nal/eschnetter/
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is is
negligible.
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his is
negligible.
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t he wants a resolution to this this issue and will
keep adding it to the agenda until it is resolved, and the old web page
replaced.
Roland mentioned that Ian Hinder worked on a replacement for the web site, and
gave the links:
https://test.cactuscode.org/
https://github.com/einsteintoolkit/ca
On 8 Jun 2020, at 14:48, Ian Hinder
mailto:ian.hin...@manchester.ac.uk>> wrote:
On 4 Jun 2020, at 16:39, Bill Gabella
mailto:b.gabe...@vanderbilt.edu>> wrote:
** [ZE] NRPyPN we use two punctures for initial data in ETK. Looking
for low ecc BBH intial data parameter solvers
be possible given an investment of time. The
VisIt ones were done by Eloisa Bentivenga
(eloisa.bentive...@ibm.com<mailto:eloisa.bentive...@ibm.com>).
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be the MPI thorn
is getting confused about which MPI to use and trying to build its own.
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ight have to uninstall mpich, but I'm not sure. There
*shouldn't* be a fundamental reason why you can't have both installed and just
use one of them, but there might be technical reasons why it doesn't work.
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it. In general, Cactus
executables will need certain environment variables set, modules loaded, etc,
and to be run with the correct mpirun command.
That being said, running the executable directly should work on a ubuntu system
like this, but it's better to use sim run.
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get accurate.
You need quite a lot of resolution, and wave extraction far enough out that you
can cleanly extrapolate it to future null infinity. There are also severe
complications due to junk radiation.
So this approach is quite hard to imple
E.g. if you have a symmetry z -> -z, then you could set zmin
= 0. You then activate ReflectionSymmetry and set
ReflectionSymmetry::reflection_z = "yes", ReflectionSymmetry::avoid_origin_z =
"no" (the need for the latter is due to an unfortunate default, from
e don't want to continue having to use a
self-maintained server.
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an start working through the
files and fixing up the php to markdown conversion, deleting old content, etc.
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ing content which is out of date would help.
We could make a website that's just a few well-chosen pages with a similar
template to the ETK.
Reducing the amount of administrative duplication is certainly desirable.
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and the extra
"baggage" that you need to learn. This wouldn't be helped by Cactus being
perceived as "a relativity code".
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played on a web page along with the CI
results, but wouldn't "break the build" or be rejected. So people can commit
freely, but the problems are tracked, and can be cleaned up later. This is
similar to how the compiler warnings are handled in Jenkins for the ET.
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onding direction with respect to the base grid.
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angular patches start at a finite radius r >
0. So if you want a 2D surface at r = 100, you need to set
CarpetIOASCII::out2D_xyplane_z = 100.
I believe the same works with HDF5. It should also work for a single point; 0d
output; see the parameters in CarpetIOASCII/param.ccl. Just r
-01 16:07:23] restart.userRun(simulationName)::numsmt = 1
In particular, ppn = 144 looks wrong.
Erik, can you confirm?
If it's trying to run on too few nodes, it will run out of memory, as Steve
suggested.
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onvert Carpet to support the "new"
reduction interface (which is probably simple as the differences seem
minor to me).
I meant to use CarpetMask; isn't this a way to mask points from reductions?
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On 15 Jun 2019, at 17:22, Haas, Roland
mailto:rh...@illinois.edu>> wrote:
The alternative is to introduce a helper grid function where you
manually zero out the regions you do not care about then compute the
norm of that grid function.
Perhaps a mask would be of use here?
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restoring the last good
backup, changing all security tokens, and bringing the system back online.
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e CTGamma arrangement:
https://bitbucket.org/llamacode/ctgamma/src/master/
but is not part of the toolkit. Just clone CTGamma into arrangements and add
CTGamma/CartesianCoordinates to the thornlist and recompile.
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messages. Get my PGP key from http://pgp.mit.edu .
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= "
ML_BSSN::ML_log_confac
ML_BSSN::ML_metric
ML_BSSN::ML_trace_curv
ML_BSSN::ML_curv
ML_BSSN::ML_Gamma
ML_BSSN::ML_lapse
ML_BSSN::ML_shift
ML_BSSN::ML_dtlapse
ML_BSSN::ML_dtshift
"
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r with min_fraction=0.9, but not significantly. I would like to
thank again everybody for the quick feedback and help.
Best Regards,
Toni.
Hi Toni,
Good to hear!
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to have the Cactus executable and simulation
result be placed outside the container. I will be happy to transfer ownership
to you, or to create a team, etc. Please advise.
Ian Hinder mentioned to me that he also created an image, but I assume he did
not upload it.
