Re: [yt-users] problem with yt update to 3.0
Dear yt:
I am currently running yt version 2.6.1 and want to update to version 3 (to read text files). Could you provide me link to so?
I tried it using yt update --all as per the link
http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-ve... .
But it wont update to 3.0 and still shows as 2.6.1
Kindly help
Thanks in advance
sushilkumar
On Thu, Dec 24, 2015 at 12:25 PM, yt-users-request@lists.spacepope.org wrote:
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Today's Topics:
- Re: problem with slices in non-unitary volumes (Nathan Goldbaum)
Message: 1 Date: Wed, 23 Dec 2015 17:17:56 -0600 From: Nathan Goldbaum nathan12343@gmail.com To: Discussion of the yt analysis package yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with slices in non-unitary volumes Message-ID: < CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
I get the same error over here. I think it's unrelated to the other error. The relevant portion of the C stack trace is here:
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff8b615286 __pthread_kill + 10 1 libsystem_c.dylib 0x00007fff8bc2a9ab abort + 129 2 libsystem_malloc.dylib 0x00007fff915d5fe2 szone_error + 625 3 libsystem_malloc.dylib 0x00007fff915cf374 small_free_list_remove_ptr + 154 4 libsystem_malloc.dylib 0x00007fff915cac3f szone_free_definite_size + 1856 5 multiarray.so 0x00000001044c2d16 npy_free_cache + 70 6 multiarray.so 0x00000001044c6ed6 array_dealloc + 182 7 selection_routines.so 0x00000001063ffe34 __pyx_pw_2yt_8geometry_18selection_routines_13SliceSelector_3fill_mask + 8804 (selection_routines.c:19749)
Line 19749 of selection_routines.c corresponds to line 1158 in selection_routines.pyx, which is the place where the fill_mask member variable of the SliceSelector extension type gets defined.
Unfortunately, I have no idea how to debug this from here...
-Nathan
On Wed, Dec 23, 2015 at 4:57 PM, Brian O'Shea bwoshea@gmail.com wrote:
Actually, interesting followup here - I have to take it back. When I do
a
projection plot:
yt.ProjectionPlot(ds,'x',("gas","temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
the behavior is perfectly fine and I get projections that look sensible. *however*, when I do a slice plot:
yt.SlicePlot(ds,'x',("gas", "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
I get a malloc error:
yt : [INFO ] 2015-12-23 17:50:59,082 Gathering a field list (this may take a moment.) yt : [INFO ] 2015-12-23 17:50:59,155 Loading field plugins. yt : [INFO ] 2015-12-23 17:50:59,155 Loaded angular_momentum (8 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded astro (16 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded cosmology (23 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded fluid (64 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded fluid_vector (96 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded geometric (112 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,157 Loaded local (112 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded magnetic_field (120 new fields) yt : [INFO ] 2015-12-23 17:50:59,158 Loaded my_plugins (120 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,158 Loaded species (122 new fields) python2.7(12254,0x7fff72d19310) malloc: *** error for object 0x103e39008: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Abort trap: 6
This happens on my Mac (OS X 10.9.5, LLVM v6.0) and also on my Linux machine (Ubuntu 13.04, gcc 4.6.3), although on the linux machine I just
get
a seg fault instead of the malloc stuff. Using pdb (python -m pdb crashing_script.py) gives me the same error with no additional
information.
On Wed, Dec 23, 2015 at 5:40 PM, Brian O'Shea bwoshea@gmail.com wrote:
Bugfix confirmed; this works for me as well. Thank you very much!
On Wed, Dec 23, 2015 at 5:18 PM, Nathan Goldbaum <nathan12343@gmail.com
wrote:
I've opened a pull request that allows me to load your dataset:
https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creatin...
On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea bwoshea@gmail.com
wrote:
Oh, interesting. Is there a way to circumvent auto-detection of
fields?
On Wed, Dec 23, 2015 at 4:35 PM, Nathan Goldbaum <
nathan12343@gmail.com
wrote:
It looks like field detection is breaking for this Enzo-3.0 active particle dataset. StoredEnergy is available on-disk as ('AGNParticle, 'StoredEnergy'), but for some reason the field detection system
isn't able
to guess that.
On Wed, Dec 23, 2015 at 3:19 PM, Nathan Goldbaum < nathan12343@gmail.com> wrote:
> > > On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea bwoshea@gmail.com > wrote: > >> Dear yt-users, >> >> I'm having a problem with making slices in non-unitary volumes. I >> have a 3D enzo simulation that has domain bounds of (-1.6...1.6)
in every
>> dimension (units of megaparsecs), and after I updated to the tip
of yt-3
>> (changeset d9502d848029) from a fairly old version of the code I
suddenly
>> have problems with making simple projections. If I run this set of >> commands: >> >> > Any idea which version you updated from? I tried on yt-3.1 and get > the same error. This is just so we can bisect and find the change
that
> introduced the regression. > > >> import yt >> ds = yt.load("DD0400/DD0400") >> proj = >>
yt.SlicePlot(ds,'x','temperature',center=[0.0,0.0,0.0],width=(0.2,'Mpc'))
>> >> I get this error: >> >> http://paste.yt-project.org/show/6115/ >> >> This seems to work fine on an Enzo cosmological dataset (domain >> bounds 0-1 in each dimension), and previously worked fine in yt-3
(using a
>> version of the code from a couple of months ago). >> >> is this a bug, or am I doing something dumb? >> >> Thanks! >> >> --Brian >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Hi Sushilkumar,
Can you try reinstalling yt from scratch?
-Nathan
On Sat, Dec 26, 2015 at 10:39 AM, Sushilkumar sushil.sush19us@gmail.com wrote:
Dear yt:
I am currently running yt version 2.6.1 and want to update to version 3 (to read text files). Could you provide me link to so?
I tried it using yt update --all as per the link
http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-ve... .
But it wont update to 3.0 and still shows as 2.6.1
Kindly help
Thanks in advance
sushilkumar
On Thu, Dec 24, 2015 at 12:25 PM, yt-users-request@lists.spacepope.org wrote:
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Today's Topics:
- Re: problem with slices in non-unitary volumes (Nathan Goldbaum)
Message: 1 Date: Wed, 23 Dec 2015 17:17:56 -0600 From: Nathan Goldbaum nathan12343@gmail.com To: Discussion of the yt analysis package yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with slices in non-unitary volumes Message-ID: < CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
I get the same error over here. I think it's unrelated to the other error. The relevant portion of the C stack trace is here:
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff8b615286 __pthread_kill + 10 1 libsystem_c.dylib 0x00007fff8bc2a9ab abort + 129 2 libsystem_malloc.dylib 0x00007fff915d5fe2 szone_error + 625 3 libsystem_malloc.dylib 0x00007fff915cf374 small_free_list_remove_ptr + 154 4 libsystem_malloc.dylib 0x00007fff915cac3f szone_free_definite_size + 1856 5 multiarray.so 0x00000001044c2d16 npy_free_cache + 70 6 multiarray.so 0x00000001044c6ed6 array_dealloc + 182 7 selection_routines.so 0x00000001063ffe34 __pyx_pw_2yt_8geometry_18selection_routines_13SliceSelector_3fill_mask + 8804 (selection_routines.c:19749)
Line 19749 of selection_routines.c corresponds to line 1158 in selection_routines.pyx, which is the place where the fill_mask member variable of the SliceSelector extension type gets defined.
Unfortunately, I have no idea how to debug this from here...
-Nathan
On Wed, Dec 23, 2015 at 4:57 PM, Brian O'Shea bwoshea@gmail.com wrote:
Actually, interesting followup here - I have to take it back. When I
do a
projection plot:
yt.ProjectionPlot(ds,'x',("gas","temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
the behavior is perfectly fine and I get projections that look sensible. *however*, when I do a slice plot:
yt.SlicePlot(ds,'x',("gas", "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
I get a malloc error:
yt : [INFO ] 2015-12-23 17:50:59,082 Gathering a field list (this
may
take a moment.) yt : [INFO ] 2015-12-23 17:50:59,155 Loading field plugins. yt : [INFO ] 2015-12-23 17:50:59,155 Loaded angular_momentum (8 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded astro (16 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded cosmology (23 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,156 Loaded fluid (64 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded fluid_vector (96 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded geometric (112 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,157 Loaded local (112 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded magnetic_field (120 new fields) yt : [INFO ] 2015-12-23 17:50:59,158 Loaded my_plugins (120 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,158 Loaded species (122 new fields) python2.7(12254,0x7fff72d19310) malloc: *** error for object
0x103e39008:
incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Abort trap: 6
This happens on my Mac (OS X 10.9.5, LLVM v6.0) and also on my Linux machine (Ubuntu 13.04, gcc 4.6.3), although on the linux machine I just
get
a seg fault instead of the malloc stuff. Using pdb (python -m pdb crashing_script.py) gives me the same error with no additional
information.
