Volume rendering
by Андрей Парамонов
Hello!
I've recently discovered yt, and I found the rendering examples really
encouraging. I'm now trying to visualize a large 3D dataset via volume
rendering technique. I have come up with the following script that is
intended to plot a part of the dataset:
---
import yt
from yt.config import ytcfg
import h5py
f = h5py.File('ims-p.hdf5')
intens = f['intensity'][:256,:256,:256]
print(intens.shape)
ds = yt.load_uniform_grid({'Intensity': intens}, intens.shape)
print(ds)
sc = yt.create_scene(ds, ('Intensity'), lens_type = 'perspective')
sc[0].set_log(True)
sc[0].tfh.plot('transfer_function.png', profile_field = 'Intensity')
sc.camera.resolution = 1024
sc.annotate_axes(alpha = 0.1)
sc.annotate_domain(ds, color = [1, 1, 1, 0.1])
sc.save_annotated('vr_grids.png', sigma_clip = 4)
---
I get some really fascinating rendering (attached), and now I want to
tweak it. I would be really happy if you could help me with the
following questions:
1) What is the best way to configure the camera viewpoint so the
complete data cube fits into the view? How to quickly render the domain
axes without performing the costly volume rendering (to find the
"optimal" viewpoint experimentally)?
2) What is the best way to specify axes scales, so that rendered volume
appears as cuboid, not cube? I want the resulting cuboid to be scaled as
3:2:2. How to specify resulting image size, e.g. how to get image of
1600x1200 pixels?
3) In my dataset, the grid is not in fact uniform, but rather X
coordinates are specified by (non-decreasing) array rettime, Y
coordinates are specified by (non-decreasing) array mz. What is the best
way to pass this information (to load_uniform_grid)?
4) Is it possible to use inverse transfer function model, i.e. white
background?
5) My complete dataset is rather large and doesn't readily fit into RAM.
However it seems that for ray-tracing algorithm, it shouldn't be
required that all data is available simultaneously. Is it possible to
feed dataset by chunks?
Your help is greatly appreciated!
Best wishes,
Andrey Paramonov
--
This message has been scanned for viruses and
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1 year, 3 months
Re: [yt-users] yt-users Digest, Vol 117, Issue 33
by Tomer Nussbaum
Hi,
Thank for answering,
My question is what are you doing now in order to have fast computations,
without changing any YT code.
Is there something That can be solved by change in the YT configurations?
(Do I understand from your answer that no?)
How are you handling many group members using the same files together? Do
you use SSD drives? Do you copy each snapshot to the node and then compute?
Do you do some of what I asked about? Do you have any other special tricks?
Thank,
Tomer
On Tue, Nov 28, 2017 at 7:53 PM, <yt-users-request(a)lists.spacepope.org>
wrote:
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> 1. Re: yt-users Digest, Vol 117, Issue 31 (Matthew Turk)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 28 Nov 2017 11:52:57 -0600
> From: Matthew Turk <matthewturk(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] yt-users Digest, Vol 117, Issue 31
> Message-ID:
> <CALO3=5Hu9VJLYA9yAZEPdACLUi+RfYwhABD78du+vsacJW=wXA@mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Tomer,
>
> Both the ARTIO frontend and the NMSU-ART frontends could definitely be
> improved in their number of disk accesses, but like Kacper said, getting a
> handle on where they are occurring would be the best first step, I think.
> Then we can take it from there.
>
> On Tue, Nov 28, 2017 at 11:25 AM, Kacper Kowalik <xarthisius.kk(a)gmail.com>
> wrote:
>
> > Hi Tomer,
> > unfortunately we don't have any means of fine tuning yt's i/o on a low
> > level. Short of profiling ART frontend and trying to decrease the number
> > of iops, I'm afraid there's not much to be done.
> >
> > Having said that, I'd try to debug your GPFS too with something
> > different than yt and simpler. Maybe a single hdf5 file with a large
> > array and simultaneous access to a random row/column with each process?
> >
> > 20 concurrent reads sounds like something that GPFS should handle
> > without degradation of performance from 10s to hours.
> >
> > Cheers,
> > Kacper
> >
> > On 11/28/2017 11:01 AM, Tomer Nussbaum wrote:
> > > Hi Nathan,
> > >
> > > Thank you for answering,
> > >
> > > 1. Does it take hours to load these files on a laptop?
> > > # Ans: Nope, It take 10 sec.
> > > # It takes us lots of time on the cluster when we parallel the jobs,
> > > above 20 yt.load calls toghter.
> > > # We toke a look at our GPFS, it looks like there are many IOP that
> > > flood the GPFS, (it is currently a serial reading at our GPFS)
> > >
> > > 2. What sort of data are you working with? How big are the data files?
> > > # Ans: We are working on Vela sims, it's ART simulations, 5GB per
> > > snapshot ruffly.
> > >
> > > 3. When you say ?load? the data, is that just doing yt.load or are you
> > > doing any I/O?
> > > # Ans: load=yt.load and then creating a sphere obj and reading gas
> > > particles from it.
> > >
> > > Thank,
> > > Tomer
> >
> > > On Tue, Nov 28, 2017 at 6:31 PM, <yt-users-request(a)lists.spacepope.org
> > > <mailto:yt-users-request@lists.spacepope.org>> wrote:
> > >
> > > Send yt-users mailing list submissions to
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> > > <mailto:yt-users@lists.spacepope.org>
> > >
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> > >
> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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> > > or, via email, send a message with subject or body 'help' to
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> > > than "Re: Contents of yt-users digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > > 1. Fwd: Cluster best configurations for YT (Tomer Nussbaum)
> > > 2. Re: Fwd: Cluster best configurations for YT (Nathan Goldbaum)
> > >
> > >
> > > ------------------------------------------------------------
> > ----------
> > >
> > > Message: 1
> > > Date: Tue, 28 Nov 2017 11:55:56 +0200
> > > From: Tomer Nussbaum <tomer.nussbaum(a)mail.huji.ac.il
> > > <mailto:tomer.nussbaum@mail.huji.ac.il>>
> > > To: yt-users(a)lists.spacepope.org <mailto:yt-users@lists.