It was very large, so I didn
at the same time (and you are
thinking of making 2 years worth of changes!), the results might be different
for many more reasons, and it's hard to reason about the problem.
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would be more than
1/min_fraction times the number of points by combining, the code does not
combine.
If you set
CarpetRegrid2::min_fraction = 1
then Carpet will never create a single enclosing box, but will always give you
a box based on the union of the points in the two boxes.
Ninja
the ET a little,
though obviously not as much as before. Please update your address books!
ian.hin...@manchester.ac.uk<mailto:ian.hin...@manchester.ac.uk>. My AEI email
address will stop working at the end of February.
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We probably would need to
blacklist those that do.
PS: there are broken links to trac tickets on the wiki. It would be good if
trac.einsteintoolkit.org<http://trac.einsteintoolkit.org> redirected a link
such as
https://trac.einsteintoolkit.org/ticket/641
to the relevant BitBucket ticke
o).
I've never used it, but it looks like simfactory provides a solution. In
simsubs.py SubAll, it looks like you can use @ENV(EBROOTHDF5)@. Let us know
how you get on with that.
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ng! There are instructions for the papers which
should be cited if you use this parameter file and code at the top of the
parameter file:
# Copyright Barry Wardell, Ian Hinder, Eloisa Bentivegna
# We ask that if you make use of the parameter file or the example
# data, then please cite
# Simulation o
reinventing the wheel),
all the information you need to place the individual component in coordinate
space is listed in attributes of the datasets. Look at the "origin" attribute
for the coordinates of the origin of the component, and the "delta" attribute
for the gr
ally means "threads") that at least two MPI processes are
used.]
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can be provided if
> needed.
Looks good. Thanks for testing this!
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sn't use notebooks; it uses textual .m files, so that they can
be version-controlled.)
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:
> https://developer.github.com/changes/2018-04-25-github-services-deprecation/
>
> Functionality will be removed from GitHub.com on January 31st, 2019.
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inful to plot in gnuplot. Before this, I would definitely
>> try to get tcmalloc running and outputting this information on the cluster
>> in a run that actually shows the OOM. My guess is that you won't get an OOM
>> with tcmalloc, and all will be fine :)
>
> o
, I would definitely try to get tcmalloc running
and outputting this information on the cluster in a run that actually shows the
OOM. My guess is that you won't get an OOM with tcmalloc, and all will be fine
:)
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er has a high rss curve, and we
don't see this on the plot. We would have to do 1D output of the grid arrays
and plot each process separately to see the full detail. One way to see if
this is necessary would be to plot both the max and min instead of
hat entire pages cannot be mapped out.
Can you set tcmalloc::report_every = 2048? The outputs a short summary of the
heap status to stdout. I would again be interested to see whether this
continues with a longer run. i.e. whether heap_size - allocated continues to
increase.
- Interesting
ith iteration 2048? HDF5 might be allocating buffers on first output
that are then not freed because they will be used again later. Can you disable
all output and see what happens?
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Can you put labels on the plot for each curve? I don’t know which variables
correspond to the different columns in the file.
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> On 2 Aug 2018, at 18:02, Miguel Zilhão
> wrote:
>
> hi Ian,
>
>> Can you do this with tcmal
ions which are
being made and not freed, or whether the rss is increasing due to fragmentation.
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ot;. This
> increases to about 2 GB after a couple of regriddings, but then stays roughly
> constant at 2 GB, which seems fine, apart from the fact that I had hoped that
> mmap was being used for all the gridfunction data
I suspect I got distracted doing my own investigations while
ibc
malloc. Try this out, and see if things are better. I also have a thorn which
hooks into the tcmalloc API. You can get it from
https://bitbucket.org/ianhinder/tcmalloc
It's very much a work in progress, and probably has some hard-coded assumptions
in it. You can
o all the freeing and
mallocing that happens during regridding when the sizes of the grids change.
Can you try using tcmalloc or jemalloc instead of glibc malloc and reporting
back? One workaround could be to run shorter simulations (i.e. set a wallt
a shell script. You should
probably use sim create-run rather than sim create-submit so that the
simulations don't run in the background at the same time.
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tomatically detect the change and use the new runscript.
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to the Cactus command line and you will get separate output and error
files from each process.
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pdate script is also failing with
Can't create session: Unable to connect to a repository at URL
'https://svn.cct.lsu.edu/repos/numrel/LSUThorns/CPUID': Error running context:
Connection timed out at /usr/share/perl5/Git/SVN.pm line 143.
