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From: Dmitry S. <Sem...@gm...> - 2020-10-20 14:41:32
|
Thank you, Pablo — I have an access and I see your nice presentations! If happens some other contributions it will be very educational not only for me but for the community :) Sincerely, Dmitry > On 20. Oct 2020, at 15:33, Pablo Conesa <pc...@cn...> wrote: > > Ok, let's do this. > > I've created a "public" folder where anyone should be able to access (read only) > > https://drive.google.com/drive/folders/1Ued4tMRW31LIepNtcHPoCuVOuMQgXvpj?usp=sharing <https://drive.google.com/drive/folders/1Ued4tMRW31LIepNtcHPoCuVOuMQgXvpj?usp=sharing> > I've put some of my recent presentations (none of them will suit you). > > But other's might be able to add more. > > > > Can you access them? > > > > On 20/10/20 15:29, Dmitry Semchonok wrote: >> Dear Pablo, >> >> I am looking for the presentation(s) that includes some theory about image formation, image processing workflow and correspondent steps in the SCIPION. >> >> Kind regards, >> Dmitry >> >> >>> On 20. Oct 2020, at 15:26, Pablo Conesa <pc...@cn... <mailto:pc...@cn...>> wrote: >>> >>> Hi Dmitry! >>> >>> We have lots of them but nothing nothing or a few publicly available (for no special reason). >>> >>> What are you exactly looking for? >>> >>> On 20/10/20 14:01, Dmitry Semchonok wrote: >>>> <>Dear colleagues, >>>> >>>> >>>> Small question – >>>> >>>> is there a place where I can find the presentations about image processing steps in SCIPION (preferably in *pptx format)? >>>> >>>> >>>> Sincerely, >>>> >>>> Dmitry >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... <mailto:sci...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> >>> -- >>> Pablo Conesa - Madrid Scipion <http://scipion.i2pc.es/> team >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... <mailto:sci...@li...> >>> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> >> >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > -- > Pablo Conesa - Madrid Scipion <http://scipion.i2pc.es/> team > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Pablo C. <pc...@cn...> - 2020-10-20 13:33:45
|
Ok, let's do this. I've created a "public" folder where anyone should be able to access (read only) https://drive.google.com/drive/folders/1Ued4tMRW31LIepNtcHPoCuVOuMQgXvpj?usp=sharing I've put some of my recent presentations (none of them will suit you). But other's might be able to add more. Can you access them? On 20/10/20 15:29, Dmitry Semchonok wrote: > Dear Pablo, > > I am looking for the presentation(s) that includes some theory about > image formation, image processing workflow and correspondent steps in > the SCIPION. > > Kind regards, > Dmitry > > >> On 20. Oct 2020, at 15:26, Pablo Conesa <pc...@cn... >> <mailto:pc...@cn...>> wrote: >> >> Hi Dmitry! >> >> We have lots of them but nothing nothing or a few publicly available >> (for no special reason). >> >> What are you exactly looking for? >> >> On 20/10/20 14:01, Dmitry Semchonok wrote: >>> >>> Dear colleagues, >>> >>> >>> Small question – >>> >>> is there a place where I can find the presentations about image >>> processing steps in SCIPION (preferably in *pptx format)? >>> >>> >>> Sincerely, >>> >>> Dmitry >>> >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >> -- >> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es/> team* >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Dmitry S. <Sem...@gm...> - 2020-10-20 13:29:41
|
Dear Pablo, I am looking for the presentation(s) that includes some theory about image formation, image processing workflow and correspondent steps in the SCIPION. Kind regards, Dmitry > On 20. Oct 2020, at 15:26, Pablo Conesa <pc...@cn...> wrote: > > Hi Dmitry! > > We have lots of them but nothing nothing or a few publicly available (for no special reason). > > What are you exactly looking for? > > On 20/10/20 14:01, Dmitry Semchonok wrote: >> <>Dear colleagues, >> >> >> Small question – >> >> is there a place where I can find the presentations about image processing steps in SCIPION (preferably in *pptx format)? >> >> >> Sincerely, >> >> Dmitry >> >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > -- > Pablo Conesa - Madrid Scipion <http://scipion.i2pc.es/> team > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Pablo C. <pc...@cn...> - 2020-10-20 13:26:40
|
Hi Dmitry! We have lots of them but nothing nothing or a few publicly available (for no special reason). What are you exactly looking for? On 20/10/20 14:01, Dmitry Semchonok wrote: > > Dear colleagues, > > Small question – > > is there a place where I can find the presentations about image > processing steps in SCIPION (preferably in *pptx format)? > > Sincerely, > > Dmitry > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Dmitry S. <Sem...@gm...> - 2020-10-20 12:17:55
|
<>Dear colleagues, Small question – is there a place where I can find the presentations about image processing steps in SCIPION (preferably in *pptx format)? Sincerely, Dmitry |
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From: Juha H. <juh...@he...> - 2020-10-17 15:15:35
|
Dear Colin, In my group all projects are shared so that we can learn from each other. This is possible as long as all users belong to the same unix project (in the example below called simply "project"). Below are some tips on how you can set the group level permissions so that new files created by Scipion get also correct permissions (no sudo required). As Pablo suggested, in my group all users use one common ScipionUserData folder. Then we share an existing project like this: 1. Change the group owner of the project folder chown -R :project ScipionUserData/projects/name-of-the-project 2. Give the proper permission (750 for read only to group) to the project folder (770 for write to group) chmod 750 ScipionUserData/projects/name-of-the-project 3. Set GID (GROUP ID), so that each new file (and folder) in this directory will inherit the same group as the parent chmod g+s ScipionUserData/projects/name-of-the-project 4. Now we set proper permissions on all subdirectories (g::r-x for read only to group, g::rwx for write) setfacl -R -d -m g::r-x -m o::--- ScipionUserData /projects/name-of-the-project If we need to transfer a project to the shared project folder, we create first the project folder in the shared folder, then transfer the project there with rsync, using the flags that honor the permissions of the target folder. rsync -rlptDzv YOUR_PROJECT/ ScipionUserData/projects/name-of-the-project Giving write permission at a group level may be risky so do this at your own risk - we have noticed database corruption if two people write files at the same time. Perhaps a feature could be added to safeguard against this. Best wishes, Juha On Sat, Oct 17, 2020 at 5:50 PM <pc...@cn...> wrote: > With scipion3 it is optional. > > It's place is scipion-home/config/scipion.conf > > You can generate one with scipion3 config > > El 16 oct. 2020 23:51, Colin Deniston <ckd...@gm...> escribió: > > Where is the scipion.conf file usually? > > On Tue, Oct 13, 2020 at 1:00 AM Pablo Conesa <pc...@cn...> wrote: > > Dear Collin, I can see 2 ways: > > 1.- By default, with your user, your projects will be created at: > ~/ScipionUserData/projects/ . You could make a link there to the other's > user project. This will work for a one time look. > > 2.