> > spacepope.org>
> > > Subject: [yt-users] Fwd: Cluster best configurations for YT
> > > Message-ID:
> > >
> > > <CAOGC2jACH1Q4QLfFNi8h7p=XhqEFvnp-6g17FUv6aDN2vSvqWg@mail.
> gmail.com
> > > <mailto:XhqEFvnp-6g17FUv6aDN2vSvqWg@mail.gmail.com>>
> > > Content-Type: text/plain; charset="utf-8"
> > >
> > > ---------- Forwarded message ----------
> > > From: Tomer Nussbaum <tomer.nussbaum(a)mail.huji.ac.il
> > > <mailto:tomer.nussbaum@mail.huji.ac.il>>
> > > Date: Thu, Nov 23, 2017 at 6:08 PM
> > > Subject: Cluster best configurations for YT
> > > To: yt-users(a)lists.spacepope.org <mailto:yt-users@lists.
> > spacepope.org>
> > >
> > >
> > >
> > > Hi,
> > >
> > > We have updated our cluster lately, but our YT platform works very
> > slow
> > > (loads one snapshot an hour, when couple of people run
> together...).
> > > I wanted to ask you if you can help solving this issue from your
> > > experience.
> > >
> > > We use infiniband, and we see that the main problem is lots of
> > > request in
> > > random access to our hard drives,
> > > so the problem can be in fine tuning YT on the Nodes, or fine
> tuning
> > the
> > > file system
> > >
> > > This brings up this couple of issues (maybe more, if you have
> > > another idea,
> > > I would be thankful to know):
> > >
> > > 1. *IO readings - *Is there a way to optimize the io readings
> > > requests
> > > to the file server?
> > > 2. *YT configurations -* Are there specific parameters in the YT
> > > configuration for this status?
> > > 3. *File server behavior -* Can we set reading server functions
> > > (we use
> > > hard drives, serial reading status)?
> > > 4. *Metadata cache -* Does using metadata cache will solve the
> > issue?
> > > 5. *zlib usage - *How can I check if this feature is activated,
> > > how much
> > > is it important in the YT platform?
> > >
> > >
> > > I will really appreciate any help with it,
> > > Thanx,
> > > Tomer
> > > -------------- next part --------------
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> > > <http://lists.spacepope.org/pipermail/yt-users-spacepope.
> > org/attachments/20171128/cde38586/attachment-0001.html>>
> > >
> > > ------------------------------
> > >
> > > Message: 2
> > > Date: Tue, 28 Nov 2017 12:42:40 +0000
> > > From: Nathan Goldbaum <nathan12343(a)gmail.com
> > > <mailto:nathan12343@gmail.com>>
> > > To: Discussion of the yt analysis package
> > > <yt-users(a)lists.spacepope.org
> > > <mailto:yt-users@lists.spacepope.org>>
> > > Subject: Re: [yt-users] Fwd: Cluster best configurations for YT
> > > Message-ID:
> > >
> > > <CAJXewOk9tCL-TCTQef9Up-mTj-qgVFJp6yHZXmwQ8SReoV4h8A@mail.
> gmail.com
> > > <mailto:CAJXewOk9tCL-TCTQef9Up-mTj-qgVFJp6yHZXmwQ8SReoV4h8A@mail.
> > gmail.com>>
> > > Content-Type: text/plain; charset="utf-8"
> > >
> > > Hi Tomer,
> > >
> > > A couple questions:
> > >
> > > 1. Does it take hours to load these files on a laptop?
> > >
> > > 2. What sort of data are you working with? How big are the data
> > files?
> > >
> > > 3. When you say ?load? the data, is that just doing yt.load or are
> > you
> > > doing any I/O?
> > >
> > > Nathan
> > >
> > > On Tue, Nov 28, 2017 at 4:56 AM Tomer Nussbaum <
> > > tomer.nussbaum(a)mail.huji.ac.il
> > > <mailto:tomer.nussbaum@mail.huji.ac.il>> wrote:
> > >
> > > >
> > > > ---------- Forwarded message ----------
> > > > From: Tomer Nussbaum <tomer.nussbaum(a)mail.huji.ac.il
> > > <mailto:tomer.nussbaum@mail.huji.ac.il>>
> > > > Date: Thu, Nov 23, 2017 at 6:08 PM
> > > > Subject: Cluster best configurations for YT
> > > > To: yt-users(a)lists.spacepope.org <mailto:yt-users@lists.
> > spacepope.org>
> > > >
> > > >
> > > >
> > > > Hi,
> > > >
> > > > We have updated our cluster lately, but our YT platform works
> very
> > > slow
> > > > (loads one snapshot an hour, when couple of people run
> > together...).
> > > > I wanted to ask you if you can help solving this issue from your
> > > > experience.
> > > >
> > > > We use infiniband, and we see that the main problem is lots of
> > > request in
> > > > random access to our hard drives,
> > > > so the problem can be in fine tuning YT on the Nodes, or fine
> > > tuning the
> > > > file system
> > > >
> > > > This brings up this couple of issues (maybe more, if you have
> > another
> > > > idea, I would be thankful to know):
> > > >
> > > > 1. *IO readings - *Is there a way to optimize the io readings
> > > requests
> > > > to the file server?
