached >> >> Il 30/09/19 15:01, Haas, Roland ha scritto: >>> Hello Villani, >>> >>>> The comman lbd release --all says: >>>> >>>> No LSB modules are available. >>>> Distributor ID: Ubuntu >>>> Description: Ubuntu 16.04.6 LTS >>>> Release: 16.04 >>>> Codename: xenial >>> I ran >>> >>> svn info https://github.com/einsteintoolkit/ExternalLibraries-GSL.git >>> >>> on a Ubuntu Xenial machine of my own and it seems to have worked fine, >>> namely I get: >>> >>> --8<-- >>> svn info https://github.com/einsteintoolkit/ExternalLibraries-GSL.git >>> Path: ExternalLibraries-GSL.git >>> URL: https://github.com/einsteintoolkit/ExternalLibraries-GSL.git >>> Relative URL: ^/ >>> Repository Root: https://github.com/einsteintoolkit/ExternalLibraries-GSL.git >>> Repository UUID: f02328a3-b203-f8a2-b1da-ce57b7db7bff >>> Revision: 756 >>> Node Kind: directory >>> Last Changed Author: roland.haas >>> Last Changed Rev: 756 >>> Last Changed Date: 2019-03-13 22:11:00 +0000 (Wed, 13 Mar 2019) >>> --8<-- >>> >>> while failure would look like so >>> >>> --8<-- >>> svn info https://github.com/einsteintoolkit/ExternalLibraries-GSL.git >>> svn: OPTIONS of 'https://github.com/einsteintoolkit/ExternalLibraries-GSL.git': SSL handshake failed: SSL error: tlsv1 alert protocol version (https://github.com) >>> --8<-- >>> >>> I have to admit I am running out of ideas. Would you mind providing the >>> two output files (svn.log and GetComponents.log) that I had asked >>> about, please? >>> >>>> The University uses G-Mail so I cannot do anything about that. >>> I feared as much, yes. I have forwarded your error message to my >>> Universities IT services with exactly that admonition (namely that >>> Universities are using GMail). >>> >>> 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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Fwd: Failed installation
by Haas, Roland 30 Sep '19

30 Sep '19

Hello , Yours, Roland Begin forwarded message: Date: Mon, 30 Sep 2019 15:36:46 +0200 From: Villani <mattia.villani(a)uniurb.it> To: "Haas, Roland" <rhaas(a)illinois.edu> Subject: Re: [Users] Failed installation Thank you I will now try to remove the installed svn and re-install through apt-get Il 30/09/19 15:31, Haas, Roland ha scritto: > Hello Villani, > >> which svn says: >> >> /usr/local/bin/svn > That sounds like you are using a self-compiled version of svn, which > explains the issues. > > You can make GetComponents use the one in /usr/bin/svn > (there will be such a one if you executed the apt-get command > that Steve and I asked you to run) by running it like so: > > PATH=/usr/bin:$PATH ./GetComponents --update ./einsteintoolkit.th > > which makes GetComponents use the copy in /usr/bin before trying to use > the copy of svn in /usr/local/bin. > > You may also want to consider removing the copy of svn > in /usr/bin/local as without https support it is not going to be very > useful. Exactly how to remove it I cannot tell you since that depends > largely on how you installed it in the first place. > > Yours, > Roland > >> Il 30/09/19 15:19, Haas, Roland ha scritto: >>> Hello Villani, >>> >>> I think you are getting this error: >>> >>> https://serverfault.com/questions/522646/svn-e170000-unrecognized-url-schem… >>> >>> ie your subversion command was built without https support. Which is >>> indeed what the output of your svn --version command confirms (since it >>> only lists ra_snv and ra_local but not ra_serf). >>> >>> This is highly unusual for subversion installed via apt-get. >>> >>> Did you perhaps compile your own? Can you check that "which svn" >>> reports /usr/bin/svn? >>> >>> Yours, >>> Roland >>> >>>> Here. Now the files should be attached >>>> >>>> Il 30/09/19 15:01, Haas, Roland ha scritto: >>>>> Hello Villani, >>>>> >>>>>> The comman lbd release --all says: >>>>>> >>>>>> No LSB modules are available. >>>>>> Distributor ID: Ubuntu >>>>>> Description: Ubuntu 16.04.6 LTS >>>>>> Release: 16.04 >>>>>> Codename: xenial >>>>> I ran >>>>> >>>>> svn info https://github.com/einsteintoolkit/ExternalLibraries-GSL.git >>>>> >>>>> on a Ubuntu Xenial machine of my own and it seems to have worked fine, >>>>> namely I get: >>>>> >>>>> --8<-- >>>>> svn info https://github.com/einsteintoolkit/ExternalLibraries-GSL.git >>>>> Path: ExternalLibraries-GSL.git >>>>> URL: https://github.com/einsteintoolkit/ExternalLibraries-GSL.git >>>>> Relative URL: ^/ >>>>> Repository Root: https://github.com/einsteintoolkit/ExternalLibraries-GSL.git >>>>> Repository UUID: f02328a3-b203-f8a2-b1da-ce57b7db7bff >>>>> Revision: 756 >>>>> Node Kind: directory >>>>> Last Changed Author: roland.haas >>>>> Last Changed Rev: 756 >>>>> Last Changed Date: 2019-03-13 22:11:00 +0000 (Wed, 13 Mar 2019) >>>>> --8<-- >>>>> >>>>> while failure would look like so >>>>> >>>>> --8<-- >>>>> svn info https://github.com/einsteintoolkit/ExternalLibraries-GSL.git >>>>> svn: OPTIONS of 'https://github.com/einsteintoolkit/ExternalLibraries-GSL.git': SSL handshake failed: SSL error: tlsv1 alert protocol version (https://github.com) >>>>> --8<-- >>>>> >>>>> I have to admit I am running out of ideas. Would you mind providing the >>>>> two output files (svn.log and GetComponents.log) that I had asked >>>>> about, please? >>>>> >>>>>> The University uses G-Mail so I cannot do anything about that. >>>>> I feared as much, yes. I have forwarded your error message to my >>>>> Universities IT services with exactly that admonition (namely that >>>>> Universities are using GMail). >>>>> >>>>> 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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HDF5 Access coordinates corresponding to data
by Kyle Nelli 30 Sep '19