On Wed, Dec 23, 2015 at 5:40 PM, Brian O'Shea bwoshea@gmail.com
wrote:
Bugfix confirmed; this works for me as well. Thank you very much!
On Wed, Dec 23, 2015 at 5:18 PM, Nathan Goldbaum <
nathan12343@gmail.com>
wrote:
I've opened a pull request that allows me to load your dataset:
https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creatin...
On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea bwoshea@gmail.com
wrote:
Oh, interesting. Is there a way to circumvent auto-detection of
fields?
On Wed, Dec 23, 2015 at 4:35 PM, Nathan Goldbaum <
nathan12343@gmail.com
> wrote:
> It looks like field detection is breaking for this Enzo-3.0 active > particle dataset. StoredEnergy is available on-disk as
('AGNParticle,
> 'StoredEnergy'), but for some reason the field detection system
isn't able
> to guess that. > > On Wed, Dec 23, 2015 at 3:19 PM, Nathan Goldbaum < > nathan12343@gmail.com> wrote: > >> >> >> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea bwoshea@gmail.com >> wrote: >> >>> Dear yt-users, >>> >>> I'm having a problem with making slices in non-unitary volumes. I >>> have a 3D enzo simulation that has domain bounds of (-1.6...1.6)
in every
>>> dimension (units of megaparsecs), and after I updated to the tip
of yt-3
>>> (changeset d9502d848029) from a fairly old version of the code I
suddenly
>>> have problems with making simple projections. If I run this set
of
>>> commands: >>> >>> >> Any idea which version you updated from? I tried on yt-3.1 and get >> the same error. This is just so we can bisect and find the change
that
>> introduced the regression. >> >> >>> import yt >>> ds = yt.load("DD0400/DD0400") >>> proj = >>>
yt.SlicePlot(ds,'x','temperature',center=[0.0,0.0,0.0],width=(0.2,'Mpc'))
>>> >>> I get this error: >>> >>> http://paste.yt-project.org/show/6115/ >>> >>> This seems to work fine on an Enzo cosmological dataset (domain >>> bounds 0-1 in each dimension), and previously worked fine in yt-3
(using a
>>> version of the code from a couple of months ago). >>> >>> is this a bug, or am I doing something dumb? >>> >>> Thanks! >>> >>> --Brian >>> >>> >>> _______________________________________________ >>> yt-users mailing list >>> yt-users@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >>> >> > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >
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Hi Nathan:
Thanks for your reply.
I had done that before installing version 2.X. I used to get errors as below. Even now I keep getting the same error after reinstalling from scratch. The error comes after "installing pip". I tried it on my pc and also on cluster but same issues.
******************************************** FAILURE REPORT: ********************************************
bootstrap(tmpdir=tmpdir) File "get-pip.py", line 82, in bootstrap import pip File "/tmp/tmpxKqAjR/pip.zip/pip/__init__.py", line 15, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/vcs/subversion.py", line 9, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/index.py", line 30, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/wheel.py", line 35, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/compat.py", line 31, in <module> ImportError: cannot import name HTTPSHandler
******************************************** ******************************************** Failure. Check /home/adrith/yt-x86_64/yt_install.log. The last 10 lines are above.
On Sat, Dec 26, 2015 at 10:41 AM, Nathan Goldbaum nathan12343@gmail.com wrote:
Hi Sushilkumar,
Can you try reinstalling yt from scratch?
-Nathan
On Sat, Dec 26, 2015 at 10:39 AM, Sushilkumar sushil.sush19us@gmail.com wrote:
Dear yt:
I am currently running yt version 2.6.1 and want to update to version 3 (to read text files). Could you provide me link to so?
I tried it using yt update --all as per the link
http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-ve... .
But it wont update to 3.0 and still shows as 2.6.1
Kindly help
Thanks in advance
sushilkumar
On Thu, Dec 24, 2015 at 12:25 PM, yt-users-request@lists.spacepope.org wrote:
Send yt-users mailing list submissions to yt-users@lists.spacepope.org
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You can reach the person managing the list at yt-users-owner@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:
- Re: problem with slices in non-unitary volumes (Nathan Goldbaum)
Message: 1 Date: Wed, 23 Dec 2015 17:17:56 -0600 From: Nathan Goldbaum nathan12343@gmail.com To: Discussion of the yt analysis package yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with slices in non-unitary volumes Message-ID: < CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
I get the same error over here. I think it's unrelated to the other error. The relevant portion of the C stack trace is here:
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff8b615286 __pthread_kill + 10 1 libsystem_c.dylib 0x00007fff8bc2a9ab abort + 129 2 libsystem_malloc.dylib 0x00007fff915d5fe2 szone_error + 625 3 libsystem_malloc.dylib 0x00007fff915cf374 small_free_list_remove_ptr + 154 4 libsystem_malloc.dylib 0x00007fff915cac3f szone_free_definite_size + 1856 5 multiarray.so 0x00000001044c2d16 npy_free_cache + 70 6 multiarray.so 0x00000001044c6ed6 array_dealloc + 182 7 selection_routines.so 0x00000001063ffe34 __pyx_pw_2yt_8geometry_18selection_routines_13SliceSelector_3fill_mask + 8804 (selection_routines.c:19749)
Line 19749 of selection_routines.c corresponds to line 1158 in selection_routines.pyx, which is the place where the fill_mask member variable of the SliceSelector extension type gets defined.
Unfortunately, I have no idea how to debug this from here...
-Nathan
On Wed, Dec 23, 2015 at 4:57 PM, Brian O'Shea bwoshea@gmail.com wrote:
Actually, interesting followup here - I have to take it back. When I
do a
projection plot:
yt.ProjectionPlot(ds,'x',("gas","temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
the behavior is perfectly fine and I get projections that look
sensible.
*however*, when I do a slice plot:
yt.SlicePlot(ds,'x',("gas", "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
I get a malloc error:
yt : [INFO ] 2015-12-23 17:50:59,082 Gathering a field list (this
may
take a moment.) yt : [INFO ] 2015-12-23 17:50:59,155 Loading field plugins. yt : [INFO ] 2015-12-23 17:50:59,155 Loaded angular_momentum (8 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded astro (16 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded cosmology (23 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,156 Loaded fluid (64 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded fluid_vector (96 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded geometric (112 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,157 Loaded local (112 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded magnetic_field (120 new fields) yt : [INFO ] 2015-12-23 17:50:59,158 Loaded my_plugins (120 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,158 Loaded species (122 new
fields)
python2.7(12254,0x7fff72d19310) malloc: *** error for object
0x103e39008:
incorrect checksum for freed object - object was probably modified
after
being freed. *** set a breakpoint in malloc_error_break to debug Abort trap: 6
This happens on my Mac (OS X 10.9.5, LLVM v6.0) and also on my Linux machine (Ubuntu 13.04, gcc 4.6.3), although on the linux machine I
just get
a seg fault instead of the malloc stuff. Using pdb (python -m pdb crashing_script.py) gives me the same error with no additional
information.
On Wed, Dec 23, 2015 at 5:40 PM, Brian O'Shea bwoshea@gmail.com
wrote:
Bugfix confirmed; this works for me as well. Thank you very much!
On Wed, Dec 23, 2015 at 5:18 PM, Nathan Goldbaum <
nathan12343@gmail.com>
wrote:
I've opened a pull request that allows me to load your dataset:
https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creatin...
On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea bwoshea@gmail.com
wrote:
> Oh, interesting. Is there a way to circumvent auto-detection of
fields?
> > On Wed, Dec 23, 2015 at 4:35 PM, Nathan Goldbaum <
nathan12343@gmail.com
> > wrote: > >> It looks like field detection is breaking for this Enzo-3.0 active >> particle dataset. StoredEnergy is available on-disk as
('AGNParticle,
>> 'StoredEnergy'), but for some reason the field detection system
isn't able
>> to guess that. >> >> On Wed, Dec 23, 2015 at 3:19 PM, Nathan Goldbaum < >> nathan12343@gmail.com> wrote: >> >>> >>> >>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea <bwoshea@gmail.com
>>> wrote: >>> >>>> Dear yt-users, >>>> >>>> I'm having a problem with making slices in non-unitary volumes.
