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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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Is there any document of TwoPuncture's code?
by 赵志超 30 Oct '17

30 Oct '17

Hello everyone, I want to change TwoPuncture's code to add some matter to BBH simulation. I think at first I should understand the method TwoPuncture used. I have read two paper about this thorn by Marcus Ansorg et.al and Vasileios Paschalidis respectively. But I still do not understand how it treat the equation contains sources and a blackhole. Another question, can TwoPuncture generate a spinning Neutron Star? I know it can generate BH-NS initial data. This question equal to "Is the source included Momentum Constraint has been writen to TwoPuncture's code? " Best Wishes, ZhiChao, Zhao. Institude of High Energy Physics, CAS, China.

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About the thorn Einstein exact
by Nisa Amir 30 Oct '17

30 Oct '17

Hello, I am new to Einstein toolkit and m doing my resarch on it for M.phil dissertion. Can you please guide me how to add a metric in polar coordinates in Einstein exact thorn in Einstein toolkit and how to generate a new thorn for this metric using kranc package. your help will be highly appreciated. <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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meeting minutes for 2017-10-30
by Roland Haas 30 Oct '17

30 Oct '17

Present: Bill. Cris, Eloisa, Gabrielle, Helvi, Ian, Miguel, Sam, Steve, Roland, Qian, Ian Discussion of the EU ET Workshop: * more discussion and presentation about ET less about "only" science results * make sure US (at GT with CRA anniversary celebration) and EU (Lisbon possibly after https://workshops.ift.uam-csic.es/222) meetings next year don't overlap * school would be good for students (requested by attendees) ** gather lectures, tutorials and lecturers ** for this we would need funds (~10-20k$), would be appropriate for COST action * for US funding for these things: https://www.nsf.gov/pubs/2018/nsf18505/nsf18505.htm?WT.mc_id=USNSF_25&WT.mc… if outside of the US needs reason, needs a focused research activity * action items: ** Roland to find out when ET workshop at CRA is going to be ** Miguel will look at local funding opportunities including COST action ** take a look at NSF funding opportunities Working groups: proposed template and groups discussed at the workshop * https://docs.google.com/document/d/1j12IEY8kH6R33qfXpD5BaDDXLEYdNceEqf9crLu… * this is currently a re-hash of the template * has a list of groups to contact * no objections to template in current form in call, Gabrielle will send around tomorrow with deadline of 1 week to report back Volunteers to answer unanswered questions on the ET list * make sure that no emails get lost, currently had one person waiting for a week which is not good at all * add this as standing item to agenda * current list: for TP can only point to Marcus Ansorg's papers (Miguel), Ian will take up the EinsteinExact one code optimization using pop-coe services * had online discussion about using these services for codes based in EU * Helvi, Ian, Erik involved (others?). Would do it at BSC which we had already discussed with BSC members at the ET meeting (Miguel and Paula) * PRACE offer starting allocations for benchmarking, next cutoff date is Dec 1st * would have one person who is really dedicated to profile code and write report. * go for Optimization allocation and code development allocation (option "C" or option "B") Change "copy" operator behaviour: * http://lists.einsteintoolkit.org/pipermail/users/2017-October/005835.html * please create a pull request / ticket so that the author's can ok it 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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defining a grid function constant in time
by Miguel Zilhão 27 Oct '17

27 Oct '17

hi all, for the purposes of trying a particular gauge condition, we'd like to have a grid function (let's call it "shift_t0") that's set to be equal to the shift at t=0. we don't want this function to evolve at all; we just want this grid function to be accessible at all times (with exactly the same values). is there something in particular that we need to watch out for, when doing this? we ask because we've noticed that when doing things in a "naive"* way, sometimes NaNs start developing at some point in the evolution (seemingly near refinement boundaries and when regriding). we noticed that exactly the same thing happens for the "puncture_u" grid function in TwoPunctures: this function is only used at t=0; however, if one activates storage for it and asks for its output, at some point NaNs start developing in the output, even though the function is never used again. so, what would be the standard way of defining a grid function that is constant in time? thanks, Miguel & Helvi * by "naive", we mean essentially the following in schedule.ccl we have STORAGE: shift_t0[1] in interface.ccl we have CCTK_REAL shift_t0 type=gf timelevels=1 tags='tensortypealias="U" tags='prolongation="none"' { betax_t0 betay_t0 betaz_t0 } "shift vector at t=0" and we set its value (on the whole grid) at a function call at CCTK_INITIAL after ADMBase_PostInitial

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meeting minutes for 2017-10-23
by Roland Haas 23 Oct '17

23 Oct '17

Present: Chris, Eloisa, Erik, Helvi, Ian, Sam, Roland, Yosef, Bill, Gabrielle NixOS: * package manager for Cactus * works a bit different from eg dpkg or rpm package manager instead it is geared towards the user that installs packages * allows sub-projects with different sets of packages (like modules) which can roll back previous OS * can be used on Supercomputers and laptops. Erik tried on Ubuntu and OSX where things seems to work mostly fine. Works with pseudo-packages for intel compilers. Still some issues. Has currently growing set of packages (10s of thousands). * needs some polishing to make fully usable * Erik will push a number of scripts into the CactusUtils scripts directory * Erik will give a hands-on presentation next week if there is time * NixOS aims at reproducibility by beginning to install specific versions of compilers so everything should be portable * link is: https://docs.einsteintoolkit.org/et-docs/meeting_agenda Youtube channel: * currently have a couple of playlists from schools and past workshops * please have a look to make sure eg you like the playlist title * want to promote this on the ET website * https://www.youtube.com/channel/UC8IObWZ7_wEbWnbIKVIQRYQ * currently have playlist by institution, suggestion to also have some per type of object * can likely have "feature" videos that are shown more prominently * suggest sending submission of videos to maintainers(a)einsteintoolkit.org or users(a)einsteintoolkit.org * incorporate youtube video into cycler Help optimization from BSC: * https://pop-coe.eu/services * PRACE offers code optimization services, and since Helvi has a large PRACE grant this may be something to take advantage of * Gabrielle mentioned that NCSA has connections to NAG for optimization as well * would be good to have a EU counterpart to the efforts in Canada and the US, also in connection Cost Action * what works best if there is a particular science driver or interest is behind it so that one has a usage case that one wants to optimize * if linked to Helvi's science project would be linked to her science goal ** multiple issues affect optimization ** different for for deep AMR runs and wide shallow runs * suggest to have a phone call between ET person(s) and center. Needs to have commitment of time by center as well. * Ian would be interested, Helvi would be interested, Erik would be interested * suggest having a common machine to test things on (Marenostrum) * BSC is part of JLESC which includes NCSA, Roland to find out what is involved * good project for optimization working group ET "starting body" for new users * reduce barriers for new users to get involved * email list suggestion was for "buddy" system to pair a new user with a more experienced user * had "virtual office hours" in the past that were however not very well attended * to revive suggest some sign up procedure * make sure that the barrier is low and that there is no perception of people being inapproachable. * announce conference attendance eg on ET website and/or facebook page * action item: link "news" and/or other changing page on starting page to document that we are not yet dead. Add facebook page and twitter feed to news page * action item: added new users to education and communication working group * action item: NCSA post communication (undergraduate level) position Next week: * ET EU workshop post-workshop discussion. Material is here: https://docs.einsteintoolkit.org/et-docs/meeting_agenda#2017-10-23 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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