[Users] meeting minutes for 2022-01-06

2022-01-06 Thread Haas, Roland
Present: Roland H, Yosef Z, Miguel G, Steve B, Federico A, Leo W * SPEC benchmark contribution [SB, RH] Steve contact SPEC group Cactus is still in the running, they were able to run the test Seem on track or inclusion * LORENE2 as default LORENE thorn in ET [RH] Roland will change to LORENE2

Re: [Users] NSNSTOHMNS(Gallery example) Plotting issues

2020-01-27 Thread Haas, Roland
Hello Atul, > Thank you for your email. > I have VisIt 3 and ETK Mayer downloaded which I believe doesn't have > CarpetHDF5. How do I use the CarpetHDF5 reader? Do I need to install it > from https://bitbucket.org/rhaas80/carpethdf5/src/multifile/ or is there a > newer version? That is still the

Re: [Users] arXiv-1111.3344 collapse example errors

2020-01-24 Thread Haas, Roland
Hello Justin, those were some thorns that were private at the time. CoreCollapseControl has been proposed for inclusion in this ticket: https://bitbucket.org/einsteintoolkit/tickets/issues/1358/import-corecollapsecontrol-into-et and you can obtain a copy using svn: svn checkout

Re: [Users] NSNSTOHMNS(Gallery example) Plotting issues

2020-01-23 Thread Haas, Roland
Hello Atul, I can venture a guess. The relevant error message seems to be: --8<-- VisIt: Message - Rendering window 1... VisIt: Error - The compute engine running on crcfe01.crc.nd.edu has exited abnorm ally. VisIt: Error - Scalable Render Request Failed (VisItException) viewer: Obtained null

Re: [Users] ET release coordinator elections

2020-01-23 Thread Haas, Roland
Hello all, I am off by one week. The next call will be Jan 30th 2020. Yours, Roland > Hello all, > > for the upcoming ET release ET_2020_04 there is no designated release > coordinator yet. > > In the past Steve has been handling this, though with this release the > idea is to spread out the

[Users] ET release coordinator elections

2020-01-23 Thread Haas, Roland
Hello all, for the upcoming ET release ET_2020_04 there is no designated release coordinator yet. In the past Steve has been handling this, though with this release the idea is to spread out the tasks a bit more. If you are interested or know someone who may be interested in coordinating the

Re: [Users] WENO-Z in GRHydro

2020-01-16 Thread Haas, Roland
Hello Bruno, Roberto, > I just discovered that GRHydro supports also WENO-Z (a different > implementation of the WENO 5th order reconstruction scheme). > > I have a master student currently looking at high order schemes and I admit > that I thought that GRHydro had only WENO5 implemented >

Re: [Users] Meeting Minutes for 2020-01-09

2020-01-09 Thread Haas, Roland
Hello all, while I was not in time to actually prepare these before the call, this: https://docs.einsteintoolkit.org/et-docs/images/3/3f/AMReX-20200109.pdf are some slides outlining the current CarpetX status. Yours, Roland > Present: Liu Haoyang, Zhao Zhi-Chao, Bill Gabella, Zach Etienne,

Re: [Users] Boundary issues solving wave equations with MoL

2020-01-08 Thread Haas, Roland
Hello Severin, sorry for the very long delay. I am no real expert on this others on this list may be better suited. My worry is that you are assuming that outside of the star (and on the star surface I guess) all time derivatives (and the spatial one in drPi it seems) vanish. This would be true

[Users] meeting minutes for 2019-12-12

2019-12-12 Thread Haas, Roland
Present: Bill, Chris, Helvi, Maria, Peter, Roland, Sam, Steve, Zach Chair: Zach Minutes: Roland status and running of working groups: * working groups have some strings attached and will be terminated for non-activity:

Re: [Users] submiting jobs in a cluster with the pbs queue

2019-12-06 Thread Haas, Roland
Hello Erik, you will want to read the "Configuring a new machine" section of the wiki https://docs.einsteintoolkit.org/et-docs/Configuring_a_new_machine If you already compiled successfully then you basically need a submission and run script. The simulation factory contains a large set of them

Re: [Users] ld error while linking simfactory on a HPC

2019-12-02 Thread Haas, Roland
Hello Alois, to fix the DSO error you would have to explicitly mention -ludev on the linker line, after hwloc. The easiest way to achieve this is to set: HWLOC_EXTRA_LIBS = udev in you option list and either do a recompile from scratch (safest) or make sure to "touch" all ccl files and