- If on the other hand, you want to see all projects of single user, > you can define in your scipion.conf: > SCIPION_USER_DATA=/home/youruser/ScipionUserData > > 3.- login as de user (sudo required). > > > NOTE: Note that Scipion will load those projects in a read only mode, you > will not be able to edit, change anything. > > And also, note that open them with sudo will allow you to make changes > but, then your user will fail to do so since "root" will own the folders > and files create > > I do fail to see a way to automatically load all projects from all users, > unless you script something using point 1. > > > All the best, Pablo. > > > On 12/10/20 19:57, Colin Deniston wrote: > > Hello, > > > > I’m wondering if there is a way in Scipion for one user to view other > users sessions (their various projects etc.). I’m a master user and will > often want to look at other users processing workflows to advise them on > issues. Can this be done within Scipion? Thanks! > > > > *Colin Deniston* > Principal Scientist I > > *GNF BIOTHERAPEUTICS & BIOTECHNOLOGY / GNF* > > Novartis Institutes for Biomed.Research, Inc. > > 10675 John Jay Hopkins Drive > > GNF Business > > San Diego, CA 92121 > > > > T +1 (858) 332-4750 > > cde...@gn... > > [image: https://saps-app.prd.nibr.novartis.net/esh/novartislogo.png] > <https://www.novartis.com/> > > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: <pc...@cn...> - 2020-10-17 14:48:07
|
<div dir='auto'>With scipion3 it is optional.<div dir="auto"><br></div><div dir="auto">It's place is scipion-home/config/scipion.conf</div><div dir="auto"><br></div><div dir="auto">You can generate one with scipion3 config</div></div><div class="gmail_extra"><br><div class="gmail_quote">El 16 oct. 2020 23:51, 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">Where is the scipion.conf file usually? </div><br /><div class="elided-text"><div dir="ltr">On Tue, Oct 13, 2020 at 1:00 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>Dear Collin, I can see 2 ways:</p>
<p>1.- By default, with your user, your projects will be created at:
~/ScipionUserData/projects/ . You could make a link there to the
other's user project. This will work for a one time look.</p>
<p>2.- If on the other hand, you want to see all projects of single
user, you can define in your scipion.conf:
SCIPION_USER_DATA=/home/youruser/ScipionUserData</p>
<p>3.- login as de user (sudo required).</p>
<p><br />
</p>
<p>NOTE: Note that Scipion will load those projects in a read only
mode, you will not be able to edit, change anything. <br />
</p>
<p>And also, note that open them with sudo will allow you to make
changes but, then your user will fail to do so since "root" will
own the folders and files create</p>
<p>I do fail to see a way to automatically load all projects from
all users, unless you script something using point 1. <br />
</p>
<p><br />
</p>
<p>All the best, Pablo.<br />
</p>
<p><br />
</p>
<div>On 12/10/20 19:57, Colin Deniston
wrote:<br />
</div>
<blockquote>
<div>
<p>Hello,<u></u><u></u></p>
<p><u></u> <u></u></p>
<p>I’m wondering if there is a way in Scipion
for one user to view other users sessions (their various
projects etc.). I’m a master user and will often want to look
at other users processing workflows to advise them on issues.
Can this be done within Scipion? 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>
<p style="background:white"><b><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 47 , 84 , 150 )">GNF
BIOTHERAPEUTICS & BIOTECHNOLOGY / GNF<u></u><u></u></span></b></p>
<p style="background:white"><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 33 , 37 , 41 )">Novartis
Institutes for Biomed.Research, Inc.<u></u><u></u></span></p>
<p style="background:white"><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 33 , 37 , 41 )">10675
John Jay Hopkins Drive<u></u><u></u></span></p>
<p style="background:white"><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 33 , 37 , 41 )">GNF
Business<u></u><u></u></span></p>
<p style="background:white"><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 33 , 37 , 41 )">San
Diego, CA 92121<u></u><u></u></span></p>
<p><u></u> <u></u></p>
<p style="background:white"><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 33 , 37 , 41 )">T
+1 (858) 332-4750<u></u><u></u></span></p>
<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 />
<br />
</span><a href="https://www.novartis.com/"><span style="font-size:9pt;font-family:'arial' , sans-serif;color:rgb( 4 , 96 , 169 );background:white;text-decoration:none"><img style="width:1.3541in;height:0.2416in" src="cid:1753364fa0c4cff311" alt="https://saps-app.prd.nibr.novartis.net/esh/novartislogo.png" width="130" height="23" border="0" /></span></a><u></u><u></u></p>
<p><u></u> <u></u></p>
</div>
<br />
<fieldset></fieldset>
<br />
<fieldset></fieldset>
<pre>_______________________________________________
scipion-users mailing list
<a href="mailto:scipion-users@lists.sourceforge.net">scipion-users@lists.sourceforge.net</a>
<a href="https://lists.sourceforge.net/lists/listinfo/scipion-users">https://lists.sourceforge.net/lists/listinfo/scipion-users</a>
</pre>
</blockquote>
<div>-- <br />
Pablo Conesa - <strong>Madrid <a href="http://scipion.i2pc.es">Scipion</a>
team</strong></div>
</div>
_______________________________________________<br />
scipion-users mailing list<br />
<a href="mailto:scipion-users@lists.sourceforge.net">scipion-users@lists.sourceforge.net</a><br />
<a href="https://lists.sourceforge.net/lists/listinfo/scipion-users">https://lists.sourceforge.net/lists/listinfo/scipion-users</a><br />
</blockquote></div>
</blockquote></div><br></div> |
|
From: Smith L. <smi...@ya...> - 2020-10-17 09:57:59
|
Dear All, It said "Scipion can be installed using conda or virtualenv". Here I ask, is using GPU mandatory for install and running Scipion v3.0? I am looking forward to getting your reply. Best wishes, Smith |
|
From: Tiru H. <tir...@gm...> - 2020-10-17 05:43:47
|
Hi, I am trying to install Scipion3 on my CPU laptop, unfortunately I couldn't succeed. Please can you guide me to installation. I have conda 4.8. Thank you and best regards Tiru |
|
From: Colin D. <ckd...@gm...> - 2020-10-16 21:51:35
|
Where is the scipion.conf file usually? On Tue, Oct 13, 2020 at 1:00 AM Pablo Conesa <pc...@cn...> wrote: > Dear Collin, I can see 2 ways: > > 1.- By default, with your user, your projects will be created at: > ~/ScipionUserData/projects/ . You could make a link there to the other's > user project. This will work for a one time look. > > 2.- If on the other hand, you want to see all projects of single user, > you can define in your scipion.conf: > SCIPION_USER_DATA=/home/youruser/ScipionUserData > > 3.- login as de user (sudo required). > > > NOTE: Note that Scipion will load those projects in a read only mode, you > will not be able to edit, change anything. > > And also, note that open them with sudo will allow you to make changes > but, then your user will fail to do so since "root" will own the folders > and files create > > I do fail to see a way to automatically load all projects from all users, > unless you script something using point 1. > > > All the best, Pablo. > > > On 12/10/20 19:57, Colin Deniston wrote: > > Hello, > > > > I’m wondering if there is a way in Scipion for one user to view other > users sessions (their various projects etc.). I’m a master user and will > often want to look at other users processing workflows to advise them on > issues. Can this be done within Scipion? Thanks! > > > > *Colin Deniston* > Principal Scientist I > > *GNF BIOTHERAPEUTICS & BIOTECHNOLOGY / GNF* > > Novartis Institutes for Biomed.Research, Inc. > > 10675 John Jay Hopkins Drive > > GNF Business > > San Diego, CA 92121 > > > > T +1 (858) 332-4750 > > cde...@gn... > > [image: https://saps-app.prd.nibr.novartis.net/esh/novartislogo.png] > <https://www.novartis.com/> > > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Colin D. <ckd...@gm...> - 2020-10-13 15:03:01