> > > > 2. *YT configurations -* Are there specific parameters in the
> YT
> > > > configuration for this status?
> > > > 3. *File server behavior -* Can we set reading server
> functions
> > (we
> > > > use hard drives, serial reading status)?
> > > > 4. *Metadata cache -* Does using metadata cache will solve the
> > > issue?
> > > > 5. *zlib usage - *How can I check if this feature is
> activated,
> > how
> > > > much is it important in the YT platform?
> > > >
> > > >
> > > > I will really appreciate any help with it,
> > > > Thanx,
> > > > Tomer
> > > >
> > > >
> > > > _______________________________________________
> > > > yt-users mailing list
> > > > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.
> spacepope.org>
> > > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> > > <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >
> > > -------------- next part --------------
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> > >
> > > ------------------------------
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> > >
> > > ------------------------------
> > >
> > > End of yt-users Digest, Vol 117, Issue 31
> > > *****************************************
> > >
> > >
> > >
> > >
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> End of yt-users Digest, Vol 117, Issue 33
> *****************************************
>
1 year, 3 months
Trouble Installing Yt with Rockstar
by Sean Larkin
I have been trying to install Rockstar with yt onto a computer running
macOS sierra 10.12, using both the install script and manually.
For the install script, I get this error:
Building Rockstar
********************************************
FAILURE REPORT:
********************************************
config=config)
File
"/Users/user1/Rockstar/yt-conda/lib/python3.6/site-packages/conda_build/build.py",
line 1147, in build
utils.check_call_env(cmd, env=env, cwd=src_dir)
File
"/Users/user1/Rockstar/yt-conda/lib/python3.6/site-packages/conda_build/utils.py",
line 628, in check_call_env
return _func_defaulting_env_to_os_environ(subprocess.check_call,
*popenargs, **kwargs)
File
"/Users/user1/Rockstar/yt-conda/lib/python3.6/site-packages/conda_build/utils.py",
line 624, in _func_defaulting_env_to_os_environ
return func(_args, **kwargs)
File "/Users/user1/Rockstar/yt-conda/lib/python3.6/subprocess.py", line
291, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/bin/bash', '-x', '-e',
'/Users/user1/Rockstar/yt-conda/conda-bld/rockstar_1511919771484/work/conda_build.sh']'
returned non-zero exit status 2.
********************************************
********************************************
Failure. Check /Users/user1/Rockstar/yt-conda/yt_install.log. The last 10
lines are above.
And when installing manually, after stating "make lib" i get this error:
/bin/sh: pkg-config: command not found
gcc -m64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64
-D_BSD_SOURCE -D_POSIX_SOURCE -D_POSIX_C_SOURCE=200809L -D_SVID_SOURCE
-D_DARWIN_C_SOURCE -Wall -fno-math-errno -fPIC -shared rockstar.c
check_syscalls.c fof.c groupies.c subhalo_metric.c potential.c nfw.c
jacobi.c fun_times.c interleaving.c universe_time.c hubble.c integrate.c
distance.c config_vars.c config.c bounds.c inthash.c io/read_config.c
client.c server.c merger.c inet/socket.c inet/rsocket.c inet/address.c
io/meta_io.c io/io_internal.c io/io_ascii.c io/stringparse.c io/io_gadget.c
io/io_generic.c io/io_art.c io/io_tipsy.c io/io_bgc2.c io/io_util.c
io/io_arepo.c io/io_hdf5.c -o librockstar.so -lm -O3 -std=c99
In file included from server.c:241:
*./load_balance.c:8:21: **warning: **using floating point absolute value
function*
* 'fabs' when argument is of integer type [-Wabsolute-value]*
i = ceil(sqrt(fabs(in)))+1;
* ^*
*./load_balance.c:8:21: **note: *use function 'llabs' instead
i = ceil(sqrt(fabs(in)))+1;
* ^~~~*
llabs
1 warning generated.
Undefined symbols for architecture x86_64:
"_GROUPIES_fast3tree_box_inside_sphere", referenced from:
_GROUPIES_fast3tree_find_sphere_offset in groupies-eb1fe8.o
ld: symbol(s) not found for architecture x86_64
clang: *error: *linker command failed with exit code 1 (use -v to see
invocation)
make: *** [lib] Error 1
I am not sure what is causing the error for install script, but for the
manual install, I think it is clang using the wrong c++ standard library. I
have attempted to change the library used, but nothing has worked for me so
far.
1 year, 3 months
Re: [yt-users] yt-users Digest, Vol 117, Issue 31
by Tomer Nussbaum
Hi Nathan,
Thank you for answering,
1. Does it take hours to load these files on a laptop?
# Ans: Nope, It take 10 sec.
# It takes us lots of time on the cluster when we parallel the jobs, above
20 yt.load calls toghter.
# We toke a look at our GPFS, it looks like there are many IOP that flood
the GPFS, (it is currently a serial reading at our GPFS)
2. What sort of data are you working with? How big are the data files?
# Ans: We are working on Vela sims, it's ART simulations, 5GB per snapshot
ruffly.
3. When you say ?load? the data, is that just doing yt.load or are you
doing any I/O?
# Ans: load=yt.load and then creating a sphere obj and reading gas
particles from it.
Thank,
Tomer
On Tue, Nov 28, 2017 at 6:31 PM, <yt-users-request(a)lists.spacepope.org>
wrote:
> Send yt-users mailing list submissions to
> yt-users(a)lists.spacepope.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> or, via email, send a message with subject or body 'help' to
> yt-users-request(a)lists.spacepope.org
>
> You can reach the person managing the list at
> yt-users-owner(a)lists.spacepope.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of yt-users digest..."