[Users] ET website down

2019-11-27 Thread Haas, Roland
Hello all, I seem to have brought down the ET webserver (with some IO error). Currently there is no ETA when it will be back. A static version of the website (so "Documentation" does not work for example) is available here: https://einsteintoolkit.bitbucket.io/ Note that the server being down

Re: [Users] Agenda for Thursday's Meeting

2019-11-25 Thread Haas, Roland
Hello all, this email was sent in error. There will not be a call this Thursday due to US Thanksgiving. Yours, Roland > Please update the Wiki with agenda items for Thursday's meeting. Thanks! > > https://docs.einsteintoolkit.org/et-docs/meeting_agenda > > --The Maintainers >

Re: [Users] No output available

2019-11-21 Thread Haas, Roland
you for your answer. > > Is there a simple and small example that produces an output file? > > Regards, > David > > Le 20/11/2019 à 16:06, Haas, Roland a écrit : >> Hello David, >> >> the HelloWorld example uses simfactory's "run" command:

Re: [Users] No output available

2019-11-20 Thread Haas, Roland
Hello David, the HelloWorld example uses simfactory's "run" command: ./simfactory/bin/sim create-run helloworld \ --parfile arrangements/CactusExamples/HelloWorld/par/HelloWorld.par which only outputs the log to screen and does not capture it to a file. Since HelloWorld itself does not

Re: [Users] Meeting Minutes for 2019-11-14

2019-11-18 Thread Haas, Roland
Hello Maria, all, > I've tested both ET_2019_10 and the development version on Mojave > with osx-homebrew.cfg and replacing gcc-8 with gcc-9. > > It looks good, run ends in less than 10 min, no test is hanging, all > tests pass, except for: > > Tests failed: > > > memspeed (from MemSpeed)

Re: [Users] GRHydro::Con2Prim question

2019-11-14 Thread Haas, Roland
Hello Giulia, this has to do with the order of timesteps when doing subcycling in time (which is what Carpet does). cctk_iteration counts RHS evaluations, and is not directly related to cctk_time ie cctk_time != cctk_iteration * DELTA_TIME. Basically the coarsest reflevel has to step first, so

[Users] Agenda for Thursday's Meeting

2019-11-05 Thread Haas, Roland
Please update the Wiki with agenda items for Thursday's meeting. Thanks! https://docs.einsteintoolkit.org/et-docs/meeting_agenda --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 .

Re: [Users] [ET Trac] #2064: Add GiRaFFE to the Einstein Toolkit

2019-11-04 Thread Haas, Roland
Hello all, there has been a lengthy discussion at one point about how to include jupyter notebooks in repositories. You may still be able to find it on the mailing list or in a ticket (if it indeed happened there, I am not sure). In the end, the solution is usually to do what Erik mentioned, i.

[Users] meeting minutes for 2019-10-31

2019-10-31 Thread Haas, Roland
Present: Bill, Chris, Helvi, Maria, Roland, Steve, Yosef, Zach New meeting software: * will use zoom, hosted by LSU (https://lsu.zoom.us/j/631356683) * volunteers for note takers - Bill - Helvi - Roland - Steve - Zach * volunteers for leads - Helvi - Roland - Steve - Peter - Zach * other tasks -

Re: [Users] Loop over the grid points of the base grid

2019-10-25 Thread Haas, Roland
Hello Erik, there is one more mode that you need to enter: LOCAL mode which is the only mode that actually has access to the grid data. This is because a single refinement level can contain multiple disjoint regions eg when there is a binary black hole system where each black hole has a set of

Re: [Users] Question about "New star location not set (18.4258, 0.763088, 0) because too far from old (15.0469, 1.82812, 0)."