|
Great, thanks for the potential avenues. I'll try them out. Read only is probably fine for now. Thanks again! On Tue, Oct 13, 2020 at 1:00 AM Pablo Conesa <pc...@cn...> wrote: > Dear Collin, I can see 2 ways: > > 1.- By default, with your user, your projects will be created at: > ~/ScipionUserData/projects/ . You could make a link there to the other's > user project. This will work for a one time look. > > 2.- If on the other hand, you want to see all projects of single user, > you can define in your scipion.conf: > SCIPION_USER_DATA=/home/youruser/ScipionUserData > > 3.- login as de user (sudo required). > > > NOTE: Note that Scipion will load those projects in a read only mode, you > will not be able to edit, change anything. > > And also, note that open them with sudo will allow you to make changes > but, then your user will fail to do so since "root" will own the folders > and files create > > I do fail to see a way to automatically load all projects from all users, > unless you script something using point 1. > > > All the best, Pablo. > > > On 12/10/20 19:57, Colin Deniston wrote: > > Hello, > > > > I’m wondering if there is a way in Scipion for one user to view other > users sessions (their various projects etc.). I’m a master user and will > often want to look at other users processing workflows to advise them on > issues. Can this be done within Scipion? Thanks! > > > > *Colin Deniston* > Principal Scientist I > > *GNF BIOTHERAPEUTICS & BIOTECHNOLOGY / GNF* > > Novartis Institutes for Biomed.Research, Inc. > > 10675 John Jay Hopkins Drive > > GNF Business > > San Diego, CA 92121 > > > > T +1 (858) 332-4750 > > cde...@gn... > > [image: https://saps-app.prd.nibr.novartis.net/esh/novartislogo.png] > <https://www.novartis.com/> > > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Pablo C. <pc...@cn...> - 2020-10-13 08:00:11
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Dear Collin, I can see 2 ways: 1.- By default, with your user, your projects will be created at: ~/ScipionUserData/projects/ . You could make a link there to the other's user project. This will work for a one time look. 2.- If on the other hand, you want to see all projects of single user, you can define in your scipion.conf: SCIPION_USER_DATA=/home/youruser/ScipionUserData 3.- login as de user (sudo required). NOTE: Note that Scipion will load those projects in a read only mode, you will not be able to edit, change anything. And also, note that open them with sudo will allow you to make changes but, then your user will fail to do so since "root" will own the folders and files create I do fail to see a way to automatically load all projects from all users, unless you script something using point 1. All the best, Pablo. On 12/10/20 19:57, Colin Deniston wrote: > > Hello, > > I’m wondering if there is a way in Scipion for one user to view other > users sessions (their various projects etc.). I’m a master user and > will often want to look at other users processing workflows to advise > them on issues. Can this be done within Scipion? Thanks! > > *Colin Deniston* > Principal Scientist I > > *GNF BIOTHERAPEUTICS & BIOTECHNOLOGY / GNF* > > Novartis Institutes for Biomed.Research, Inc. > > 10675 John Jay Hopkins Drive > > GNF Business > > San Diego, CA 92121 > > T +1 (858) 332-4750 > > cde...@gn... <mailto:cde...@gn...> > > https://saps-app.prd.nibr.novartis.net/esh/novartislogo.png > <https://www.novartis.com/> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Colin D. <cde...@gn...> - 2020-10-12 21:33:08
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Hello, I'm wondering if there is a way in Scipion for one user to view other users sessions (their various projects etc.). I'm a master user and will often want to look at other users processing workflows to advise them on issues. Can this be done within Scipion? Thanks! Colin Deniston Principal Scientist I GNF BIOTHERAPEUTICS & BIOTECHNOLOGY / GNF Novartis Institutes for Biomed.Research, Inc. 10675 John Jay Hopkins Drive GNF Business San Diego, CA 92121 T +1 (858) 332-4750 cde...@gn...<mailto:cde...@gn...> [https://saps-app.prd.nibr.novartis.net/esh/novartislogo.png]<https://www.novartis.com/> |
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From: Jose M. de la R. T. <del...@gm...> - 2020-10-09 16:08:26
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Great! There are a couple bugfixes algo coming in 3.0.0b4. Have a nice weekend, Jose Miguel On Fri, Oct 9, 2020, 3:55 PM Lugmayr, Wolfgang <w.l...@uk...> wrote: > dear all, > > its fixed with scipion-em-relion 3.0.0b3 plugin version. > > thanks, > wolfgang > > > ------------------------------ > *From: *"Lugmayr, Wolfgang" <w.l...@uk...> > *To: *"Mailing list for Scipion users" < > sci...@li...> > *Sent: *Friday, 9 October, 2020 15:45:09 > *Subject: *Re: [scipion-users] scipion3 - relion protocol viewer - > chimerax script problem > > hi pablo, > > yes i got my volumes and can view the results with chimera and the > chimera_angular_distribution.cxc script. > the other views like slices, show in scipion etc. give reasonable views on > my original data. > > the test produces for me in the scipion gui also a "tile" only file. > see attached screenshot. > it does not matter if i choose class 1 or all. > the behaviour is the same. > > the line "runnning ChimeraX" comes from my vglrun wrapper but does not > modify the cxc file. > > cheers, > wolfgang > > > > ------------------------------ > *From: *"Pablo Conesa" <pc...@cn...> > *To: *"Mailing list for Scipion users" < > sci...@li...> > *Sent: *Friday, 9 October, 2020 14:01:57 > *Subject: *Re: [scipion-users] scipion3 - relion protocol viewer - > chimerax script problem > > Hi Wolfgang, > > I've run the tests: > > scipion3 tests relion.tests.test_protocols_relion.TestRelionClassify3D > > And got a proper output: > > pablo@youyou:~/desarrollo/scipion-em-relion$ cat > ~/ScipionUserData/projects/TestRelionClassify3D/Runs/000294_ProtRelionClassify3D/extra/chimera_volumes.cxc > > open relion_it008_class001.mrc > open relion_it008_class002.mrc > open relion_it008_class003.mrc > tile > > > I'm guessing....did you actually get any volume? > > > On 9/10/20 11:17, Lugmayr, Wolfgang wrote: > > hi, > > i run relion class3d and run into the following problem when looking at the volume that the chimerax cxc script only contains the word "tile": > > $ cat Runs/003565_ProtRelionClassify3D/tmp/chimera_angular_distribution.cxc > open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/tmp/axis.bild > open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/tmp/spheres.bild > cofr 0,0,0 > open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/extra/relion_it025_class001.mrc > volume #3 voxelSize 0.87 > volume #3 origin -104.4,-104.4,-104.4 > > $ cat Runs/003565_ProtRelionClassify3D/extra/chimera_volumes.cxc > tile > > settings used: > 3D classes to visualize: -> selection -> Classes used: 1 > Display volume with: chimera > > pressing the eye button calls: > ChimeraX Runs/003565_ProtRelionClassify3D/extra/chimera_volumes.cxc > with no other arguments so i assume the open statements are overwritten > > the same behaviour is also when looking at the initial model, so i assume its the same code statement. > > cheers, > wolfgang > > p.s. fyi: i am working on a virtual desktop on the cluster, so i had to replace ChimeraX by a script > vglrun +xcb /.../ChimeraX.orig $* > to overcome the usual ChimeraX problem: > WARNING: WebEngineContext? used before QtWebEngine::initialize() or OpenGL context creation failed. > ERROR: Could not create OpenGL context > > > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Lugmayr, W. <w.l...@uk...> - 2020-10-09 13:55:20