>
>
> Today's Topics:
>
> 1. Fwd: Cluster best configurations for YT (Tomer Nussbaum)
> 2. Re: Fwd: Cluster best configurations for YT (Nathan Goldbaum)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 28 Nov 2017 11:55:56 +0200
> From: Tomer Nussbaum <tomer.nussbaum(a)mail.huji.ac.il>
> To: yt-users(a)lists.spacepope.org
> Subject: [yt-users] Fwd: Cluster best configurations for YT
> Message-ID:
> <CAOGC2jACH1Q4QLfFNi8h7p=XhqEFvnp-6g17FUv6aDN2vSvqWg@mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> ---------- Forwarded message ----------
> From: Tomer Nussbaum <tomer.nussbaum(a)mail.huji.ac.il>
> Date: Thu, Nov 23, 2017 at 6:08 PM
> Subject: Cluster best configurations for YT
> To: yt-users(a)lists.spacepope.org
>
>
>
> Hi,
>
> We have updated our cluster lately, but our YT platform works very slow
> (loads one snapshot an hour, when couple of people run together...).
> I wanted to ask you if you can help solving this issue from your
> experience.
>
> We use infiniband, and we see that the main problem is lots of request in
> random access to our hard drives,
> so the problem can be in fine tuning YT on the Nodes, or fine tuning the
> file system
>
> This brings up this couple of issues (maybe more, if you have another idea,
> I would be thankful to know):
>
> 1. *IO readings - *Is there a way to optimize the io readings requests
> to the file server?
> 2. *YT configurations -* Are there specific parameters in the YT
> configuration for this status?
> 3. *File server behavior -* Can we set reading server functions (we use
> hard drives, serial reading status)?
> 4. *Metadata cache -* Does using metadata cache will solve the issue?
> 5. *zlib usage - *How can I check if this feature is activated, how much
> is it important in the YT platform?
>
>
> I will really appreciate any help with it,
> Thanx,
> Tomer
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.
> org/attachments/20171128/cde38586/attachment-0001.html>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 28 Nov 2017 12:42:40 +0000
> From: Nathan Goldbaum <nathan12343(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] Fwd: Cluster best configurations for YT
> Message-ID:
> <CAJXewOk9tCL-TCTQef9Up-mTj-qgVFJp6yHZXmwQ8SReoV4h8A@mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Tomer,
>
> A couple questions:
>
> 1. Does it take hours to load these files on a laptop?
>
> 2. What sort of data are you working with? How big are the data files?
>
> 3. When you say ?load? the data, is that just doing yt.load or are you
> doing any I/O?
>
> Nathan
>
> On Tue, Nov 28, 2017 at 4:56 AM Tomer Nussbaum <
> tomer.nussbaum(a)mail.huji.ac.il> wrote:
>
> >
> > ---------- Forwarded message ----------
> > From: Tomer Nussbaum <tomer.nussbaum(a)mail.huji.ac.il>
> > Date: Thu, Nov 23, 2017 at 6:08 PM
> > Subject: Cluster best configurations for YT
> > To: yt-users(a)lists.spacepope.org
> >
> >
> >
> > Hi,
> >
> > We have updated our cluster lately, but our YT platform works very slow
> > (loads one snapshot an hour, when couple of people run together...).
> > I wanted to ask you if you can help solving this issue from your
> > experience.
> >
> > We use infiniband, and we see that the main problem is lots of request in
> > random access to our hard drives,
> > so the problem can be in fine tuning YT on the Nodes, or fine tuning the
> > file system
> >
> > This brings up this couple of issues (maybe more, if you have another
> > idea, I would be thankful to know):
> >
> > 1. *IO readings - *Is there a way to optimize the io readings requests
> > to the file server?
> > 2. *YT configurations -* Are there specific parameters in the YT
> > configuration for this status?
> > 3. *File server behavior -* Can we set reading server functions (we
> > use hard drives, serial reading status)?
> > 4. *Metadata cache -* Does using metadata cache will solve the issue?
> > 5. *zlib usage - *How can I check if this feature is activated, how
> > much is it important in the YT platform?
> >
> >
> > I will really appreciate any help with it,
> > Thanx,
> > Tomer
> >
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users(a)lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
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>
> Subject: Digest Footer
>
> _______________________________________________
> yt-users mailing list
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>
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> ------------------------------
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> End of yt-users Digest, Vol 117, Issue 31
> *****************************************
>
1 year, 3 months
Fwd: Cluster best configurations for YT
by Tomer Nussbaum
---------- Forwarded message ----------
From: Tomer Nussbaum <tomer.nussbaum(a)mail.huji.ac.il>
Date: Thu, Nov 23, 2017 at 6:08 PM
Subject: Cluster best configurations for YT
To: yt-users(a)lists.spacepope.org
Hi,
We have updated our cluster lately, but our YT platform works very slow
(loads one snapshot an hour, when couple of people run together...).
I wanted to ask you if you can help solving this issue from your experience.
We use infiniband, and we see that the main problem is lots of request in
random access to our hard drives,
so the problem can be in fine tuning YT on the Nodes, or fine tuning the
file system
This brings up this couple of issues (maybe more, if you have another idea,
I would be thankful to know):
1. *IO readings - *Is there a way to optimize the io readings requests
to the file server?
2. *YT configurations -* Are there specific parameters in the YT
configuration for this status?
3. *File server behavior -* Can we set reading server functions (we use
hard drives, serial reading status)?
4. *Metadata cache -* Does using metadata cache will solve the issue?
5. *zlib usage - *How can I check if this feature is activated, how much
is it important in the YT platform?