2019-10-24 Thread Haas, Roland
Hello ZhiChao, > However, I found a lot of logs that likes : “New star location not set > (18.4258,0.763088,0) because too far from old (15.0469,1.82812,0).” > > I think maybe it shows there is some error. > > Could you list some possible unreasonable uses that that can cause this > error? My

Re: [Users] The simulation stops suddenly, problem with restarting from checkpoint, and with number of processors

2019-10-23 Thread Haas, Roland
htop" was > showing that only a portion of cores are being used and non was performing > on 100%, however, the simulation was *running faster more than fourfold. * > I am still confused about specifying the number of cores. > > Bests, > Hassan > > On Thu

Re: [Users] Stop MoL after tolerance is reached

2019-10-22 Thread Haas, Roland
fferent variable with the option alias, so, I try > > IO::filereader_ID_vars = "BrillEvolve::brillpsi{alias='IDBRILLMOL::phi'}" > > but I got the error above described. Can you help me with this? Am I > misunderstanding how the readingfile interface works? > > Eri

[Users] meeting minutes for 2019-10-17

2019-10-17 Thread Haas, Roland
Present: Bill, Chris, Erik, Maria, Peter, Philipp, Roland, Steve, Yosef, Zach ET release * scheduled for Oct 27th * BBH, Poisson equation still in the works * BNS, needs to be re-run. Maria and Roland will do so, Roland to push fixes in pull requests needed * testsuite status: no unexpected

Re: [Users] Output file for one specific grid point

2019-10-15 Thread Haas, Roland
Hello Severin, > However if I want to choose a point inside the spherical part > (outside of the cartesian grid) I can not gather any data. > > I assume that the output thorn is only aware of the cartesian > coordinates? Do you (or anyone else) know if there is a way to bypass > this issue? The

Re: [Users] Output file for one specific grid point

2019-10-15 Thread Haas, Roland
Hello Severin, CarpetIOASCII's out0d_vars will do that, there are out0d_x etc options to specify the location. You should also use the compact_ firmat option to make nicer files. Yours, Roland - Original Message - From: Severin Frank Sent: 2019-10-15 - 03:18 To:

Re: [Users] Stop MoL after tolerance is reached

2019-10-14 Thread Haas, Roland
Hello Erik, as to how to decide to stop: the simplest way would be to compute a pointwise stopping criterion (maybe magnitude of the right-hand-side or so) then do a reduction on it using the CCTK_Reduce function (assuming you are using Carpet), see eg. the code in Hydro_Analysis to compute the

Re: [Users] Possible performance issue

2019-10-09 Thread Haas, Roland
Hello Vaishak, > 1. In the link ( > https://docs.einsteintoolkit.org/et-docs/Configuring_a_new_machine), I see > that not only optimization flags but also CFLAGS, CXXFLAGS, FPPFLAGS are > set to ( -g3 -march=native ...) . Would it help to change these too? -g3 gives you extra debugging

Re: [Users] Err logs like "[83bdcfc58a2e:19025] Read -1, expected 4096, errno = 1" when running ET.

2019-10-09 Thread Haas, Roland
Hello zhichao, good to hear that things are now working even without the workaround. It is quite possible that OpenMPI updated itself and the new version no longer triggers the warning. Thank you for letting us know of the changes. Yours, Roland > Thanks Roland, > > A host with CentOS 7 and a

Re: [Users] Possible performance issue

2019-10-08 Thread Haas, Roland
Hello Vaishak, > I have made the changes as suggested. In fact I compiled using a Intel MPI > ( which was compiled by myself locally) using the optionlist of Stanpede 2 > cluster as suggested by you , without OpenMP and with appropriate library > paths.I am glad that the speed has improved. I am

Re: [Users] compilation fails on supermuc-ng due to hdf5 library

2019-10-08 Thread Haas, Roland
Hello Giuseppe, > HDF5_LIBS = /lrz/sys/io_tools/hdf5/1.8.15/serial_icc17/lib > HDF5_INC = /lrz/sys/io_tools/hdf5/1.8.15/serial_icc17/include these variables should be called HDF5_LIB_DIRS and HDF5_INC_DIRS (see eg

Re: [Users] LSU ETK meeting

2019-10-08 Thread Haas, Roland
Hello Steve, all, no preference from my side, both dates are outside of the teaching period for classes at UIUC. Looking at hyperspace (https://hyperspace.uni-frankfurt.de/) I do not see an obvious conflict. I have tried to find out if there is a LIGO conflict but have been unable to find a

Re: [Users] Possible performance issue

2019-10-07 Thread Haas, Roland
PI mvapich and intel-mpi have similar options) to find out which libraries the official mpi compiler wrapper would use. Yours, Roland > Dear Sir, > > Please find the config-info file attached herewith... > > > Yours, > > Vaishak > > On Mon, Oct 7, 2019 at 7:56 PM H