30 Sep '19

Hello, I have vector data in the form of h5 files as such vx.file_0.h5 vy.file_0.h5 vz.file_0.h5 vx.file_1.h5 vy.file_1.h5 vz.file_1.h5 and so on. I am trying to use a python script to access the actual position of each data point so I can use it in a calculation but I'm not sure how to access it. I imagine it is buried somewhere in the attributes of each refinement level of the dataset, but I'm not sure where. Much appreciated, Kyle Nelli

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Re: [Users] Failed installation
by Haas, Roland 30 Sep '19

30 Sep '19

Hello Villani, just before the error at the end you can see a couple of lines: --8<-- [...] CST error 43: -> Thorn 'TwoPunctures_KerrProca' requires the capability 'GSL'. Please add a thorn that provides 'GSL' to your ThornList or remove 'TwoPunctures_KerrProca' from it ! CST error 44: -> Thorn 'WatchDog' requires the capability 'PTHREADS'. Please add a thorn that provides 'PTHREADS' to your ThornList or remove 'WatchDog' from it ! --8<-- and at the beginning of that list of errors you can see the following: --8<-- ------------------------------------------------------ Warnings were generated during execution of the CST ------------------------------------------------------ CST error in /home/mattia/Cactus/lib/sbin/CST (at 376) -> Missing thorn ExternalLibraries/BLAS CST error in /home/mattia/Cactus/lib/sbin/CST (at 376) -> Missing thorn ExternalLibraries/FFTW3 CST error in /home/mattia/Cactus/lib/sbin/CST (at 376) -> Missing thorn ExternalLibraries/GSL --8<-- indicating that some modules (thorns) could not be downloaded and are missing. Those missing are downloaded using subversion (using the svn command) and possibly you are missing it. Steve already asked this, but can you double check that you ran the command (all in one line): sudo apt-get install -y libjpeg-turbo?-dev gcc git liblapack-dev make subversion g++ libpapi-dev libhwloc-dev libopenmpi-dev libhdf5-openmpi-dev libssl-dev numactl gfortran libhdf5-dev libfftw3-dev patch rsync libgsl-dev pkg-config and that svn --version works? If that works, can you please provide the log files generated by: cd $HOME ./GetComponents --update ./einsteintoolkit.th &>GetComponents.log and svn info https://github.com/einsteintoolkit/ExternalLibraries-GSL.git &>svn.log ie the two files GetComponents.log and svn.log . 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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Texas2019: Deadline for abstract submission now extended to 7th October
by Witek, Helvi 27 Sep '19