I will really appreciate any help with it,
Thanx,
Tomer
1 year, 3 months
Exodus file Couldn't figure out output type
by Jaron Senecal
Hi,
I just installed yt and immediately ran into the following problem. The
following script
#viz1.py
import yt
from yt.mods import *
ds = yt.load("stnd_2d_out.e", step=-1)
gives this error:
yt : [ERROR ] 2017-11-21 09:34:33,950 Couldn't figure out output type
for stnd_2d_out.e
Traceback (most recent call last):
File "viz1.py", line 27, in <module>
ds = yt.load("stnd_2d_out.e", step=-1)
File
"/home/jaron/.conda/envs/py36/lib/python3.6/site-packages/yt/convenience.py",
line 98, in load
raise YTOutputNotIdentified(args, kwargs)
yt.utilities.exceptions.YTOutputNotIdentified: Supplied
('stnd_2d_out.e',) {'step': -1}, but could not load!
Please let me know how to resolve this.
-Jaron
1 year, 4 months
Readline on Pleiades
by David Collins
Hi, Everybody!
I'm running yt on Pleiades, and I'm running into a readline error (below)
Has anyone else run into this, and do you know what I can do to fix this?
This is a recent build, not from source.
Thanks!
pleiades:~/yt3_scripts>python
Python 2.7.13 | packaged by conda-forge | (default, May 2 2017, 12:48:11)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Traceback (most recent call last):
File "/etc/pythonstart", line 7, in <module>
import readline
ImportError: /u/dccolli1/local-yt-2017-09-28/yt-conda/lib/python2.7/lib-
dynload/../../libreadline.so.6: undefined symbol: PC
>>>
--
-- Sent from a computer.
1 year, 4 months
ANN: Trident CGM/IGM Analysis Code v1.1 Released
by Cameron Hummels
On behalf of the Trident development team, I am happy to announce a new
stable release of Trident, a python-based code suite for analyzing
astrophysical hydro simulations to investigate the CGM/IGM and produce
synthetic absorption spectra. This release is accompanied by a shift in
development from mercurial/bitbucket to git/github, continuous integration
and testing with travis, and a number of bugfixes and additional features.
Our changelog (below) has a full description of the changes in this
version.
Full installation instructions are available in our documentation, as are
instructions for a number of common use cases in working with your
datasets: e.g., adding arbitrary ion fields, making column density maps,
calculating column densities of individual sightlines, generating
absorption line spectra.
There has also been recent development in the yt community to treat
particle-based datasets more natively rather than by depositing to a grid
and then processing. This effort, nicknamed "*demeshening*", is being led
by Nathan Goldbaum, Meagan Lang, and Matt Turk, with Trident contributions
by Bili Dong and myself. Not only does it get more accurate results, but
it is faster and uses less memory since particle fields don't need to be
deposited to a global grid. This code is now in beta, and users are
encouraged to use it and give bug reports. There are full instructions for
installation of it available in the Trident docs, and we expect the next
stable release of Trident will incorporate it.
Please don't hesitate to contact the mailing list with any questions or
problems you may encounter with the code, and I encourage you to share this
announcement with other scientists who may be interested in using Trident.
*Trident Page:* http://trident-project.org
*Trident Code:* https://github.com/trident-project/trident/
*Trident Docs:* https://trident.readthedocs.io/en/latest/
*Trident Paper*: http://adsabs.harvard.edu/abs/2017ApJ...847...59H
*Changelog to Trident 1.1:*
https://trident.readthedocs.io/en/latest/changelog.html
*Installation Docs for beta "demeshened" yt and Trident:*
https://nbviewer.jupyter.org/url/trident-project.org/notebooks/trident_de...
--The Trident Developer Team:
Cameron Hummels
Britton Smith
Devin Silvia
Matthew Turk
Nathan Goldbaum
Kacper Kowalik
Lauren Corlies
Bili Dong
Hilary Egan
Clayton Strawn
--
Cameron Hummels
NSF Postdoctoral Fellow
Department of Astronomy
California Institute of Technology
http://chummels.org
1 year, 4 months
how to add halo quantity
by Daegene Koh
Hi all,
I’m trying to add a new quantity to a halo catalog following the docs as such,
23 def _total_mass(halo):
24 gasmass, dmmass = halo.data_object.quantities.total_mass()
25 return gasmass+dmmass
26
27 add_quantity('total_mass',_total_mass)
28 hc.add_quantity('total_mass’)
however, it seems at add_quantity is not defined. How do I go about doing this?
Cheers,
DK
1 year, 4 months
Re: [yt-users] yt-users Digest, Vol 117, Issue 22
by Matias Enrique Suazo Campos
Thanks Everybody!!!
There was no problem after all :P
I hope this to be useful for someone else.
Matías Suazo,
MSc student at Universidad de Chile
2017-11-14 17:42 GMT-03:00 <yt-users-request(a)lists.spacepope.org>:
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of yt-users digest..."
>
>
> Today's Topics:
>
> 1. Re: Projection (Jos? Mauricio Utreras)
> 2. Re: Projection (Nathan Goldbaum)
> 3. Re: Projection (Matthew Turk)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 14 Nov 2017 15:45:23 -0300
> From: Jos? Mauricio Utreras <jutreras(a)ug.uchile.cl>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] Projection
> Message-ID:
> <CANhQbF5OzXEhNzguuXR8iNRrAryy74iQ=sVg8zZg5QCzyzqvJg@mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi everyone,
>
> I got the same result using the IsolatedGalaxy dataset
>
> ds=yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
> disk = ds.disk('c',[0,0,1],(1000,'pc'),(100,'pc'))
> proj=ds.proj('density',axis='z',weight_field='density',
> data_source=disk,method='integrate')
> proj['density']
> >>> YTArray([ nan, nan, nan, ..., nan, nan, nan]) g/cm**3
>
> 2017-11-14 15:38 GMT-03:00, Nathan Goldbaum <nathan12343(a)gmail.com>:
> > Can I get one of you to open an issue?