Re: [Users] Possible performance issue

2019-10-07 Thread Haas, Roland
hanking you > > Regards, > Vaishak > > > On Fri, Oct 4, 2019 at 8:05 PM Haas, Roland wrote: > > > Hello Vaishak, > > > > I do not see anything obviously wrong with the setup. > > > > It uses 128 MPI ranks for the 4 nodes which fits with there b

Re: [Users] problem in analysis thorn

2019-10-04 Thread Haas, Roland
Hello Fabrizio, I am not quite sure what may be happening, but here's my guess: options: global loop-local will call your scheduled function once on each refinement level (and component) at every since iteration. This includes calling on reflevel 0 at iteration 1 (at which point an normal

Re: [Users] Possible performance issue

2019-10-04 Thread Haas, Roland
Hello Vaishak, I do not see anything obviously wrong with the setup. It uses 128 MPI ranks for the 4 nodes which fits with there being 2x16 cores per node. Lookin at the timer tree output at iteration 1024 (search for "gettimeof " and you will find the spot) out of 5977s spend during Evolve

Re: [Users] meeting minutes for 2019-10-03

2019-10-03 Thread Haas, Roland
Hello all, trying to get a better idea of the failing tests, I ran the comparison tool (n testsuite_results): perl ./compare_results.pl ET_2019_03_v0 master results/bluewaters__{1_8,2_8}.log results/comet__{1_24,2_12}.log results/golub__1_10.log:results/golub__1_12.log

Re: [Users] The simulation stops suddenly, problem with restarting from checkpoint, and with number of processors

2019-10-03 Thread Haas, Roland
Hello Hassan, Erik, does this issue still persist? Since there are no *.out and no *.err file, would you mind providing a list of the files that are present? Ie the output of somehing like: ls -lR /home/cosmo/simulations/the-last-one/output-0001/ as well as the simfactory log file

Re: [Users] Warning: Cannot output variable because it has no storage (ADMAnalysis OR ADMMass)

2019-10-03 Thread Haas, Roland
Hello Yu Liu, sorry for the very late response. There seem to be two questions in your email: 1. how to output a particular variable 2. about the layout of output directories in simfactory To output ADMMass::ADMMass_box the varariable needs to first be computed (or more accurate have storage

Re: [Users] meeting minutes for 2019-10-03

2019-10-03 Thread Haas, Roland
Hello all, > Present: Bill, Chris, Maria, Peter, Roland, Yosef, Zach > > ET release: > * gallery examples: Guiseppe and Helvi are running gallery examples, at > least two done. Not sure if will also run BBH example, will cross > check with Sam > * HMNS still under investigation, Maria in

[Users] meeting minutes for 2019-10-03

2019-10-03 Thread Haas, Roland
Present: Bill, Chris, Maria, Peter, Roland, Yosef, Zach ET release: * gallery examples: Guiseppe and Helvi are running gallery examples, at least two done. Not sure if will also run BBH example, will cross check with Sam * HMNS still under investigation, Maria in process of testing on local

Re: [Users] [External] Checkpointing with parameter change 8%

2019-10-03 Thread Haas, Roland
Hello DG, > I noticed that the ReadInterpolate Thorn only works with Carpet. Is > it possible to get something like it for Pugh? What would be the > differences? I have not tried it with PUGH. PUGH implements a subset of what Carpet offers and at the very basic level one could think of having

Re: [Users] Checkpointing with parameter change

2019-10-02 Thread Haas, Roland
Hello DG, > Is it possible to restart a checkpointed run with a few parameters > changed? For example, can you run a simulation with checkpoint, then > restart it from the last checkpoint using different values of maximum > and minimum grid range values (as well as different grid spacing) if >

Re: [Users] Failed installation

2019-09-30 Thread Haas, Roland
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

Re: [Users] Failed installation

2019-09-30 Thread Haas, Roland
s 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

Re: [Users] Failed installation

2019-09-30 Thread Haas, Roland
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

[Users] Fwd: Failed installation

2019-09-30 Thread Haas, Roland
Begin forwarded message: Date: Mon, 30 Sep 2019 14:44:44 +0200 From: Villani To: "Haas, Roland" 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:    16.0

[Users] Fwd: Failed installation

2019-09-30 Thread Haas, Roland
Begin forwarded message: Date: Mon, 30 Sep 2019 15:06:18 +0200 From: Villani To: "Haas, Roland" Subject: Re: [Users] Failed installation Here. Now the files should be attached Il 30/09/19 15:01, Haas, Roland ha scritto: > Hello Villani, > >> The comman lbd release --

