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From: 范宏成 <187...@16...> - 2021-06-21 02:07:39
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Hi Grigory and Pablo, Thanks for your response and help! I will try it Best regards, Hongcheng Fan | | 范宏成 | | m18...@16... | 签名由网易邮箱大师定制 On 6/21/2021 04:49，<pc...@cn...> wrote： You're great! This is called fast response time! I actually didn't know there was a cryoEF plugin. 🤦♂️ El 20 jun. 2021 15:22, Grigory Sharov <sha...@gm...> escribió: Hi again, I've added the color plot in the new cryoEF plugin release (3.0.12), which should be available in a few minutes. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 e-mail: gs...@mr... On Fri, Jun 18, 2021 at 11:45 AM Pablo Conesa <pc...@cn...> wrote: Thanks! this is an interesting plot. Not yet available in Scipion, but I guess doable. On 18/6/21 10:10, 范宏成 wrote: Dear colleagues, I recently used the cryo-EF program in Scipion to try to quantify my protein's orientation distribution. I found it very useful compared to relion-orientation output and told me whether the preferential orientation influenced my protein's high resolution structure determination when using the single particle analysis. Recently, I found this paper <<Multifunctional graphene supports for electron cryomicroscopy>>. The Figure3 ( Mapping the surface interaction profile of the 30S ribosomal subunit on a multifunctional graphene grid) was impressive. However, I found the cryoEF output was a single color picture ( see my result in the attachment, I already had the pdb model). I am curious about how to draw this multi-color picture (especially for the surface interaction site) based on the cryo-EF results . I did't find this in the cryoEF output folder. Does anyone have some ideas or other programs in scipion which can help me find the preferential orientation site (euler angles values). Thank you! Best regards, Hongcheng Fan | | 范宏成 | | m18...@16... | 签名由 网易邮箱大师 定制 _______________________________________________ scipion-users mailing list sci...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - Madrid Scipion team _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: <pc...@cn...> - 2021-06-20 20:49:08
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<div dir='auto'>You're great! This is called fast response time!<div dir="auto"><br></div><div dir="auto">I actually didn't know there was a cryoEF plugin.</div><div dir="auto"><br></div><div dir="auto">🤦♂️</div></div><div class="gmail_extra"><br><div class="gmail_quote">El 20 jun. 2021 15:22, Grigory Sharov <sha...@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">Hi again,<div><br /></div><div>I've added the color plot in the new cryoEF plugin release (3.0.12), which should be available in a few minutes.</div><div><br clear="all" /><div><div dir="ltr" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div style="color:rgb( 0 , 0 , 0 )"><font face="arial, helvetica, sans-serif" size="2"><span style="font-size:10pt">Best regards,<br />Grigory</span></font></div><div style="color:rgb( 0 , 0 , 0 )"><font face="arial, helvetica, sans-serif" size="2"><span style="font-size:10pt"><br /></span></font></div><div style="color:rgb( 0 , 0 , 0 )"><font face="arial, helvetica, sans-serif" size="2"><span style="font-size:10pt">--------------------------------------------------------------------------------</span></font></div><div style="color:rgb( 0 , 0 , 0 )"><span style="font-size:12.8px">Grigory Sharov, Ph.D.</span><br style="font-size:12.8px" /><br style="font-size:12.8px" /><span style="font-size:12.8px">MRC Laboratory of Molecular Biology,</span><br style="font-size:12.8px" /><span style="font-size:12.8px">Francis Crick Avenue,</span><br style="font-size:12.8px" /><span style="font-size:12.8px">Cambridge Biomedical Campus,</span><br style="font-size:12.8px" /><span style="font-size:12.8px">Cambridge CB2 0QH, UK.</span><br style="font-size:12.8px" /><span style="font-size:12.8px">tel. </span><a href="tel:+44%201223%20267228" style="color:rgb( 17 , 85 , 204 );font-size:12.8px">+44 (0) 1223 267228</a></div><div style="color:rgb( 0 , 0 , 0 )"><span style="font-size:12.8px">e-mail: </span><a href="mailto:gsharov@mrc-lmb.cam.ac.uk" style="color:rgb( 17 , 85 , 204 );font-size:12.8px">gsharov@mrc-lmb.cam.ac.uk</a><br /></div></div></div></div></div></div></div></div></div></div></div></div></div><br /></div></div><br /><div class="elided-text"><div dir="ltr">On Fri, Jun 18, 2021 at 11:45 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! this is an interesting plot. Not yet available in Scipion, but I guess doable.<br /> </p> <div>On 18/6/21 10:10, 范宏成 wrote:<br /> </div> <blockquote> <div> <div> <div> <div style="font-family:'微软雅黑' , 'verdana' , 'microsoft yahei' , 'simsun' , sans-serif;line-height:22.4px;color:rgb( 49 , 53 , 59 )">Dear colleagues<span style="line-height:1.6">,</span></div> <div style="font-family:'微软雅黑' , 'verdana' , 'microsoft yahei' , 'simsun' , sans-serif;line-height:22.4px"><font style="color:rgb( 49 , 53 , 59 )" face="Arial"><span style="line-height:23.8px">I recently used the cryo-EF program in Scipion to try to quantify my protein's orientation distribution. I found it very useful compared to relion-orientation output and told me whether the preferential orientation influenced my protein's high resolution structure determination when using the single particle analysis. Recently, I found this paper <<</span></font><span style="color:rgb( 49 , 53 , 59 );font-family:'arial';line-height:23.8px">Multifunctional graphene supports for electron cryomicroscopy>>. The Figure3 ( </span><span style="color:rgb( 49 , 53 , 59 );font-family:'arial';line-height:1.7">Mapping the surface interaction profile of the 30S ribosomal subunit on a multifunctional graphene grid) was impressive. However, I found the cryoEF output was a single color picture ( see my result in the attachment, I already had the pdb model). I am curious about how to draw this multi-color picture (especially for the surface interaction site) based on the cryo-EF results . </span> <span style="color:rgb( 49 , 53 , 59 );font-family:'arial';line-height:1.7">I did't find this in the cryoEF output folder. Does anyone have some ideas or other programs in scipion which can help me find the preferential orientation site (euler angles values). Thank you! </span></div> <div style="font-family:'微软雅黑' , 'verdana' , 'microsoft yahei' , 'simsun' , sans-serif;line-height:22.4px;color:rgb( 49 , 53 , 59 )"><span style="line-height:1.7;font-family:'arial'">Best regards,</span></div> <div style="font-family:'微软雅黑' , 'verdana' , 'microsoft yahei' , 'simsun' , sans-serif;line-height:22.4px;color:rgb( 49 , 53 , 59 )"><font face="Arial"><span style="line-height:23.8px">Hongcheng Fan</span></font></div> </div> <div> <br /> </div> <div style="font-family:'微软雅黑'"> <div style="font-size:14px;padding:0px;margin:0px;line-height:14px"> <div style="padding-bottom:6px;margin-bottom:10px;border-bottom:1px solid rgb( 230 , 230 , 230 );display:inline-block"> <a href="https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=%E8%8C%83%E5%AE%8F%E6%88%90&uid=m18717124574%40163.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fsm9cc9cc9db2766bf0072c27595c17827b.jpg&items=%5B%22m18717124574%40163.com%22%5D" style="display:block;background:rgb( 255 , 255 , 255 );max-width:400px;padding:15px 0px 10px;text-decoration:none;outline:none"> <table style="width:100%;max-width:100%;table-layout:fixed;border-collapse:collapse;color:rgb( 155 , 158 , 161 );font-size:14px;line-height:1.3" cellpadding="0"><tbody><tr><td style="padding:0px;width:38px" width="38"> <img style="vertical-align:middle;width:38px;height:38px;border-radius:50%" src="https://mail-online.nosdn.127.net/sm9cc9cc9db2766bf0072c27595c17827b.jpg" width="38" height="38" /> </td><td style="padding:0px 0px 0px 10px;color:rgb( 49 , 53 , 59 )"> <div style="font-size:16px;font-weight:bold;width:100%;white-space:nowrap;text-overflow:ellipsis">范宏成</div> </td></tr><tr style="width:100%;font-size:14px"><td colspan="2" style="padding:10px 0px 0px;width:100%;font-size:14px"> <div style="width:100%;font-size:14px">m18717124574@163.com</div> </td></tr></tbody></table> </a> </div> </div> <div style="font-size:12px;color:rgb( 181 , 185 , 189 );line-height:18px"> 签名由 <a style="text-decoration:none;color:rgb( 65 , 150 , 255 );padding:0px 5px" href="https://mail.163.com/dashi/dlpro.html?from=mail81">网易邮箱大师</a> 定制 </div> </div> </div> </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> |
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From: Grigory S. <sha...@gm...> - 2021-06-20 13:23:10
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Hi again, I've added the color plot in the new cryoEF plugin release (3.0.12), which should be available in a few minutes. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Fri, Jun 18, 2021 at 11:45 AM Pablo Conesa <pc...@cn...> wrote: > Thanks! this is an interesting plot. Not yet available in Scipion, but I > guess doable. > On 18/6/21 10:10, 范宏成 wrote: > > Dear colleagues, > I recently used the cryo-EF program in Scipion to try to quantify my > protein's orientation distribution. I found it very useful compared to > relion-orientation output and told me whether the preferential orientation > influenced my protein's high resolution structure determination when using > the single particle analysis. Recently, I found this paper <<Multifunctional > graphene supports for electron cryomicroscopy>>. The Figure3 ( Mapping > the surface interaction profile of the 30S ribosomal subunit on a > multifunctional graphene grid) was impressive. However, I found the cryoEF > output was a single color picture ( see my result in the attachment, I > already had the pdb model). I am curious about how to draw this > multi-color picture (especially for the surface interaction site) based > on the cryo-EF results . I did't find this in the cryoEF output folder. > Does anyone have some ideas or other programs in scipion which can help me > find the preferential orientation site (euler angles values). Thank you! > Best regards, > Hongcheng Fan > > 范宏成 > m18...@16... > > <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=%E8%8C%83%E5%AE%8F%E6%88%90&uid=m18717124574%40163.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fsm9cc9cc9db2766bf0072c27595c17827b.jpg&items=%5B%22m18717124574%40163.com%22%5D> > 签名由 网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail81> 定制 > > > _______________________________________________ > 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 > |
