Clear memory?
by Elizabeth Tasker
Hi,
Is there any way in yt to get a script to delete (or ignore) all the .yt
and .harray files and clear its memory? I run into errors when I'm
re-doing a plot or I've re-run the simulation and over-written the last
data set I looked at with yt. I have to exit yt, delete the above files
by hand and restart, which is a bit of a pain.
Elizabeth
7 years, 6 months
new fields in output
by Elizabeth Tasker
Hi,
I've added PotentialField to the data that gets outputted. I'd like to
read this into yt, but how does this work when yt won't be expecting
PotentialField to be one of the data sets?
Elizabeth
7 years, 8 months
Reason
by Christine Simpson
Hi all,
I'm not sure if this is the right list to send this to, but I think a
bunch of knowledgeable people read this one, and hopefully one of you
can help me. I'm trying to use Reason and I'm kind of confused about
the ssh tunneling part. I start up yt serve on a remote machine
(ranger) and I'm told to create a ssh tunnel by executing these
commands:
~C
-L55185:localhost:55185
My local machine doesn't recognize "~C" and I'm not sure what it is
either. I tried creating an ssh tunnel with this:
ssh tg803911(a)ranger.tacc.utexas.edu -L 55185:localhost:55185
I was then able to successfully open the gui in a browser with the url
provided, but I am unable to load data (I can view the help though). In
order to do the ssh tunnel properly do I need to install something on my
local machine?
Christine
7 years, 9 months
yt Logo Contest, and possibly a free mug!
by Sam Skillman
Hi all,
yt is in need of an awesome new logo, which is why we are announcing the
first ever new logo contest! So here's the deal:
We'll accept entries for the next two weeks. Let's arbitrarily say Tuesday,
May 10th, at 11:59:59 pm EST. If there is more than one entry, we will put
it up for a community vote at that time.
Oh, and the most important part -- the winner will get a coffee mug with
their new logo front and center!!!
Please email yt(a)enzotools.org with your image attached. Good luck, and happy
logo-ing!
Sam
7 years, 10 months
ray problem with cell volume
by Elizabeth Tasker
Hi,
When using the ray feature in yt, we hit problems if we try to plot any
variable that contains the cell volume. e.g.
def _Momentum(field, data):
return (data["Density"]*data["CellVolume"]*sqrt(
data["x-velocity"]**2.0
+ data["y-velocity"]**2.0
+ data["z-velocity"]**2.0 ))
ray = pf.h.ray([0.5, 0.5, 0.5], [1.0,1.0,1.0], "Momentum")
pylab.plot(ray["RadiusCode"], ray["Momentum"], 'o')
Gives:
IndexError Traceback (most recent call
last)
/saw_sfs/work/chris/yt/scripts/iyt in <module>()
----> 1
2
3
4
5
/saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in
__getitem__(self, key)
274 if key not in
self.fields:
275
self.fields.append(key)
--> 276
self.get_data(key)
277 return
self.data[key]
278
/saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in
get_data(self, fields, in_grids)
445 mylog.info("Getting field %s from %s", field,
len(self._grids))
446 if field not in self.hierarchy.field_list and not
in_grids:
--> 447 if field not in ("dts", "t") and
self._generate_field(field):
448 continue # True means we already assigned
it
449 self[field] =
na.concatenate(
/saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in
_generate_field(self, field)
423 return
False
424
else:
--> 425 self[field] =
self.pf.field_info[field](self)
426 return
True
427 else: # Can't find the field, try as it
might
/saw_sfs/work/chris/yt/yt/data_objects/field_info_container.pyc in
__call__(self, data)
292 ii =
self.check_available(data)
293 original_fields = data.keys() #
Copy
--> 294 dd = self._function(self,
data)
295 dd *=
self._convert_function(data)
296 for field_name in
data.keys():
/saw_sfs/work/chris/yt/scripts/iyt in _Momentum(field, data)
14
15 def _Momentum(field, data):
---> 16 return (data["Density"]*data["CellVolume"]*sqrt(
17
data["x-velocity"]**2.0
18 +
data["y-velocity"]**2.0
/saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in
__getitem__(self, key)
274 if key not in
self.fields:
275
self.fields.append(key)
--> 276
self.get_data(key)
277 return
self.data[key]
278
/saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in
get_data(self, fields, in_grids)
445 mylog.info("Getting field %s from %s", field,
len(self._grids))
446 if field not in self.hierarchy.field_list and not
in_grids:
--> 447 if field not in ("dts", "t") and
self._generate_field(field):
448 continue # True means we already assigned
it
449 self[field] =
na.concatenate(
/saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in
_generate_field(self, field)
423 return
False
424
else:
--> 425 self[field] =
self.pf.field_info[field](self)
426 return True
427 else: # Can't find the field, try as it might
/saw_sfs/work/chris/yt/yt/data_objects/field_info_container.pyc in
__call__(self, data)
292 ii = self.check_available(data)
293 original_fields = data.keys() # Copy
--> 294 dd = self._function(self, data)
295 dd *= self._convert_function(data)
296 for field_name in data.keys():
/saw_sfs/work/chris/yt/yt/data_objects/universal_fields.pyc in
_CellVolume(field, data)
392
393 def _CellVolume(field, data):
--> 394 if data['dx'].size == 1:
395 try:
396 return data['dx']*data['dy']*data['dx']*\
/saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in
__getitem__(self, key)
274 if key not in self.fields:
275 self.fields.append(key)
--> 276 self.get_data(key)
277 return self.data[key]
278
/saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in
get_data(self, fields, in_grids)
449 self[field] = na.concatenate(
450 [self._get_data_from_grid(grid, field)
--> 451 for grid in self._grids])
452 if not self.data.has_key(field):
453 continue
/saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in
_get_data_from_grid(self, grid, field)
558 if field == 'dts': return self._dts[grid.id][mask]
559 if field == 't': return self._ts[grid.id][mask]
--> 560 return grid[field][mask]
561
562 @cache_mask
IndexError: invalid index to scalar variable.
