Users May 2018

users@lists.einsteintoolkit.org

17 participants
31 discussions

DSO not found compile question
by Jared Coughlin 14 May '18

14 May '18

Hello! I've just started using the Einstein toolkit and I'm new to the whole cactus and thorn way of compiling code, so forgive me if these questions seem stupid. I downloaded the code onto my laptop and followed the new users Jupyter notebook instructions to compile it, and it worked like a charm. I then downloaded the code to my University's compute cluster to try and run some of the test problems. When compiling, at the very end, I get an error about DSO not being found. As far as I can tell from Google, this is a linker error where the proper library (libnuma, it appears) has not been correctly linked. I was just wondering if this is the case and, if so, where I tell the code which libraries to link? I'm used to more traditional makefiles, so I was unsure where this sort of thing should go. The relevant part of the error message is as follows: 1 /usr/bin/ld: /path/to/einsteintoolkit/Cactus/con figs/sim/scratch/external/hwloc/lib/libhwloc.a(topology-linux.o): undefined refe rence to symbol 'mbind@@libnuma_1.1' 2 //usr/lib64/libnuma.so.1: error adding symbols: DSO missing from command line 3 collect2: error: ld returned 1 exit status I just went with the default ./simfactory/bin/sim setup-silent So I'm not sure if that needs to change (since I saw there are versions for other clusters). Thank you! Sincerely, -Jared

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Re: [Users] einstein toolkit error
by Steven R. Brandt 14 May '18

14 May '18

Since the code was running from the workbench, the only explanation that makes sense to me is that you encoutnered a network error. If you re-run the commands, everything should work. --Steve On 05/13/2018 04:10 AM, Emad Mahdavi wrote: > > Dear sir > > > we are trying to download and use the Einstein toolkit with labs > workbench account: rsaffari (email: reza.saffari.khomirani(a)gmail.com > <mailto:reza.saffari.khomirani@gmail.com>), but on this way, we > encountered a problem that is expressed bellow. > > > After the initial stages, we reached the stage : > > “GetComponents accepts a thorn list as an argument. To check out the > needed components:“ > > and used the code > > “.*/*GetComponents *--*parallel https:*//*bitbucket.org > <http://bitbucket.org>*/*einsteintoolkit*/*manifest*/*raw*/*ET_2018_02*/*einsteintoolkit.th > <http://einsteintoolkit.th>” > > and after about 20 minutes we encountered this error message: > > “ Wide character in print at ./getcomponent line 2695 > > Error: couldn’t download > https://bitbucket.org/einsteintoolkit/manifest/raw/ET_2018_02/einsteintoolk… > correctly.” > > > we hope that with the help of your suggestions, the problem be solved > and … run properly. > > > Sincerely, > > rsaffari > > > P.S: we attached a photo of encountered error. > >

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meeting minutes for 2018-05-14
by Roland Haas 14 May '18

14 May '18

Present: Bhavesh, Peter, Sam, Roland, Steve, Yosef, Zach, Qian * planning for next ET release (due in June or August) ** August is next possible date ** collect milestones for ET release: https://trac.einsteintoolkit.org/query?status=accepted&status=assigned&stat… * Giraffe tests ** Zach is working on this ** will be couple of weeks * status of NSNS gallery example: http://einsteintoolkit.org/mp.html Peter will try and get this done this week. * status of download page for ET MHD paper: http://einsteintoolkit.org/mp.html Roland to look into this. Roland to update page. * server status ** ssl on trac and wiki sites ** captchas on trac and wiki sites Steve is in contact with IT at CCT about sites. Captchas rely on mod_php which has been deprecated. For now, disable catpchas in trac and hope for the best as far as receiving spam goes. * standing item: unanswered / ongoing questions on mailing list No open emails. ET workshops: * Bhavesh has sent out a reminder about registration * how to review codes On wiki: https://docs.einsteintoolkit.org/et-docs/How_to_Review_a_Patch Guidelines or code contributions http://einsteintoolkit.org/contribute.html * Components should be of sufficient quality to be used for peer-reviewed and published science. This includes a basic standard of software engineering, documentation of the software including algorithms and methods, tutorials and examples, and self-tests to demonstrate that the software works correctly. * To focus development and support, optimize resources, and provide best practises, the Einstein Toolkit components should be of current interest to the community. * All components must be distributed under an open source licence so that others can use these components without restrictions (except as mandated by scientific integrity), can modify and improve them as necessary, and can pass on these modifications to their collaborators as they see fit. * ET call attendance fluctuates significantly suggestion to base skipping on number of agenda items having the regular meeting once a week makes scheduling easier and harder to forget tentative agreement is to keep the weekly meeting 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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ET Workshop Registration Reminder
by Khamesra, Bhavesh 14 May '18

14 May '18

Hi everyone, the registration for the North American ET workshop are currently ongoing. The last date for the registration is June 1st, 2018. The workshop will be hosted at Georgia Tech from June 18th - 20th. We are also offering travel support to a few participants. If you wish to apply for travel support, please submit an application along with your registration briefly describing 1. Your interest in this workshop 2. Your research work 3. The type of support requested (registration/travel/both) and estimated expense. 4. The reason for requesting the support. The last date for applying for travel support is May 20th, 2018. You can find more information about the workshop and registration at this link - http://et-workshop18.physics.gatech.edu/ Please let us know if you have any questions. Thanks, Bhavesh Khamesra Graduate Student Center of Relativistic Astrophysics Georgia Institute of Technology