27 Sep '19

Dear Colleagues, (apologies if you receive the same information multiple times) The extended abstract submission deadline for the 30th Texas Symposium is 7th October 2019. The 30th Texas Symposium on Relativistic Astrophysics takes place in Portsmouth, UK, from Sunday 15 to Friday 20 December 2019. As convener of the parallel session on Gravity / Numerical Relativity, I would like to encourage you and your colleagues to submit an abstract for this session. Registration for early-bird fees will end on 25 October 2019, and general registration will close on 22 November 2019. See the web site http://texas2019.org/<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftexas2019.…> for more details and the information appended below. I hope to see you in Portsmouth in December. Best wishes, Helvi -- =========================================== Dr. Helvi Witek Royal Society University Research Fellow Theoretical Particle Physics and Cosmology. Department of Physics King's College London =========================================== The extended abstract submission deadline is 7th October 2019. Early-bird registration fee payment deadline is 25th October. Registration closes 22nd of November. See the web site http://texas2019.org/<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftexas2019.…> for more details. The Texas meetings have covered topics such as black holes, gravitational waves, neutron stars, cosmic rays, dark matter and the early Universe since the first symposium, held in Dallas in 1963. Following the tradition of previous meetings, the 2019 Symposium will cover a broad range of subjects in relativistic astrophysics, including: Gravity: Test of Gravity, Modified Gravity, Quantum Gravity, Numerical Relativity Cosmology: CMB, Reionisation, Early Universe, LSS, Lensing, Supernovae, Dark Energy, Simulations Gravitational Waves: Modelling, Sources, Experiments, Pulsar timing Messengers: Cosmic Rays, Gamma Rays, X-Rays, Neutrinos Relativity At Work: Black holes, AGN, Quasars, Neutron stars, Discs, Jets & Magnetic Fields Participants are invited to submit abstracts for presentations in parallel sessions covering topics listed below. Participants can each submit one abstract for consideration under one or more topics, to be selected by the convenor(s) named below for each session. We may create additional parallel sessions where there is sufficient demand. GRAVITY – TESTS OF GRAVITY – Leonardo Gualtieri GRAVITY – MODIFIED GRAVITY – Thomas Sotiriou GRAVITY – QUANTUM GRAVITY – Mairi Sakellariadou GRAVITY – NUMERICAL RELATIVITY – Helvi Witek COSMOLOGY – COSMIC MICROWAVE BACKGROUND & RE-IONIZATION – Emanuela Dimastrogiovanni COSMOLOGY – EARLY UNIVERSE AND THE ORIGIN OF STRUCTURE – Matteo Fasiello COSMOLOGY – LARGE SCALE STRUCTURE THEORY – Matteo Viel and Chris Clarkson COSMOLOGY – GALAXY SURVEYS, LENSING, SUPERNOVAE – Hendrik Hildebrandt COSMOLOGY – DARK ENERGY, COSMIC CONCORDANCE AND TENSIONS – Lucas Lombriser COSMOLOGY – NUMERICAL COSMOLOGY AND SIMULATIONS – Christian Fidler and Jim Mertens GRAVITATIONAL WAVES – MODELLING AND SOURCES – Kostas Kokkotas GRAVITATIONAL WAVES – GROUND BASED EXPERIMENTS – Jess McIver GRAVITATIONAL WAVES – SPACE BASED EXPERIMENTS, PULSAR TIMING – Carlos Sopuerta MESSENGERS – COSMIC RAYS – Matthew Baring MESSENGERS – GAMMA RAYS – Emma de Oña-Wilhelmi MESSENGERS – X-RAYS – Paolo d’Avanzo MESSENGERS – NEUTRINOS – Anna Franckowiak RELATIVITY AT WORK – DISKS, JETS AND MAGNETIC FIELDS – Matt Middleton RELATIVITY AT WORK – NEUTRON STARS – Vanessa Graber RELATIVITY AT WORK – SUPERMASSIVE BLACKHOLES, AGN AND QUASARS – tba The extended abstract submission deadline is 7th October 2019. Please register http://texas2019.org/registration/<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftexas2019.…> then submit your abstract http://texas2019.org/abstract-submission/<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftexas2019.…> Deadline for payment for early-bird registration fees 25th October. (Requests for financial support please email texas2019(a)port.ac.uk<mailto:texas2019@port.ac.uk>) Invited Speakers Antony Lewis (University of Sussex, UK) Astrid Eichorn (University of Southern Denmark & Heidelberg University, Germany) Chris Reynolds (University of Cambridge, UK) Claudia De Rham (Imperial College London, UK) Dany Page (National Autonomous University, Mexico) Elena Gallo (University of Michigan, USA) Elena Rossi (Leiden University, Netherlands) Elisa Resconi (Technical University Munich, Germany) Elisabeth Krause (University of Arizona, USA) Giovanni Losurdo (INFN Pisa, Italy) Juan Garcia-Bellido (University of Madrid, Spain) Luciano Rezzolla (University of Frankfurt, Germany) Martin Lemoine (IAP, France) Raffaella Margutti (Northwestern University, USA) Rennan Barkana (Tel Aviv University, Israel) Takahiro Tanaka (Kyoto University, Japan) Tanja Hinderer (University of Amsterdam, Netherlands) Tom Giblin (Kenyon College Ohio, USA) Ulisses Barres de Almeida (CBPF, Brazil) We look forward to seeing you in Portsmouth this December! Marco Bruni and David Wands on behalf of the Scientific and Local Organising Committees