It works fine from my laptop, but not from
> On 30 May 2018, at 15:35, Feyisso Sado wrote:
>
> Dear Ian Hinder
>
> Many Thanks
>
> I'm searching google, but still not resolved
>
> My Ubuntu version: Ubuntu 14.04.5 LTS
> and
> curl --version: curl 7.52.1 (x86_64-pc-linux-gnu) libcurl/7.52.1
&
to access an http server with https. Is it possible that there is some
firewall or redirection happening on your network to prevent you from accessing
https servers?
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#x27;m reinstalling Toolkit, but I faced the
>> following error.
>> curl: (35) error:140770FC:SSL routines:SSL23_GET_SERVER_HELLO:unknown
>> protocol
>> Please he me resolve
>
> Please can you tell us the command that you ran to get this error message?
>
>
23_GET_SERVER_HELLO:unknown protocol
> Please he me resolve
Please can you tell us the command that you ran to get this error message?
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the same with optionlists
and thornlists. This is so that the simulation is self-contained, and no
longer depends on external files once it has been created unless the user
explicitly asks for something to be updated.
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ou using simfactory? If so, then I usually just edit the
parameter file in /SIMFACTORY/par then submit the next segment.
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does "which gcc" give you?
If it is indeed compiling OK with Clang, it's interesting, because when I tried
to compile just Cactus, not even the whole ET, using Clang on a Mac, I ran into
several incompatibilities. This was a couple of years ago now, and maybe they
have all be
> On 30 Apr 2018, at 16:30, Einstein Toolkit
> wrote:
>
> #1471: Cactus should auto-detect newer versions of GCC from MacPorts
> --+-
> Reporter: Ian Hinder | Owner: (none)
> Type: enhancemen
Hi Steve,
If I push to the ET website repo, does it automatically get reflected on the
web? Or do I need to click the button on
http://einsteintoolkit.org/update.php <http://einsteintoolkit.org/update.php>
?
What else does that button do?
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ner levels?
Hi,
I have never tried to do this with mesh refinement, no. This might be a
limitation in Carpet, because perhaps it tries to prolongate with the same
order in every direction.
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e equation
(i.e. it doesn't take derivatives in the z direction):
https://github.com/ianhinder/Kranc/blob/master/Examples/laplace.par
I have not tried this recently, but it worked at one point.
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of those repositories,
which allows users to make changes which don't conflict with other people, but
then also to share those changes in a controlled way.
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ow:
> <螢幕快照 2018-02-10 下午2.03.30.png>
> It failed, so SimulationTools seems to be required to move to Application
> directory of Mathematica.
Yes, that should fix the problem.
NX is good; that should be fast enough to use Mathematica remotely.
Good luck, and pleas
rnel runs on the cluster, where
it can directly access the data. This way, only the visualisation needs to be
sent over the network, not the original raw data. Of course, Mathematica is
very expensive, so this might not be an ideal solution for you.
rnel runs on the cluster, where
it can directly access the data. This way, only the visualisation needs to be
sent over the network, not the original raw data. Of course, Mathematica is
very expensive, so this might not be an ideal solution for you.
there was a way to avoid this by first "slicing" the
NxMx1 3D dataset that Carpet produces to be an NxM 2D dataset, so that VisIt
knows it is 2D, but I think when I tried this, it didn't work. Perhaps someone
who is more expert in VisIt could suggest something?
--
Slight correction: Wednesday 2/7/2018.
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> below:
> #module load cray-petsc/3.7.6.0
> #module load curl/7.28.1
> #module load hwloc/1.7.2
> #module load numactl/2.0.10
> I wonder whether this module commended resulted in the disappearance of .vtk
> files.
No, this should be
would allow the machine to be used for science now by people just running
"git pull" in the simfactory directory, rather than waiting until the end of
February for the next release.
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nk below.
>
> https://docs.einsteintoolkit.org/et-docs/Main_Page#Weekly_Users_Call
> <https://docs.einsteintoolkit.org/et-docs/Main_Page#Weekly_Users_Call>
Hi,
I am unable to join the call; is it happening?
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Hi Roland,
Shouldn't these changes be backported to the current release?
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which ones we have time to work on
for this release, and which ones will be bumped to the next release.
Thanks!
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olkit.th)
Were you following a particular tutorial? If so, can you give more details?
If you found a thornlist on one of the Cactus or ET websites along with a
WaveDemo tutorial, I'm afraid to say that many of these are unfortunately very
out of date, which is likely the reason for t
utely
necessary for a strict reproducibility test, we could probably get the 2008
version of the toolkit running. But this will be a large amount of work. It's
probably much less work to get it working with the current release.
What error message do you get if you try to use the current release?
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gt; users.
Are we yet in a position where we can have just a single tutorial, to avoid
confusion?