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From: Pablo C. <pc...@cn...> - 2021-06-18 10:45:38
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Thanks! this is an interesting plot. Not yet available in Scipion, but I guess doable. On 18/6/21 10:10, 范宏成 wrote: > Dear colleagues, > I recently used the cryo-EF program in Scipion to try to quantify my > protein's orientation distribution. I found it very useful compared to > relion-orientation output and told me whether the preferential > orientation influenced my protein's high resolution structure > determination when using the single particle analysis. Recently, I > found this paper <<Multifunctional graphene supports for electron > cryomicroscopy>>. The Figure3 ( Mapping the surface interaction > profile of the 30S ribosomal subunit on a multifunctional graphene > grid) was impressive. However, I found the cryoEF output was a > single color picture ( see my result in the attachment, I already had > the pdb model). I am curious about how to draw this multi-color > picture (especially for the surface interaction site) based on the > cryo-EF results . I did't find this in the cryoEF output folder. Does > anyone have some ideas or other programs in scipion which can help me > find the preferential orientation site (euler angles values). Thank you! > Best regards, > Hongcheng Fan > > > 范宏成 > m18...@16... > > <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=%E8%8C%83%E5%AE%8F%E6%88%90&uid=m18717124574%40163.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fsm9cc9cc9db2766bf0072c27595c17827b.jpg&items=%5B%22m18717124574%40163.com%22%5D> > > 签名由 网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail81> > 定制 > > > _______________________________________________ > 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: Grigory S. <sha...@gm...> - 2021-06-18 08:36:23
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Hello Hongcheng, The color plot is currently not implemented in Scipion, thank you for letting me know about it. In the meantime you can use PlotOD.py script from https://www.mrc-lmb.cam.ac.uk/crusso/cryoEF/downloads.html to generat such a plot yourself. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Fri, Jun 18, 2021 at 9:13 AM 范宏成 <187...@16...> wrote: > Dear colleagues, > I recently used the cryo-EF program in Scipion to try to quantify my > protein's orientation distribution. I found it very useful compared to > relion-orientation output and told me whether the preferential orientation > influenced my protein's high resolution structure determination when using > the single particle analysis. Recently, I found this paper <<Multifunctional > graphene supports for electron cryomicroscopy>>. The Figure3 ( Mapping > the surface interaction profile of the 30S ribosomal subunit on a > multifunctional graphene grid) was impressive. However, I found the cryoEF > output was a single color picture ( see my result in the attachment, I > already had the pdb model). I am curious about how to draw this > multi-color picture (especially for the surface interaction site) based > on the cryo-EF results . I did't find this in the cryoEF output folder. > Does anyone have some ideas or other programs in scipion which can help me > find the preferential orientation site (euler angles values). Thank you! > Best regards, > Hongcheng Fan > > 范宏成 > m18...@16... > > <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=%E8%8C%83%E5%AE%8F%E6%88%90&uid=m18717124574%40163.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fsm9cc9cc9db2766bf0072c27595c17827b.jpg&items=%5B%22m18717124574%40163.com%22%5D> > 签名由 网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail81> 定制 > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: 范宏成 <187...@16...> - 2021-06-18 08:11:03
|
Dear colleagues, I recently used the cryo-EF program in Scipion to try to quantify my protein's orientation distribution. I found it very useful compared to relion-orientation output and told me whether the preferential orientation influenced my protein's high resolution structure determination when using the single particle analysis. Recently, I found this paper <<Multifunctional graphene supports for electron cryomicroscopy>>. The Figure3 ( Mapping the surface interaction profile of the 30S ribosomal subunit on a multifunctional graphene grid) was impressive. However, I found the cryoEF output was a single color picture ( see my result in the attachment, I already had the pdb model). I am curious about how to draw this multi-color picture (especially for the surface interaction site) based on the cryo-EF results . I did't find this in the cryoEF output folder. Does anyone have some ideas or other programs in scipion which can help me find the preferential orientation site (euler angles values). Thank you! Best regards, Hongcheng Fan | | 范宏成 | | m18...@16... | 签名由网易邮箱大师定制 |
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From: Dmitry A. S. <sem...@gm...> - 2021-06-10 19:52:44
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<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><!--[if !mso]><style>v\:* {behavior:url(#default#VML);} o\:* {behavior:url(#default#VML);} w\:* {behavior:url(#default#VML);} .shape {behavior:url(#default#VML);} </style><![endif]--><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal><span lang=EN-GB>NO, not yet.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>That is the next thing I plan to do.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Thank you!<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>I will check the RAM while running the polishing protocol.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Sincerely,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>Dmitry</span><o:p></o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><b>From: </b><a href="mailto:sha...@gm...">Grigory Sharov</a><br><b>Sent: </b>Thursday, June 10, 2021 9:36 PM<br><b>To: </b><a href="mailto:sci...@li...">Mailing list for Scipion users</a><br><b>Subject: </b>Re: [scipion-users] Bayesian polishing</p></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>I see, thanks for the clarification. Have you tried to run with all frames (default) but with a smaller particle subset, e.g. 3000-5000 particles?</p><div><p class=MsoNormal>You can monitor RAM usage when the protocol starts to see if that is an issue.</p></div><div><p class=MsoNormal><br clear=all></p><div><div><div><div><div><div><div><div><div><div><div><div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>Best regards,<br>Grigory</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>--------------------------------------------------------------------------------</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.5pt;color:black'>Grigory Sharov, Ph.D.<br><br>MRC Laboratory of Molecular Biology,<br>Francis Crick Avenue,<br>Cambridge Biomedical Campus,<br>Cambridge CB2 0QH, UK.<br>tel. </span><span style='color:black'><a href="tel:+44%201223%20267228" target="_blank"><span style='font-size:9.5pt;color:#1155CC'>+44 (0) 1223 267228</span></a><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.5pt;color:black'>e-mail: </span><span style='color:black'><a href="mailto:gs...@mr..." target="_blank"><span style='font-size:9.5pt;color:#1155CC'>gs...@mr...</span></a><o:p></o:p></span></p></div></div></div></div></div></div></div></div></div></div></div></div></div><p class=MsoNormal><o:p> </o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Thu, Jun 10, 2021 at 8:32 PM Dmitry A. Semchonok <<a href="mailto:sem...@gm...">sem...@gm...</a>> wrote:</p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB>Sorry Grigory,</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB> </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB>I would have explained that abbreviation. </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB>This means a) 1 movie frame and b) 5 movie frames.</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB> </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB>a)</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><img border=0 width=369 height=255 style='width:3.8385in;height:2.651in' id="gmail-m_3230183901105949274Picture_x0020_3" src="cid:image005.png@01D75E42.E7190CB0"></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><img border=0 width=234 height=233 style='width:2.4322in;height:2.4218in' id="gmail-m_3230183901105949274Picture_x0020_4" src="cid:image006.png@01D75E42.E7190CB0"></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB> </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB>And even with Threads 1 MPI 1 the 5 movie frames fail</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB> </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><img border=0 width=362 height=238 style='width:3.7656in;height:2.4739in' id="gmail-m_3230183901105949274Picture_x0020_5" src="cid:image007.png@01D75E42.E7190CB0"></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><img border=0 width=1213 height=176 style='width:12.6302in;height:1.8333in' id="gmail-m_3230183901105949274Picture_x0020_6" src="cid:image008.png@01D75E42.E7190CB0"></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB> </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB>Thanks again</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB> </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB> </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB> </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB>Sincerely,</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB>Dmitry</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986" target="_blank">Mail</a> for Windows 10</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b>From: </b><a href="mailto:sha...