I
>>>> have a 3D enzo simulation that has domain bounds of (-1.6...1.6)
in every
>>>> dimension (units of megaparsecs), and after I updated to the tip
of yt-3
>>>> (changeset d9502d848029) from a fairly old version of the code I
suddenly
>>>> have problems with making simple projections. If I run this set
of
>>>> commands: >>>> >>>> >>> Any idea which version you updated from? I tried on yt-3.1 and get >>> the same error. This is just so we can bisect and find the change
that
>>> introduced the regression. >>> >>> >>>> import yt >>>> ds = yt.load("DD0400/DD0400") >>>> proj = >>>>
yt.SlicePlot(ds,'x','temperature',center=[0.0,0.0,0.0],width=(0.2,'Mpc'))
>>>> >>>> I get this error: >>>> >>>> http://paste.yt-project.org/show/6115/ >>>> >>>> This seems to work fine on an Enzo cosmological dataset (domain >>>> bounds 0-1 in each dimension), and previously worked fine in
yt-3 (using a
>>>> version of the code from a couple of months ago). >>>> >>>> is this a bug, or am I doing something dumb? >>>> >>>> Thanks! >>>> >>>> --Brian >>>> >>>> >>>> _______________________________________________ >>>> yt-users mailing list >>>> yt-users@lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>>> >>> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >
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-- *SK2*
*"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
This is happening because python is unable to link against an openSSL library.
Can you try using the get_yt.sh script install of the install_script.sh script:
https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73a...
This script installs yt using the miniconda python distribution, which includes a precompiled python and openSSL library.
-Nathan
On Sat, Dec 26, 2015 at 11:40 AM, Sushilkumar sushil.sush19us@gmail.com wrote:
Hi Nathan:
Thanks for your reply.
I had done that before installing version 2.X. I used to get errors as below. Even now I keep getting the same error after reinstalling from scratch. The error comes after "installing pip". I tried it on my pc and also on cluster but same issues.
FAILURE REPORT:
bootstrap(tmpdir=tmpdir)File "get-pip.py", line 82, in bootstrap import pip File "/tmp/tmpxKqAjR/pip.zip/pip/__init__.py", line 15, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/vcs/subversion.py", line 9, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/index.py", line 30, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/wheel.py", line 35, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/compat.py", line 31, in
<module> ImportError: cannot import name HTTPSHandler
Failure. Check /home/adrith/yt-x86_64/yt_install.log. The last 10 lines are above.
On Sat, Dec 26, 2015 at 10:41 AM, Nathan Goldbaum nathan12343@gmail.com wrote:
Hi Sushilkumar,
Can you try reinstalling yt from scratch?
-Nathan
On Sat, Dec 26, 2015 at 10:39 AM, Sushilkumar sushil.sush19us@gmail.com wrote:
Dear yt:
I am currently running yt version 2.6.1 and want to update to version 3 (to read text files). Could you provide me link to so?
I tried it using yt update --all as per the link
http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-ve... .
But it wont update to 3.0 and still shows as 2.6.1
Kindly help
Thanks in advance
sushilkumar
On Thu, Dec 24, 2015 at 12:25 PM, yt-users-request@lists.spacepope.org wrote:
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Today's Topics:
- Re: problem with slices in non-unitary volumes (Nathan Goldbaum)
Message: 1 Date: Wed, 23 Dec 2015 17:17:56 -0600 From: Nathan Goldbaum nathan12343@gmail.com To: Discussion of the yt analysis package yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with slices in non-unitary volumes Message-ID: < CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
I get the same error over here. I think it's unrelated to the other error. The relevant portion of the C stack trace is here:
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff8b615286 __pthread_kill + 10 1 libsystem_c.dylib 0x00007fff8bc2a9ab abort + 129 2 libsystem_malloc.dylib 0x00007fff915d5fe2 szone_error + 625 3 libsystem_malloc.dylib 0x00007fff915cf374 small_free_list_remove_ptr + 154 4 libsystem_malloc.dylib 0x00007fff915cac3f szone_free_definite_size + 1856 5 multiarray.so 0x00000001044c2d16 npy_free_cache + 70 6 multiarray.so 0x00000001044c6ed6 array_dealloc + 182 7 selection_routines.so 0x00000001063ffe34 __pyx_pw_2yt_8geometry_18selection_routines_13SliceSelector_3fill_mask + 8804 (selection_routines.c:19749)
Line 19749 of selection_routines.c corresponds to line 1158 in selection_routines.pyx, which is the place where the fill_mask member variable of the SliceSelector extension type gets defined.
Unfortunately, I have no idea how to debug this from here...
-Nathan
On Wed, Dec 23, 2015 at 4:57 PM, Brian O'Shea bwoshea@gmail.com wrote:
Actually, interesting followup here - I have to take it back. When I
do a
projection plot:
yt.ProjectionPlot(ds,'x',("gas","temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
the behavior is perfectly fine and I get projections that look
sensible.
*however*, when I do a slice plot:
yt.SlicePlot(ds,'x',("gas", "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
I get a malloc error:
yt : [INFO ] 2015-12-23 17:50:59,082 Gathering a field list (this
may
take a moment.) yt : [INFO ] 2015-12-23 17:50:59,155 Loading field plugins. yt : [INFO ] 2015-12-23 17:50:59,155 Loaded angular_momentum (8
new
fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded astro (16 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded cosmology (23 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,156 Loaded fluid (64 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded fluid_vector (96 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded geometric (112 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,157 Loaded local (112 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded magnetic_field (120
new
fields) yt : [INFO ] 2015-12-23 17:50:59,158 Loaded my_plugins (120 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,158 Loaded species (122 new
fields)
python2.7(12254,0x7fff72d19310) malloc: *** error for object
0x103e39008:
incorrect checksum for freed object - object was probably modified
after
being freed. *** set a breakpoint in malloc_error_break to debug Abort trap: 6
This happens on my Mac (OS X 10.9.5, LLVM v6.0) and also on my Linux machine (Ubuntu 13.04, gcc 4.6.3), although on the linux machine I
just get
a seg fault instead of the malloc stuff. Using pdb (python -m pdb crashing_script.py) gives me the same error with no additional
information.
On Wed, Dec 23, 2015 at 5:40 PM, Brian O'Shea bwoshea@gmail.com
wrote:
Bugfix confirmed; this works for me as well. Thank you very much!
On Wed, Dec 23, 2015 at 5:18 PM, Nathan Goldbaum <
nathan12343@gmail.com>
wrote:
> I've opened a pull request that allows me to load your dataset: > > >
https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creatin...
> > On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea bwoshea@gmail.com
wrote:
> >> Oh, interesting. Is there a way to circumvent auto-detection of
fields?
>> >> On Wed, Dec 23, 2015 at 4:35 PM, Nathan Goldbaum <
nathan12343@gmail.com
>> > wrote: >> >>> It looks like field detection is breaking for this Enzo-3.0 active >>> particle dataset. StoredEnergy is available on-disk as
('AGNParticle,
>>> 'StoredEnergy'), but for some reason the field detection system
isn't able
>>> to guess that. >>> >>> On Wed, Dec 23, 2015 at 3:19 PM, Nathan Goldbaum < >>> nathan12343@gmail.com> wrote: >>> >>>> >>>> >>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea <
bwoshea@gmail.com>
>>>> wrote: >>>> >>>>> Dear yt-users, >>>>> >>>>> I'm having a problem with making slices in non-unitary
volumes. I
>>>>> have a 3D enzo simulation that has domain bounds of
(-1.6...1.6) in every
>>>>> dimension (units of megaparsecs), and after I updated to the
tip of yt-3
>>>>> (changeset d9502d848029) from a fairly old version of the code
I suddenly
>>>>> have problems with making simple projections. If I run this
set of
>>>>> commands: >>>>> >>>>> >>>> Any idea which version you updated from? I tried on yt-3.1 and
get
>>>> the same error. This is just so we can bisect and find the
change that
>>>> introduced the regression. >>>> >>>> >>>>> import yt >>>>> ds = yt.load("DD0400/DD0400") >>>>> proj = >>>>>
yt.SlicePlot(ds,'x','temperature',center=[0.0,0.0,0.0],width=(0.2,'Mpc'))
>>>>> >>>>> I get this error: >>>>> >>>>> http://paste.yt-project.org/show/6115/ >>>>> >>>>> This seems to work fine on an Enzo cosmological dataset (domain >>>>> bounds 0-1 in each dimension), and previously worked fine in
yt-3 (using a
>>>>> version of the code from a couple of months ago). >>>>> >>>>> is this a bug, or am I doing something dumb? >>>>> >>>>> Thanks! >>>>> >>>>> --Brian >>>>> >>>>> >>>>> _______________________________________________ >>>>> yt-users mailing list >>>>> yt-users@lists.spacepope.org >>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>> >>>>> >>>> >>> >>> _______________________________________________ >>> yt-users mailing list >>> yt-users@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >>> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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End of yt-users Digest, Vol 94, Issue 24
-- *SK2*
*"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- *SK2*
*"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Dear Nathan:
I will try it and let you know. In the meanwhile, could you let me know if yt supports loading text file for version 2.6.1? If so could you point me to examples for the same.
Thanks in advance
On Sat, Dec 26, 2015, 11:44 Nathan Goldbaum nathan12343@gmail.com wrote:
This is happening because python is unable to link against an openSSL library.
