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<p>Dear Ryan,</p>
<p>Thanks for your suggestion. I looked into the python tool in <i>tools/python/output.py
& yt_derived_fields.py</i>. I tried to import those files
into my jupyter notebook. I find most of them is outdated (in
FLASH4.6.2), even the <i>yt</i> command such as <i>from
yt.data_objects.field_info_container import add_field </i>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.<br>
</p>
<pre class="moz-signature" cols="72">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
<a class="moz-txt-link-abbreviated" href="http://www.eli-np.ro">www.eli-np.ro</a></pre>
<div class="moz-cite-prefix">On 01/06/2021 6:08 pm, Ryan Farber
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAF9W8=1Nh9qSzXVRjUEHLvKqmP_kxL-O2KJEKJBV4nSVAjXMMg@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hi Jian,
<div><br>
</div>
<div>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: <a
href="http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug_4p62/node13.html"
moz-do-not-send="true">http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug_4p62/node13.html</a>
(or for the corresponding version of FLASH you're using).</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Best,</div>
<div>
<div>
<div dir="ltr" class="gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr">--------
<div>Ryan</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Jun 1, 2021 at 2:04 AM
Jian Fuh Ong <<a href="mailto:jianfuh.ong@eli-np.ro"
moz-do-not-send="true">jianfuh.ong@eli-np.ro</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="overflow-wrap: break-word;">Hi Ryan,
<div><br>
</div>
<div>
<div>I just downloaded FLASH4.6 and <i>python setup.py install<i> <span
style="background-color:rgb(246,252,252)">--</span></i></i><span><i>user</i> return </span></div>
<div><span><br>
</span></div>
<div>
<div
style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
style="font-variant-ligatures:no-common-ligatures"> File
"setup.py", line 42</span></div>
<div
style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
style="font-variant-ligatures:no-common-ligatures">
print "RELEASE file not found at " + release_path</span></div>
<div
style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
style="font-variant-ligatures:no-common-ligatures">
^</span></div>
<div
style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
style="font-variant-ligatures:no-common-ligatures">SyntaxError:
Missing parentheses in call to 'print'. Did you mean
print("RELEASE file not found at " + release_path)?</span></div>
<div
style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
style="font-variant-ligatures:no-common-ligatures"><br>
</span></div>
<span>The <> operator still appear in utils.py. I
am not sure if this python tool also changed to
python3. Using python2.7 gives</span></div>
<div><span><br>
</span></div>
<div>
<div
style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
style="font-variant-ligatures:no-common-ligatures">Traceback
(most recent call last):</span></div>
<div
style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
style="font-variant-ligatures:no-common-ligatures">
File "setup.py", line 207, in <module></span></div>
<div
style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
style="font-variant-ligatures:no-common-ligatures">
run_setup()</span></div>
<div
style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
style="font-variant-ligatures:no-common-ligatures">
File "setup.py", line 199, in run_setup</span></div>
<div
style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
style="font-variant-ligatures:no-common-ligatures">
make_bash_completion()</span></div>
<div
style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
style="font-variant-ligatures:no-common-ligatures">
File "setup.py", line 118, in make_bash_completion</span></div>
<div
style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
style="font-variant-ligatures:no-common-ligatures">
import flash.flmake.__init__</span></div>
<div
style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
style="font-variant-ligatures:no-common-ligatures">ImportError:
No module named flash.flmake.__init__</span></div>
</div>
<span> </span></div>
<div><span>I see the flamake lines here.</span></div>
<div><span><a
href="http://flash.uchicago.edu/site/flashcode/user_support/tools4b/usersguide/output.html#"
target="_blank" moz-do-not-send="true">http://flash.uchicago.edu/site/flashcode/user_support/tools4b/usersguide/output.html#</a></span></div>
<div><span><br>
</span></div>
<div>All I need to do is to extract the data from hdf5 file
for plotting, i.e.</div>
<div><br>
</div>
<div>
<pre style="overflow:auto hidden;padding:5px;background-color:rgb(246,252,252);border-style:solid;border-color:rgb(128,133,138);border-width:1px 1px 1px 4px;color:rgb(0,0,0);line-height:15.6px"><span style="font-size:12px"><span style="color:rgb(0,136,0);font-weight:bold">from</span> <span style="color:rgb(187,0,102);font-weight:bold">flash</span> <span style="color:rgb(0,136,0);font-weight:bold">import</span> <span>output</span>
<span style="color:rgb(0,136,0);font-weight:bold">import</span> <span style="color:rgb(187,0,102);font-weight:bold">matplotlib.pyplot</span> <span style="color:rgb(0,136,0);font-weight:bold">as</span> <span style="color:rgb(187,0,102);font-weight:bold">plt</span>