@gm..." target="_blank">Grigory Sharov</a><br><b>Sent: </b>Thursday, June 10, 2021 8:27 PM<br><b>To: </b><a href="mailto:sci...@li..." target="_blank">Mailing list for Scipion users</a><br><b>Subject: </b>Re: [scipion-users] Bayesian polishing</p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I have no idea what 1e or 5e means, I see you are using 14 threads..</p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><br clear=all></p><div><div><div><div><div><div><div><div><div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>Best regards,<br>Grigory</span></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:black'> </span></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>--------------------------------------------------------------------------------</span></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:9.5pt;color:black'>Grigory Sharov, Ph.D.<br><br>MRC Laboratory of Molecular Biology,<br>Francis Crick Avenue,<br>Cambridge Biomedical Campus,<br>Cambridge CB2 0QH, UK.<br>tel. </span><span style='color:black'><a href="tel:+44%201223%20267228" target="_blank"><span style='font-size:9.5pt;color:#1155CC'>+44 (0) 1223 267228</span></a></span></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:9.5pt;color:black'>e-mail: </span><span style='color:black'><a href="mailto:gs...@mr..." target="_blank"><span style='font-size:9.5pt;color:#1155CC'>gs...@mr...</span></a></span></p></div></div></div></div></div></div></div></div></div></div></div></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>On Thu, Jun 10, 2021 at 7:25 PM Dmitry A. Semchonok <<a href="mailto:sem...@gm..." target="_blank">sem...@gm...</a>> wrote:</p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0in;margin-bottom:5.0pt'><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Thank you Grigory,</p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>The interesting point is that if the one uses 1e - the process finishes without error.</p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>But 5e seems too be too much. </p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Sincerely,</p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dmitry</p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div><div id="gmail-m_3230183901105949274gmail-m_-6395269166704044080aqm-original"><div><div><p style='margin-bottom:8.0pt'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>On June 10, 2021 5:20:06 PM Grigory Sharov <<a href="mailto:sha...@gm..." target="_blank">sha...@gm...</a>> wrote:</span></p><blockquote style='border:none;border-left:solid gray 1.0pt;padding:0in 0in 0in 5.0pt;margin-left:4.5pt;margin-top:5.0pt;margin-right:0in;margin-bottom:5.0pt'><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:black'>Hi Dmitry,</span></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:black'> </span></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:black'>I think you posted a similar error before. You are using too many particles for training and running out of RAM, hence your process is killed by Linux kernel.</span></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:black'><br clear=all></span></p><div><div><div><div><div><div><div><div><div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>Best regards,<br>Grigory</span></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:black'> </span></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>--------------------------------------------------------------------------------</span></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:9.5pt;color:black'>Grigory Sharov, Ph.D.<br><br>MRC Laboratory of Molecular Biology,<br>Francis Crick Avenue,<br>Cambridge Biomedical Campus,<br>Cambridge CB2 0QH, UK.<br>tel. </span><span style='color:black'><a href="tel:+44%201223%20267228" target="_blank"><span style='font-size:9.5pt;color:#1155CC'>+44 (0) 1223 267228</span></a></span></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:9.5pt;color:black'>e-mail: </span><span style='color:black'><a href="mailto:gs...@mr..." target="_blank"><span style='font-size:9.5pt;color:#1155CC'>gs...@mr...</span></a></span></p></div></div></div></div></div></div></div></div></div></div></div></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:black'> </span></p></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:black'> </span></p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:black'>On Thu, Jun 10, 2021 at 4:02 PM Dmitry Semchonok <<a href="mailto:Sem...@gm..." target="_blank">Sem...@gm...</a>> wrote:</span></p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0in;margin-bottom:5.0pt'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:black'>Dear colleagues,<br><br>After running Bayesian polishing script with 5e I got the following error<br><br><br><br>2232: GridSquare_26409500_Data_FoilHole_26633166_Data_26416121_26416123_20210330_110202_Fractions.mrc<br>02591: 1914: GridSquare_26409382_Data_FoilHole_26635345_Data_26416121_26416123_20210330_172633_Fractions.mrc<br>02592: 1985: GridSquare_26409382_Data_FoilHole_26635480_Data_26416121_26416123_20210330_201730_Fractions.mrc<br>02593: 2253: GridSquare_26409500_Data_FoilHole_26633222_Data_26416121_26416123_20210330_123213_Fractions.mrc<br>02594: 1404: GridSquare_26409268_Data_FoilHole_26621354_Data_26416121_26416123_20210329_092746_Fractions.mrc<br>02595: 361: GridSquare_26409080_Data_FoilHole_26614677_Data_26416121_26416123_20210328_095659_Fractions.mrc<br>02596: <br>02597: - Warning: this dataset does not contain 217187 particles (--min_p) in micrographs with at least 2 particles<br>02598: + preparing alignment data... <br>02599: Traceback (most recent call last):<br>02600: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run<br>02601: self._run()<br>02602: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run<br>02603: resultFiles = self._runFunc()<br>02604: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc<br>02605: return self._func(*self._args)<br>02606: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", line 351, in trainOrPolishStep<br>02607: self.runJob(self._getProgram('relion_motion_refine'), args)<br>02608: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1388, in runJob<br>02609: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)<br>02610: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob<br>02611: process.runJob(log, programName, params,<br>02612: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob<br>02613: return runCommand(command, env, cwd)<br>02614: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand<br>02615: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,<br>02616: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call<br>02617: raise CalledProcessError(retcode, cmd)<br>02618: subprocess.CalledProcessError: Command ' relion_motion_refine --i Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o Runs/004833_ProtRelionBayesianPolishing/extra --f Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.59200 --corr_mic Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>.<br>02619: Protocol failed: Command ' relion_motion_refine --i Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o Runs/004833_ProtRelionBayesianPolishing/extra --f Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.59200 --corr_mic Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>.<br>02620: FAILED: trainOrPolishStep, step 2, time 2021-06-09 11:27:00.176491<br>02621: *** Last status is failed <br>02622: ------------------- PROTOCOL FAILED (DONE 2/2)<br><br>Do you know how to fix that?<br><br><br>Thank you<br><br>Sincerely,<br>Dmitry<br><br><br><br><br>_______________________________________________<br>scipion-users mailing list<br><a href="mailto:sci...@li..." target="_blank">sci...@li...</a><br><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users" target="_blank">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></span></p></blockquote></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:black'>_______________________________________________</span></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:black'>scipion-users mailing list</span></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:black'><a href="mailto:scipion-users%40lists.sourceforge.net" target="_blank">sci...@li...</a></span></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:black'><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users" target="_blank">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></span></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:black'> </span></p></div></blockquote></div></div></div></div></div></blockquote></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:4.8pt'> </p></div></div></blockquote></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:4.8pt'> </p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
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From: Grigory S. <sha...@gm...> - 2021-06-10 19:36:31