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dear all, its fixed with scipion-em-relion 3.0.0b3 plugin version. thanks, wolfgang From: "Lugmayr, Wolfgang" <w.l...@uk...> To: "Mailing list for Scipion users" <sci...@li...> Sent: Friday, 9 October, 2020 15:45:09 Subject: Re: [scipion-users] scipion3 - relion protocol viewer - chimerax script problem hi pablo, yes i got my volumes and can view the results with chimera and the chimera_angular_distribution.cxc script. the other views like slices, show in scipion etc. give reasonable views on my original data. the test produces for me in the scipion gui also a "tile" only file. see attached screenshot. it does not matter if i choose class 1 or all. the behaviour is the same. the line "runnning ChimeraX" comes from my vglrun wrapper but does not modify the cxc file. cheers, wolfgang From: "Pablo Conesa" <pc...@cn...> To: "Mailing list for Scipion users" <sci...@li...> Sent: Friday, 9 October, 2020 14:01:57 Subject: Re: [scipion-users] scipion3 - relion protocol viewer - chimerax script problem Hi Wolfgang, I've run the tests: scipion3 tests relion.tests.test_protocols_relion.TestRelionClassify3D And got a proper output: pablo@youyou:~/desarrollo/scipion-em-relion$ cat ~/ScipionUserData/projects/TestRelionClassify3D/Runs/000294_ProtRelionClassify3D/extra/chimera_volumes.cxc open relion_it008_class001.mrc open relion_it008_class002.mrc open relion_it008_class003.mrc tile I'm guessing....did you actually get any volume? On 9/10/20 11:17, Lugmayr, Wolfgang wrote: hi, i run relion class3d and run into the following problem when looking at the volume that the chimerax cxc script only contains the word "tile": $ cat Runs/003565_ProtRelionClassify3D/tmp/chimera_angular_distribution.cxc open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/tmp/axis.bild open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/tmp/spheres.bild cofr 0,0,0 open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/extra/relion_it025_class001.mrc volume #3 voxelSize 0.87 volume #3 origin -104.4,-104.4,-104.4 $ cat Runs/003565_ProtRelionClassify3D/extra/chimera_volumes.cxc tile settings used: 3D classes to visualize: -> selection -> Classes used: 1 Display volume with: chimera pressing the eye button calls: ChimeraX Runs/003565_ProtRelionClassify3D/extra/chimera_volumes.cxc with no other arguments so i assume the open statements are overwritten the same behaviour is also when looking at the initial model, so i assume its the same code statement. cheers, wolfgang p.s. fyi: i am working on a virtual desktop on the cluster, so i had to replace ChimeraX by a script vglrun +xcb /.../ChimeraX.orig $* to overcome the usual ChimeraX problem: WARNING: WebEngineContext? used before QtWebEngine::initialize() or OpenGL context creation failed. ERROR: Could not create OpenGL context -- Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Lugmayr, W. <w.l...@uk...> - 2020-10-09 13:45:21
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hi pablo, yes i got my volumes and can view the results with chimera and the chimera_angular_distribution.cxc script. the other views like slices, show in scipion etc. give reasonable views on my original data. the test produces for me in the scipion gui also a "tile" only file. see attached screenshot. it does not matter if i choose class 1 or all. the behaviour is the same. the line "runnning ChimeraX" comes from my vglrun wrapper but does not modify the cxc file. cheers, wolfgang From: "Pablo Conesa" <pc...@cn...> To: "Mailing list for Scipion users" <sci...@li...> Sent: Friday, 9 October, 2020 14:01:57 Subject: Re: [scipion-users] scipion3 - relion protocol viewer - chimerax script problem Hi Wolfgang, I've run the tests: scipion3 tests relion.tests.test_protocols_relion.TestRelionClassify3D And got a proper output: pablo@youyou:~/desarrollo/scipion-em-relion$ cat ~/ScipionUserData/projects/TestRelionClassify3D/Runs/000294_ProtRelionClassify3D/extra/chimera_volumes.cxc open relion_it008_class001.mrc open relion_it008_class002.mrc open relion_it008_class003.mrc tile I'm guessing....did you actually get any volume? On 9/10/20 11:17, Lugmayr, Wolfgang wrote: hi, i run relion class3d and run into the following problem when looking at the volume that the chimerax cxc script only contains the word "tile": $ cat Runs/003565_ProtRelionClassify3D/tmp/chimera_angular_distribution.cxc open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/tmp/axis.bild open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/tmp/spheres.bild cofr 0,0,0 open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/extra/relion_it025_class001.mrc volume #3 voxelSize 0.87 volume #3 origin -104.4,-104.4,-104.4 $ cat Runs/003565_ProtRelionClassify3D/extra/chimera_volumes.cxc tile settings used: 3D classes to visualize: -> selection -> Classes used: 1 Display volume with: chimera pressing the eye button calls: ChimeraX Runs/003565_ProtRelionClassify3D/extra/chimera_volumes.cxc with no other arguments so i assume the open statements are overwritten the same behaviour is also when looking at the initial model, so i assume its the same code statement. cheers, wolfgang p.s. fyi: i am working on a virtual desktop on the cluster, so i had to replace ChimeraX by a script vglrun +xcb /.../ChimeraX.orig $* to overcome the usual ChimeraX problem: WARNING: WebEngineContext? used before QtWebEngine::initialize() or OpenGL context creation failed. ERROR: Could not create OpenGL context -- Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Pablo C. <pc...@cn...> - 2020-10-09 12:02:30
