[FLASH-USERS] FLASH's python tools
Ong Jian Fuh
jianfuh.ong at eli-np.ro
Mon Jun 7 02:29:07 EDT 2021
Dear Ryan,
Thanks for your suggestion. I looked into the python tool in
/tools/python/output.py & yt_derived_fields.py/. I tried to import those
files into my jupyter notebook. I find most of them is outdated (in
FLASH4.6.2), even the /yt/ command such as /from
yt.data_objects.field_info_container import add_field /does not exist
anymore. Only part of the file is compatible with python3 (e.g.
tools/scripts/extract_rays.py). I will try out yt for the plotting.
Regards,
Dr. Ong Jian Fuh
Extreme Light Infrastructure - Nuclear Physics
"Horia Hulubei" National Institute for Physics and Nuclear Engineering
30 Reactorului Street, 077125 Magurele (Ilfov), Romania
www.eli-np.ro
On 01/06/2021 6:08 pm, Ryan Farber wrote:
> Hi Jian,
>
> I'd recommend copy pasting the exact command you're using at the
> command line, similar to how you've been copy-pasting the Traceback
> error messages. I'd also recommend following the instructions in the
> quickstart guide here:
> http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug_4p62/node13.html
> <http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug_4p62/node13.html>
> (or for the corresponding version of FLASH you're using).
>
> The flmake documentation you linked to is from FLASH4 ***beta*** which
> I would guess is around 10+ years old, so it's unsurprising to me that
> it doesn't work with FLASH4.6+. The good news is plotting natively
> with yt is simple enough, and the yt community is pretty helpful.
>
> Best,
> --------
> Ryan
>
>
> On Tue, Jun 1, 2021 at 2:04 AM Jian Fuh Ong <jianfuh.ong at eli-np.ro
> <mailto:jianfuh.ong at eli-np.ro>> wrote:
>
> Hi Ryan,
>
> I just downloaded FLASH4.6 and
> /python setup.py install/--///user/ return
>
> File "setup.py", line 42
> print "RELEASE file not found at " + release_path
> ^
> SyntaxError: Missing parentheses in call to 'print'. Did you mean
> print("RELEASE file not found at " + release_path)?
>
> The <> operator still appear in utils.py. I am not sure if this
> python tool also changed to python3. Using python2.7 gives
>
> Traceback (most recent call last):
> File "setup.py", line 207, in <module>
> run_setup()
> File "setup.py", line 199, in run_setup
> make_bash_completion()
> File "setup.py", line 118, in make_bash_completion
> import flash.flmake.__init__
> ImportError: No module named flash.flmake.__init__
> I see the flamake lines here.
> http://flash.uchicago.edu/site/flashcode/user_support/tools4b/usersguide/output.html#
> <http://flash.uchicago.edu/site/flashcode/user_support/tools4b/usersguide/output.html#>
>
> All I need to do is to extract the data from hdf5 file for
> plotting, i.e.
>
> from flash import output import matplotlib.pyplot as plt x, y, z =
> output.slice(2, 0.0, 'dens', "<path to chk>") plt.imshow(z) plt.show()
>
>
> Regards,
> Jian Fuh
>
>
>
>> On 31 May 2021, at 7:14 PM, Ryan Farber <rjfarber at umich.edu
>> <mailto:rjfarber at umich.edu>> wrote:
>>
>> Hi Ong,
>>
>> Unfortunately, I appear to have deleted my FLASH 4.6.2
>> installation. I had thought it should be fine with python3
>> but can't confirm at this time. However, the user guide suggests
>> python3 compatibility since FLASH 4.6 as I had thought so perhaps
>> there is some improper link for the download of FLASH 4.6.2
>> pointing to an older version?
>> http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug_4p62/node6.html
>> <http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug_4p62/node6.html>
>>
>> Regarding the flmake lines in the user guide, where do you see
>> that? I haven't used that tool before. I don't see flmake
>> referenced in the quickstart guide (just double-checked)
>> http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug_4p62/node13.html
>> <http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug_4p62/node13.html>.
>>
>> If you don't require FLASH 4.6.2 you can see if FLASH4.6 setup
>> works with your python3 environment (there shouldn't be those
>> diamond operators except in older version of FLASH). However, I'm
>> pretty sure python 2.7 will work if you don't use flmake since
>> the error you reported had to do with that tool.