Can you try using the get_yt.sh script install of the install_script.sh script:
https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73a...
This script installs yt using the miniconda python distribution, which includes a precompiled python and openSSL library.
-Nathan
On Sat, Dec 26, 2015 at 11:40 AM, Sushilkumar sushil.sush19us@gmail.com wrote:
Hi Nathan:
Thanks for your reply.
I had done that before installing version 2.X. I used to get errors as below. Even now I keep getting the same error after reinstalling from scratch. The error comes after "installing pip". I tried it on my pc and also on cluster but same issues.
FAILURE REPORT:
bootstrap(tmpdir=tmpdir)File "get-pip.py", line 82, in bootstrap import pip File "/tmp/tmpxKqAjR/pip.zip/pip/__init__.py", line 15, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/vcs/subversion.py", line 9, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/index.py", line 30, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/wheel.py", line 35, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/compat.py", line 31, in <module> ImportError: cannot import name HTTPSHandler
Failure. Check /home/adrith/yt-x86_64/yt_install.log. The last 10 lines are above.
On Sat, Dec 26, 2015 at 10:41 AM, Nathan Goldbaum nathan12343@gmail.com wrote:
Hi Sushilkumar,
Can you try reinstalling yt from scratch?
-Nathan
On Sat, Dec 26, 2015 at 10:39 AM, Sushilkumar <sushil.sush19us@gmail.com
wrote:
Dear yt:
I am currently running yt version 2.6.1 and want to update to version 3 (to read text files). Could you provide me link to so?
I tried it using yt update --all as per the link
http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-ve... .
But it wont update to 3.0 and still shows as 2.6.1
Kindly help
Thanks in advance
sushilkumar
On Thu, Dec 24, 2015 at 12:25 PM, <yt-users-request@lists.spacepope.org
wrote:
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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:
- Re: problem with slices in non-unitary volumes (Nathan Goldbaum)
Message: 1 Date: Wed, 23 Dec 2015 17:17:56 -0600 From: Nathan Goldbaum nathan12343@gmail.com To: Discussion of the yt analysis package yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with slices in non-unitary volumes Message-ID: < CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
I get the same error over here. I think it's unrelated to the other error. The relevant portion of the C stack trace is here:
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff8b615286 __pthread_kill + 10 1 libsystem_c.dylib 0x00007fff8bc2a9ab abort + 129 2 libsystem_malloc.dylib 0x00007fff915d5fe2 szone_error + 625 3 libsystem_malloc.dylib 0x00007fff915cf374 small_free_list_remove_ptr + 154 4 libsystem_malloc.dylib 0x00007fff915cac3f szone_free_definite_size + 1856 5 multiarray.so 0x00000001044c2d16 npy_free_cache + 70 6 multiarray.so 0x00000001044c6ed6 array_dealloc + 182 7 selection_routines.so 0x00000001063ffe34 __pyx_pw_2yt_8geometry_18selection_routines_13SliceSelector_3fill_mask
8804 (selection_routines.c:19749)
Line 19749 of selection_routines.c corresponds to line 1158 in selection_routines.pyx, which is the place where the fill_mask member variable of the SliceSelector extension type gets defined.
Unfortunately, I have no idea how to debug this from here...
-Nathan
On Wed, Dec 23, 2015 at 4:57 PM, Brian O'Shea bwoshea@gmail.com wrote:
Actually, interesting followup here - I have to take it back. When
I do a
projection plot:
yt.ProjectionPlot(ds,'x',("gas","temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
the behavior is perfectly fine and I get projections that look
sensible.
*however*, when I do a slice plot:
yt.SlicePlot(ds,'x',("gas", "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
I get a malloc error:
yt : [INFO ] 2015-12-23 17:50:59,082 Gathering a field list
(this may
take a moment.) yt : [INFO ] 2015-12-23 17:50:59,155 Loading field plugins. yt : [INFO ] 2015-12-23 17:50:59,155 Loaded angular_momentum (8
new
fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded astro (16 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded cosmology (23 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,156 Loaded fluid (64 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded fluid_vector (96 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded geometric (112 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,157 Loaded local (112 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,157 Loaded magnetic_field (120
new
fields) yt : [INFO ] 2015-12-23 17:50:59,158 Loaded my_plugins (120 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,158 Loaded species (122 new
fields)
python2.7(12254,0x7fff72d19310) malloc: *** error for object
0x103e39008:
incorrect checksum for freed object - object was probably modified
after
being freed. *** set a breakpoint in malloc_error_break to debug Abort trap: 6
This happens on my Mac (OS X 10.9.5, LLVM v6.0) and also on my Linux machine (Ubuntu 13.04, gcc 4.6.3), although on the linux machine I
just get
a seg fault instead of the malloc stuff. Using pdb (python -m pdb crashing_script.py) gives me the same error with no additional
information.
On Wed, Dec 23, 2015 at 5:40 PM, Brian O'Shea bwoshea@gmail.com
wrote:
> Bugfix confirmed; this works for me as well. Thank you very much! > > On Wed, Dec 23, 2015 at 5:18 PM, Nathan Goldbaum <
nathan12343@gmail.com>
> wrote: > >> I've opened a pull request that allows me to load your dataset: >> >> >>
https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creatin...
>> >> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea bwoshea@gmail.com
wrote:
>> >>> Oh, interesting. Is there a way to circumvent auto-detection of
fields?
>>> >>> On Wed, Dec 23, 2015 at 4:35 PM, Nathan Goldbaum <
nathan12343@gmail.com
>>> > wrote: >>> >>>> It looks like field detection is breaking for this Enzo-3.0
active
>>>> particle dataset. StoredEnergy is available on-disk as
('AGNParticle,
>>>> 'StoredEnergy'), but for some reason the field detection system
isn't able
>>>> to guess that. >>>> >>>> On Wed, Dec 23, 2015 at 3:19 PM, Nathan Goldbaum < >>>> nathan12343@gmail.com> wrote: >>>> >>>>> >>>>> >>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea <
bwoshea@gmail.com>
>>>>> wrote: >>>>> >>>>>> Dear yt-users, >>>>>> >>>>>> I'm having a problem with making slices in non-unitary
volumes. I
>>>>>> have a 3D enzo simulation that has domain bounds of
(-1.6...1.6) in every
>>>>>> dimension (units of megaparsecs), and after I updated to the
tip of yt-3
>>>>>> (changeset d9502d848029) from a fairly old version of the code
I suddenly
>>>>>> have problems with making simple projections. If I run this
set of
>>>>>> commands: >>>>>> >>>>>> >>>>> Any idea which version you updated from? I tried on yt-3.1 and
get
>>>>> the same error. This is just so we can bisect and find the
change that
>>>>> introduced the regression. >>>>> >>>>> >>>>>> import yt >>>>>> ds = yt.load("DD0400/DD0400") >>>>>> proj = >>>>>>
yt.SlicePlot(ds,'x','temperature',center=[0.0,0.0,0.0],width=(0.2,'Mpc'))
>>>>>> >>>>>> I get this error: >>>>>> >>>>>> http://paste.yt-project.org/show/6115/ >>>>>> >>>>>> This seems to work fine on an Enzo cosmological dataset (domain >>>>>> bounds 0-1 in each dimension), and previously worked fine in
yt-3 (using a
>>>>>> version of the code from a couple of months ago). >>>>>> >>>>>> is this a bug, or am I doing something dumb? >>>>>> >>>>>> Thanks! >>>>>> >>>>>> --Brian >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> yt-users mailing list >>>>>> yt-users@lists.spacepope.org >>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>>> >>>>>> >>>>> >>>> >>>> _______________________________________________ >>>> yt-users mailing list >>>> yt-users@lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>>> >>> >>> _______________________________________________ >>> yt-users mailing list >>> yt-users@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >>> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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End of yt-users Digest, Vol 94, Issue 24
-- *SK2*
*"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- *SK2*
*"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
If you can format your data as numpy arrays, there are examples of how to load your data into yt here:
http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=l...
yt (2.6.1 or newer) does not support i/o from arbitrary text files.
On Sat, Dec 26, 2015 at 12:30 PM, Sushilkumar sushil.sush19us@gmail.com wrote:
Dear Nathan:
I will try it and let you know. In the meanwhile, could you let me know if yt supports loading text file for version 2.6.1? If so could you point me to examples for the same.
Thanks in advance
On Sat, Dec 26, 2015, 11:44 Nathan Goldbaum nathan12343@gmail.com wrote:
This is happening because python is unable to link against an openSSL library.
Can you try using the get_yt.sh script install of the install_script.sh script:
https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73a...
This script installs yt using the miniconda python distribution, which includes a precompiled python and openSSL library.
-Nathan
On Sat, Dec 26, 2015 at 11:40 AM, Sushilkumar sushil.sush19us@gmail.com wrote:
Hi Nathan:
Thanks for your reply.