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I see, thanks for the clarification. Have you tried to run with all frames (default) but with a smaller particle subset, e.g. 3000-5000 particles? You can monitor RAM usage when the protocol starts to see if that is an issue. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Jun 10, 2021 at 8:32 PM Dmitry A. Semchonok <sem...@gm...> wrote: > Sorry Grigory, > > > > I would have explained that abbreviation. > > This means a) 1 movie frame and b) 5 movie frames. > > > > a) > > > > And even with Threads 1 MPI 1 the 5 movie frames fail > > > > > > Thanks again > > > > > > > > Sincerely, > > Dmitry > > > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > *From: *Grigory Sharov <sha...@gm...> > *Sent: *Thursday, June 10, 2021 8:27 PM > *To: *Mailing list for Scipion users <sci...@li...> > *Subject: *Re: [scipion-users] Bayesian polishing > > > > I have no idea what 1e or 5e means, I see you are using 14 threads.. > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Thu, Jun 10, 2021 at 7:25 PM Dmitry A. Semchonok <sem...@gm...> > wrote: > > Thank you Grigory, > > > > The interesting point is that if the one uses 1e - the process finishes > without error. > > But 5e seems too be too much. > > > > Sincerely, > > Dmitry > > > > On June 10, 2021 5:20:06 PM Grigory Sharov <sha...@gm...> > wrote: > > Hi Dmitry, > > > > I think you posted a similar error before. You are using too many > particles for training and running out of RAM, hence your process is > killed by Linux kernel. > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Thu, Jun 10, 2021 at 4:02 PM Dmitry Semchonok <Sem...@gm...> > wrote: > > Dear colleagues, > > After running Bayesian polishing script with 5e I got the following error > > > > 2232: > GridSquare_26409500_Data_FoilHole_26633166_Data_26416121_26416123_20210330_110202_Fractions.mrc > 02591: 1914: > GridSquare_26409382_Data_FoilHole_26635345_Data_26416121_26416123_20210330_172633_Fractions.mrc > 02592: 1985: > GridSquare_26409382_Data_FoilHole_26635480_Data_26416121_26416123_20210330_201730_Fractions.mrc > 02593: 2253: > GridSquare_26409500_Data_FoilHole_26633222_Data_26416121_26416123_20210330_123213_Fractions.mrc > 02594: 1404: > GridSquare_26409268_Data_FoilHole_26621354_Data_26416121_26416123_20210329_092746_Fractions.mrc > 02595: 361: > GridSquare_26409080_Data_FoilHole_26614677_Data_26416121_26416123_20210328_095659_Fractions.mrc > 02596: > 02597: - Warning: this dataset does not contain 217187 particles > (--min_p) in micrographs with at least 2 particles > 02598: + preparing alignment data... > 02599: Traceback (most recent call last): > 02600: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 197, in run > 02601: self._run() > 02602: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 248, in _run > 02603: resultFiles = self._runFunc() > 02604: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 244, in _runFunc > 02605: return self._func(*self._args) > 02606: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", > line 351, in trainOrPolishStep > 02607: self.runJob(self._getProgram('relion_motion_refine'), args) > 02608: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 1388, in runJob > 02609: self._stepsExecutor.runJob(self._log, program, arguments, > **kwargs) > 02610: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", > line 65, in runJob > 02611: process.runJob(log, programName, params, > 02612: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 52, in runJob > 02613: return runCommand(command, env, cwd) > 02614: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 67, in runCommand > 02615: check_call(command, shell=True, stdout=sys.stdout, > stderr=sys.stderr, > 02616: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, > in check_call > 02617: raise CalledProcessError(retcode, cmd) > 02618: subprocess.CalledProcessError: Command ' relion_motion_refine --i > Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o > Runs/004833_ProtRelionBayesianPolishing/extra --f > Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref > 0.59200 --corr_mic > Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star > --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500 > --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>. > 02619: Protocol failed: Command ' relion_motion_refine --i > Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o > Runs/004833_ProtRelionBayesianPolishing/extra --f > Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref > 0.59200 --corr_mic > Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star > --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500 > --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>. > 02620: FAILED: trainOrPolishStep, step 2, time 2021-06-09 11:27:00.176491 > 02621: *** Last status is failed > 02622: ------------------- PROTOCOL FAILED (DONE 2/2) > > Do you know how to fix that? > > > Thank you > > Sincerely, > Dmitry > > > > > _______________________________________________ > 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: Dmitry A. S. <sem...@gm...> - 2021-06-10 19:32:16
|
<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><!--[if !mso]><style>v\:* {behavior:url(#default#VML);} o\:* {behavior:url(#default#VML);} w\:* {behavior:url(#default#VML);} .shape {behavior:url(#default#VML);} </style><![endif]--><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal><span lang=EN-GB>Sorry Grigory,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>I would have explained that abbreviation. <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>This means a) 1 movie frame and b) 5 movie frames.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>a)<o:p></o:p></span></p><p class=MsoNormal><img width=368 height=254 style='width:3.8333in;height:2.6458in' id="Picture_x0020_3" src="cid:image003.png@01D75E40.0C29E8B0"><span lang=EN-GB><o:p></o:p></span></p><p class=MsoNormal><img width=233 height=232 style='width:2.427in;height:2.4166in' id="Picture_x0020_4" src="cid:image005.png@01D75E40.0C29E8B0"><span lang=EN-GB><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>And even with Threads 1 MPI 1 the 5 movie frames fail<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><img width=361 height=237 style='width:3.7604in;height:2.4635in' id="Picture_x0020_5" src="cid:image008.png@01D75E40.0C29E8B0"><span lang=EN-GB><o:p></o:p></span></p><p class=MsoNormal><img width=1212 height=176 style='width:12.625in;height:1.8281in' id="Picture_x0020_6" src="cid:image012.png@01D75E40.0C29E8B0"><span lang=EN-GB><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Thanks again<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Sincerely,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>Dmitry<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><b>From: </b><a href="mailto:sha...@gm...">Grigory Sharov</a><br><b>Sent: </b>Thursday, June 10, 2021 8:27 PM<br><b>To: </b><a href="mailto:sci...@li...">Mailing list for Scipion users</a><br><b>Subject: </b>Re: [scipion-users] Bayesian polishing</p></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>I have no idea what 1e or 5e means, I see you are using 14 threads..</p><div><p class=MsoNormal><br clear=all></p><div><div><div><div><div><div><div><div><div><div><div><div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>Best regards,<br>Grigory</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>--------------------------------------------------------------------------------</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.5pt;color:black'>Grigory Sharov, Ph.D.<br><br>MRC Laboratory of Molecular Biology,<br>Francis Crick Avenue,<br>Cambridge Biomedical Campus,<br>Cambridge CB2 0QH, UK.<br>tel. </span><span style='color:black'><a href="tel:+44%201223%20267228" target="_blank"><span style='font-size:9.5pt;color:#1155CC'>+44 (0) 1223 267228</span></a><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.5pt;color:black'>e-mail: </span><span style='color:black'><a href="mailto:gs...@mr..." target="_blank"><span style='font-size:9.5pt;color:#1155CC'>gs...@mr...</span></a><o:p></o:p></span></p></div></div></div></div></div></div></div></div></div></div></div></div></div><p class=MsoNormal><o:p> </o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Thu, Jun 10, 2021 at 7:25 PM Dmitry A. Semchonok <<a href="mailto:sem...@gm...">sem...@gm...</a>> wrote:</p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><div><div><p class=MsoNormal>Thank you Grigory,</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>The interesting point is that if the one uses 1e - the process finishes without error.</p></div><div><p class=MsoNormal>But 5e seems too be too much. </p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Sincerely,</p></div><div><p class=MsoNormal>Dmitry</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div id="gmail-m_-6395269166704044080aqm-original"><div><div><p style='mso-margin-top-alt:8.0pt;margin-right:0in;margin-bottom:8.0pt;margin-left:0in'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>On June 10, 2021 5:20:06 PM Grigory Sharov <<a href="mailto:sha...@gm..." target="_blank">sha...@gm...</a>> wrote:<o:p></o:p></span></p><blockquote style='border:none;border-left:solid gray 1.0pt;padding:0in 0in 0in 5.0pt;margin-left:4.5pt;margin-right:0in'><div><p class=MsoNormal><span style='color:black'>Hi Dmitry,</span><span style='color:black'><o:p></o:p></span></p><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>I think you posted a similar error before. You are using too many particles for training and running out of RAM, hence your process is killed by Linux kernel.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><br clear=all><o:p></o:p></span></p><div><div><div><div><div><div><div><div><div><div><div><div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>Best regards,<br>Grigory</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>--------------------------------------------------------------------------------</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.5pt;color:black'>Grigory Sharov, Ph.D.<br><br>MRC Laboratory of Molecular Biology,<br>Francis Crick Avenue,<br>Cambridge Biomedical Campus,<br>Cambridge CB2 0QH, UK.<br>tel. </span><span style='color:black'><a href="tel:+44%201223%20267228" target="_blank"><span style='font-size:9.5pt;color:#1155CC'>+44 (0) 1223 267228</span></a><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.5pt;color:black'>e-mail: </span><span style='color:black'><a href="mailto:gs...