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Hi Wolfgang, I've run the tests: scipion3 tests relion.tests.test_protocols_relion.TestRelionClassify3D And got a proper output: pablo@youyou:~/desarrollo/scipion-em-relion$ cat ~/ScipionUserData/projects/TestRelionClassify3D/Runs/000294_ProtRelionClassify3D/extra/chimera_volumes.cxc open relion_it008_class001.mrc open relion_it008_class002.mrc open relion_it008_class003.mrc tile I'm guessing....did you actually get any volume? On 9/10/20 11:17, Lugmayr, Wolfgang wrote: > hi, > > i run relion class3d and run into the following problem when looking at the volume that the chimerax cxc script only contains the word "tile": > > $ cat Runs/003565_ProtRelionClassify3D/tmp/chimera_angular_distribution.cxc > open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/tmp/axis.bild > open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/tmp/spheres.bild > cofr 0,0,0 > open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/extra/relion_it025_class001.mrc > volume #3 voxelSize 0.87 > volume #3 origin -104.4,-104.4,-104.4 > > $ cat Runs/003565_ProtRelionClassify3D/extra/chimera_volumes.cxc > tile > > settings used: > 3D classes to visualize: -> selection -> Classes used: 1 > Display volume with: chimera > > pressing the eye button calls: > ChimeraX Runs/003565_ProtRelionClassify3D/extra/chimera_volumes.cxc > with no other arguments so i assume the open statements are overwritten > > the same behaviour is also when looking at the initial model, so i assume its the same code statement. > > cheers, > wolfgang > > p.s. fyi: i am working on a virtual desktop on the cluster, so i had to replace ChimeraX by a script > vglrun +xcb /.../ChimeraX.orig $* > to overcome the usual ChimeraX problem: > WARNING: WebEngineContext? used before QtWebEngine::initialize() or OpenGL context creation failed. > ERROR: Could not create OpenGL context > > -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Lugmayr, W. <w.l...@uk...> - 2020-10-09 09:18:04
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hi, i run relion class3d and run into the following problem when looking at the volume that the chimerax cxc script only contains the word "tile": $ cat Runs/003565_ProtRelionClassify3D/tmp/chimera_angular_distribution.cxc open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/tmp/axis.bild open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/tmp/spheres.bild cofr 0,0,0 open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/extra/relion_it025_class001.mrc volume #3 voxelSize 0.87 volume #3 origin -104.4,-104.4,-104.4 $ cat Runs/003565_ProtRelionClassify3D/extra/chimera_volumes.cxc tile settings used: 3D classes to visualize: -> selection -> Classes used: 1 Display volume with: chimera pressing the eye button calls: ChimeraX Runs/003565_ProtRelionClassify3D/extra/chimera_volumes.cxc with no other arguments so i assume the open statements are overwritten the same behaviour is also when looking at the initial model, so i assume its the same code statement. cheers, wolfgang p.s. fyi: i am working on a virtual desktop on the cluster, so i had to replace ChimeraX by a script vglrun +xcb /.../ChimeraX.orig $* to overcome the usual ChimeraX problem: WARNING: WebEngineContext? used before QtWebEngine::initialize() or OpenGL context creation failed. ERROR: Could not create OpenGL context -- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Deutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 Gebäude 15 22607 Hamburg, Germany Tel.: +49 40 8998-87652 Email: wol...@cs... http://www.cssb-hamburg.de/ |
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From: David M. <dma...@cn...> - 2020-10-07 08:23:25
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Hi Tao, Which OS are you using? Someone reported a similar problem in Centos. He fixed it by removing hdf5 from the conda environment and installing it in the system (sudo yum install hdf5-devel). Please try this. Thank you for reporting. <http://ucm.es/> *_____Dr. David Maluenda Niubó* dma...@cn... - (+34) 619 029 310 CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es> BioComputing Unit <http://biocomputingunit.es/> This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. On Mon, Oct 5, 2020 at 10:08 AM Pablo Conesa <pc...@cn...> wrote: > This is just a guess. > > hdf5 files might be provided by the system (yum/apt-get install hdf5-dev) > > But actual hdf5 libraries....are taken from conda? > > What if they do differ? Is this what is happening? > > David Maluenda, others, could this be the case? > > > On 5/10/20 9:35, Jorge wrote: > > Hello Tao, > > We've been updating the documentation these days. The following link > contains detailed information and instructions about how to install > Scipion3 in different Linux distributions, and may solve your hdf5 issue. > > https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install.html > > Please have a look and in case the problem remains, do not hesitate to > contact us. We'll be pleased to help you. > > Have a good day! > > Jorge > > > On 10/3/20 8:48 PM, 王涛 wrote: > > hello everyone, > I got a problem while installing scipion3 with miniconda. > I installed conda at first,then: > > pip install --user scipion-installer > python3 -m scipioninstaller /path/where/you/want/scipion -j 4 > > then program failed in compiling module 'xmipp',and log showed that there may be some errors in linking > > hdf5 library,but I have hdf5 installed by conda with default channel. There is another warning about > > libjpeg.so at /usr/lib64 in error logs, so I think program may not find library in .scipion3env as normal,and > > I don't know which file should I configure.(maybe xmipp.conf or SConscript or SConstruct?) > > (.scipion3env) [raozh@mgmt01 scipion3]$ conda list hdf5 > # packages in environment at /home/raozh/wtao/conda/miniconda/envs/.scipion3env: > # > # Name Version Build Channel > hdf5 1.10.7 hb1b8bf9_0 > > Anybody got any idea about this? > > Thanks for any help. > > Tao Wang > > Ph.D candidate, > > Tsinghua University > > here are logs: > > (.scipion3env) [raozh@mgmt01 scipion3]$ python3 -m scipioninstaller /home/raozh/wtao/scipion3/ -j 4 > conda detected. Favouring it. If you want a virtualenv installation cancel installation and pass --venv . > WARNING: A conda environment already exists at '/home/raozh/wtao/conda/miniconda/envs/.scipion3env' > Remove existing environment (y/[n])? > > > CondaSystemExit: Exiting. > > Requirement already satisfied: scipion-pyworkflow in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (3.0.4) > Requirement already satisfied: matplotlib<=3.2.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (3.2.2) > Requirement already satisfied: configparser<=5.0.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (5.0.0) > Requirement already satisfied: pillow<=7.1.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (7.1.2) > Requirement already satisfied: psutil<=5.7.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (5.7.0) > Requirement already satisfied: requests<=2.23.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (2.23.0) > Requirement already satisfied: numpy<=1.18.4 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (1.18.4) > Requirement already satisfied: bibtexparser<=1.2.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (1.2.0) > Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.4.7) > Requirement already satisfied: python-dateutil>=2.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.8.1) > Requirement already satisfied: kiwisolver>=1.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (1.2.0) > Requirement already satisfied: cycler>=0.10 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (0.10.0) > Requirement already satisfied: chardet<4,>=3.0.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (3.0.4) > Requirement already satisfied: certifi>=2017.4.17 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2020.6.20) > Requirement already satisfied: idna<3,>=2.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2.10) > Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (1.25.10) > Requirement already satisfied: future>=0.16.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow) (0.18.2) > Requirement already satisfied: six>=1.