[Users] Fwd: Failed installation

2019-09-30 Thread Haas, Roland
Hello , Yours, Roland Begin forwarded message: Date: Mon, 30 Sep 2019 15:36:46 +0200 From: Villani To: "Haas, Roland" 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

[Users] Fwd: Failed installation

2019-09-30 Thread Haas, Roland
Begin forwarded message: Date: Mon, 30 Sep 2019 15:20:30 +0200 From: Villani To: "Haas, Roland" 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 th

Re: [Users] HDF5 Access coordinates corresponding to data

2019-09-30 Thread Haas, Roland
Hello Kyle, coordinates are not normally explicitly stored in hdf5 files. However if you asked for output of the coordinates grid functions (those defined in CartGrid3D) then you will have output files name like this: x.file_0.h5 ... y.file_0.h5 ... z.file_0.h5 and those datasets do indeed

Re: [Users] Failed installation

2019-09-30 Thread Haas, Roland
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

[Users] meeting minutes for 2019-09-26

2019-09-26 Thread Haas, Roland
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

[Users] tutorial server and Jenkins server down Saturday September 28th

2019-09-25 Thread Haas, Roland
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

Re: [Users] Failed installation

2019-09-25 Thread Haas, Roland
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:

Re: [Users] Failed installation

2019-09-25 Thread Haas, Roland
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

Re: [Users] Failed installation

2019-09-25 Thread Haas, Roland
Hello Villani, I can get a somewhat similar error if I add a thorn that does not exist to my thornlist file. In that case there is an initial error from the CST stage that may have scrolled out of your window. It looks somewhat like this: --8<--

[Users] Fwd: Failed installation

2019-09-24 Thread Haas, Roland
Begin forwarded message: Date: Tue, 24 Sep 2019 15:07:32 +0200 From: Villani To: "Haas, Roland" Subject: Re: [Users] Failed installation Thanks for the prompt answer. I did what you wrote, but I still get the same error. I am trying to install ET on a Ubuntu 16.04 mach

[Users] Fwd: Failed installation

2019-09-24 Thread Haas, Roland
Begin forwarded message: Date: Tue, 24 Sep 2019 15:26:24 +0200 From: "Villani, Mattia" To: "Haas, Roland" Subject: Re: [Users] Failed installation I have tried everything you wrote, but nothing has changed. Il mar 24 set 2019, 15:23 Haas, Roland ha scritto: > Hello

Re: [Users] Failed installation

2019-09-24 Thread Haas, Roland
Hello Villani, > I am trying to install Einstein ToolKit on my laptop following these > instructions: > > https://nbviewer.jupyter.org/github/nds-org/jupyter-et/blob/master/CactusTutorial.ipynb > > but I run into errors when using the (last) command: > > ./simfactory/bin/sim build --mdbkey

Re: [Users] Err logs like "[83bdcfc58a2e:19025] Read -1, expected 4096, errno = 1" when running ET.

2019-09-20 Thread Haas, Roland
es, for example, > > BBHHighRes.par, the error also occurs. > > > > 83bdcfc58a2e is the identification of this machine (this node), so I guess > > it is something wrong with Docker ( I run ET in a docker ) ? > > > > I have upload an err file generated by simfactory(locate

Re: [Users] Err logs like "[83bdcfc58a2e:19025] Read -1, expected 4096, errno = 1" when running ET.

2019-09-20 Thread Haas, Roland
without docker ? > > Thanks again for your help. > > Yours, > Zhichao. > > > > Haas, Roland 于2019年9月10日周二 下午8:14写道: > > > Hello ZhiChao, > > > > > > + date +%s > > > > + export CACTUS_STARTTIME=1567761511 > > > > + [ 14 =

[Users] meeting minutes for 2019-09-19

2019-09-19 Thread Haas, Roland
Present: Bill, Chris, Helvi, Maria, Peter, Roland, Steve, Toni. Yosef, Yu Liu, Zach ET release: * Steve is reviewing Peter's self-force code, may open up ticket system in code repo * no one assigned yet to review Zach's Fishbone-Moncrief disk code, needs volunteer * DOI: proceed as planned *