@mr..." target="_blank"><span style='font-size:9.5pt;color:#1155CC'>gs...@mr...</span></a><o:p></o:p></span></p></div></div></div></div></div></div></div></div></div></div></div></div></div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div></div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p><div><div><p class=MsoNormal><span style='color:black'>On Thu, Jun 10, 2021 at 4:02 PM Dmitry Semchonok <<a href="mailto:Sem...@gm..." target="_blank">Sem...@gm...</a>> wrote:<o:p></o:p></span></p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><p class=MsoNormal><span style='color:black'>Dear colleagues,<br><br>After running Bayesian polishing script with 5e I got the following error<br><br><br><br>2232: GridSquare_26409500_Data_FoilHole_26633166_Data_26416121_26416123_20210330_110202_Fractions.mrc<br>02591: 1914: GridSquare_26409382_Data_FoilHole_26635345_Data_26416121_26416123_20210330_172633_Fractions.mrc<br>02592: 1985: GridSquare_26409382_Data_FoilHole_26635480_Data_26416121_26416123_20210330_201730_Fractions.mrc<br>02593: 2253: GridSquare_26409500_Data_FoilHole_26633222_Data_26416121_26416123_20210330_123213_Fractions.mrc<br>02594: 1404: GridSquare_26409268_Data_FoilHole_26621354_Data_26416121_26416123_20210329_092746_Fractions.mrc<br>02595: 361: GridSquare_26409080_Data_FoilHole_26614677_Data_26416121_26416123_20210328_095659_Fractions.mrc<br>02596: <br>02597: - Warning: this dataset does not contain 217187 particles (--min_p) in micrographs with at least 2 particles<br>02598: + preparing alignment data... <br>02599: Traceback (most recent call last):<br>02600: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run<br>02601: self._run()<br>02602: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run<br>02603: resultFiles = self._runFunc()<br>02604: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc<br>02605: return self._func(*self._args)<br>02606: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", line 351, in trainOrPolishStep<br>02607: self.runJob(self._getProgram('relion_motion_refine'), args)<br>02608: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1388, in runJob<br>02609: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)<br>02610: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob<br>02611: process.runJob(log, programName, params,<br>02612: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob<br>02613: return runCommand(command, env, cwd)<br>02614: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand<br>02615: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,<br>02616: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call<br>02617: raise CalledProcessError(retcode, cmd)<br>02618: subprocess.CalledProcessError: Command ' relion_motion_refine --i Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o Runs/004833_ProtRelionBayesianPolishing/extra --f Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.59200 --corr_mic Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>.<br>02619: Protocol failed: Command ' relion_motion_refine --i Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o Runs/004833_ProtRelionBayesianPolishing/extra --f Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.59200 --corr_mic Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>.<br>02620: FAILED: trainOrPolishStep, step 2, time 2021-06-09 11:27:00.176491<br>02621: *** Last status is failed <br>02622: ------------------- PROTOCOL FAILED (DONE 2/2)<br><br>Do you know how to fix that?<br><br><br>Thank you<br><br>Sincerely,<br>Dmitry<br><br><br><br><br>_______________________________________________<br>scipion-users mailing list<br><a href="mailto:sci...@li..." target="_blank">sci...@li...</a><br><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users" target="_blank">https://lists.sourceforge.net/lists/listinfo/scipion-users</a><o:p></o:p></span></p></blockquote></div><div><p class=MsoNormal><span style='color:black'>_______________________________________________<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>scipion-users mailing list<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><a href="mailto:scipion-users%40lists.sourceforge.net" target="_blank">sci...@li...</a><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users" target="_blank">https://lists.sourceforge.net/lists/listinfo/scipion-users</a><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div></blockquote></div></div></div></div></div></blockquote></div><p class=MsoNormal style='margin-left:4.8pt'><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
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From: Grigory S. <sha...@gm...> - 2021-06-10 18:27:00
|
I have no idea what 1e or 5e means, I see you are using 14 threads..
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...
On Thu, Jun 10, 2021 at 7:25 PM Dmitry A. Semchonok <sem...@gm...>
wrote:
> Thank you Grigory,
>
> The interesting point is that if the one uses 1e - the process finishes
> without error.
> But 5e seems too be too much.
>
> Sincerely,
> Dmitry
>
> On June 10, 2021 5:20:06 PM Grigory Sharov <sha...@gm...>
> wrote:
>
>> Hi Dmitry,
>>
>> I think you posted a similar error before. You are using too many
>> particles for training and running out of RAM, hence your process is
>> killed by Linux kernel.
>>
>> Best regards,
>> Grigory
>>
>>
>> --------------------------------------------------------------------------------
>> Grigory Sharov, Ph.D.
>>
>> MRC Laboratory of Molecular Biology,
>> Francis Crick Avenue,
>> Cambridge Biomedical Campus,
>> Cambridge CB2 0QH, UK.
>> tel. +44 (0) 1223 267228 <+44%201223%20267228>
>> e-mail: gs...@mr...
>>
>>
>> On Thu, Jun 10, 2021 at 4:02 PM Dmitry Semchonok <Sem...@gm...>
>> wrote:
>>
>>> Dear colleagues,
>>>
>>> After running Bayesian polishing script with 5e I got the following error
>>>
>>>
>>>
>>> 2232:
>>> GridSquare_26409500_Data_FoilHole_26633166_Data_26416121_26416123_20210330_110202_Fractions.mrc
>>> 02591: 1914:
>>> GridSquare_26409382_Data_FoilHole_26635345_Data_26416121_26416123_20210330_172633_Fractions.mrc
>>> 02592: 1985:
>>> GridSquare_26409382_Data_FoilHole_26635480_Data_26416121_26416123_20210330_201730_Fractions.mrc
>>> 02593: 2253:
>>> GridSquare_26409500_Data_FoilHole_26633222_Data_26416121_26416123_20210330_123213_Fractions.mrc
>>> 02594: 1404:
>>> GridSquare_26409268_Data_FoilHole_26621354_Data_26416121_26416123_20210329_092746_Fractions.mrc
>>> 02595: 361:
>>> GridSquare_26409080_Data_FoilHole_26614677_Data_26416121_26416123_20210328_095659_Fractions.mrc
>>> 02596:
>>> 02597: - Warning: this dataset does not contain 217187 particles
>>> (--min_p) in micrographs with at least 2 particles
>>> 02598: + preparing alignment data...
>>> 02599: Traceback (most recent call last):
>>> 02600: File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
>>> line 197, in run
>>> 02601: self._run()
>>> 02602: File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
>>> line 248, in _run
>>> 02603: resultFiles = self._runFunc()
>>> 02604: File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
>>> line 244, in _runFunc
>>> 02605: return self._func(*self._args)
>>> 02606: File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py",
>>> line 351, in trainOrPolishStep
>>> 02607: self.runJob(self._getProgram('relion_motion_refine'), args)
>>> 02608: File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
>>> line 1388, in runJob
>>> 02609: self._stepsExecutor.runJob(self._log, program, arguments,
>>> **kwargs)
>>> 02610: File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py",
>>> line 65, in runJob
>>> 02611: process.runJob(log, programName, params,
>>> 02612: File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
>>> line 52, in runJob
>>> 02613: return runCommand(command, env, cwd)
>>> 02614: File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
>>> line 67, in runCommand
>>> 02615: check_call(command, shell=True, stdout=sys.stdout,
>>> stderr=sys.stderr,
>>> 02616: File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364,
>>> in check_call
>>> 02617: raise CalledProcessError(retcode, cmd)
>>> 02618: subprocess.CalledProcessError: Command ' relion_motion_refine
>>> --i Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o
>>> Runs/004833_ProtRelionBayesianPolishing/extra --f
>>> Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
>>> 0.59200 --corr_mic
>>> Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star
>>> --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500
>>> --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>.
>>> 02619: Protocol failed: Command ' relion_motion_refine --i
>>> Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o
>>> Runs/004833_ProtRelionBayesianPolishing/extra --f
>>> Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
>>> 0.59200 --corr_mic
>>> Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star
>>> --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500
>>> --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>.
>>> 02620: FAILED: trainOrPolishStep, step 2, time 2021-06-09
>>> 11:27:00.176491
>>> 02621: *** Last status is failed
>>> 02622: ------------------- PROTOCOL FAILED (DONE 2/2)
>>>
>>> Do you know how to fix that?
>>>
>>>
>>> Thank you
>>>
>>> Sincerely,
>>> Dmitry
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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: Dmitry A. S. <sem...@gm...> - 2021-06-10 18:25:12
|
Thank you Grigory,
The interesting point is that if the one uses 1e - the process finishes
without error.
But 5e seems too be too much.
Sincerely,
Dmitry
On June 10, 2021 5:20:06 PM Grigory Sharov <sha...@gm...> wrote:
> Hi Dmitry,
>
> I think you posted a similar error before. You are using too many particles
> for training and running out of RAM, hence your process is killed by Linux
> kernel.
