Trac May 2021

trac@lists.einsteintoolkit.org

1 participants
79 discussions

#2528: ExternalLibraries/libjpeg thorn adds problematic system library path to Cactus
by Michael Müller 12 May '21

12 May '21

#2528: ExternalLibraries/libjpeg thorn adds problematic system library path to Cactus Reporter: Michael Müller Status: new Milestone: Version: ET_2020_11 Type: bug Priority: major Component: EinsteinToolkit thorn I have been trying to work with the new ET\_2020\_11 version, but while the compilation seems to work, upon submission of a run, MPI immediately generates an error message connected to a failure of the MPI\_INIT routine $output in "run\_name".err$: ``` *** An error occurred in MPI_Init_thread *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) [cn076:4193] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed! *** An error occurred in MPI_Init_thread *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) [cn076:4192] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed! -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[62070,1],1] Exit code: 1 -------------------------------------------------------------------------- ``` This is indicating some clash with OpenMPI. This turned out to be connected to the ExternalLibraries/libjpeg thorn. The thorn ExternalLibraries/libjpeg finds a jpeg library in the directory "/usr/lib/x86\_64-linux-gnu", and adds this path via the -L option to the library search path of Cactus. Unfortunately, this is a system library path. As a consequence, the linker then picks the MPI library in this directory instead of the one specified via MPI\_DIR, which creates the inconsistencies that cause the failure. Upon exclusion of this thorn and the connected CactusIO/IOJpeg thorn and recompilation this error does not occur anymore and all libraries are imported correctly. I do not use these thorns, so this is not a problem for me, but it would be great, if someone could have a look at this. $error encountered by me and source identified by @{557058:56049c54-f8c2-4b6c-9b88-ab697c967495} $ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2528/externallibraries…

1 0

#2526: McLachlan has incorrect READ declarations for presync.
by Roland Haas 12 May '21

12 May '21

#2526: McLachlan has incorrect READ declarations for presync. Reporter: Peter Diener Status: new Milestone: ET_2021_05 Version: development version Type: bug Priority: major Component: EinsteinToolkit thorn Comment (by Roland Haas): The `READS` generation is somewhat related to using Tmunu in expression as of commit hash [e69182c](https://github.com/ianhinder/Kranc/commits/e69182cf0e78e4120d6d3e5… "generate READS statement for stress\_energy\_state if needed" of [Kranc](https://github.com/ianhinder/Kranc) which is in ET\_2020\_05\_v0. While that commit does _not_ produce `READS: TmunuBase:eTxx` it queries the `RequireGroups` variable for their presence and that variable is the one used to generate the `READS` and itself generates a `READS: TmunuBase::stress_energy_state`. Meaning: if there is a `READS: TmunuBase::stress_energy_state` then `RequireGroups` contained TmunuBase variables and `READS` for them will be generated. This seems to be what happens for ML\_BSSN\_ADMBaseEverywhere. That commit $once one ignores whitespace changes and putting code in a `Module`$ adds: ```mathematica (* must match list in CodeGenCalculation.m *) ignoreGroups = {"TmunuBase::eTtt", "TmunuBase::eTxx", "TmunuBase::eTxy", "TmunuBase::eTxz", "TmunuBase::eTyy", "TmunuBase::eTyz", "TmunuBase::eTzz", "TmunuBase::eTtx", "TmunuBase::eTty", "TmunuBase::eTtz"}; If[ContainsAny[lookupDefault[spec, RequiredGroups, {}], ignoreGroups], "READS: " <> "TmunuBase::stress_energy_state" <> "\n", ""], ``` ‌ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2526/mclachlan-has-inc…

1 0

#2176: Test "Binary neutron star" example
by Roland Haas 12 May '21

12 May '21

#2176: Test "Binary neutron star" example Reporter: Roland Haas Status: open Milestone: ET_2021_05 Version: development version Type: task Priority: major Component: EinsteinToolkit website Comment (by Roland Haas): For now I have put a copy of the required thorn $only the most recent revision which is all I had a copy of$ to: [https://bitbucket.org/rhaas80/lsuthorns/src/master/](https://bitbucket.org/… and you should be able to use it with a GetComponents line like so: ``` # LSU Thorns !TARGET = $ARR !TYPE = git !URL = https://bitbucket.org/rhaas80/lsuthorns.git !REPO_PATH= $2 !CHECKOUT = LSUThorns/NSTracker ``` ‌ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2176/test-binary-neutr…

1 0

#2176: Test "Binary neutron star" example
by Roland Haas 12 May '21

12 May '21

#2176: Test "Binary neutron star" example Reporter: Roland Haas Status: open Milestone: ET_2021_05 Version: development version Type: task Priority: major Component: EinsteinToolkit website Comment (by Roland Haas): Uh right. The svn server [svn.cct.lsu.edu](http://svn.cct.lsu.edu) was recently moved behind a firewall and is no longer publicly accessible. Though right now even when trying to access it from inside of LSU IP space $which worked fine yesterday$ I get a error 500 internal server error. @{557058:f7fd5133-6eee-4385-a5e5-3e03342a0b24} @{557058:1671c5c3-29cc-4e83-9850-a152d33a6235} is there a LSUThorns Bitbucket or github place where the thorns that wwere in [https://svn.cct.lsu.edu/repos/numrel](https://svn.cct.lsu.edu/repos/numrel) could be hosted? From the email that I received from IT support it seemed to me that the svn server would not be made public again $“svn access is restricted to internal users now.”$. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2176/test-binary-neutr…