I had done that before installing version 2.X. I used to get errors as below. Even now I keep getting the same error after reinstalling from scratch. The error comes after "installing pip". I tried it on my pc and also on cluster but same issues.
FAILURE REPORT:
bootstrap(tmpdir=tmpdir)File "get-pip.py", line 82, in bootstrap import pip File "/tmp/tmpxKqAjR/pip.zip/pip/__init__.py", line 15, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/vcs/subversion.py", line 9, in
<module> File "/tmp/tmpxKqAjR/pip.zip/pip/index.py", line 30, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/wheel.py", line 35, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/compat.py", line 31, in <module> ImportError: cannot import name HTTPSHandler
Failure. Check /home/adrith/yt-x86_64/yt_install.log. The last 10 lines are above.
On Sat, Dec 26, 2015 at 10:41 AM, Nathan Goldbaum <nathan12343@gmail.com
wrote:
Hi Sushilkumar,
Can you try reinstalling yt from scratch?
-Nathan
On Sat, Dec 26, 2015 at 10:39 AM, Sushilkumar < sushil.sush19us@gmail.com> wrote:
Dear yt:
I am currently running yt version 2.6.1 and want to update to version 3 (to read text files). Could you provide me link to so?
I tried it using yt update --all as per the link
http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-ve... .
But it wont update to 3.0 and still shows as 2.6.1
Kindly help
Thanks in advance
sushilkumar
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Today's Topics:
- Re: problem with slices in non-unitary volumes (Nathan Goldbaum)
Message: 1 Date: Wed, 23 Dec 2015 17:17:56 -0600 From: Nathan Goldbaum nathan12343@gmail.com To: Discussion of the yt analysis package yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with slices in non-unitary volumes Message-ID: < CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
I get the same error over here. I think it's unrelated to the other error. The relevant portion of the C stack trace is here:
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff8b615286 __pthread_kill
- 10
1 libsystem_c.dylib 0x00007fff8bc2a9ab abort + 129 2 libsystem_malloc.dylib 0x00007fff915d5fe2 szone_error + 625 3 libsystem_malloc.dylib 0x00007fff915cf374 small_free_list_remove_ptr + 154 4 libsystem_malloc.dylib 0x00007fff915cac3f szone_free_definite_size + 1856 5 multiarray.so 0x00000001044c2d16 npy_free_cache + 70 6 multiarray.so 0x00000001044c6ed6 array_dealloc + 182 7 selection_routines.so 0x00000001063ffe34 __pyx_pw_2yt_8geometry_18selection_routines_13SliceSelector_3fill_mask
8804 (selection_routines.c:19749)
Line 19749 of selection_routines.c corresponds to line 1158 in selection_routines.pyx, which is the place where the fill_mask member variable of the SliceSelector extension type gets defined.
Unfortunately, I have no idea how to debug this from here...
-Nathan
On Wed, Dec 23, 2015 at 4:57 PM, Brian O'Shea bwoshea@gmail.com wrote:
> Actually, interesting followup here - I have to take it back. When I do a > projection plot: > > yt.ProjectionPlot(ds,'x',("gas", > "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save() > > the behavior is perfectly fine and I get projections that look sensible. > *however*, when I do a slice plot: > > yt.SlicePlot(ds,'x',("gas", > "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save() > > I get a malloc error: > > yt : [INFO ] 2015-12-23 17:50:59,082 Gathering a field list (this may > take a moment.) > yt : [INFO ] 2015-12-23 17:50:59,155 Loading field plugins. > yt : [INFO ] 2015-12-23 17:50:59,155 Loaded angular_momentum (8 new > fields) > yt : [INFO ] 2015-12-23 17:50:59,156 Loaded astro (16 new fields) > yt : [INFO ] 2015-12-23 17:50:59,156 Loaded cosmology (23 new fields) > yt : [INFO ] 2015-12-23 17:50:59,156 Loaded fluid (64 new fields) > yt : [INFO ] 2015-12-23 17:50:59,157 Loaded fluid_vector (96 new > fields) > yt : [INFO ] 2015-12-23 17:50:59,157 Loaded geometric (112 new fields) > yt : [INFO ] 2015-12-23 17:50:59,157 Loaded local (112 new fields) > yt : [INFO ] 2015-12-23 17:50:59,157 Loaded magnetic_field (120 new > fields) > yt : [INFO ] 2015-12-23 17:50:59,158 Loaded my_plugins (120 new fields) > yt : [INFO ] 2015-12-23 17:50:59,158 Loaded species (122 new fields) > python2.7(12254,0x7fff72d19310) malloc: *** error for object 0x103e39008: > incorrect checksum for freed object - object was probably modified after > being freed. > *** set a breakpoint in malloc_error_break to debug > Abort trap: 6 > > This happens on my Mac (OS X 10.9.5, LLVM v6.0) and also on my Linux > machine (Ubuntu 13.04, gcc 4.6.3), although on the linux machine I just get > a seg fault instead of the malloc stuff. Using pdb (python -m pdb > crashing_script.py) gives me the same error with no additional information. > > > On Wed, Dec 23, 2015 at 5:40 PM, Brian O'Shea bwoshea@gmail.com wrote: > >> Bugfix confirmed; this works for me as well. Thank you very much! >> >> On Wed, Dec 23, 2015 at 5:18 PM, Nathan Goldbaum < nathan12343@gmail.com> >> wrote: >> >>> I've opened a pull request that allows me to load your dataset: >>> >>> >>> https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creatin... >>> >>> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea bwoshea@gmail.com wrote: >>> >>>> Oh, interesting. Is there a way to circumvent auto-detection of fields? >>>> >>>> On Wed, Dec 23, 2015 at 4:35 PM, Nathan Goldbaum < nathan12343@gmail.com >>>> > wrote: >>>> >>>>> It looks like field detection is breaking for this Enzo-3.0 active >>>>> particle dataset. StoredEnergy is available on-disk as ('AGNParticle, >>>>> 'StoredEnergy'), but for some reason the field detection system isn't able >>>>> to guess that. >>>>> >>>>> On Wed, Dec 23, 2015 at 3:19 PM, Nathan Goldbaum < >>>>> nathan12343@gmail.com> wrote: >>>>> >>>>>> >>>>>> >>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea < bwoshea@gmail.com> >>>>>> wrote: >>>>>> >>>>>>> Dear yt-users, >>>>>>> >>>>>>> I'm having a problem with making slices in non-unitary volumes. I >>>>>>> have a 3D enzo simulation that has domain bounds of (-1.6...1.6) in every >>>>>>> dimension (units of megaparsecs), and after I updated to the tip of yt-3 >>>>>>> (changeset d9502d848029) from a fairly old version of the code I suddenly >>>>>>> have problems with making simple projections. If I run this set of >>>>>>> commands: >>>>>>> >>>>>>> >>>>>> Any idea which version you updated from? I tried on yt-3.1 and get >>>>>> the same error. This is just so we can bisect and find the change that >>>>>> introduced the regression. >>>>>> >>>>>> >>>>>>> import yt >>>>>>> ds = yt.load("DD0400/DD0400") >>>>>>> proj = >>>>>>> yt.SlicePlot(ds,'x','temperature',center=[0.0,0.0,0.0],width=(0.2,'Mpc')) >>>>>>> >>>>>>> I get this error: >>>>>>> >>>>>>> http://paste.yt-project.org/show/6115/ >>>>>>> >>>>>>> This seems to work fine on an Enzo cosmological dataset (domain >>>>>>> bounds 0-1 in each dimension), and previously worked fine in yt-3 (using a >>>>>>> version of the code from a couple of months ago). >>>>>>> >>>>>>> is this a bug, or am I doing something dumb? >>>>>>> >>>>>>> Thanks! >>>>>>> >>>>>>> --Brian >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> yt-users mailing list >>>>>>> yt-users@lists.spacepope.org >>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> yt-users mailing list >>>>> yt-users@lists.spacepope.org >>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> yt-users mailing list >>>> yt-users@lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>>> >>> >>> _______________________________________________ >>> yt-users mailing list >>> yt-users@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >>> >> > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > -------------- next part -------------- An HTML attachment was scrubbed... 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Dear Nathan:
Thank you for your help
Dear Nathan:
As per your advice I am trying to load my text file to numpy array. But there are two ways to so using numpy.loadtxt and numpy.fromfile. Could you suggest which of them is more efficient for large files and more suitable for yt (if any)?
Thanks in advance
On Sat, Dec 26, 2015 at 6:43 PM, Sushilkumar Sreekumar < sushil.sush19us@gmail.com> wrote:
Dear Nathan:
Thank you for your help
-- SK2
"Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein."