Re: [Users] HDF5 and submission/runtime issues on a PBS cluster

2019-09-19 Thread Haas, Roland
LIBDIRS' used > for? > > > Thankyou for you support again > > Yours Sincerely > Vaishak > > On Fri, Sep 13, 2019 at 6:42 PM Haas, Roland wrote: > > > Hello Vaishak, > > > > looking at you .ini and .cfg files you need to add extra option

Re: [Users] make -utils failing with "RNS" error (ET_2019_03)

2019-09-18 Thread Haas, Roland
Hello Bernard, > You're right; that was a non-standard version of RNSID I made to > remove the GRHydro dependence some time ago. Ah ok. In theory this dependence should now also have been removed from the vanilla version (there should be a ticket about this). > Interestingly, this new failure

Re: [Users] make -utils failing with "RNS" error (ET_2019_03)

2019-09-18 Thread Haas, Roland
Hello Bernard, I am not quite sure what could cause this. The RNS utility in the Einstein Toolkit is part of einsteininitialdata/Hydro_RNSID is your thorn the same or a older / modified version of that thorn? I am not sure how SystemTopology itself could be responsible, however removing it from

Re: [Users] CarpetIOHDF5 recover failure with manual topology

2019-09-13 Thread Haas, Roland
Hello all, map=51 seems like a bug to me (access to uninitialized variables most likely) since the "map" is Llama's coordinate patch (with the Cartesian patch being map 0). Unless your really have at least 52 patches (and are using Llama) this thus seems like a bug. Yours, Roland > Do you want

[Users] symmetries and IllinoisGRMHD

2019-09-13 Thread Haas, Roland
Hello all, since this came up at the ET meeting in London: can someone please remind me what the support for (Cactus) symmetries in IllinoisGRMHD is? My recollection is that, due to the way that the staggered field work, that none of the ReflectionSymmetry, RotatingSymmetry90,

Re: [Users] HDF5 and submission/runtime issues on a PBS cluster

2019-09-13 Thread Haas, Roland
Hello Vaishak, looking at you .ini and .cfg files you need to add extra options to make sure that the correct hdf5 libraries are found at runtime (not just at compile time). Often on clusters there will be "environment modules" that you should load to set the correct settings. The command to do

[Users] meeting minutes for 2019-09-12

2019-09-12 Thread Haas, Roland
Present: Bill, Chris, Maria, Peter, Roland, Steve, Yosef software citation project: * can be used to find citations for open source software used in papers * the ET has some support for this ET release Modules to include: * Peter's self-force code ** Steve is reviewing ** Peter is creating a

Re: [Users] errors while compiling Einstein toolkit

2019-09-11 Thread Haas, Roland
Hello Nattia, all, did Steve's suggestion fix the problem for you? > On 8/26/2019 3:00 AM, Mattia wrote: > > After the compilation I get the following list of errors: > > > > CST error 1: > >   -> Missing thorn ExternalLibraries/BLAS To me this can also be caused errors during the

Re: [Users] Err logs like "[83bdcfc58a2e:19025] Read -1, expected 4096, errno = 1" when running ET.

2019-09-10 Thread Haas, Roland
Hello ZhiChao, > > + date +%s > > + export CACTUS_STARTTIME=1567761511 > > + [ 14 = 1 ] > > + mpirun -np 14 /home/zhaozc/simulations/bnstest/SIMFACTORY/exe/cactus_sim > > -L 3 /home/zhaozc/simulations/bnstest /output-/bnstest.par > > [83bdcfc58a2e:19025] Read -1, expected 4096, errno = 1 > >

[Users] user map code

2019-09-09 Thread Haas, Roland
Hello Niels, after the discussion at the ET meeting in London last week, would you mind sharing the scripts (or instructions if you have any) that were used to produce the user map at: https://bhptoolkit.org/users.html For the ET we would like to have a similar life map:

Re: [Users] Macport openmpi error

2019-09-04 Thread Haas, Roland
Hello Robyn, yes, that was it. I responded on stackexchange but basically the solution is to make sure that the "default" version of gcc is installed. You'd run sudo port uninstall gcc8 sudo port install gcc9 sudo port install openmpi-gcc9 then can select the version using: sudo port select

Re: [Users] Error running nsns_test.par with file resu.d

2019-08-29 Thread Haas, Roland
Hello Atul, just in case this is still an issue: the Meudo_Bin_NS thorn's parameter's description (see arrangements/EinsteinInitialData/Meudon_Bin_NS/param.ccl) says: --8<-- STRING filename "Input file name containing LORENE data" { "" :: "Any filename, potentially including path" } "" --8<--