> >
> > https://github.com/yt-project/yt/issues/new
> >
> > If you can, please include a script to reproduce the problem, making use
> of
> > one of the public datasets on yt-project.org/data.
> >
> > -Nathan
> >
> > On Tue, Nov 14, 2017 at 12:34 PM, Andrew James Emerick
> > <aje2123(a)columbia.edu
> >> wrote:
> >
> >> Hello Matias and Nathan,
> >>
> >> I was able to reproduce this error on my own Enzo data set(s) using
> >> similar code. I did a little more playing around and it looks like it
> >> only
> >> breaks when having a weight_field. weight_field = None seems to be O.K.
> .
> >> It also occurs for the "region" objects, in addition to the disk.
> >> Interestingly, as Matias pointed out, doing something like this works:
> >>
> >> region = ds.region([0.5,0.5,0.5], [0.0, 0.0, 0.0], [1.0, 1.0, 1.0])
> >> proj=ds.proj('density',axis='z',weight_field='density',data_
> >> source=region,method='integrate')
> >>
> >> but this does not:
> >>
> >> region = ds.region([0.5,0.5,0.5], [0.1,0.1,0.1], [0.9,0.9,0.9] )
> >> proj =ds.proj('density',axis='z',weight_field='density',data_
> >> source=region,method='integrate')
> >>
> >> In short, this indeed appears to be a bug, and possibly not specific to
> a
> >> single dataset.
> >>
> >>
> >>
> >>
> >> Andrew
> >>
> >>
> >> On Tue, Nov 14, 2017 at 12:40 PM, Nathan Goldbaum <
> nathan12343(a)gmail.com>
> >> wrote:
> >>
> >>> This sounds like a bug. I don't think you should ever get back NaNs
> from
> >>> a projection operation.
> >>>
> >>> Is there any chance you can share the dataset that's triggering this
> >>> behavior?
> >>>
> >>> On Tue, Nov 14, 2017 at 11:34 AM, Matias Enrique Suazo Campos <
> >>> matias.suazo(a)ug.uchile.cl> wrote:
> >>>
> >>>> Dear YT users,
> >>>>
> >>>> I'm trying to make a density projection, in the following lines I show
> >>>> you the lines that I have.
> >>>>
> >>>> #Ramses output
> >>>> ds = yt.load(path+"output_%05d"%snap+"/info_%05d.txt" %snap)
> >>>> disk = ds.disk('max',[0,0,1],(20,'pc'),(5,'pc'))
> >>>> proj=ds.proj('density',axis='z',weight_field='density',data_
> >>>> source=disk,method='integrate')
> >>>>
> >>>> However when I print proj["density"] I get a list of nan, however when
> >>>> I
> >>>> use the whole domain as my data_source I get reasonable numbers.
> >>>>
> >>>> Thanks,
> >>>> Mat?as Suazo
> >>>> MSc student at Universidad de Chile
> >>>>
> >>>> _______________________________________________
> >>>> yt-users mailing list
> >>>> yt-users(a)lists.spacepope.org
> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>>
> >>>>
> >>>
> >>> _______________________________________________
> >>> yt-users mailing list
> >>> yt-users(a)lists.spacepope.org
> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>
> >>>
> >>
> >>
> >> --
> >> NSF Graduate Fellow
> >> Columbia University
> >> Department of Astronomy
> >>
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users(a)lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> >>
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 14 Nov 2017 13:04:04 -0600
> From: Nathan Goldbaum <nathan12343(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] Projection
> Message-ID:
> <CAJXewOm3f91Z66L8WPYZ3ztnVx=BPaKAO9FuZ1Lq28qJZHNVZg@mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Ah, so this isn't actually a bug. There's even a comment in the code
> indicating that this is the intended behavior:
>
> https://github.com/yt-project/yt/blob/master/yt/data_
> objects/construction_data_containers.py#L373
>
> So the choices about what to do here are, in my opinion:
>
> * Change this behavior to fill the array with zeros instead of NaNs
> * Improve the documentation to make this choice clearer
>
> I'm not sure offhand what is the best approach, especially given that
> changing this behavior would be a backward compatibility break.
>
> For the original question: your data aren't all NaNs I suspect. E.g. take a
> look at this example script:
>
> import yt
> import numpy as np
> ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
> disk = ds.disk('c', [0, 0, 1], (1000, 'pc'), (100, 'pc'))
> proj = ds.proj('density', axis='z', weight_field='density',
> data_source=disk,
> method='integrate')
> dens_proj = proj['density']
> print(dens_proj[np.isfinite(dens_proj)])
> print(np.nanmax(dens_proj))
> print(np.nanmin(dens_proj))
>
> Which prints out values in regions where the projection isn't filled with
> NaNs.
>
>
> On Tue, Nov 14, 2017 at 12:45 PM, Jos? Mauricio Utreras <
> jutreras(a)ug.uchile.cl> wrote:
>
> > Hi everyone,
> >
> > I got the same result using the IsolatedGalaxy dataset
> >
> > ds=yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
> > disk = ds.disk('c',[0,0,1],(1000,'pc'),(100,'pc'))
> > proj=ds.proj('density',axis='z',weight_field='density',
> > data_source=disk,method='integrate')
> > proj['density']
> > >>> YTArray([ nan, nan, nan, ..., nan, nan, nan]) g/cm**3
> >
> > 2017-11-14 15:38 GMT-03:00, Nathan Goldbaum <nathan12343(a)gmail.com>:
> > > Can I get one of you to open an issue?