>
> Best regards,
> Grigory
>
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
>
> MRC Laboratory of Molecular Biology,
> Francis Crick Avenue,
> Cambridge Biomedical Campus,
> Cambridge CB2 0QH, UK.
> tel. +44 (0) 1223 267228
> e-mail: gs...@mr...
>
>
> On Thu, Jun 10, 2021 at 4:02 PM Dmitry Semchonok <Sem...@gm...> wrote:
> Dear colleagues,
>
> After running Bayesian polishing script with 5e I got the following error
>
>
>
> 2232:
> GridSquare_26409500_Data_FoilHole_26633166_Data_26416121_26416123_20210330_110202_Fractions.mrc
> 02591: 1914:
> GridSquare_26409382_Data_FoilHole_26635345_Data_26416121_26416123_20210330_172633_Fractions.mrc
> 02592: 1985:
> GridSquare_26409382_Data_FoilHole_26635480_Data_26416121_26416123_20210330_201730_Fractions.mrc
> 02593: 2253:
> GridSquare_26409500_Data_FoilHole_26633222_Data_26416121_26416123_20210330_123213_Fractions.mrc
> 02594: 1404:
> GridSquare_26409268_Data_FoilHole_26621354_Data_26416121_26416123_20210329_092746_Fractions.mrc
> 02595: 361:
> GridSquare_26409080_Data_FoilHole_26614677_Data_26416121_26416123_20210328_095659_Fractions.mrc
> 02596:
> 02597: - Warning: this dataset does not contain 217187 particles
> (--min_p) in micrographs with at least 2 particles
> 02598: + preparing alignment data...
> 02599: Traceback (most recent call last):
> 02600: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 197, in run
> 02601: self._run()
> 02602: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 248, in _run
> 02603: resultFiles = self._runFunc()
> 02604: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 244, in _runFunc
> 02605: return self._func(*self._args)
> 02606: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py",
> line 351, in trainOrPolishStep
> 02607: self.runJob(self._getProgram('relion_motion_refine'), args)
> 02608: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 1388, in runJob
> 02609: self._stepsExecutor.runJob(self._log, program, arguments,
> **kwargs)
> 02610: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py",
> line 65, in runJob
> 02611: process.runJob(log, programName, params,
> 02612: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 52, in runJob
> 02613: return runCommand(command, env, cwd)
> 02614: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 67, in runCommand
> 02615: check_call(command, shell=True, stdout=sys.stdout,
> stderr=sys.stderr,
> 02616: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364,
> in check_call
> 02617: raise CalledProcessError(retcode, cmd)
> 02618: subprocess.CalledProcessError: Command ' relion_motion_refine --i
> Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o
> Runs/004833_ProtRelionBayesianPolishing/extra --f
> Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
> 0.59200 --corr_mic
> Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star
> --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500
> --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>.
> 02619: Protocol failed: Command ' relion_motion_refine --i
> Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o
> Runs/004833_ProtRelionBayesianPolishing/extra --f
> Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
> 0.59200 --corr_mic
> Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star
> --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500
> --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>.
> 02620: FAILED: trainOrPolishStep, step 2, time 2021-06-09 11:27:00.176491
> 02621: *** Last status is failed
> 02622: ------------------- PROTOCOL FAILED (DONE 2/2)
>
> Do you know how to fix that?
>
>
> Thank you
>
> Sincerely,
> Dmitry
>
>
>
>
> _______________________________________________
> 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: Grigory S. <sha...@gm...> - 2021-06-10 15:19:52
|
Hi Dmitry,
I think you posted a similar error before. You are using too many particles
for training and running out of RAM, hence your process is killed by Linux
kernel.
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...
On Thu, Jun 10, 2021 at 4:02 PM Dmitry Semchonok <Sem...@gm...>
wrote:
> Dear colleagues,
>
> After running Bayesian polishing script with 5e I got the following error
>
>
>
> 2232:
> GridSquare_26409500_Data_FoilHole_26633166_Data_26416121_26416123_20210330_110202_Fractions.mrc
> 02591: 1914:
> GridSquare_26409382_Data_FoilHole_26635345_Data_26416121_26416123_20210330_172633_Fractions.mrc
> 02592: 1985:
> GridSquare_26409382_Data_FoilHole_26635480_Data_26416121_26416123_20210330_201730_Fractions.mrc
> 02593: 2253:
> GridSquare_26409500_Data_FoilHole_26633222_Data_26416121_26416123_20210330_123213_Fractions.mrc
> 02594: 1404:
> GridSquare_26409268_Data_FoilHole_26621354_Data_26416121_26416123_20210329_092746_Fractions.mrc
> 02595: 361:
> GridSquare_26409080_Data_FoilHole_26614677_Data_26416121_26416123_20210328_095659_Fractions.mrc
> 02596:
> 02597: - Warning: this dataset does not contain 217187 particles
> (--min_p) in micrographs with at least 2 particles
> 02598: + preparing alignment data...
> 02599: Traceback (most recent call last):
> 02600: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 197, in run
> 02601: self._run()
> 02602: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 248, in _run
> 02603: resultFiles = self._runFunc()
> 02604: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 244, in _runFunc
> 02605: return self._func(*self._args)
> 02606: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py",
> line 351, in trainOrPolishStep
> 02607: self.runJob(self._getProgram('relion_motion_refine'), args)
> 02608: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 1388, in runJob
> 02609: self._stepsExecutor.runJob(self._log, program, arguments,
> **kwargs)
> 02610: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py",
> line 65, in runJob
> 02611: process.runJob(log, programName, params,
> 02612: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 52, in runJob
> 02613: return runCommand(command, env, cwd)
> 02614: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 67, in runCommand
> 02615: check_call(command, shell=True, stdout=sys.stdout,
> stderr=sys.stderr,
> 02616: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364,
> in check_call
> 02617: raise CalledProcessError(retcode, cmd)
> 02618: subprocess.CalledProcessError: Command ' relion_motion_refine --i
> Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o
> Runs/004833_ProtRelionBayesianPolishing/extra --f
> Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
> 0.59200 --corr_mic
> Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star
> --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500
> --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>.
> 02619: Protocol failed: Command ' relion_motion_refine --i
> Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o
> Runs/004833_ProtRelionBayesianPolishing/extra --f
> Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
> 0.59200 --corr_mic
> Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star
> --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500
> --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>.
> 02620: FAILED: trainOrPolishStep, step 2, time 2021-06-09 11:27:00.176491
> 02621: *** Last status is failed
> 02622: ------------------- PROTOCOL FAILED (DONE 2/2)
>
> Do you know how to fix that?
>
>
> Thank you
>
> Sincerely,
> Dmitry
>
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: Dmitry S. <Sem...@gm...> - 2021-06-10 15:02:42
|
Dear colleagues,
After running Bayesian polishing script with 5e I got the following error
2232: GridSquare_26409500_Data_FoilHole_26633166_Data_26416121_26416123_20210330_110202_Fractions.mrc
02591: 1914: GridSquare_26409382_Data_FoilHole_26635345_Data_26416121_26416123_20210330_172633_Fractions.mrc
02592: 1985: GridSquare_26409382_Data_FoilHole_26635480_Data_26416121_26416123_20210330_201730_Fractions.mrc
02593: 2253: GridSquare_26409500_Data_FoilHole_26633222_Data_26416121_26416123_20210330_123213_Fractions.mrc
02594: 1404: GridSquare_26409268_Data_FoilHole_26621354_Data_26416121_26416123_20210329_092746_Fractions.mrc
02595: 361: GridSquare_26409080_Data_FoilHole_26614677_Data_26416121_26416123_20210328_095659_Fractions.mrc
02596:
02597: - Warning: this dataset does not contain 217187 particles (--min_p) in micrographs with at least 2 particles
02598: + preparing alignment data...
02599: Traceback (most recent call last):
02600: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run
02601: self._run()
02602: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run
02603: resultFiles = self._runFunc()
02604: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc
02605: return self._func(*self._args)
02606: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", line 351, in trainOrPolishStep
02607: self.runJob(self._getProgram('relion_motion_refine'), args)
02608: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1388, in runJob
02609: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
02610: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob
02611: process.runJob(log, programName, params,
02612: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob
02613: return runCommand(command, env, cwd)
02614: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand
02615: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
02616: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call
02617: raise CalledProcessError(retcode, cmd)
02618: subprocess.CalledProcessError: Command ' relion_motion_refine --i Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o Runs/004833_ProtRelionBayesianPolishing/extra --f Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.59200 --corr_mic Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>.