[Users] meeting minutes for 2019-08-29

2019-08-29 Thread Haas, Roland
Present: Chris, Frank, Helvi, Maria, Roland, Toni, Zach ET meeting at KCL: * will have zoom set up for remote participation: https://zoom.us/j/355206842 * program is available at: https://sites.google.com/view/eetm2019/home Upcoming ET release: * planned for October * pan to add Peter

Re: [Users] CactusTutorial

2019-08-28 Thread Haas, Roland
Hello Tomas, to run the tutorial online (ie via http://etkhub.ndslabs.org/) you do not need to install any software. The "Prerequisites" section is only used when you want to run the tutorial on your own laptop. The section talking about xcode in particular is only used on OSX systems (Macs).

Re: [Users] Issues compiling ETK on Blue Waters

2019-08-15 Thread Haas, Roland
Hello Federico, > Can anyone give me some hint? I can compile the ET_Proca release of the ET one BW using the release option list. this change is likely due to a change in the BW programming environment (which may have slipped proper announcement channels). The error you describe (incorrect

[Users] meeting minutes for 2019-08-08

2019-08-08 Thread Haas, Roland
Present: Bill, Chris, Helvi, Peter, Roland, Steve, Zach Steve, Helvi, Roland discussed plans for tutorial machines for the KCL workshop Zach reported work on NRPy which may speed up SpehericalBSSN Issues with docs.einsteintoolkit.org should resolved, please respond if this is not the case ET

[Users] meeting minutes for 2019-08-01

2019-08-01 Thread Haas, Roland
Present: Eric, Peter, Roland, Steve, Toni ET citation: * discussed author list on proposed Zenodo citation * please send author suggestions to Steve * current data for Zenodo: http://cct.lsu.edu/~sbrandt/Zenodo.pdf * have two tiers of authors, contributors who are on the release team get moved

Re: [Users] Einstein Toolkit Meeting Reminder

2019-08-01 Thread Haas, Roland
Hello all, since the wiki is still acting up for me (about every second request fails), here's the call-in link: https://bluejeans.com/194244555 and full information: Connection Details We are using Blue Jeans to host the Einstein Toolkit meetings. The meeting is sponsored by the Perimeter

Re: [Users] MareNostrum4 compilation Error

2019-07-29 Thread Haas, Roland
Hello Alejandro, > ExternalLibraries/pthreads WVUThorns_Diagnostics/smallbPoynET > ExternalLibraries/zlib > /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: > cannot find -lsz > collect2: error: ld returned 1 exit status sz (libsz) is part of HDF5. It should be provided

[Users] meeting minutes for 2019-07-18

2019-07-18 Thread Haas, Roland
Present: Roland, Bill, Eric, Helvi, Peter, Steve, Yosef Tutorial notebooks: * Eric worked on a couple of extended notebooks for new ET users * currently in Eric's github repo: https://github.com/EricJWest/ETKNotebooks * will include in tutorial server Self-force code: * Peter's code is ready to

Re: [Users] hwloc: necessary?; explicit dependencies

2019-07-02 Thread Haas, Roland
Hello Bernard, > (1) When do I *need* hwloc? Is it only relevant to systems using > OpenMPI? The machine Pleiades uses SGI mpi. It is very helpful for SystemTopology. SystemTopology in turn makes sure that a sane thread-to-core binding is used (most important on clusters where hypterthreading is

Re: [Users] x86_64 link-time errors on MacOS Mojave

2019-07-02 Thread Haas, Roland
_LIBS=hdf5 hdf5_cpp hdf5_hl > HDF5_LIB_DIRS=/opt/local/lib > > That is, it wasn't enough to just say "HDF5_DIR=/opt/local" > > Hope this helps if someone else runs into problems (and thanks for the > help getting here), > > Bernard > > On Fri, 21 Jun 2019 at 14:20

[Users] number of thesis using the Einstein Toolkit codes

2019-06-27 Thread Haas, Roland
Hello all, for a report to the NSF I am trying to obtain an idea of who many student thesis were using (were enabled by) the Einstein Toolkit. So if you are a student or are working with a student and have used the Einstein Toolkit as part of your thesis work in between 2018-07-01 and 2019-06-30