> > >
> > > https://github.com/yt-project/yt/issues/new
> > >
> > > If you can, please include a script to reproduce the problem, making
> use
> > of
> > > one of the public datasets on yt-project.org/data.
> > >
> > > -Nathan
> > >
> > > On Tue, Nov 14, 2017 at 12:34 PM, Andrew James Emerick
> > > <aje2123(a)columbia.edu
> > >> wrote:
> > >
> > >> Hello Matias and Nathan,
> > >>
> > >> I was able to reproduce this error on my own Enzo data set(s) using
> > >> similar code. I did a little more playing around and it looks like it
> > >> only
> > >> breaks when having a weight_field. weight_field = None seems to be
> O.K.
> > .
> > >> It also occurs for the "region" objects, in addition to the disk.
> > >> Interestingly, as Matias pointed out, doing something like this works:
> > >>
> > >> region = ds.region([0.5,0.5,0.5], [0.0, 0.0, 0.0], [1.0, 1.0, 1.0])
> > >> proj=ds.proj('density',axis='z',weight_field='density',data_
> > >> source=region,method='integrate')
> > >>
> > >> but this does not:
> > >>
> > >> region = ds.region([0.5,0.5,0.5], [0.1,0.1,0.1], [0.9,0.9,0.9] )
> > >> proj =ds.proj('density',axis='z',weight_field='density',data_
> > >> source=region,method='integrate')
> > >>
> > >> In short, this indeed appears to be a bug, and possibly not specific
> to
> > a
> > >> single dataset.
> > >>
> > >>
> > >>
> > >>
> > >> Andrew
> > >>
> > >>
> > >> On Tue, Nov 14, 2017 at 12:40 PM, Nathan Goldbaum <
> > nathan12343(a)gmail.com>
> > >> wrote:
> > >>
> > >>> This sounds like a bug. I don't think you should ever get back NaNs
> > from
> > >>> a projection operation.
> > >>>
> > >>> Is there any chance you can share the dataset that's triggering this
> > >>> behavior?
> > >>>
> > >>> On Tue, Nov 14, 2017 at 11:34 AM, Matias Enrique Suazo Campos <
> > >>> matias.suazo(a)ug.uchile.cl> wrote:
> > >>>
> > >>>> Dear YT users,
> > >>>>
> > >>>> I'm trying to make a density projection, in the following lines I
> show
> > >>>> you the lines that I have.
> > >>>>
> > >>>> #Ramses output
> > >>>> ds = yt.load(path+"output_%05d"%snap+"/info_%05d.txt" %snap)
> > >>>> disk = ds.disk('max',[0,0,1],(20,'pc'),(5,'pc'))
> > >>>> proj=ds.proj('density',axis='z',weight_field='density',data_
> > >>>> source=disk,method='integrate')
> > >>>>
> > >>>> However when I print proj["density"] I get a list of nan, however
> when
> > >>>> I
> > >>>> use the whole domain as my data_source I get reasonable numbers.
> > >>>>
> > >>>> Thanks,
> > >>>> Mat?as Suazo
> > >>>> MSc student at Universidad de Chile
> > >>>>
> > >>>> _______________________________________________
> > >>>> yt-users mailing list
> > >>>> yt-users(a)lists.spacepope.org
> > >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> > >>>>
> > >>>>
> > >>>
> > >>> _______________________________________________
> > >>> yt-users mailing list
> > >>> yt-users(a)lists.spacepope.org
> > >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> > >>>
> > >>>
> > >>
> > >>
> > >> --
> > >> NSF Graduate Fellow
> > >> Columbia University
> > >> Department of Astronomy
> > >>
> > >> _______________________________________________
> > >> yt-users mailing list
> > >> yt-users(a)lists.spacepope.org
> > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> > >>
> > >>
> > >
> > _______________________________________________
> > yt-users mailing list
> > yt-users(a)lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
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>
> ------------------------------
>
> Message: 3
> Date: Tue, 14 Nov 2017 14:42:01 -0600
> From: Matthew Turk <matthewturk(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] Projection
> Message-ID:
> <CALO3=5GimZpK9u2i40ZWfECXx3btj1GFT1jLO+6OhVn6_DqQGg@mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> On Tue, Nov 14, 2017 at 1:04 PM, Nathan Goldbaum <nathan12343(a)gmail.com>
> wrote:
>
> > Ah, so this isn't actually a bug. There's even a comment in the code
> > indicating that this is the intended behavior:
> >
> > https://github.com/yt-project/yt/blob/master/yt/data_
> > objects/construction_data_containers.py#L373
> >
> > So the choices about what to do here are, in my opinion:
> >
> > * Change this behavior to fill the array with zeros instead of NaNs
> >
>
> I think this would give the wrong impression, especially for things like
> weighted average velocity fields.
>
>
> > * Improve the documentation to make this choice clearer
> >
>
> Probably a good thing.
>
> I think I would suggest another option, which would be to filter it based
> on which values are non-NaN. In the cases identified in the emails, I
> would *suspect* that what's happening is that there are elements in the
> quad tree that are initialized from the tree initialization step (which
> just looks at the mesh from the container, not the selected elements in the
> mesh) and left at zero following initialization. We could either have a
> "touched" flag on all of the mesh elements (i.e., "has this been touched by
> data, or is it left at initialized value) and filter in the conversion of
> the quad tree to the flat arrays, or we could filter in the python code
> based on NaNs. My preference would be to filter it in the creation of the
> flat arrays, as then it will be uniformly applied even without weight
> fields.
>
>
> >
> > I'm not sure offhand what is the best approach, especially given that
> > changing this behavior would be a backward compatibility break.
