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Re: [scipion-users] Scipion 3.0 Issue with Commands Waiting for Eachother
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From: <pc...@cn...> - 2020-10-03 06:43:17
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<div dir='auto'>I think we have implemented that functionality. Once reviewed and approved we will release a new version with it. <div dir="auto"><br></div><div dir="auto">If you want to test it before that I can give you the command to install the patch</div></div><div class="gmail_extra"><br><div class="gmail_quote">El 2 oct. 2020 23:20, Colin Deniston <ckd...@gm...> escribió:<br type="attribution" /><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thanks for the info. Integrating the wait command in the templates somehow would definitely be useful. I'll take a better look at the python script but I'm not much of a coder and at first glance that script doesn't appear to have a way to sequentially run the protocols. Not sure how to implement that in the script myself. Also, my colors appear different from what you've mentioned, maybe because I'm using Scipion 3.0? Peach is scheduled for me, orange is running, and green is finished. Thanks for all the help!</div><br /><div class="elided-text"><div dir="ltr">On Fri, Oct 2, 2020 at 12:58 AM Pablo Conesa <<a href="mailto:pconesa@cnb.csic.es">pconesa@cnb.csic.es</a>> wrote:<br /></div><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb( 204 , 204 , 204 );padding-left:1ex">
<div>
<p>Thanks Colin, see anwser in line.<br />
</p>
<div>On 1/10/20 23:49, Colin Deniston wrote:<br />
</div>
<blockquote>
<div>
<p>Hello,<u></u><u></u></p>
<p><u></u> <u></u></p>
<p>First off, I’m new to Scipion and have been
loving the flexibility, streaming, monitoring, and reporting
abilities of the program! However, I’m currently trying to run
a custom built workflow in Scipion 3.0.3 and I’m running into
a few issues. <u></u><u></u></p>
<p><u></u> <u></u></p>
<p>1) I don’t see in the actual .json.template
file a line to designate what ID to wait for under each
protocol (I want each job to wait for the prior job to
completely finish before running). Is this something I can
add? If so, what is the command I should use? </p>
</div>
</blockquote>
Certainly something to Implement. Jose Miguel is right about the ids
potentially been changes, but I think we can update the "wait for"
attribute too (and export it/import it). I've created and <a href="https://github.com/scipion-em/scipion-pyworkflow/issues/151">issue</a>
and will look at it: <br />
<blockquote>
<div>
<p><u></u><u></u></p>
<p>2) When I try and circumvent that by simply
typing the ID in the GUI once the workflow is loaded (in the
“wait for” box of each protocol), nothing seems to wait. They
all run while the previous job is still going. Am I doing
something wrong? I’ve been entering them as just the ID number
like “432” but should they be entered differently? Also, I see
multiple IDs for the same job/protocol under different menus,
not sure if that is a bug or not or whether it is maybe
related to the issue of jobs not waiting. </p>
</div>
</blockquote>
<p>The expected behavior is all should be "scheduled" (orange). This
does not mean they are running, but they are actively checking is
they can start once all validation passes (wait for should be part
of the validation)</p>
<p>Do the box with the "wait for" turns orange (scheduled,this would
be correct) or green (running, thus not waiting)?<br />
</p>
<blockquote>
<div>
<p><u></u><u></u></p>
<p><u></u> <u></u></p>
<p>Any feedback would be helpful, my end goal
is just to make a reproducible workflow that can be loaded and
run on multiple Appoferritin calibration datasets all the way
to 3D refinement without any user intervention. However, at
the moment one job will try to run too soon and fail and then
lead to a cascade of downstream jobs failing. Thanks!<u></u><u></u></p>
<p><u></u> <u></u></p>
<p><b><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 33 , 37 , 41 );background:white">Colin
Deniston</span></b><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 33 , 37 , 41 )"><br />
<span style="background:white">Principal Scientist I</span><br />
<br />
</span><u></u><u></u></p>
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Institutes for Biomed.Research, Inc.<u></u><u></u></span></p>
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<p><a href="mailto:cdeniston@gnf.org"><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 47 , 84 , 150 );background:white">cdeniston@gnf.org</span></a><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 33 , 37 , 41 )"><br />
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</blockquote>
<div>-- <br />
Pablo Conesa - <strong>Madrid <a href="http://scipion.i2pc.es">Scipion</a>
team</strong></div>
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