Users November 2017

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23 participants
28 discussions

Cactus Tutorial
by Steven R. Brandt 04 Nov '17

04 Nov '17

The attached file is the html rendering of a Jupyter notebook version of Cactus tutorials advocated by Ian and Roland. It is my proposal to use this going forward. To run this tutorial, you can either go to the NDS machine (which I propose should be the default tutorial machine from now on): https://www.einsteintoolkit.nationaldataservice.org/#/ Alternatively, you may run it in docker. docker run --name myjupyter -d -p 8888:8888 ndslabs/jupyter-et If you don't like Jupyter, you can open a console on the NDS machine, or you can get a command line interface by doing this docker run -it ndslabs/jupyter-et bash Which is a machine that already has the requisite cactus packages installed. You can then use the attached html to enter instructions one by one. Please send comments, flames, etc. Thanks. --Steve

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Cannot access x,y,z,r when inheriting grid in c
by Chris Stevens 03 Nov '17

03 Nov '17

Hi all, this hopefully is a dumb question, but I cannot for the life of me get access to the x,y,z,r coordinates defined in CartGrid3D. Suppose I have a thorn X that wants to access these coordinates from test.cc, then the thorn should inherit: grid, the .cc should #include "cctk_Arguments.h" and the line that accesses, say x[0], should be called after DECLARE_CCTK_ARGUMENTS. Unfortunately doing this results in an error: [maths02:86267] *** Process received signal *** [maths02:86267] Signal: Segmentation fault (11) [maths02:86267] Signal code: Address not mapped (1) [maths02:86267] Failing at address: (nil) Which is analogous to the error message you get by defining a grid variable in interface.ccl without the accompanying STORAGE: in schedule.ccl, i.e. the memory is not allocated. I am using Llama as my coordinate system, but I know this basically is a wrapper for CartGrid3D and these coordinates are still set. I see the printout from CartGrid3D. I try to access these coordinates at, for example, CCTK_INITIAL, when the grid structure is already setup. I have also tried later time bins such as CCTK_POSTSTEP. Example files that access these coordinates are: CTGBase::debug.cc ADMDerivatives::calc_derivs.cc Coordinates::cylinderinbox.cc However I am not having any luck reverse-engineering these. Any ideas would be appreciated. Chris -- Dr Chris Stevens Department of Mathematics Rhodes University Room 5 Ph: +27 46 603 8932 Web: www.chrisdoesmaths.com <http://www.chrisdoesmaths.com>

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Re: [Users] Carpet options to switch off mesh refinement
by dumsani 02 Nov '17

02 Nov '17

On 02/11/2017 10:46, Ian Hinder wrote: > On 2 Nov 2017, at 01:41, dumsani <g14n8326(a)campus.ru.ac.za> wrote: > >> I think I have figured it out eventually. Thanks, Ian. > Good to hear! Would it be useful to summarise the cause of the problem to the mailing list, in case it helps others? > The following 3 options were enough, as you suggested. Carpet::max_refinement_levels = 1 Carpet::refinement_factor = 1 CarpetRegrid2::num_centres = 0 After setting these properly, it turned out the crash wasn't due to Carpet. It was now due to inappropriate memory allocation by the scheduler in my initial data code. Thanks

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Carpet options to switch off mesh refinement
by dumsani 01 Nov '17

01 Nov '17

Hi, I am to run a simulation with Carpet in "ungrid" mode, that is, without mesh refinement. I don't seem to get it right. What's options do I need to set? Apart from setting Carpet::max_refinement_levels = 1, what else does one have to specify in orer to get a run with only one grid? Regards, Dumsani

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Fwd: ProbPhysGrav code optimisation on Prace
by helvi witek 01 Nov '17