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from python-dateutil>=2.1->matplotlib<=3.2.2->scipion-pyworkflow) (1.15.0) > Requirement already satisfied: scipion-app in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (3.0.4) > Requirement already satisfied: scipion-em in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-app) (3.0.3) > Requirement already satisfied: outdated==0.2.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-app) (0.2.0) > Requirement already satisfied: scipion-pyworkflow in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em->scipion-app) (3.0.4) > Requirement already satisfied: biopython==1.76 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em->scipion-app) (1.76) > Requirement already satisfied: littleutils in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from outdated==0.2.0->scipion-app) (0.2.2) > Requirement already satisfied: requests in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from outdated==0.2.0->scipion-app) (2.23.0) > Requirement already satisfied: configparser<=5.0.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (5.0.0) > Requirement already satisfied: pillow<=7.1.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (7.1.2) > Requirement already satisfied: numpy<=1.18.4 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.18.4) > Requirement already satisfied: psutil<=5.7.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (5.7.0) > Requirement already satisfied: matplotlib<=3.2.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (3.2.2) > Requirement already satisfied: bibtexparser<=1.2.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.2.0) > Requirement already satisfied: idna<3,>=2.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (2.10) > Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (1.25.10) > Requirement already satisfied: certifi>=2017.4.17 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (2020.6.20) > Requirement already satisfied: chardet<4,>=3.0.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (3.0.4) > Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.4.7) > Requirement already satisfied: python-dateutil>=2.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.8.1) > Requirement already satisfied: cycler>=0.10 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (0.10.0) > Requirement already satisfied: kiwisolver>=1.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.2.0) > Requirement already satisfied: future>=0.16.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow->scipion-em->scipion-app) (0.18.2) > Requirement already satisfied: six>=1.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from python-dateutil>=2.1->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.15.0) > Scipion v3.0.4 () devel > > >>> WARNING: Image library not found! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) > > > Building scipion-em-xmipp ... > /home/raozh/wtao/conda/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-xmipp==20.7rc1 > Requirement already satisfied: scipion-em-xmipp==20.7rc1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (20.7rc1) > Requirement already satisfied: scons in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (4.0.1) > Requirement already satisfied: plotter in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (1.3.17) > Requirement already satisfied: joblib in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (0.17.0) > Requirement already satisfied: scikit-learn==0.22.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (0.22.1) > Requirement already satisfied: peppercorn in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (0.6) > Requirement already satisfied: setuptools in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scons->scipion-em-xmipp==20.7rc1) (49.6.0.post20200925) > Requirement already satisfied: numpy>=1.11.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7rc1) (1.18.4) > Requirement already satisfied: scipy>=0.17.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7rc1) (1.5.2) > Done (0.78 seconds) > Building xmippSrc-3.20.07rc ... > Skipping command: wget -nv -c -O /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07rc.tgz > mv -v /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc.tgz.part /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc.tgz > All targets exist. > Skipping command: tar -xf xmippSrc-v3.20.07rc.tgz > All targets exist. > cd /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc > cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srf build /home/raozh/wtao/scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null > Configuring ----------------------------------------- > gcc detected > g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include > OpenCV not found > rm -v xmipp_test_opencv* > > 'mpirun' and 'mpiexec' not found in the PATH > Using '/usr/lib64/openmpi/bin'. > > 'mpicc' not found in the PATH > Using '/usr/lib64/openmpi/bin'. > > 'mpicxx' not found in the PATH > Using '/usr/lib64/openmpi/bin'. > Java detected at: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64 > > 'nvcc' not found in the PATH (either in CUDA_BIN/XMIPP_CUDA_BIN) > Using '/usr/local/cuda/bin'. > CUDA-10.1.168 detected. > CUDA-8.0 is recommended. > Using '/usr/local/cuda-10.1/targets/x86_64-linux/lib'. > Configuration completed..... > Checking configuration ------------------------------ > Checking compiler configuration ... > g++ 4.8.5 detected > g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_main.cpp -o xmipp_test_main.o -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include/python3.8 -I/home/raozh/wtao/c > onda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/numpy/core/include g++ -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib xmipp_test_main.o -o xmipp_test_main -lfftw3 -lfftw3_threads -lhdf5 -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread > /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > rm xmipp_test_main* > Checking MPI configuration ... > /usr/lib64/openmpi/bin/mpicxx -c -w -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include -mtune=native -march=native -std=c++11 -O3 xmipp_mpi_test_main.cpp -o xmipp_mpi_test_main.o > /usr/lib64/openmpi/bin/mpicxx -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib xmipp_mpi_test_main.o -o xmipp_mpi_test_main -lfftw3 -lfftw3_threads -lhdf5 -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread > /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > rm xmipp_mpi_test_main* > /usr/lib64/openmpi/bin/mpirun -np 2 echo ' > This sentence should be printed 2 times if mpi runs fine.' > > This sentence should be printed 2 times if mpi runs fine. > > This sentence should be printed 2 times if mpi runs fine. > Checking Java configuration... > /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/bin/javac Xmipp.java > rm Xmipp.java Xmipp.class > g++ -c -w -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/include/linux -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include xmipp_jni_test.cpp -o xmipp_jn > i_test.o rm xmipp_jni_test* > Checking CUDA configuration ... > /usr/local/cuda-10.1/bin/nvcc -c -w --x cu -D_FORCE_INLINES -Xcompiler -fPIC -ccbin g++ -std=c++11 --expt-extended-lambda -gencode=arch=compute_30,code=compute_30 -gencode=arch=compute_35,code=compute_35 -gencode=arch=compute_50,code=compute_50 -gencod > e=arch=compute_60,code=compute_60 -gencode=arch=compute_61,code=compute_61 -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include