*From: *Nathan Goldbaum nathan12343@gmail.com *Sent: *Saturday, December 26, 2015 12:34 PM *To: *Sushilkumar sushil.sush19us@gmail.com *Cc: *Discussion of the yt analysis package yt-users@lists.spacepope.org *Subject: *Re: [yt-users] problem with yt update to 3.0
If you can format your data as numpy arrays, there are examples of how to load your data into yt here:
http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=l...
yt (2.6.1 or newer) does not support i/o from arbitrary text files.
On Sat, Dec 26, 2015 at 12:30 PM, Sushilkumar sushil.sush19us@gmail.com wrote:
Dear Nathan:
I will try it and let you know. In the meanwhile, could you let me know if yt supports loading text file for version 2.6.1? If so could you point me to examples for the same.
Thanks in advance
On Sat, Dec 26, 2015, 11:44 Nathan Goldbaum nathan12343@gmail.com wrote:
This is happening because python is unable to link against an openSSL library.
Can you try using the get_yt.sh script install of the install_script.sh script:
https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73a...
This script installs yt using the miniconda python distribution, which includes a precompiled python and openSSL library.
-Nathan
On Sat, Dec 26, 2015 at 11:40 AM, Sushilkumar sushil.sush19us@gmail.com wrote:
Hi Nathan:
Thanks for your reply.
I had done that before installing version 2.X. I used to get errors as below. Even now I keep getting the same error after reinstalling from scratch. The error comes after "installing pip". I tried it on my pc and also on cluster but same issues.
FAILURE REPORT:
bootstrap(tmpdir=tmpdir)File "get-pip.py", line 82, in bootstrap import pip File "/tmp/tmpxKqAjR/pip.zip/pip/__init__.py", line 15, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/vcs/subversion.py", line 9, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/index.py", line 30, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/wheel.py", line 35, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/compat.py", line 31, in
<module> ImportError: cannot import name HTTPSHandler
Failure. Check /home/adrith/yt-x86_64/yt_install.log. The last 10 lines are above.
On Sat, Dec 26, 2015 at 10:41 AM, Nathan Goldbaum nathan12343@gmail.com wrote:
Hi Sushilkumar,
Can you try reinstalling yt from scratch?
-Nathan
On Sat, Dec 26, 2015 at 10:39 AM, Sushilkumar sushil.sush19us@gmail.com wrote:
Dear yt:
I am currently running yt version 2.6.1 and want to update to version 3 (to read text files). Could you provide me link to so?
I tried it using yt update --all as per the link
http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-ve... .
But it wont update to 3.0 and still shows as 2.6.1
Kindly help
Thanks in advance
sushilkumar
On Thu, Dec 24, 2015 at 12:25 PM, yt-users-request@lists.spacepope.org wrote:
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Today's Topics:
- Re: problem with slices in non-unitary volumes (Nathan Goldbaum)
Message: 1 Date: Wed, 23 Dec 2015 17:17:56 -0600 From: Nathan Goldbaum nathan12343@gmail.com To: Discussion of the yt analysis package yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with slices in non-unitary volumes Message-ID: < CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
I get the same error over here. I think it's unrelated to the other error. The relevant portion of the C stack trace is here:
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff8b615286 __pthread_kill + 10 1 libsystem_c.dylib 0x00007fff8bc2a9ab abort + 129 2 libsystem_malloc.dylib 0x00007fff915d5fe2 szone_error + 625 3 libsystem_malloc.dylib 0x00007fff915cf374 small_free_list_remove_ptr + 154 4 libsystem_malloc.dylib 0x00007fff915cac3f szone_free_definite_size + 1856 5 multiarray.so 0x00000001044c2d16 npy_free_cache + 70 6 multiarray.so 0x00000001044c6ed6 array_dealloc + 182 7 selection_routines.so 0x00000001063ffe34 __pyx_pw_2yt_8geometry_18selection_routines_13SliceSelector_3fill_mask + 8804 (selection_routines.c:19749)
Line 19749 of selection_routines.c corresponds to line 1158 in selection_routines.pyx, which is the place where the fill_mask member variable of the SliceSelector extension type gets defined.
Unfortunately, I have no idea how to debug this from here...
-Nathan
On Wed, Dec 23, 2015 at 4:57 PM, Brian O'Shea bwoshea@gmail.com wrote:
Actually, interesting followup here - I have to take it back. When I do
a
projection plot:
yt.ProjectionPlot(ds,'x',("gas","temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
the behavior is perfectly fine and I get projections that look sensible. *however*, when I do a slice plot:
yt.SlicePlot(ds,'x',("gas", "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
I get a malloc error:
yt : [INFO ] 2015-12-23 17:50:59,082 Gathering a field list (this may take a moment.) yt : [INFO ] 2015-12-23 17:50:59,155 Loading field plugins. yt : [INFO ] 2015-12-23 17:50:59,155 Loaded angular_momentum (8 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded astro (16 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded cosmology (23 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded fluid (64 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded fluid_vector (96 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded geometric (112 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,157 Loaded local (112 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded magnetic_field (120 new fields) yt : [INFO ] 2015-12-23 17:50:59,158 Loaded my_plugins (120 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,158 Loaded species (122 new fields) python2.7(12254,0x7fff72d19310) malloc: *** error for object 0x103e39008: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Abort trap: 6
This happens on my Mac (OS X 10.9.5, LLVM v6.0) and also on my Linux machine (Ubuntu 13.04, gcc 4.6.3), although on the linux machine I just
get
a seg fault instead of the malloc stuff. Using pdb (python -m pdb crashing_script.py) gives me the same error with no additional
information.
On Wed, Dec 23, 2015 at 5:40 PM, Brian O'Shea bwoshea@gmail.com wrote:
Bugfix confirmed; this works for me as well. Thank you very much!
On Wed, Dec 23, 2015 at 5:18 PM, Nathan Goldbaum <nathan12343@gmail.com
wrote:
I've opened a pull request that allows me to load your dataset:
https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creatin...
On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea bwoshea@gmail.com
wrote:
Oh, interesting. Is there a way to circumvent auto-detection of
fields?
On Wed, Dec 23, 2015 at 4:35 PM, Nathan Goldbaum <
nathan12343@gmail.com
wrote:
It looks like field detection is breaking for this Enzo-3.0 active particle dataset. StoredEnergy is available on-disk as ('AGNParticle, 'StoredEnergy'), but for some reason the field detection system
isn't able
to guess that.
On Wed, Dec 23, 2015 at 3:19 PM, Nathan Goldbaum < nathan12343@gmail.com> wrote:
> > > On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea bwoshea@gmail.com > wrote: > >> Dear yt-users, >> >> I'm having a problem with making slices in non-unitary volumes. I >> have a 3D enzo simulation that has domain bounds of (-1.6...1.6)
in every
>> dimension (units of megaparsecs), and after I updated to the tip
of yt-3
>> (changeset d9502d848029) from a fairly old version of the code I
suddenly
>> have problems with making simple projections. If I run this set of >> commands: >> >> > Any idea which version you updated from? I tried on yt-3.1 and get > the same error. This is just so we can bisect and find the change
that
> introduced the regression. > > >> import yt >> ds = yt.load("DD0400/DD0400") >> proj = >>
yt.SlicePlot(ds,'x','temperature',center=[0.0,0.0,0.0],width=(0.2,'Mpc'))
>> >> I get this error: >> >> http://paste.yt-project.org/show/6115/ >> >> This seems to work fine on an Enzo cosmological dataset (domain >> bounds 0-1 in each dimension), and previously worked fine in yt-3
(using a
>> version of the code from a couple of months ago). >> >> is this a bug, or am I doing something dumb? >> >> Thanks! >> >> --Brian >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >
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--
*SK2*
*"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein."*
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
--
*SK2*
*"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein."*
Dear Nathan:
I am trying to load my data from a file by formatting it as numpy array (using np.genfromtxt).
But when I try to load a uniform grid using pf = load_uniform_grid(data, vector.shape, cm_per_mpc, bbox=bbox, nprocs=64).
I get the following error AttributeError: 'module' object has no attribute 'load_uniform_grid'.
Can you suggest the source of the error?
Thank you in advance
On Wed, Dec 30, 2015 at 11:01 AM, Sushilkumar sushil.sush19us@gmail.com wrote:
Dear Nathan:
As per your advice I am trying to load my text file to numpy array. But there are two ways to so using numpy.loadtxt and numpy.fromfile. Could you suggest which of them is more efficient for large files and more suitable for yt (if any)?
Thanks in advance
On Sat, Dec 26, 2015 at 6:43 PM, Sushilkumar Sreekumar < sushil.sush19us@gmail.com> wrote:
Dear Nathan:
Thank you for your help
-- SK2
"Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein."
*From: *Nathan Goldbaum nathan12343@gmail.com *Sent: *Saturday, December 26, 2015 12:34 PM *To: *Sushilkumar sushil.sush19us@gmail.com *Cc: *Discussion of the yt analysis package yt-users@lists.spacepope.org *Subject: *Re: [yt-users] problem with yt update to 3.0
If you can format your data as numpy arrays, there are examples of how to load your data into yt here:
http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=l...
yt (2.6.1 or newer) does not support i/o from arbitrary text files.