01 Nov '17

Dear Bruno, everyone, please find a bit more information about the optimization services they offer via the pop-ceu project below. They offer free services for groups based in the EU. Sorry, I had only forwarded the email to those who signaled interest in the performance optimization to not spam the list. Anyway, instead of running it via my PRACE grant we decided to apply for PRACE Preparatory Access, Type B or C; see http://www.prace-ri.eu/prace-preparatory-access/ There is no official deadline but the next cutoff date is 1 December 2017, and I'll draft a a proposal in the next few days. Anyone who is interested in getting involved, please contact me. cheers, Helvi =========================================== Dr. Helvi Witek Marie-Curie Research Fellow Dep. Fisica Quantica i Astrofisica & ICCUB Universitat de Barcelona =========================================== ---------- Forwarded message ---------- From: Wadud Miah <wadud.miah(a)nag.co.uk> Date: Fri, Oct 27, 2017 at 4:05 PM Subject: RE: ProbPhysGrav code optimisation on Prace To: helvi witek <hwitek(a)icc.ub.edu> Hi Helvi, Let me attempt to answer your questions: > - what the services would include exactly? The service will provide a report identifying root causes of performance issues and recommendations on how to address them. In some cases where not much effort is involved, we will be making the code changes to increase the performance. To give you some idea on what is included in the report, you can find some sample reports at: https://pop-coe.eu/target-customers/customer-code-list > - what is the manpower involved, i.e., would we have a computer scientist from your side > dedicated to the service? All we require from you is either the code or the executable. In addition, we will need a test case so we can run your code and any special instructions for a successful run. You will get a dedicated person who will profile your code and write the report. > - what would be the involvement from, e.g., the BSC (our grant is for MareNostrum)? BSC will need to set up a temporary account so that a POP partner can log in and run the profiling. As BSC are part of this project, they may be selected to do this profiling in which case no temporary account will be required. All the profiling tools are already installed on MareNostrum. > - would using your services entail any follow-up costs? The service is completely free to use as it is fully funded by the EU. Let me know if you have any further questions. If you would like to proceed with using this service, you can fill in a simple application form at: https://pop-coe.eu/request-service-form Regards, Wadud. *From:* helvi witek [mailto:hwitek@icc.ub.edu] *Sent:* 27 October 2017 14:36 *To:* Wadud Miah <wadud.miah(a)nag.co.uk> *Subject:* Re: ProbPhysGrav code optimisation on Prace Dear Wadud, I talked with my colleagues developing and maintaining the Einstein Toolkit, and we would in principle be interested in your profiling and optimization services. If we use it, we would probably handle it through my PRACE grant, with the group based in the EU. Could you please give us a bit more information on - what the services would include exactly? - what is the manpower involved, i.e., would we have a computer scientist from your side dedicated to the service? - what would be the involvement from, e.g., the BSC (our grant is for MareNostrum)? - would using your services entail any follow-up costs? Best wishes, Helvi =========================================== Dr. Helvi Witek Marie-Curie Research Fellow Dep. Fisica Quantica i Astrofisica & ICCUB Universitat de Barcelona =========================================== On Thu, Oct 19, 2017 at 6:28 PM, Wadud Miah <wadud.miah(a)nag.co.uk> wrote: Hi Helvi, Thanks for your reply. The Performance Optimisation and Productivity (POP) service is for any parallel code as long as you are based in the EU. Looking at the Web page you listed, the Einstein Toolkit has an MPI implementation, so we can certainly profile it for you. Please do forward the details of the POP service to your colleagues. Let me know if you have any further questions. Wadud. *From:* helvi witek [mailto:hwitek@icc.ub.edu] *Sent:* 19 October 2017 17:20 *To:* Wadud Miah <wadud.miah(a)nag.co.uk> *Subject:* Re: ProbPhysGrav code optimisation on Prace Dear Wadud, thank you very much for your offer. This would certainly be of interest to our group. Let me discuss it with them first. Is this for EU/PRACE funded projects only? One of the codes that we are using and further developing, the Einstein Toolkit ( http://einsteintoolkit.org/), is a publicly available code and our community might be interested in further improving its performance. With your permission I would put it forward to them, with me as contact person. Best wishes, Helvi =========================================== Dr. Helvi Witek Marie-Curie Research Fellow Dep. Fisica Quantica i Astrofisica & ICCUB Universitat de Barcelona =========================================== On Thu, Oct 19, 2017 at 3:15 PM, Wadud Miah <wadud.miah(a)nag.co.uk> wrote: Dear Helvi, I am contacting you because you are listed as the PI for the ProbPhysGrav project on Prace. I am working on a European Commission (EC) funded project which analyses HPC computer applications and makes recommendations on how to improve their speed and performance, as demonstrated by our success stories: https://pop-coe.eu/target-customers/success-stories As the project is funded by the EC, it is completely free to use by organisations based in the EU. Further information on the application analysis service can be found below with case studies for computational/HPC codes: https://pop-coe.eu/services If there are intellectual property issues involved, I am happy to sign any reasonable NDAs. If this service is of interest to you or your colleagues, when would be a good time to discuss this further? If you know of anyone who might be interested in this service, please feel free to forward it to them. Best regards, Wadud. ----------------------------------- Dr. Wadud Miah Numerical Algorithms Group *Disclaimer* The Numerical Algorithms Group Ltd is a company registered in England and Wales with company number 1249803. The registered office is: Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom. This e-mail has been scanned for all viruses and malware, and may have been automatically archived by Mimecast Ltd, an innovator in Software as a Service (SaaS) for business. *Disclaimer* The Numerical Algorithms Group Ltd is a company registered in England and Wales with company number 1249803. The registered office is: Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom. This e-mail has been scanned for all viruses and malware, and may have been automatically archived by Mimecast Ltd, an innovator in Software as a Service (SaaS) for business. *Disclaimer* The Numerical Algorithms Group Ltd is a company registered in England and Wales with company number 1249803. The registered office is: Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom. This e-mail has been scanned for all viruses and malware, and may have been automatically archived by Mimecast Ltd, an innovator in Software as a Service (SaaS) for business.