xmipp_cuda_test.cpp -o xmipp_cuda_test.o /usr/local/cuda-10.1/bin/nvcc -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs xmipp_cuda_test.o -o xmipp_cuda_test -lcudart -lcublas -lcufft -lcurand -lcusparse -lnvToolsExt > g++ -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs xmipp_cuda_test.o -o xmipp_cuda_test -lcudart -lcublas -lcufft -lcurand -lcusparse -lnvToolsExt > rm xmipp_cuda_test* > Setting VERIFIED=True > Building Dependencies ------------------------------------- > make all > mkdir -p build/ > nvcc --cudart static -shared -link -Wno-deprecated-gpu-targets -o build/libcuFFTAdvisor.so obj/benchmarkResult.o obj/inputParser.o obj/transform.o obj/advisor.o obj/validator.o obj/cudaAsserts.o obj/transformGenerator.o obj/benchmarker.o obj/generalTran > sform.o obj/sizeOptimizer.o obj/main.omkdir -p build/ > nvcc -o build/cuFFTAdvisor obj/benchmarkResult.o obj/inputParser.o obj/transform.o obj/advisor.o obj/validator.o obj/cudaAsserts.o obj/transformGenerator.o obj/benchmarker.o obj/generalTransform.o obj/sizeOptimizer.o obj/main.o -lcufft -Wno-deprecated-g > pu-targets cp src/cuFFTAdvisor/build/libcuFFTAdvisor.so src/xmipp/lib/ > Compiling ------------------------------------------- > scons -j4 > scons: Reading SConscript files ... > scons: done reading SConscript files. > scons: Building targets ... > scons: `lib/libXmippCore.so' is up to date. > scons: `lib/xmippCore.so' is up to date. > scons: done building targets. > scons -j4 > scons: Reading SConscript files ... > scons: done reading SConscript files. > scons: Building targets ... > scons: `lib/libXmipp.so' is up to date. > scons: `lib/_swig_frm.so' is up to date. > scons: `lib/libXmippCuda.a' is up to date. > scons: `lib/libXmippInterfaceCuda.so' is up to date. > scons: `lib/libXmippParallelCuda.so' is up to date. > scons: `lib/libXmippParallel.so' is up to date. > g++ -o bin/xmipp_volume_from_pdb applications/programs/volume_from_pdb/volume_from_pdb_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib -lXmipp -lhd > f5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCoreg++ -o bin/xmipp_idr_xray_tomo applications/programs/idr_xray_tomo/idr_xray_tomo_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib -lXmipp -lhdf5 -lh > df5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCoreg++ -o bin/xmipp_image_separate_objects applications/programs/image_separate_objects/image_separate_objects_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion > 3env/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCoreg++ -o bin/xmipp_pdb_reduce_pseudoatoms applications/programs/pdb_reduce_pseudoatoms/pdb_reduce_pseudoatoms_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion > 3env/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore/usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' > lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' > /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' > collect2: error: ld returned 1 exit status > scons: *** [bin/xmipp_volume_from_pdb] Error 1 > /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' > lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' > /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' > collect2: error: ld returned 1 exit status > scons: *** [bin/xmipp_idr_xray_tomo] Error 1 > /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' > lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' > /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' > collect2: error: ld returned 1 exit status > scons: *** [bin/xmipp_image_separate_objects] Error 1 > /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' > lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' > /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' > collect2: error: ld returned 1 exit status > scons: *** [bin/xmipp_pdb_reduce_pseudoatoms] Error 1 > scons: building terminated because of errors. > > Some error occurred during the compilation of 'xmipp' ('bin/xmipp_pdb_reduce_pseudoatoms'). > > Traceback (most recent call last): > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 449, in <module> > main() > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 292, in main > installPluginMethods() > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods > plugin.installBin({'args': ['-j', numberProcessor]}) > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin > environment.execute() > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute > self._executeTargets(targetList) > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets > tgt.execute() > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 220, in execute > command.execute() > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 160, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target '/home/raozh/wtao/scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srf build /home/raozh/wtao/scip > ion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')Error at main: target '/home/raozh/wtao/scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srf build /home/raozh/wtao/scipi > on3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') > Something went wrong running: > eval "$(/home/raozh/wtao/conda/miniconda/condabin/conda shell.bash hook)" && > conda create -n .scipion3env python=3 && > conda activate .scipion3env && > cd /home/raozh/wtao/scipion3 && > mkdir -p software/lib && > mkdir -p software/bindings && > mkdir -p software/em && > export SCIPION_HOME=/home/raozh/wtao/scipion3 && > pip install scipion-pyworkflow && > pip install scipion-app && > python -m scipion installp -p scipion-em-xmipp -j 4 > Installation cancelled. > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Nicholas P. <pro...@gm...> - 2020-10-07 01:23:51
|
Dear all, I’m trying to use Localized Reconstruction plugin in Scipion 3. I imported particles from Relion 3.1, defined subparticles, filtered them and extracted with a new box size. Everything worked seemingly okay. But when I try and do 2D or 3D classification or 3D auto-refine the subparticles are treated as if they have the size of the original imported particles - 972 px instead of 168 px. For instance, in 3D auto-refine I have "ERROR The reference box size is 168 A, but the box size of the first optics group of the data is 972 A!” (which is btw not correct as the reference box size is 168 px and the pixel size is 1.1 A) Particles in particles.mrcs have correct dimensions and the problem seems to be in metadata. I opened particles.sqlite from the extraction job and it looks like every particle has its own relion optics group header. I changed rlnImageSize from 972 to 168 in all entries but still have the same error from 3D auto-refine when I try using corrected particles.sqlite. What would be the simplest way to overcome the bug? Thank you, Nikolai |
|
From: Roberto M. <ro...@cn...> - 2020-10-06 15:20:51
|
hi,
1) select analyze results
2) show classification in Scipion
3) select the class you are interested in
4) save the particles assigned to the class (+particles, red button)
5) close analyze
6) a new protocol appear, the output is the selected particles
7) select the new protocol
8) press analyze results
9) select tools -> avg & std images
10 you are done
On Tue, Oct 6, 2020 at 4:52 PM Dmitry A. Semchonok <sem...@gm...> wrote:
>
> Dear colleagues,
>
> Can we get the result relion 2D classification without mask?
> If yes then how?
>
> Thank you in advance.