Any ideas?
Elizabeth
7 years, 10 months
FLASH and spherical coords
by Massimo Gaspari
Hi all,
I am using FLASH3.3, testing the (3D) spherical coordinate system.
Is it possible with YT to make a slice with this kind of coords (r,theta,phi)?
If so, how can I do that? Could you provide a template?
Thank you in advance,
Massimo Gaspari
7 years, 11 months
Re: [yt-users] yt-users Digest, Vol 38, Issue 38
by Wolfram Schmidt
Hi Matt,
thanks a lot for your reply! Of course, I am aware that you cannot
account for every special situation in the design of yt right from the
beginning, so sometimes we have to resort to provisional solutions.
I followed the procedure you suggested on the machine behind the
firewall (I think there was a confusion of A and B - never mind;-).
After removing and re-creating the yt-hg subdirectory and changing into
this directory, the execution of
~/yt/bin/hg unbundle ~/yt/yt-20110428.hg
yielded the error message:
abort: There is no Mercurial repository here (.hg not found)!
Now, one thing is for sure: yt-20110428.hg is right where it is supposed
to be:
ls -l ~/yt/yt-20110428.hg
-rw-r--r-- 1 lu78tar3 pr47bi 25682789 2011-04-29 19:18
/home/hlrb2/pr47bi/lu78tar3/yt/yt-20110428.hg
So that's curious...
Wolfram
7 years, 11 months
h5py from install script on kraken
by Britton Smith
Hi everyone,
I just tried a new install of yt on kraken form the install script. It
failed on installing h5py 1.3 with the following error:
******************************************
Configure: Autodetecting HDF5 settings...
Custom HDF5 dir: /lustre/scratch/britton/local-dev
Custom API level: None
/opt/cray/xt-asyncpe/4.0/bin/cc: INFO: linux target is being used
/opt/cray/xt-asyncpe/4.0/bin/cc: INFO: linux target is being used
/lustre/scratch/britton/local-dev/lib/libhdf5.a(H5Zdeflate.o): In function
`H5Z_filter_deflate':
H5Zdeflate.c:(.text+0x134): undefined reference to `compress2'
H5Zdeflate.c:(.text+0x1ee): undefined reference to `inflateInit_'
H5Zdeflate.c:(.text+0x209): undefined reference to `inflate'
H5Zdeflate.c:(.text+0x270): undefined reference to `inflateEnd'
H5Zdeflate.c:(.text+0x3de): undefined reference to `inflateEnd'
H5Zdeflate.c:(.text+0x410): undefined reference to `inflateEnd'
/usr/bin/ld: link errors found, deleting executable `detect/vers'
collect2: ld returned 1 exit status
Failed to compile HDF5 test program. Please check to make sure:
* You have a C compiler installed
* A development version of Python is installed (including header files)
* A development version of HDF5 is installed (including header files)
* If HDF5 is not in a default location, supply the argument
--hdf5=<path>
******************************************
error: command 'cc' failed with exit status 1
I checked that the kraken yt install from the yt module is using h5py 1.2,
which I believe suffers from the h5py bug that was mentioned not too long
ago. I double checked that I had gnu compiler module loaded, so I don't
think that's it. Does anyone have any ideas?
Britton
7 years, 11 months
FixedResolutionBuffer problem
by Stephen Skory
Hi all,
I am attempting to follow the examples of how to make a fixed
resolution buffer, and I have run into a problem. If I follow the
first example on this page
<http://yt.enzotools.org/doc/analyzing/generating_processed_data.html>:
sl = pf.h.proj(0, 0.6)
frb = FixedResolutionBuffer(sl, (0.3, 0.5, 0.6, 0.8), (512, 512))
my_image = frb["Density"]
I get this error <http://paste.enzotools.org/show/1603/> which makes
it look like it's trying to use the second term of .proj() '0.6' as a
data field. So, if I change things to:
sl = pf.h.proj(0, 'Density')
I get this error <http://paste.enzotools.org/show/1604/> complaining
about 'px'. Am I doing something wrong, or is this a bug? I am using
4216:5c6f932b9f34. Thanks!
--
Stephen Skory
s(a)skory.us
http://stephenskory.com/
510.621.3687 (google voice)
7 years, 11 months
installing yt behind a firewall
by Wolfram Schmidt
Hi everyone,
perhaps, others also have encountered the situation of having to install
yt on a machine with tight security measures that do not allow access to
the internet through its firewall.
An awkward, yet doable workaround is to mount the installation directory
via sshfs on a machine outside the firewall (let's call it machine B) to
download the required packages and to execute everything else on machine
A behind the firewall.
With the most recent yt version, I encountered a problem once the
installation of Python was completed. Going back to machine B to
download the yt distribution, I found that the previously installed hg
wouldn't work. The last lines of the installation log (see attachment)
show that hg, running on machine B, attempts to use Python under the
path that applies to machine A (/home/hlrb2/pr47bi/lu78tar3/yt/...
instead of /home/raid2/schmidt/hlrb2/yt/...), athough I set DEST_DIR to
the (sshfs-mounted) path that applies to machine B. What should I do
about that?
Cheers,
Wolfram
7 years, 11 months