>>
>> Best,
>> --------
>> Ryan
>>
>>
>> On Sun, May 30, 2021 at 11:46 PM Ong Jian Fuh
>> <jianfuh.ong at eli-np.ro <mailto:jianfuh.ong at eli-np.ro>> wrote:
>> Dear Ryan,
>>
>> Thanks for your reply. I am using FLASH4.6.2 and I believe
>> this is the latest version. I still need to
>> replace print msg to print(msg), which is still in python2.7.
>> Fixing the symbol with "!=" then many more issues exist as
>> you suggested. Such as
>>
>> File "/home/ong/.local/lib/python3.8/site-packages/flash/flmake/setup_globals.py", line
>> 204, in set
>> if type(value) != types.StringType:
>> AttributeError: module 'types' has no attribute 'StringType'
>>
>> Then I try using python2.7. and return the following error
>>
>> Writing /home/ong/.local/lib/python2.7/site-packages/flash-0.1.egg-info
>> Traceback (most recent call last):
>> File "setup.py", line 207, in <module>
>> run_setup()
>> File "setup.py", line 199, in run_setup
>> make_bash_completion()
>> File "setup.py", line 118, in make_bash_completion
>> import flash.flmake.__init__
>> ImportError: No module named flash.flmake.__init__
>>
>> Is there any update from FLASH's python tools to python3? I
>> am using jupyter notebook which run on python3.8.8. Switching
>> from one version to another would be quite troublesome.
>>
>> In addition, I am not clear what the following lines in
>> the user's guide do and how it relate to the simulation
>>
>> $ mkdir temp
>> $ cd temp
>> $ flmake setup -auto Sedov
>> $ flmake build -j 20
>> $ flmake run -n 20
>>
>> Regards,
>>
>> Dr. Ong Jian Fuh
>> Extreme Light Infrastructure - Nuclear Physics
>> "Horia Hulubei" National Institute for Physics and Nuclear
>> Engineering
>> 30 Reactorului Street, 077125 Magurele (Ilfov), Romania
>>
>> www.eli-np.ro <http://www.eli-np.ro>
>> On 28/05/2021 6:06 pm, Ryan Farber wrote:
>>> Hi Ong,
>>>
>>> I remember being mystified the first time I encountered that
>>> archaic "diamond operator."
>>>
>>> The easiest solutions are:
>>> 1. Use the latest FLASH, where they updated the python code to
>>> be compatible with python3
>>> 2. Use python2 if you need to use an old version of FLASH (like
>>> me :))
>>>
>>> Or, you can replace "<>" with "!=", although there will be many
>>> more issues you'll subsequently need to convert.
>>>
>>> Best,
>>> --------
>>> Ryan
>>>
>>>
>>> On Fri, May 28, 2021 at 8:33 AM Ong Jian Fuh
>>> <jianfuh.ong at eli-np.ro <mailto:jianfuh.ong at eli-np.ro>> wrote:
>>> Dear all,
>>>
>>> Good afternoon. I am trying to install the FLASH python tools
>>> for the plotting.
>>>
>>> Doing python setup.py install --user
>>>
>>> return
>>>
>>> running install
>>> running build
>>> running build_py
>>> copying python/metadata.json -> build/lib/flash
>>> running build_scripts
>>> running install_lib
>>> copying build/lib/flash/metadata.json
>>> -> /home/ong/.local/lib/python3.8/site-packages/flash
>>> byte-compiling /home/ong/.local/lib/python3.8/site-packages/flash/flmake/utils.py to
>>> utils.cpython-38.pyc
>>> File "/home/ong/.local/lib/python3.8/site-packages/flash/flmake/utils.py", line
>>> 423
>>> if len(parts) <> 2:
>>> ^
>>> SyntaxError: invalid syntax
>>>
>>> I am using python3.8. What can I do to fix this or use it with
>>> new python? Thanks.
>>>
>>> --
>>> Regards,
>>>
>>> Dr. Ong Jian Fuh
>>> Extreme Light Infrastructure - Nuclear Physics
>>> "Horia Hulubei" National Institute for Physics and Nuclear
>>> Engineering
>>> 30 Reactorului Street, 077125 Magurele (Ilfov), Romania
>>>
>>> www.eli-np.ro <http://www.eli-np.ro>
>
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