[FLASH-USERS] FLASH's python tools

Mon Jun 7 06:37:24 EDT 2021

Hi Ong,

Even the python tools related to yt in the FLASH code repository are very out of date (I originally put them there years ago). I would not recommend using them.

You can check out the yt website at https://yt-project.org to get lots of examples on how to carry out many different kinds of analysis.

John 

> On Jun 7, 2021, at 2:29 AM, Ong Jian Fuh <jianfuh.ong at eli-np.ro> wrote:
> 
> 
> 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 I find most of them is outdated (in FLASH4.6.2), even the yt command such as from yt.data_objects.field_info_container import add_field does not exist anymore.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 (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> 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#
>>> 
>>> 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> 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
>>>> 
>>>> 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.
>>>> 
>>>> 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> 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
>>>> 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> 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
>>> 
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