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Fwd: ProbPhysGrav code optimisation on Prace
by helvi witek 01 Nov '17

01 Nov '17

Dear all, as PI of a PRACE grant I have been contacted by Wadud Miah who is working on a European Commission (EC) funded project which analyses HPC computer applications and makes recommendations on how to improve their speed and performance. Their project is free to use for organizations based in the EU. Since part of my team is using the Einstein Toolkit and since we discussed options for improving its performance and possible industry involvement for upcoming EC grant applications last week, I was wondering whether this could interesting for our community in general. You can find more information about the service here: https://pop-coe.eu/services and the correspondence below. Have you come across them before? What do you think? cheers, Helvi =========================================== Dr. Helvi Witek Marie-Curie Research Fellow Dep. Fisica Quantica i Astrofisica & ICCUB Universitat de Barcelona =========================================== ---------- Forwarded message ---------- From: Wadud Miah <wadud.miah(a)nag.co.uk> Date: Thu, Oct 19, 2017 at 6:28 PM Subject: RE: ProbPhysGrav code optimisation on Prace To: helvi witek <hwitek(a)icc.ub.edu> Hi Helvi, Thanks for your reply. The Performance Optimisation and Productivity (POP) service is for any parallel code as long as you are based in the EU. Looking at the Web page you listed, the Einstein Toolkit has an MPI implementation, so we can certainly profile it for you. Please do forward the details of the POP service to your colleagues. Let me know if you have any further questions. Wadud. *From:* helvi witek [mailto:hwitek@icc.ub.edu] *Sent:* 19 October 2017 17:20 *To:* Wadud Miah <wadud.miah(a)nag.co.uk> *Subject:* Re: ProbPhysGrav code optimisation on Prace Dear Wadud, thank you very much for your offer. This would certainly be of interest to our group. Let me discuss it with them first. Is this for EU/PRACE funded projects only? One of the codes that we are using and further developing, the Einstein Toolkit ( http://einsteintoolkit.org/), is a publicly available code and our community might be interested in further improving its performance. With your permission I would put it forward to them, with me as contact person. Best wishes, Helvi =========================================== Dr. Helvi Witek Marie-Curie Research Fellow Dep. Fisica Quantica i Astrofisica & ICCUB Universitat de Barcelona =========================================== On Thu, Oct 19, 2017 at 3:15 PM, Wadud Miah <wadud.miah(a)nag.co.uk> wrote: Dear Helvi, I am contacting you because you are listed as the PI for the ProbPhysGrav project on Prace. I am working on a European Commission (EC) funded project which analyses HPC computer applications and makes recommendations on how to improve their speed and performance, as demonstrated by our success stories: https://pop-coe.eu/target-customers/success-stories As the project is funded by the EC, it is completely free to use by organisations based in the EU. Further information on the application analysis service can be found below with case studies for computational/HPC codes: https://pop-coe.eu/services If there are intellectual property issues involved, I am happy to sign any reasonable NDAs. If this service is of interest to you or your colleagues, when would be a good time to discuss this further? If you know of anyone who might be interested in this service, please feel free to forward it to them. Best regards, Wadud. ----------------------------------- Dr. Wadud Miah Numerical Algorithms Group *Disclaimer* The Numerical Algorithms Group Ltd is a company registered in England and Wales with company number 1249803. The registered office is: Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom. This e-mail has been scanned for all viruses and malware, and may have been automatically archived by Mimecast Ltd, an innovator in Software as a Service (SaaS) for business. *Disclaimer* The Numerical Algorithms Group Ltd is a company registered in England and Wales with company number 1249803. The registered office is: Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom. This e-mail has been scanned for all viruses and malware, and may have been automatically archived by Mimecast Ltd, an innovator in Software as a Service (SaaS) for business.

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Re: [Users] About the thorn Einstein exact
by Ian Hinder 01 Nov '17

01 Nov '17

On 1 Nov 2017, at 16:43, Nisa Amir <nisaamir(a)math.qau.edu.pk> wrote: > I want to do the evaluation in polar coordinates. Please include users(a)einsteintoolkit.org in CC, so that other benefit from the discussion. I am still not sure what you mean: I was asking about the *evolution*, i.e. the solution of the Einstein evolution equations from one time to another time. Do you want to do this in polar coordinates? Or just the "evaluation" of the initial data, where you have polar coordinates available. -- Ian Hinder http://members.aei.mpg.de/ianhin

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Re: [Users] About the thorn Einstein exact
by Ian Hinder 01 Nov '17

01 Nov '17

On 31 Oct 2017, at 17:16, Nisa Amir <nisaamir(a)math.qau.edu.pk> wrote: > Yes exactly, I want to add a space time non kerr to Einstein Exact thorn, but as you have already said, it considers only cartesian coordinates. What should I do ? (Please include users(a)einsteintoolkit.org in CC, so that other benefit from the discussion) Hi, I'm afraid I still don't understand which of the two options you want. Do you want to perform the evolution in polar or Cartesian coordinates? -- Ian Hinder http://members.aei.mpg.de/ianhin

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