> >
>
> I think filtering NaNs is not a big change in compatibility. I think we'd
> just need to make sure that the cmap normalization has the same behavior
> for missing values as for NaN values, which I think it does.
>
>
> >
> > For the original question: your data aren't all NaNs I suspect. E.g. take
> > a look at this example script:
> >
> > import yt
> > import numpy as np
> > ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
> > disk = ds.disk('c', [0, 0, 1], (1000, 'pc'), (100, 'pc'))
> > proj = ds.proj('density', axis='z', weight_field='density',
> > data_source=disk,
> > method='integrate')
> > dens_proj = proj['density']
> > print(dens_proj[np.isfinite(dens_proj)])
> > print(np.nanmax(dens_proj))
> > print(np.nanmin(dens_proj))
> >
> > Which prints out values in regions where the projection isn't filled with
> > NaNs.
> >
> >
> > On Tue, Nov 14, 2017 at 12:45 PM, Jos? Mauricio Utreras <
> > jutreras(a)ug.uchile.cl> wrote:
> >
> >> Hi everyone,
> >>
> >> I got the same result using the IsolatedGalaxy dataset
> >>
> >> ds=yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
> >> disk = ds.disk('c',[0,0,1],(1000,'pc'),(100,'pc'))
> >> proj=ds.proj('density',axis='z',weight_field='density',data_
> >> source=disk,method='integrate')
> >> proj['density']
> >> >>> YTArray([ nan, nan, nan, ..., nan, nan, nan]) g/cm**3
> >>
> >> 2017-11-14 15:38 GMT-03:00, Nathan Goldbaum <nathan12343(a)gmail.com>:
> >> > Can I get one of you to open an issue?
> >> >
> >> > https://github.com/yt-project/yt/issues/new
> >> >
> >> > If you can, please include a script to reproduce the problem, making
> >> use of
> >> > one of the public datasets on yt-project.org/data.
> >> >
> >> > -Nathan
> >> >
> >> > On Tue, Nov 14, 2017 at 12:34 PM, Andrew James Emerick
> >> > <aje2123(a)columbia.edu
> >> >> wrote:
> >> >
> >> >> Hello Matias and Nathan,
> >> >>
> >> >> I was able to reproduce this error on my own Enzo data set(s) using
> >> >> similar code. I did a little more playing around and it looks like it
> >> >> only
> >> >> breaks when having a weight_field. weight_field = None seems to be
> >> O.K. .
> >> >> It also occurs for the "region" objects, in addition to the disk.
> >> >> Interestingly, as Matias pointed out, doing something like this
> works:
> >> >>
> >> >> region = ds.region([0.5,0.5,0.5], [0.0, 0.0, 0.0], [1.0, 1.0, 1.0])
> >> >> proj=ds.proj('density',axis='z',weight_field='density',data_
> >> >> source=region,method='integrate')
> >> >>
> >> >> but this does not:
> >> >>
> >> >> region = ds.region([0.5,0.5,0.5], [0.1,0.1,0.1], [0.9,0.9,0.9] )
> >> >> proj =ds.proj('density',axis='z',weight_field='density',data_
> >> >> source=region,method='integrate')
> >> >>
> >> >> In short, this indeed appears to be a bug, and possibly not specific
> >> to a
> >> >> single dataset.
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> Andrew
> >> >>
> >> >>
> >> >> On Tue, Nov 14, 2017 at 12:40 PM, Nathan Goldbaum <
> >> nathan12343(a)gmail.com>
> >> >> wrote:
> >> >>
> >> >>> This sounds like a bug. I don't think you should ever get back NaNs
> >> from
> >> >>> a projection operation.
> >> >>>
> >> >>> Is there any chance you can share the dataset that's triggering this
> >> >>> behavior?
> >> >>>
> >> >>> On Tue, Nov 14, 2017 at 11:34 AM, Matias Enrique Suazo Campos <
> >> >>> matias.suazo(a)ug.uchile.cl> wrote:
> >> >>>
> >> >>>> Dear YT users,
> >> >>>>
> >> >>>> I'm trying to make a density projection, in the following lines I
> >> show
> >> >>>> you the lines that I have.
> >> >>>>
> >> >>>> #Ramses output
> >> >>>> ds = yt.load(path+"output_%05d"%snap+"/info_%05d.txt" %snap)
> >> >>>> disk = ds.disk('max',[0,0,1],(20,'pc'),(5,'pc'))
> >> >>>> proj=ds.proj('density',axis='z',weight_field='density',data_
> >> >>>> source=disk,method='integrate')
> >> >>>>
> >> >>>> However when I print proj["density"] I get a list of nan, however
> >> when
> >> >>>> I
> >> >>>> use the whole domain as my data_source I get reasonable numbers.
> >> >>>>
> >> >>>> Thanks,
> >> >>>> Mat?as Suazo
> >> >>>> MSc student at Universidad de Chile
> >> >>>>
> >> >>>> _______________________________________________
> >> >>>> yt-users mailing list
> >> >>>> yt-users(a)lists.spacepope.org
> >> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >>>>
> >> >>>>
> >> >>>
> >> >>> _______________________________________________
> >> >>> yt-users mailing list
> >> >>> yt-users(a)lists.spacepope.org
> >> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >>>
> >> >>>
> >> >>
> >> >>
> >> >> --
> >> >> NSF Graduate Fellow
> >> >> Columbia University
> >> >> Department of Astronomy
> >> >>
> >> >> _______________________________________________
> >> >> yt-users mailing list
> >> >> yt-users(a)lists.spacepope.org
> >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >>
> >> >>
> >> >
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users(a)lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> >
> >
> > _______________________________________________
> > yt-users mailing list
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> >
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1 year, 4 months