[Users] meeting minutes for 2019-06-27

2019-06-27 Thread Haas, Roland
Present: Eric, Helvi, Peter, Roland, Sam, Steve, Zach Neutron star star: * Zach provided details on HARM3D evolution, currently no NR yet, but development on multiple fronts * provided update on Vassili's SpherecalBSNN and SphericalGRMHD codes that will be made public sometime after September

Re: [Users] boundary conditions with Llama

2019-06-25 Thread Haas, Roland
ly does "outer boundary points" mean for the Sn function? is > there a bug, or did i just misinterpreted that "outer boundary" means the > "physical" boundary? > > - what would be the canonical way of checking whether a point belongs to > the phy

Re: [Users] Achieve Cell-Center in NR simulation

2019-06-24 Thread Haas, Roland
Hello Steve, using Carpet's cell centered refinement you should enable the CarpetLib parameter: CarpetLib::use_higher_order_restriction = "yes" and possibly increase the default value of CarpetLib::restriction_order_space from its default value of 3. Note that values larger than 3 can be

Re: [Users] Failed to Download Proca

2019-06-24 Thread Haas, Roland
Hello Arshad, you will need to have the subversion version control system installed. Given that OSX has a built in subversion client (so the exact message that you see if not shown) I am assuming that you are using a version of GNU/Linux (either natively or as Windows 10's Linux subsystem). In

Re: [Users] x86_64 link-time errors on MacOS Mojave

2019-06-21 Thread Haas, Roland
f installed ports (a bit longer than yours) > > Bernard > > On Thu, 20 Jun 2019 at 12:44, Haas, Roland wrote: > > > > Hello Bernard, > > > > > I did a clean, from-scratch compilation after copying that 18.2.0 > > > Darwin architecture file to

Re: [Users] x86_64 link-time errors on MacOS Mojave

2019-06-20 Thread Haas, Roland
Hello Bernard, > I did a clean, from-scratch compilation after copying that 18.2.0 > Darwin architecture file to 18.6.0. > > Sadly, no change. Still fails at link time with all the "Undefined > _H5" errors. Ok. Since it starts with at "_" I almost suspected it may be some Fortran binding but

Re: [Users] x86_64 link-time errors on MacOS Mojave

2019-06-20 Thread Haas, Roland
Hello Bernard, I am still in the process of trying to reproduce your error. However one thing I noticed is that (yet again) Cactus needs a new architecture file (once for each Apple update) and reports that darwin 18.6.0 is not a known architecture. This may be part of the reason for failure.

Re: [Users] ToV Collapse Example Parfile

2019-06-19 Thread Haas, Roland
Hello Cole, While I still do now have a reproduced my original plot of the collapsing NS that was in in the ET paper, if you issue is that the fluid speed exceeds the speed of light, you may see a benefit in setting GRHydro::reconstruct_Wv = "yes" Yours, Roland > On Thu, May 23, 2019 at 9:55

Re: [Users] boundary conditions with Llama

2019-06-18 Thread Haas, Roland
Hello Miguel, > oh, but won't this be handled by the > >if (Sn(i,j,k) == -2) > > line above? I see. I had no idea that this is what the grid function does. > from the description of the Sn function in the Interpolate2 thorn: > > CCTK_INT source_patch TYPE=gf TAGS='Checkpoint="no" >

Re: [Users] boundary conditions with Llama

2019-06-18 Thread Haas, Roland
Hello Miguel, > i now have a follow-up question... i would like to experiment with > different boundary conditions, which i would like to implement > myself. i had a look at LlamaWaveToy to see how it's implemented > therein; would the following be a correct way of looping through the > outer

Re: [Users] boundary conditions with Llama

2019-06-17 Thread Haas, Roland
Hello Miguel, assuming that your outer boundary is spherical, your should set: NewRad::z_is_radial = "yes" Yours, Roland > hi all, > > i've been implementing a scalar wave evolution code to work with the Llama > multipatch > infrastructure. i think i have it working except for the boundary

Re: [Users] How to add thorn CarpetAdaptiveRegrid to simulate

2019-06-16 Thread Haas, Roland
Hello Xiaoxiao, I am not sure if CarpetAdaptiveRegrid is still the way to go. The most recent use of adaptive mesh refinement is the AMRToy thorn that you can find in the Carpet repository. That thorn uses the "level_mask" grid function of CarpetRegrid2. Basically at each point on the grid you

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