>
> Sincerely,
> Dmitry
>
|
|
From: Dmitry A. S. <sem...@gm...> - 2020-10-06 14:53:02
|
Dear colleagues, Can we get the result relion 2D classification without mask? If yes then how? Thank you in advance. Sincerely, Dmitry |
|
From: Colin D. <ckd...@gm...> - 2020-10-05 16:25:17
|
Sure, I'd be happy to give it a whirl. Thanks! On Fri, Oct 2, 2020 at 11:43 PM <pc...@cn...> wrote: > I think we have implemented that functionality. Once reviewed and approved > we will release a new version with it. > > If you want to test it before that I can give you the command to install > the patch > > El 2 oct. 2020 23:20, Colin Deniston <ckd...@gm...> escribió: > > 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! > > On Fri, Oct 2, 2020 at 12:58 AM Pablo Conesa <pc...@cn...> wrote: > > Thanks Colin, see anwser in line. > On 1/10/20 23:49, Colin Deniston wrote: > > Hello, > > > > 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. > > > > 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? > > 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 issue > <https://github.com/scipion-em/scipion-pyworkflow/issues/151> and will > look at it: > > 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. > > 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) > > Do the box with the "wait for" turns orange (scheduled,this would be > correct) or green (running, thus not waiting)? > > > > 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! > > > > *Colin Deniston* > Principal Scientist I > > *GNF BIOTHERAPEUTICS & BIOTECHNOLOGY / GNF* > > Novartis Institutes for Biomed.Research, Inc. > > 10675 John Jay Hopkins Drive > > GNF Business > > San Diego, CA 92121 > > > > T +1 (858) 332-4750 > > cde...@gn... > > [image: https://saps-app.prd.nibr.novartis.net/esh/novartislogo.png] > <https://www.novartis.com/> > > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Pablo C. <pc...@cn...> - 2020-10-05 14:57:48
|
hi
On 5/10/20 16:22, Lugmayr, Wolfgang wrote:
> hi,
>
> now it works, but only if you have a "default" entry in the queue
> section of the hosts.conf. i have renamed this one and then the
> "Execute" selection does not work.
> maybe add a comment in the hosts.conf template.
Thanks Wolfgang, we then need to review this behavior. Certainly,
"default" shouldn't be "that important".
>
> i found also the "Edit" button beside the "Use queue" entry. so we can
> re-submit/continue also existing jobs to gpus or cpus depending what's
> available.
>
> good work ;-)
>
Thank you, it was a last addition based on other user/developer
feedback. Scipion3 is far more agile to incorporate new features quickly.
> cheers,
> wolfgang
All the best, Pablo
>
>
> ------------------------------------------------------------------------
> *From: *"Pablo Conesa" <pc...@cn...>
> *To: *"Mailing list for Scipion users"
> <sci...@li...>
> *Sent: *Monday, 5 October, 2020 12:15:24
> *Subject: *Re: [scipion-users] scipion 3.0.3+ does not support
> multiple queue configurations anymore?
>
> Hi Wolfgang ... we have recently added a new feature that is releated
> to the queue parameters.
>
> With the latest version you can edit the parameters before
> "executing/scheduling" the protocol.
>
> If they are populated (copying a protocol will keep the parameters)
> the user is not asked.
>
> We were currenlty discussing this, and Jose Miguel already suggested
> to ask, at least once to verify de queue parameters and we will do so.
>
> Maybe, with current code (3.0.4), you can remove the queue parameters
> in the template, so users will be asked. (I'm guessing you have
> queueParams poplated in your template)
>
> Does it make sense?
>
>
>
>
>
> On 5/10/20 11:29, Lugmayr, Wolfgang wrote:
>
> hi,
>
> we have 2 queues on our cluster, one for cpu jobs and one for gpu jobs.
> so far my template was working fine, but since 3.0.3 and now 3.0.4 scipion always takes the last entry in the QUEUES section of the hosts.conf file.
>
> before a window pop-up appeared after pressing the Execute button and users could choose which queue and which parameters they want to have.
> this defines the nodes the users will get.
>
> now the pop-up window is gone and the job script is generated with the settings of the last queue entry.
> in this case maxwell-gpu.
>
> QUEUES = {
> "maxwell-cpu": [
> ["JOB_QUEUE","cssb,all","Queue Name:","Select the target queue/partition"],
> ["JOB_TIME", "168", "Time (hours)", "Select the time expected (in hours) for this job"],
> ["JOB_NODES","48","Total cores:","MPI tasks"],
> ["JOB_CONS","Gold-6126","Constraints:","Call sinfo_detailed on the commandline for the options"]
> ],
> "maxwell-gpu": [
> ["JOB_QUEUE","cssbgpu,allgpu","Queue Name:","Select the target queue/partition"],
> ["JOB_TIME", "168", "Time (hours)", "Select the time expected (in hours) for this job"],
> ["JOB_NODES","1","Total cores:","1: Single program call with threads and no MPI"],
> ["JOB_CONS","GPUx1","Constraints:","Call sinfo_detailed on the commandline for the options"]
> ]
> }
>
> is there a new way to do this, so i have to update my template?
>
> cheers,
> wolfgang
>
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Lugmayr, W. <w.l...@uk...> - 2020-10-05 14:23:10
|
hi,
now it works, but only if you have a "default" entry in the queue section of the hosts.conf. i have renamed this one and then the "Execute" selection does not work.
maybe add a comment in the hosts.conf template.
i found also the "Edit" button beside the "Use queue" entry. so we can re-submit/continue also existing jobs to gpus or cpus depending what's available.
good work ;-)
cheers,
wolfgang
From: "Pablo Conesa" <pc...@cn...>
To: "Mailing list for Scipion users" <sci...@li...>
Sent: Monday, 5 October, 2020 12:15:24
Subject: Re: [scipion-users] scipion 3.0.3+ does not support multiple queue configurations anymore?
Hi Wolfgang ... we have recently added a new feature that is releated to the queue parameters.
With the latest version you can edit the parameters before "executing/scheduling" the protocol.
If they are populated (copying a protocol will keep the parameters) the user is not asked.
We were currenlty discussing this, and Jose Miguel already suggested to ask, at least once to verify de queue parameters and we will do so.
Maybe, with current code (3.0.4), you can remove the queue parameters in the template, so users will be asked. (I'm guessing you have queueParams poplated in your template)
Does it make sense?
On 5/10/20 11:29, Lugmayr, Wolfgang wrote:
hi,
we have 2 queues on our cluster, one for cpu jobs and one for gpu jobs.
so far my template was working fine, but since 3.0.3 and now 3.0.4 scipion always takes the last entry in the QUEUES section of the hosts.conf file.
before a window pop-up appeared after pressing the Execute button and users could choose which queue and which parameters they want to have.
this defines the nodes the users will get.
now the pop-up window is gone and the job script is generated with the settings of the last queue entry.
in this case maxwell-gpu.
QUEUES = {
"maxwell-cpu": [
["JOB_QUEUE","cssb,all","Queue Name:","Select the target queue/partition"],
["JOB_TIME", "168", "Time (hours)", "Select the time expected (in hours) for this job"],
["JOB_NODES","48","Total cores:","MPI tasks"],
["JOB_CONS","Gold-6126","Constraints:","Call sinfo_detailed on the commandline for the options"]
],
"maxwell-gpu": [
["JOB_QUEUE","cssbgpu,allgpu","Queue Name:","Select the target queue/partition"],
["JOB_TIME", "168", "Time (hours)", "Select the time expected (in hours) for this job"],
["JOB_NODES","1","Total cores:","1: Single program call with threads and no MPI"],
["JOB_CONS","GPUx1","Constraints:","Call sinfo_detailed on the commandline for the options"]
]
}
is there a new way to do this, so i have to update my template?
cheers,
wolfgang
--
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team
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