02619: Protocol failed: Command ' relion_motion_refine --i Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o Runs/004833_ProtRelionBayesianPolishing/extra --f Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.59200 --corr_mic Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>.
02620: FAILED: trainOrPolishStep, step 2, time 2021-06-09 11:27:00.176491
02621: *** Last status is failed
02622: ------------------- PROTOCOL FAILED (DONE 2/2)
Do you know how to fix that?
Thank you
Sincerely,
Dmitry
|
|
From: Morgan B. <m....@im...> - 2021-06-03 16:14:06
|
Hi Teige, Grigory, Pablo, Many thanks for helping me untie myself. Turns out the key was Teige's astute observation: I have multiple Python installs (not for the first time...), and root was referencing a different install to standard users. Fixing that and it all worked nicely. I then enabled all users to install (and, therefore, break...) scipion modules. All seems to work a treat now. Thanks again, all. Morgan On 03/06/2021 10:18, Pablo Conesa wrote: > > All seems to be around what Grigory and Teige are saying. > > I'm curious about what is going on there and learn how to do that > setup with virtualenv. > > If you like, I'm available for a shared desktop session to find out, > and later document how to do that setup. > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > On 3/6/21 10:54, Grigory Sharov wrote: >> I think you should have a folder >> /usr/local/bin/scipion3/.venv/scipion3 where the venv is located.. >> >> Best regards, >> Grigory >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> >> e-mail: gs...@mr... <mailto:gs...@mr...> >> >> >> On Thu, Jun 3, 2021 at 9:52 AM Teige Matthews-Palmer >> <tei...@gm... <mailto:tei...@gm...>> wrote: >> >> Hi Morgan, >> >> I installed scipion3 and its packages a while ago and remember it >> was a bit tricky/fussy on Centos7 too. >> >> Just some ideas, it seems like user’s python is not searching the >> directory where the scipion module is, or permissions stop it >> from finding the module? >> >> The scipion launcher /usr/local/scipion3/scipion3 starts with the >> shebang #!/usr/bin/env python3, which should invoke the default >> python3 of the user’s environment. I don’t think this would be >> the issue, but maybe user has a different default python binary? >> >> Or, you could use /python -c ‘import sys; print(sys.path)’/ to >> print out the directories where python will search for modules. >> Is it different between root and user? >> For me, it includes …/python3.8/site-packages , which contains >> scipioninstaller, and I think that eventually leads to it finding >> scipion3. I can’t tell exactly where the module referred to as >> “scipion” is located, but specifying its directory in PYTHONPATH >> could solve it? >> >> Otherwise, potentially the directory where the scipion module is >> found has permissions that deny user access, and need chmod? >> >> Hope it doesn’t take too many more knots before it’s working! >> Teige >> >> >>> On 2 Jun 2021, at 22:50, Morgan Beeby <m....@im... >>> <mailto:m....@im...>> wrote: >>> >>> Dear all, >>> >>> I wondered if anyone could help point me in the direction of >>> installing scipion3 for all users on a machine (ultimately for >>> cluster install for all users)? I seem to be tying myself in >>> knots with what seems to be a trivial install. >>> >>> As root, I am doing the following to install on Linux Mint 20 >>> (after insuring all prequisite libraries are installed): >>> >>> * >>> pip install scipion-installer >>> * >>> python -m scipioninstaller /usr/local/bin/scipion3 -venv -j 4 >>> >>> Then as user: >>> >>> * alias scipion3=/usr/local/bin/scipion3/scipion3 >>> * scipion3 >>> >>> But I get an error: >>> >>> * /usr/bin/python: No module named scipion >>> >>> (it runs ok for root) >>> >>> It seems like this should just work, but after hours of playing >>> around, I've had no success, and I cannot find anything on >>> multiuser installs on linux. >>> >>> thanks, >>> >>> Morgan >>> >>> >>> -- >>> Dr Morgan Beeby >>> Department of Life Sciences >>> c/o Department of Chemistry Stores >>> Imperial College London >>> Frankland Road >>> London, SW7 2AZ >>> United Kingdom >>> >>> Office: +44 (0)20 7594 5251 >>> Web : www.beebylab.org >>> >>> ~ ~ ~ >>> >>> Schedule a meeting with me: https://go.oncehub.com/MorganBeeby >>> <https://go.oncehub.com/MorganBeeby> >>> >>> ~ ~ ~ >>> >>> Drop in office hours, no appointment necessary, over the next 7 >>> days: >>> >>> (Teams link >>> <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NzA4MjI4OGItZmYwOC00Yjk5LThkMzQtNmU1MGI1YjJkYTZh%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) >>> 12:30pm - 1:00pm (Europe/London), Wednesday 02 Jun >>> (Teams link >>> <https://teams.microsoft.com/l/meetup-join/19%3ameeting_OTExZWZhZjctYjdhNC00YmZmLTg3MmUtYzc5NjE1NDkzNWI2%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) >>> 1:15pm - 1:45pm (Europe/London), Monday 07 Jun >>> (Teams link >>> <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NWZlNGZmYzMtMWJjZS00M2Q4LWFhNGQtNTdlYmE2YTFmZjc4%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) >>> 1:15pm - 1:45pm (Europe/London), Tuesday 08 Jun >>> >>> Full schedule and links: http://www.beebylab.org/contact/ >>> <http://www.beebylab.org/contact/> >>> _______________________________________________ >>> 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> >> >> >> >> _______________________________________________ >> 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 -- Dr Morgan Beeby Department of Life Sciences c/o Department of Chemistry Stores Imperial College London Frankland Road London, SW7 2AZ United Kingdom Office: +44 (0)20 7594 5251 Web : www.beebylab.org <www.beebylab.org> ~ ~ ~ Schedule a meeting with me: https://go.oncehub.com/MorganBeeby <https://go.oncehub.com/MorganBeeby> ~ ~ ~ Drop in office hours, no appointment necessary, over the next 7 days: (Teams link <https://teams.microsoft.com/l/meetup-join/19%3ameeting_OTExZWZhZjctYjdhNC00YmZmLTg3MmUtYzc5NjE1NDkzNWI2%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) 1:15pm - 1:45pm (Europe/London), Monday 07 Jun (Teams link <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NWZlNGZmYzMtMWJjZS00M2Q4LWFhNGQtNTdlYmE2YTFmZjc4%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) 1:15pm - 1:45pm (Europe/London), Tuesday 08 Jun (Teams link <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NzA4MjI4OGItZmYwOC00Yjk5LThkMzQtNmU1MGI1YjJkYTZh%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) 1:15pm - 1:45pm (Europe/London), Wednesday 09 Jun Full schedule and links: http://www.beebylab.org/contact/ <http://www.beebylab.org/contact/> |
|
From: Pablo C. <pc...@cn...> - 2021-06-03 12:51:49
|
Hi, ...
…/scipion3/.scipion3env/bin/scipion is a "shell compatible" shortcut to
scipion3/.scipion3env/lib/python3.6/site-packages/scipion/ (python
module). Only when the environement is activated,
"scipion3/.scipion3env/bin" is added to the PATH variable, so from then,
"scipion" is available as a command in a shell. But without the
environment activated that command is missing.
Using chmod will not harm, unless you do not trust the users. Anyone
could break the installation.
We have in our severs installations done with one user (not root, but
"admin"), protected to the rest of the users and they are working fine.
In theory , to run python code is not needed write permissions.
My guess, is that, for some reason, Morgan setup is not able to activate
the environment.
Morgan, I'd say all is around the content of "scipion3" launcher. This
is a file that might look like more or less like this:
___________________________________
#!/usr/bin/env python
# Scipion launcher
import os
import sys
from os.path import dirname, abspath, join, basename
# Set SCIPION_HOME to the location of this file
scipionHome = dirname(abspath(__file__))
os.environ["SCIPION_TESTS_CMD"] = basename(__file__) + " tests"
os.environ["LD_LIBRARY_PATH"] =
":".join([os.environ.get("LD_LIBRARY_PATH", ""), join(scipionHome,
"software", "lib")])
os.environ["PYTHONPATH"] = ":".join([os.environ.get("PYTHONPATH", ""),
join(scipionHome, "software", "bindings")])
cmd = ""
if len(sys.argv) > 1 and sys.argv[1] == 'git':
for repo in ['scipion-app', 'scipion-pyworkflow', 'scipion-em']:
cmd += ("(cd "+join(scipionHome, repo)+" ; echo ' > in
"+repo+":' ;"
" git "+' '.join(sys.argv[2:])+" ; echo) ; ")
else:
# Activate the environment
cmd = '. /home/pablo/software/scipion/.scipion3/bin/activate && '
cmd += "python -m scipion %s" % " ".join(sys.argv[1:])
# Set SCIPION_HOME
os.environ["SCIPION_HOME"] = scipionHome
_____________________________________
You can try the equivalent to my: .