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building on wheeler @ caltech
by Bela Szilagyi 11 May '18

11 May '18

Hello, I am trying to build Cactus on wheeler @ caltech. Does anyone have experience with this system? I tried the standard download, created a configuration (using "make null") and edited the thornlist to have only PUGH, HDF5 and zlib. At link time the build system complains of no libz. I do see those on the system, listed under /usr/lib64/ . Thanks for any input. Bela

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Error on Ubuntu subsystem
by 徐泽坤 11 May '18

11 May '18

Hello all, I'm using the Ubuntu subsystem of Win10 and something is wrong during the step: ./simfactory/bin/sim build --mdbkey make 'make -j2' --thornlist ../einsteintoolkit.th The error is showed in the picture: I'm a beginner of Ubuntu, so I will appreciate it if make your advice simple. Thanks in advance. -Zekun Xu

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Meeting Minutes
by Steven R. Brandt 07 May '18

07 May '18

Attendees: Steve, Zach, Sam Cupp, Bhavesh, Yosef Started registration, there are 2 registrations. http://et-workshop18.physics.gatech.edu/register/ Zach and Giraffe: He will add test cases and then submit his pending thorns to the development master. NRPY: Zach is working on a rewrite of NRPY and plans to make a Maclachlin to test against Kranc. Planning to have new versions with Jupyter notebooks. Plan to make it interactive. Request that he use PreSync. Sam will send email to make sure that this happens.

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Calling a function in Thorn A from Thorn B
by Chris Stevens 06 May '18

06 May '18

Hi everyone, I am in a situation where I want to call a function whose argument is just CCTK_ARGUMENTS from another thorn. I am aware of the following: -- I can share functions defined between thorns through the interface.ccl of the thorns, but I do not know how to specify CCTK_ARGUMENTS in the interface file. I cannot seem to find the cctk_arguments.h header anywhere in the Cactus directory to see what the definition of this is? -- I can call functions with argument CCTK_ARGUMENTS within the same thorn by using CCTK_PASS_CTOC. As a current fix (copied from CTGamma code), I can write the function like void test(CCTK_POINTER_TO_CONST _cctkGH) { const cGH* const cctkGH = _cctkGH; DECLARE_CCTK_ARGUMENTS; DECLARE_CCTK_PARAMETERS; } where this argument can now be passed through the interface file and seems to do a similar thing to CCTK_ARGUMENTS. Any help to figure out the best way to do this would be much appreciated! Thanks, Chris -- Dr Chris Stevens Claude Leon Postdoctoral Fellow Department of Mathematics Rhodes University Room 5 Ph: +27 46 603 8932 Web: www.chrisdoesmaths.com <http://www.chrisdoesmaths.com>

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Any Documents of Meudon_Mag_NS ?
by ZHAO Zhichao 03 May '18

03 May '18

Hello everyone, I am trying to simulating an isolate rotating mag neutron star. I used Lorene to produce an initial data. However, when I tring to use Meudon_Mag_NS import the initial data, I encount a trouble. The "bbig.par" file in "par" folder of Meudon_Mag_NS does not work, the err message is : ``` Coordinate polar radius a3 = 9.5691471042209 km Axis ratio a2/a1 = 1.0000000000000 a3/a1 = 0.9864200902433 Baryon mass : 1.4000000005901 M_sol Gravitational mass : 1.2922339017494 M_sol Uniformly rotating star ----------------------- Omega : 0.0000000000000 rad/s f : 0.0000000000000 Hz Rotation period : inf ms Central N^phi : 0.0000000000000 Error on the virial identity GRV2 : -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 15482 on node chaoge-MS-7A72 exited on signal 11 (Segmentation fault). ``` The error is so 'suddenly' that I have no idea to debug it.. Is there any Documents of Meudon_Mag_NS ? --- By the way, I have also tried arrangements/EinsteinEvolve/GRHydro_InitData/par/MagTOVstar.par . When I change Cactus::terminate to "never", I found it will crash at "Time 9~10". The error message says Bvec became Nan. Thanks to all of you ~

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ET summer workshop 2018 - Registration starting today
by Khamesra, Bhavesh 01 May '18

01 May '18

Hi Everyone, Registration for the North American ET Workshop 2018 is now open. You can find the link to the registration here - http://et-workshop18.physics.gatech.edu/register/ Registration Fee: There is a nominal registration fee of $60. The instructions for the payment will be sent to you by email once you submit the registration form. Note that registration is not complete until the registration fee is paid. The last date of registration is June 1st, 2018. Support: We also have some funds available to support registration/travel for the participants. Since the funds are limited, we request you to submit an application for the same. Check the registration page for more details. The last date for submitting the applications is May 20th, 2018. It is advised to use Firefox/Chrome browser for registration as we have encountered some issues with Safari. Please let us know if you have any questions. Thanks, Bhavesh ............................. Bhavesh Khamesra Graduate Student Center of Relativistic Astrophysics Georgia Institute of Technology

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Users May 2018