1 0

#2176: Test "Binary neutron star" example
by Atul Kedia 11 May '21

11 May '21

#2176: Test "Binary neutron star" example Reporter: Roland Haas Status: open Milestone: ET_2021_05 Version: development version Type: task Priority: major Component: EinsteinToolkit website Comment (by Atul Kedia): There is some issue with the nsnstohmns.th thornlist that is disrupting the download of NSTracker. The issue, as I understand, is that [http://einsteintoolkit.org/gallery/bns/nsnstohmns.th](http://einsteintoolki… accesses the link [https://svn.cct.lsu.edu/repos/numrel/$1/$2/trunk](https://svn.cct.lsu.edu/r… which is dead and needs to be replaced with a new one. I last downloaded ET with the nsnstohmns.th a couple weeks ago and all went well, so this must have come up recently. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2176/test-binary-neutr…

1 0

#2527: Perl undefined variables warnings when tyring to inherit from a non existing thorn
by Roland Haas 11 May '21

11 May '21

#2527: Perl undefined variables warnings when tyring to inherit from a non existing thorn Reporter: Roland Haas Status: new Milestone: Version: development version Type: bug Priority: minor Component: Cactus Changes (by Roland Haas): Erik Schnetter reported warnings from Perl of the sort: ``` Use of uninitialized value in concatenation (.) or string at /Users/eschnett/src/CarpetX/Cactus/repos/flesh/lib/sbin/interface_parser.pl line 176. ``` on Gitter. These seem triggered by trying to inherit from a non-existing thorn ``` CST error in /Users/eschnett/src/CarpetX/Cactus/repos/flesh/lib/sbin/interface_parser.pl (at 296) -> IDBRILLDATA (thorn IDBrillData) inherits from ellbase No thorn in your current ThornList implements ellbase Either remove IDBrillData, or add a thorn to your ThornList implementing ellbase No thorns in arrangements directory implement ellbase ``` and Perl trying to use a not yet defined array hash value when constructing the list of thorn ancestors. There are no such warnings when the code builds, yet the Perl code should not produce these warning even in the case of a later build failure. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2527/perl-undefined-va…

1 0

#2527: Perl undefined variables warnings when tyring to inherit from a non existing thorn
by Roland Haas 11 May '21

11 May '21

#2527: Perl undefined variables warnings when tyring to inherit from a non existing thorn Reporter: Roland Haas Status: new Milestone: Version: development version Type: bug Priority: minor Component: Cactus Comment (by Roland Haas): oops, wrong string in the copy and paste buffer. I will update the description… -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2527/perl-undefined-va…

1 0

#2527: Perl undefined variables warnings when tyring to inherit from a non existing thorn
by Erik Schnetter 10 May '21

10 May '21

1 0

#2527: Perl undefined variables warnings when tyring to inherit from a non existing thorn
by Roland Haas 10 May '21

10 May '21

#2527: Perl undefined variables warnings when tyring to inherit from a non existing thorn Reporter: Roland Haas Status: new Milestone: Version: development version Type: bug Priority: minor Component: Cactus Erik Schnetter reported warnings from Perl of the sort: ``` The Einstein Toolkit ecosystem: Enabling fundamental research in the era of multi-messenger astrophysics ``` on Gitter. These seem triggered by trying to inherit from a non-existing thorn ``` CST error in /Users/eschnett/src/CarpetX/Cactus/repos/flesh/lib/sbin/interface_parser.pl (at 296) -> IDBRILLDATA (thorn IDBrillData) inherits from ellbase No thorn in your current ThornList implements ellbase Either remove IDBrillData, or add a thorn to your ThornList implementing ellbase No thorns in arrangements directory implement ellbase ``` and Perl trying to use a not yet defined array hash value when constructing the list of thorn ancestors. There are no such warnings when the code builds, yet the Perl code should not produce these warning even in the case of a later build failure. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2527/perl-undefined-va…

1 0

#2413: Include "POWER" code to extrapolate waveforms to scri+ into ET
by Maria 06 May '21

06 May '21

#2413: Include "POWER" code to extrapolate waveforms to scri+ into ET Reporter: Roland Haas Status: open Milestone: Version: Type: task Priority: major Component: EinsteinToolkit thorn Comment (by Maria): If f0 is what will enable using Power to calculate the strain from BNS runs, then that’s it. Knowing the command line that should be used for this would be helpful too. And also, explaining how to manipulate Power in an IPython or Jupyter Notebook environment, making TwoPunctures.bbh and QLM output optional would be a good addition to the Documentation. ‌ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2413/include-power-cod…

1 0

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

Trac May 2021