On Sat, Dec 26, 2015 at 12:30 PM, Sushilkumar sushil.sush19us@gmail.com wrote:
Dear Nathan:
I will try it and let you know. In the meanwhile, could you let me know if yt supports loading text file for version 2.6.1? If so could you point me to examples for the same.
Thanks in advance
On Sat, Dec 26, 2015, 11:44 Nathan Goldbaum nathan12343@gmail.com wrote:
This is happening because python is unable to link against an openSSL library.
Can you try using the get_yt.sh script install of the install_script.sh script:
https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73a...
This script installs yt using the miniconda python distribution, which includes a precompiled python and openSSL library.
-Nathan
On Sat, Dec 26, 2015 at 11:40 AM, Sushilkumar sushil.sush19us@gmail.com wrote:
Hi Nathan:
Thanks for your reply.
I had done that before installing version 2.X. I used to get errors as below. Even now I keep getting the same error after reinstalling from scratch. The error comes after "installing pip". I tried it on my pc and also on cluster but same issues.
FAILURE REPORT:
bootstrap(tmpdir=tmpdir)File "get-pip.py", line 82, in bootstrap import pip File "/tmp/tmpxKqAjR/pip.zip/pip/__init__.py", line 15, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/vcs/subversion.py", line 9, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/index.py", line 30, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/wheel.py", line 35, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/compat.py", line 31, in <module> ImportError: cannot import name HTTPSHandler
Failure. Check /home/adrith/yt-x86_64/yt_install.log. The last 10 lines are above.
On Sat, Dec 26, 2015 at 10:41 AM, Nathan Goldbaum nathan12343@gmail.com wrote:
Hi Sushilkumar,
Can you try reinstalling yt from scratch?
-Nathan
On Sat, Dec 26, 2015 at 10:39 AM, Sushilkumar sushil.sush19us@gmail.com wrote:
Dear yt:
I am currently running yt version 2.6.1 and want to update to version 3 (to read text files). Could you provide me link to so?
I tried it using yt update --all as per the link
http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-ve... .
But it wont update to 3.0 and still shows as 2.6.1
Kindly help
Thanks in advance
sushilkumar
On Thu, Dec 24, 2015 at 12:25 PM, yt-users-request@lists.spacepope.org wrote:
Send yt-users mailing list submissions to yt-users@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@lists.spacepope.org
You can reach the person managing the list at yt-users-owner@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:
- Re: problem with slices in non-unitary volumes (Nathan Goldbaum)
Message: 1 Date: Wed, 23 Dec 2015 17:17:56 -0600 From: Nathan Goldbaum nathan12343@gmail.com To: Discussion of the yt analysis package yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with slices in non-unitary volumes Message-ID: < CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
I get the same error over here. I think it's unrelated to the other error. The relevant portion of the C stack trace is here:
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff8b615286 __pthread_kill + 10 1 libsystem_c.dylib 0x00007fff8bc2a9ab abort + 129 2 libsystem_malloc.dylib 0x00007fff915d5fe2 szone_error + 625 3 libsystem_malloc.dylib 0x00007fff915cf374 small_free_list_remove_ptr + 154 4 libsystem_malloc.dylib 0x00007fff915cac3f szone_free_definite_size + 1856 5 multiarray.so 0x00000001044c2d16 npy_free_cache + 70 6 multiarray.so 0x00000001044c6ed6 array_dealloc + 182 7 selection_routines.so 0x00000001063ffe34 __pyx_pw_2yt_8geometry_18selection_routines_13SliceSelector_3fill_mask + 8804 (selection_routines.c:19749)
Line 19749 of selection_routines.c corresponds to line 1158 in selection_routines.pyx, which is the place where the fill_mask member variable of the SliceSelector extension type gets defined.
Unfortunately, I have no idea how to debug this from here...
-Nathan
On Wed, Dec 23, 2015 at 4:57 PM, Brian O'Shea bwoshea@gmail.com wrote:
Actually, interesting followup here - I have to take it back. When I
do a
projection plot:
yt.ProjectionPlot(ds,'x',("gas","temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
the behavior is perfectly fine and I get projections that look sensible. *however*, when I do a slice plot:
yt.SlicePlot(ds,'x',("gas", "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
I get a malloc error:
yt : [INFO ] 2015-12-23 17:50:59,082 Gathering a field list (this
may
take a moment.) yt : [INFO ] 2015-12-23 17:50:59,155 Loading field plugins. yt : [INFO ] 2015-12-23 17:50:59,155 Loaded angular_momentum (8 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded astro (16 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded cosmology (23 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,156 Loaded fluid (64 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded fluid_vector (96 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded geometric (112 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,157 Loaded local (112 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded magnetic_field (120 new fields) yt : [INFO ] 2015-12-23 17:50:59,158 Loaded my_plugins (120 new
fields)
yt : [INFO ] 2015-12-23 17:50:59,158 Loaded species (122 new fields) python2.7(12254,0x7fff72d19310) malloc: *** error for object
0x103e39008:
incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Abort trap: 6
This happens on my Mac (OS X 10.9.5, LLVM v6.0) and also on my Linux machine (Ubuntu 13.04, gcc 4.6.3), although on the linux machine I just
get
a seg fault instead of the malloc stuff. Using pdb (python -m pdb crashing_script.py) gives me the same error with no additional
information.
On Wed, Dec 23, 2015 at 5:40 PM, Brian O'Shea bwoshea@gmail.com
wrote:
Bugfix confirmed; this works for me as well. Thank you very much!
On Wed, Dec 23, 2015 at 5:18 PM, Nathan Goldbaum <
nathan12343@gmail.com>
wrote:
I've opened a pull request that allows me to load your dataset:
https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creatin...
On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea bwoshea@gmail.com
wrote:
Oh, interesting. Is there a way to circumvent auto-detection of
fields?
On Wed, Dec 23, 2015 at 4:35 PM, Nathan Goldbaum <
nathan12343@gmail.com
> wrote:
> It looks like field detection is breaking for this Enzo-3.0 active > particle dataset. StoredEnergy is available on-disk as
('AGNParticle,
> 'StoredEnergy'), but for some reason the field detection system
isn't able
> to guess that. > > On Wed, Dec 23, 2015 at 3:19 PM, Nathan Goldbaum < > nathan12343@gmail.com> wrote: > >> >> >> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea bwoshea@gmail.com >> wrote: >> >>> Dear yt-users, >>> >>> I'm having a problem with making slices in non-unitary volumes. I >>> have a 3D enzo simulation that has domain bounds of (-1.6...1.6)
in every
>>> dimension (units of megaparsecs), and after I updated to the tip
of yt-3
>>> (changeset d9502d848029) from a fairly old version of the code I
suddenly
>>> have problems with making simple projections. If I run this set
of
>>> commands: >>> >>> >> Any idea which version you updated from? I tried on yt-3.1 and get >> the same error. This is just so we can bisect and find the change
that
>> introduced the regression. >> >> >>> import yt >>> ds = yt.load("DD0400/DD0400") >>> proj = >>>
yt.SlicePlot(ds,'x','temperature',center=[0.0,0.0,0.0],width=(0.2,'Mpc'))
>>> >>> I get this error: >>> >>> http://paste.yt-project.org/show/6115/ >>> >>> This seems to work fine on an Enzo cosmological dataset (domain >>> bounds 0-1 in each dimension), and previously worked fine in yt-3
(using a
>>> version of the code from a couple of months ago). >>> >>> is this a bug, or am I doing something dumb? >>> >>> Thanks! >>> >>> --Brian >>> >>> >>> _______________________________________________ >>> yt-users mailing list >>> yt-users@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >>> >> > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >
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-- *SK2*
*"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*
In the current development version of yt there is also yt.loadtxt, which is essentially a wrapper for numpy.loadtxt which also accepts unit information.
See http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html#Saving-an... http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html#Saving-and-Loading-YTArrays-to/from-disk
On Dec 30, 2015, at 12:01 PM, Sushilkumar sushil.sush19us@gmail.com wrote:
Dear Nathan:
As per your advice I am trying to load my text file to numpy array. But there are two ways to so using numpy.loadtxt and numpy.fromfile. Could you suggest which of them is more efficient for large files and more suitable for yt (if any)?
Thanks in advance
On Sat, Dec 26, 2015 at 6:43 PM, Sushilkumar Sreekumar <sushil.sush19us@gmail.com mailto:sushil.sush19us@gmail.com> wrote: Dear Nathan:
Thank you for your help
-- SK2
"Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein."