<span>x</span><span>,</span> <span>y</span><span>,</span> <span>z</span> <span>=</span> <span>output</span><span>.</span><span>slice</span><span>(</span><span style="color:rgb(0,0,221);font-weight:bold">2</span><span>,</span> <span style="color:rgb(0,0,221);font-weight:bold">0.0</span><span>,</span> <span style="color:rgb(221,34,0);background-color:rgb(255,240,240)">'dens'</span><span>,</span> <span style="color:rgb(221,34,0);background-color:rgb(255,240,240)">"<path to chk>"</span><span>)</span>
<span>plt</span><span>.</span><span>imshow</span><span>(</span><span>z</span><span>)</span>
<span>plt</span><span>.</span><span>show</span><span>()</span></span></pre>
</div>
<div><span><br>
</span><span>
<div>Regards,<br>
Jian Fuh<br>
<br>
<br>
</div>
</span><span></span><span><br>
<blockquote type="cite">On 31 May 2021, at 7:14 PM, Ryan
Farber <<a href="mailto:rjfarber@umich.edu"
target="_blank" moz-do-not-send="true">rjfarber@umich.edu</a>>
wrote:<br>
<br>
Hi Ong,<br>
<br>
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?<br>
<a
href="http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug_4p62/node6.html"
target="_blank" moz-do-not-send="true">http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug_4p62/node6.html</a><br>
<br>
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)<br>
<a
href="http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug_4p62/node13.html"
target="_blank" moz-do-not-send="true">http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug_4p62/node13.html</a>.<br>
<br>
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.<br>
<br>
Best,<br>
--------<br>
Ryan<br>
<br>
<br>
On Sun, May 30, 2021 at 11:46 PM Ong Jian Fuh <<a
href="mailto:jianfuh.ong@eli-np.ro" target="_blank"
moz-do-not-send="true">jianfuh.ong@eli-np.ro</a>>
wrote:<br>
Dear Ryan,<br>
<br>
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 <br>
<br>
File "/home/ong/.local/lib/python3.8/site-packages/flash/flmake/setup_globals.py", line
204, in set<br>
if type(value) != types.StringType:<br>
AttributeError: module 'types' has no attribute
'StringType'<br>
<br>
Then I try using python2.7. and return the following
error<br>
<br>
Writing /home/ong/.local/lib/python2.7/site-packages/flash-0.1.egg-info<br>
Traceback (most recent call last):<br>
File "setup.py", line 207, in <module><br>
run_setup()<br>
File "setup.py", line 199, in run_setup<br>
make_bash_completion()<br>
File "setup.py", line 118, in make_bash_completion<br>
import flash.flmake.__init__<br>
ImportError: No module named flash.flmake.__init__<br>
<br>
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. <br>
<br>
In addition, I am not clear what the following lines
in the user's guide do and how it relate to the
simulation<br>
<br>
<div>$ mkdir temp</div>
<div>$ cd temp</div>
<div>$ flmake setup -auto Sedov</div>
<div>$ flmake build -j 20</div>
<div>$ flmake run -n 20</div>
<br>
<div>Regards,</div>
<div><br>
</div>
<div>Dr. Ong Jian Fuh</div>
<div>Extreme Light Infrastructure - Nuclear Physics</div>
<div>"Horia Hulubei" National Institute for Physics
and Nuclear Engineering</div>
<div>30 Reactorului Street, 077125 Magurele (Ilfov),
Romania</div>
<br>
<a href="http://www.eli-np.ro" target="_blank"
moz-do-not-send="true">www.eli-np.ro</a><br>
On 28/05/2021 6:06 pm, Ryan Farber wrote:<br>
<blockquote type="cite">Hi Ong,<br>
<br>
I remember being mystified the first time I
encountered that archaic "diamond operator."<br>
<br>
The easiest solutions are:<br>
1. Use the latest FLASH, where they updated the
python code to be compatible with python3<br>
2. Use python2 if you need to use an old version of
FLASH (like me :))<br>
<br>
Or, you can replace "<>" with "!=", although
there will be many more issues you'll subsequently
need to convert.<br>
<br>
Best,<br>
--------<br>
Ryan<br>
<br>
<br>
On Fri, May 28, 2021 at 8:33 AM Ong Jian Fuh <<a
href="mailto:jianfuh.ong@eli-np.ro"
target="_blank" moz-do-not-send="true">jianfuh.ong@eli-np.ro</a>>
wrote:<br>
Dear all,<br>
<br>
Good afternoon. I am trying to install the FLASH
python tools for the plotting. <br>
<br>
Doing python setup.py install --user <br>
<br>
return <br>
<br>
running install<br>
running build<br>
running build_py<br>
copying python/metadata.json -> build/lib/flash<br>
running build_scripts<br>
running install_lib<br>
copying build/lib/flash/metadata.json
-> /home/ong/.local/lib/python3.8/site-packages/flash<br>
byte-compiling /home/ong/.local/lib/python3.8/site-packages/flash/flmake/utils.py to
utils.cpython-38.pyc<br>
File "/home/ong/.local/lib/python3.8/site-packages/flash/flmake/utils.py", line
423<br>
if len(parts) <> 2:<br>
^<br>
SyntaxError: invalid syntax<br>
<br>
I am using python3.8. What can I do to fix this or
use it with new python? Thanks. <br>
<br>
<div>-- </div>
<div>Regards,</div>
<div><br>
</div>
<div>Dr. Ong Jian Fuh</div>
<div>Extreme Light Infrastructure - Nuclear Physics</div>
<div>"Horia Hulubei" National Institute for Physics
and Nuclear Engineering</div>
<div>30 Reactorului Street, 077125 Magurele (Ilfov),
Romania</div>
<br>
<a href="http://www.eli-np.ro" target="_blank"
moz-do-not-send="true">www.eli-np.ro</a><br>
</blockquote>
</blockquote>
</span><br>
</div>
</div>
</blockquote>
</div>
</blockquote>
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