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meeting minutes for 2019-09-26
by Haas, Roland 26 Sep '19

26 Sep '19

Present: Bill, Helvi, Maria, Peter, Roland, Steve, Yu Liu, Zach ET release: * Fishbone Moncrief: - code is not self-contained since NRPy+ is not part of the toolkit - NRPy+ itself is BSD license and available * self-force code - Steve could not checkout and and compile code, was missing effective source code, needs to be organized yet, could be done next week - Peter is addressing issues raised in tickets https://bitbucket.org/peterdiener/selfforce-1d/issues - will go ahead with inclusion - code will not be part of the default thornlist, will use its own issue tracker - will provide download instructions on ET website, will be mentioned in release announcement - Roland suggests to add Cactus-like "Author", "Maintainer" and "License" information to the README file (which are in somewhat machine parseable) * release date: move complete freeze to Oct 14th * Helvi's group will start running gallery examples * Helvi will run test suites on SuperMUC Tickets relevant to : * https://bitbucket.org/einsteintoolkit/tickets/issues/2119/ has made some progress tracking down, have old code so that we can compare, currently do not have a current run with the current evolution code * https://bitbucket.org/einsteintoolkit/tickets/issues/2274/ will be reviewed by Steve BaikalETK: * Zach has code done far enough that comparison to McLachlan was possible and waveforms agree for qc0-mclachlan.par * removed symmetries, 6th order accurate finite differencing, Dissipation to 7th order, increased final time (crash is after t=200M which is normally not reached), found crash in McLachlan (BSSN). Using Dissipation thorn, will send email to mailing list 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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Re: [Users] [ET Trac] #2285: Add the Self-Force code to the ET
by Peter Diener 25 Sep '19

25 Sep '19

When we asked for reviewers on the ET call, I mentioned that the code is still private on the bit buckets and that people interested in looking at the code should contact me so I could grant permissions. The reason being that I'm still finishing up the code test paper. If you send me your bitbucket user name, I can add you. Cheers, Peter On Tuesday 2019-09-24 16:43, Roland Haas wrote: >Date: Tue, 24 Sep 2019 16:43:03 >From: Roland Haas <trac-noreply(a)einsteintoolkit.org> >Reply-To: users(a)einsteintoolkit.org >To: trac(a)einsteintoolkit.org >Subject: [ET Trac] #2285: Add the Self-Force code to the ET > >#2285: Add the Self-Force code to the ET >Reporter: >Steven R. Brandt >Status: >new >Milestone: >ET_2019_10 >Version: >Type: >enhancement >Priority: >major >Component: >Other > >Comment (by Roland Haas): > >The code in the repository seems private I get (being logged in as @rhaas80 >to bitbucket): > > We can't let you see this page > >To access this page, you may need to log in with another account. You can >also return to the previous page or go back to your dashboard. > > >‌-- >Ticket URL:https://bitbucket.org/einsteintoolkit/tickets/issues/2285/add-the-self-… >e-code-to-the-et > > >

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tutorial server and Jenkins server down Saturday September 28th
by Haas, Roland 25 Sep '19

25 Sep '19

Hello all, due to maintenance work that will happen at the NCSA building, the tutorial server https://etkhub.ndslabs.org and https://build.barrywwardell.net (password protected so the link will not get you far) will be unavailable on Saturday September 28th. 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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Re: [Users] Failed installation
by Haas, Roland 25 Sep '19

25 Sep '19

Hello Villani, sorry, I gave the wrong command. It should have been: ./simfactory/bin/sim build &>sim.log Yours, Roland > done > > Il 25/09/19 14:51, Haas, Roland ha scritto: > > ./simfactory/sim/build &>sim.log -- 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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