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> -D_USE_MATH_DEFINES
> -D_XOPEN_SOURCE
> -DM_PI = 3.14149265358979323847
>
> I also tried to change c11 to c99 at CFLAGS and add
> -stdlib=libc++ at LIBCXX.
>
> None of those worked.
>
> Please let me know what is to be done.
Hi Maria,
Have you installed all the
ot;KerrSchild", "Minkowski", "ShiftedGaugeWave",
"Vaidya", "ModifiedSchwarzschildBL"};
+(* spacetimes = {"GaugeWave", "KerrSchild", "Minkowski", "ShiftedGaugeWave",
"Vaidya", "ModifiedSchwarzschildB
coordinates will just not work (e.g. the horizon finder). That is why I asked
you what you are trying to do. Please can you answer that, before we go into a
lot of detail about how to do it in one particular way, which may in the end
not help you?
Thanks!
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of the list check to see what the setting
is? If people need to subscribe, then we should give instructions on the web
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On 6 Nov 2017, at 17:31, Ian Hinder wrote:
>
> On 6 Nov 2017, at 17:06, Roland Haas wrote:
>
>> * 6 failing tests
>> ** prolongation one is new, need input from Erik, want trac ticket
>
> It turns out that this was already discussed in the original ticke
t or something, which
really had no optimisations at all.
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er what you are trying to
do is feasible? Maybe you could give more details about what you are trying to
do?
PS: *please* include users@einsteintoolkit.org in the CC when you reply. If
you reply just to me, then nobody else benefits from the discussion, and nobody
else has the opportun
through each of the 23 packages one by one. Also, the table
format, while quite attractive, won't scale to adding columns for more
operating systems, such as Mac OS.
One question:
- Is this tutorial in a repository somewhere?
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When you schedule a function in local
mode ("OPTIONS: LOCAL"), it is called once per component, and then you can
access grid data.
I spent hours recently trying to track down exactly this problem!
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_
.cc
>
> However I am not having any luck reverse-engineering these.
> Any ideas would be appreciated.
>
Hi,
Thanks for the detailed report!
What mode are you calling your function in? i.e. can you show us the block in
schedule.ccl that schedules your function? If it is not loca
On 2 Nov 2017, at 11:20, dumsani wrote:
>
>
> On 02/11/2017 10:46, Ian Hinder wrote:
>> On 2 Nov 2017, at 01:41, dumsani wrote:
>>
>>> I think I have figured it out eventually. Thanks, Ian.
>> Good to hear! Would it be useful to summarise the cause of
= 1, what else
> does one have to specify in orer to get a run with only one grid?
Hi Dumsani,
What goes wrong? Do you get an error message? You don't even have to set
max_refinement_levels to 1; you just have to make sure you don't ask for any
more than 1 refinemen
ein 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.
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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?
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Ian Hinder
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want to express your
initial data in Cartesian-type coordinates. So, for example, if you had Kerr
in Boyer-Lindquist coordinates, you would first change coordinates and basis
using the usual transformation, and then evaluate the metric and extrinsic
curvature on the x,y,z grid. Is that what you
n in the
case of "op_copy". The problem here likely resulted in confusion due to the
operator being badly named (https://martinfowler.com/bliki/TwoHardThings.html).
In arrangements/Carpet/CarpetLib/src/operators.hh, the implication is that the
"copy" in op_copy refers to the time interpolation only, but the code in
patched in the above commit assumes that "copy" means don't interpolate at all.
It's not clear how this can make sense when the data comes from another
refinement level, which will always have a different resolution, but maybe
there is some case where this would have made sense.
Erik, should this commit be merged to master?
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Ian Hinder
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regridding? By not prolongating the refinement
boundaries, it's not clear how the "new" bits of the grid are supposed to be
filled when the fine grids move. Could this be the problem? If you give the
gridfunction 3 timelevels and remove "prolongation=none", do the NaNs go away?
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Ian Hinder
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.
For submissions, you can:
1. Ask on the list;
2. Create a bitbucket pull request; or
3. Create a ticket on TRAC.
Up to you! Probably (2) is the preferred option.
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Ian Hinder
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.
>
>
> https://docs.einsteintoolkit.org/et-docs/Main_Page#Weekly_Users_Call
Hi Steve,
The call this week conflicts with the LIGO press conference, which is at 10:00
am EST (9:00 am CT). I expect many people will not attend; should we just
cancel the call?
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Ian Hinder
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On 3 Jul 2017, at 17:32, Ian Hinder wrote:
>
> On 20 Jun 2017, at 13:45, Ian Hinder wrote:
>
>> On Fri, Jun 2, 2017 at 11:25 AM, Ian Hinder wrote:
>>
>>> Hi all,
>>>
>>> The security team at NCSA have blocked access to the ET Jenkins server
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