From: Nathan Goldbaum mailto:nathan12343@gmail.com Sent: Saturday, December 26, 2015 12:34 PM To: Sushilkumar mailto:sushil.sush19us@gmail.com Cc: Discussion of the yt analysis package mailto:yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with yt update to 3.0
If you can format your data as numpy arrays, there are examples of how to load your data into yt here:
http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=l... http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=load_uniform_grid
yt (2.6.1 or newer) does not support i/o from arbitrary text files.
On Sat, Dec 26, 2015 at 12:30 PM, Sushilkumar <sushil.sush19us@gmail.com mailto:sushil.sush19us@gmail.com> wrote:
Dear Nathan:
I will try it and let you know. In the meanwhile, could you let me know if yt supports loading text file for version 2.6.1? If so could you point me to examples for the same.
Thanks in advance
On Sat, Dec 26, 2015, 11:44 Nathan Goldbaum <nathan12343@gmail.com mailto:nathan12343@gmail.com> wrote:
This is happening because python is unable to link against an openSSL library.
Can you try using the get_yt.sh script install of the install_script.sh script:
https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73a... https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73a6bd08/doc/get_yt.sh
This script installs yt using the miniconda python distribution, which includes a precompiled python and openSSL library.
-Nathan
On Sat, Dec 26, 2015 at 11:40 AM, Sushilkumar <sushil.sush19us@gmail.com mailto:sushil.sush19us@gmail.com> wrote:
Hi Nathan:
Thanks for your reply.
I had done that before installing version 2.X. I used to get errors as below. Even now I keep getting the same error after reinstalling from scratch. The error comes after "installing pip". I tried it on my pc and also on cluster but same issues.
FAILURE REPORT:
bootstrap(tmpdir=tmpdir)File "get-pip.py", line 82, in bootstrap import pip File "/tmp/tmpxKqAjR/pip.zip/pip/__init__.py", line 15, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/vcs/subversion.py", line 9, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/index.py", line 30, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/wheel.py", line 35, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in <module> File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/compat.py", line 31, in <module> ImportError: cannot import name HTTPSHandler
Failure. Check /home/adrith/yt-x86_64/yt_install.log. The last 10 lines are above.
On Sat, Dec 26, 2015 at 10:41 AM, Nathan Goldbaum <nathan12343@gmail.com mailto:nathan12343@gmail.com> wrote:
Hi Sushilkumar,
Can you try reinstalling yt from scratch?
-Nathan
On Sat, Dec 26, 2015 at 10:39 AM, Sushilkumar <sushil.sush19us@gmail.com mailto:sushil.sush19us@gmail.com> wrote:
Dear yt:
I am currently running yt version 2.6.1 and want to update to version 3 (to read text files). Could you provide me link to so?
I tried it using yt update --all as per the link
http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-ve... http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-versions-and-going-back .
But it wont update to 3.0 and still shows as 2.6.1
Kindly help
Thanks in advance
sushilkumar
On Thu, Dec 24, 2015 at 12:25 PM, <yt-users-request@lists.spacepope.org mailto:yt-users-request@lists.spacepope.org> wrote:
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Today's Topics:
- Re: problem with slices in non-unitary volumes (Nathan Goldbaum)
Message: 1 Date: Wed, 23 Dec 2015 17:17:56 -0600 From: Nathan Goldbaum <nathan12343@gmail.com mailto:nathan12343@gmail.com> To: Discussion of the yt analysis package <yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> Subject: Re: [yt-users] problem with slices in non-unitary volumes Message-ID: <CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@mail.gmail.com mailto:CAJXewOmVEX-qB41doTk%2B7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
I get the same error over here. I think it's unrelated to the other error. The relevant portion of the C stack trace is here:
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff8b615286 __pthread_kill + 10 1 libsystem_c.dylib 0x00007fff8bc2a9ab abort + 129 2 libsystem_malloc.dylib 0x00007fff915d5fe2 szone_error + 625 3 libsystem_malloc.dylib 0x00007fff915cf374 small_free_list_remove_ptr + 154 4 libsystem_malloc.dylib 0x00007fff915cac3f szone_free_definite_size + 1856 5 multiarray.so 0x00000001044c2d16 npy_free_cache + 70 6 multiarray.so 0x00000001044c6ed6 array_dealloc + 182 7 selection_routines.so 0x00000001063ffe34 __pyx_pw_2yt_8geometry_18selection_routines_13SliceSelector_3fill_mask + 8804 (selection_routines.c:19749)
Line 19749 of selection_routines.c corresponds to line 1158 in selection_routines.pyx, which is the place where the fill_mask member variable of the SliceSelector extension type gets defined.
Unfortunately, I have no idea how to debug this from here...
-Nathan
On Wed, Dec 23, 2015 at 4:57 PM, Brian O'Shea <bwoshea@gmail.com mailto:bwoshea@gmail.com> wrote:
Actually, interesting followup here - I have to take it back. When I do a projection plot:
yt.ProjectionPlot(ds,'x',("gas","temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
the behavior is perfectly fine and I get projections that look sensible. *however*, when I do a slice plot:
yt.SlicePlot(ds,'x',("gas", "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
I get a malloc error:
yt : [INFO ] 2015-12-23 17:50:59,082 Gathering a field list (this may take a moment.) yt : [INFO ] 2015-12-23 17:50:59,155 Loading field plugins. yt : [INFO ] 2015-12-23 17:50:59,155 Loaded angular_momentum (8 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded astro (16 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded cosmology (23 new fields) yt : [INFO ] 2015-12-23 17:50:59,156 Loaded fluid (64 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded fluid_vector (96 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded geometric (112 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded local (112 new fields) yt : [INFO ] 2015-12-23 17:50:59,157 Loaded magnetic_field (120 new fields) yt : [INFO ] 2015-12-23 17:50:59,158 Loaded my_plugins (120 new fields) yt : [INFO ] 2015-12-23 17:50:59,158 Loaded species (122 new fields) python2.7(12254,0x7fff72d19310) malloc: *** error for object 0x103e39008: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Abort trap: 6
This happens on my Mac (OS X 10.9.5, LLVM v6.0) and also on my Linux machine (Ubuntu 13.04, gcc 4.6.3), although on the linux machine I just get a seg fault instead of the malloc stuff. Using pdb (python -m pdb crashing_script.py) gives me the same error with no additional information.
On Wed, Dec 23, 2015 at 5:40 PM, Brian O'Shea <bwoshea@gmail.com mailto:bwoshea@gmail.com> wrote:
Bugfix confirmed; this works for me as well. Thank you very much!
On Wed, Dec 23, 2015 at 5:18 PM, Nathan Goldbaum <nathan12343@gmail.com mailto:nathan12343@gmail.com> wrote:
I've opened a pull request that allows me to load your dataset:
https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creatin... https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creating-particle-unions-for/diff
On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea <bwoshea@gmail.com mailto:bwoshea@gmail.com> wrote:
Oh, interesting. Is there a way to circumvent auto-detection of fields?
On Wed, Dec 23, 2015 at 4:35 PM, Nathan Goldbaum <nathan12343@gmail.com mailto:nathan12343@gmail.com
wrote:
It looks like field detection is breaking for this Enzo-3.0 active particle dataset. StoredEnergy is available on-disk as ('AGNParticle, 'StoredEnergy'), but for some reason the field detection system isn't able to guess that.
On Wed, Dec 23, 2015 at 3:19 PM, Nathan Goldbaum < nathan12343@gmail.com mailto:nathan12343@gmail.com> wrote:
> > > On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea <bwoshea@gmail.com mailto:bwoshea@gmail.com> > wrote: > >> Dear yt-users, >> >> I'm having a problem with making slices in non-unitary volumes. I >> have a 3D enzo simulation that has domain bounds of (-1.6...1.6) in every >> dimension (units of megaparsecs), and after I updated to the tip of yt-3 >> (changeset d9502d848029) from a fairly old version of the code I suddenly >> have problems with making simple projections. If I run this set of >> commands: >> >> > Any idea which version you updated from? I tried on yt-3.1 and get > the same error. This is just so we can bisect and find the change that > introduced the regression. > > >> import yt >> ds = yt.load("DD0400/DD0400") >> proj = >> yt.SlicePlot(ds,'x','temperature',center=[0.0,0.0,0.0],width=(0.2,'Mpc')) >> >> I get this error: >> >> http://paste.yt-project.org/show/6115/ http://paste.yt-project.org/show/6115/ >> >> This seems to work fine on an Enzo cosmological dataset (domain >> bounds 0-1 in each dimension), and previously worked fine in yt-3 (using a >> version of the code from a couple of months ago). >> >> is this a bug, or am I doing something dumb? >> >> Thanks! >> >> --Brian >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@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 >> >> >
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"Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein."
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--
SK2
"Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein."
-- SK2
"Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein."
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participants (4)
-
John ZuHone -
Nathan Goldbaum -
Sushilkumar -
Sushilkumar Sreekumar