/home/pablo/software/scipion/.scipion3/bin/activate
This is meant to source and activate the environment, and maybe from
another user it does not work
What happens if you do this?
. /usr/local/bin/scipion3/.scipion3/bin/activate
which python
On 3/6/21 11:21, Teige Matthews-Palmer wrote:
> Soz for spam - think I’m wrong to say
> …/scipion3/.scipion3env/bin/scipion is the module, I think it’s rather
> in scipion3/.scipion3env/lib/python3.6/site-packages/scipion/
> I guess that if users are denied permission to any of this, then it
> will fail to load the module.
>
> Open question: is it OK generally to do chmod -R 755 to the whole
> scipion directory - and maybe it solves the problem Morgan has?
>
>> On 3 Jun 2021, at 18:14, Teige Matthews-Palmer <tei...@gm...
>> <mailto:tei...@gm...>> wrote:
>>
>> That sounds probably right! On my install the module called scipion
>> is found in …/scipion3/.scipion3env/bin/scipion , it and everything
>> alongside it are owned by root and 755 permission and it works fine
>> (I think it’s a venv install - at least I know I wanted to avoid
>> miniconda).
>>
>> Good luck
>> Teige
>>
>>> On 3 Jun 2021, at 17:54, Grigory Sharov <sha...@gm...
>>> <mailto:sha...@gm...>> wrote:
>>>
>>> I think you should have a folder
>>> /usr/local/bin/scipion3/.venv/scipion3 where the venv is located..
>>>
>>> Best regards,
>>> Grigory
>>>
>>> --------------------------------------------------------------------------------
>>> Grigory Sharov, Ph.D.
>>>
>>> MRC Laboratory of Molecular Biology,
>>> Francis Crick Avenue,
>>> Cambridge Biomedical Campus,
>>> Cambridge CB2 0QH, UK.
>>> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228>
>>> e-mail: gs...@mr... <mailto:gs...@mr...>
>>>
>>>
>>> On Thu, Jun 3, 2021 at 9:52 AM Teige Matthews-Palmer
>>> <tei...@gm... <mailto:tei...@gm...>> wrote:
>>>
>>> Hi Morgan,
>>>
>>> I installed scipion3 and its packages a while ago and remember
>>> it was a bit tricky/fussy on Centos7 too.
>>>
>>> Just some ideas, it seems like user’s python is not searching
>>> the directory where the scipion module is, or permissions stop
>>> it from finding the module?
>>>
>>> The scipion launcher /usr/local/scipion3/scipion3 starts with
>>> the shebang #!/usr/bin/env python3, which should invoke the
>>> default python3 of the user’s environment. I don’t think this
>>> would be the issue, but maybe user has a different default
>>> python binary?
>>>
>>> Or, you could use /python -c ‘import sys; print(sys.path)’/ to
>>> print out the directories where python will search for modules.
>>> Is it different between root and user?
>>> For me, it includes …/python3.8/site-packages , which contains
>>> scipioninstaller, and I think that eventually leads to it
>>> finding scipion3. I can’t tell exactly where the module referred
>>> to as “scipion” is located, but specifying its directory in
>>> PYTHONPATH could solve it?
>>>
>>> Otherwise, potentially the directory where the scipion module is
>>> found has permissions that deny user access, and need chmod?
>>>
>>> Hope it doesn’t take too many more knots before it’s working!
>>> Teige
>>>
>>>
>>>> On 2 Jun 2021, at 22:50, Morgan Beeby <m....@im...
>>>> <mailto:m....@im...>> wrote:
>>>>
>>>> Dear all,
>>>>
>>>> I wondered if anyone could help point me in the direction of
>>>> installing scipion3 for all users on a machine (ultimately for
>>>> cluster install for all users)? I seem to be tying myself in
>>>> knots with what seems to be a trivial install.
>>>>
>>>> As root, I am doing the following to install on Linux Mint 20
>>>> (after insuring all prequisite libraries are installed):
>>>>
>>>> *
>>>> pip install scipion-installer
>>>> *
>>>> python -m scipioninstaller /usr/local/bin/scipion3 -venv -j 4
>>>>
>>>> Then as user:
>>>>
>>>> * alias scipion3=/usr/local/bin/scipion3/scipion3
>>>> * scipion3
>>>>
>>>> But I get an error:
>>>>
>>>> * /usr/bin/python: No module named scipion
>>>>
>>>> (it runs ok for root)
>>>>
>>>> It seems like this should just work, but after hours of playing
>>>> around, I've had no success, and I cannot find anything on
>>>> multiuser installs on linux.
>>>>
>>>> thanks,
>>>>
>>>> Morgan
>>>>
>>>>
>>>> --
>>>> Dr Morgan Beeby
>>>> Department of Life Sciences
>>>> c/o Department of Chemistry Stores
>>>> Imperial College London
>>>> Frankland Road
>>>> London, SW7 2AZ
>>>> United Kingdom
>>>>
>>>> Office: +44 (0)20 7594 5251
>>>> Web : www.beebylab.org
>>>>
>>>> ~ ~ ~
>>>>
>>>> Schedule a meeting with me: https://go.oncehub.com/MorganBeeby
>>>> <https://go.oncehub.com/MorganBeeby>
>>>>
>>>> ~ ~ ~
>>>>
>>>> Drop in office hours, no appointment necessary, over the next 7
>>>> days:
>>>>
>>>> (Teams link
>>>> <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NzA4MjI4OGItZmYwOC00Yjk5LThkMzQtNmU1MGI1YjJkYTZh%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>)
>>>> 12:30pm - 1:00pm (Europe/London), Wednesday 02 Jun
>>>> (Teams link
>>>> <https://teams.microsoft.com/l/meetup-join/19%3ameeting_OTExZWZhZjctYjdhNC00YmZmLTg3MmUtYzc5NjE1NDkzNWI2%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>)
>>>> 1:15pm - 1:45pm (Europe/London), Monday 07 Jun
>>>> (Teams link
>>>> <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NWZlNGZmYzMtMWJjZS00M2Q4LWFhNGQtNTdlYmE2YTFmZjc4%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>)
>>>> 1:15pm - 1:45pm (Europe/London), Tuesday 08 Jun
>>>>
>>>> Full schedule and links: http://www.beebylab.org/contact/
>>>> <http://www.beebylab.org/contact/>
>>>> _______________________________________________
>>>> 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>
>>>
>>> _______________________________________________
>>> 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...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Teige Matthews-P. <tei...@gm...> - 2021-06-03 09:21:51
|
Soz for spam - think I’m wrong to say …/scipion3/.scipion3env/bin/scipion is the module, I think it’s rather in scipion3/.scipion3env/lib/python3.6/site-packages/scipion/ I guess that if users are denied permission to any of this, then it will fail to load the module. Open question: is it OK generally to do chmod -R 755 to the whole scipion directory - and maybe it solves the problem Morgan has? > On 3 Jun 2021, at 18:14, Teige Matthews-Palmer <tei...@gm...> wrote: > > That sounds probably right! On my install the module called scipion is found in …/scipion3/.scipion3env/bin/scipion , it and everything alongside it are owned by root and 755 permission and it works fine (I think it’s a venv install - at least I know I wanted to avoid miniconda). > > Good luck > Teige > >> On 3 Jun 2021, at 17:54, Grigory Sharov <sha...@gm... <mailto:sha...@gm...>> wrote: >> >> I think you should have a folder /usr/local/bin/scipion3/.venv/scipion3 where the venv is located.. >> >> Best regards, >> Grigory >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> >> e-mail: gs...@mr... <mailto:gs...@mr...> >> >> >> On Thu, Jun 3, 2021 at 9:52 AM Teige Matthews-Palmer <tei...@gm... <mailto:tei...@gm...>> wrote: >> Hi Morgan, >> >> I installed scipion3 and its packages a while ago and remember it was a bit tricky/fussy on Centos7 too. >> >> Just some ideas, it seems like user’s python is not searching the directory where the scipion module is, or permissions stop it from finding the module? >> >> The scipion launcher /usr/local/scipion3/scipion3 starts with the shebang #!/usr/bin/env python3, which should invoke the default python3 of the user’s environment. I don’t think this would be the issue, but maybe user has a different default python binary? >> >> Or, you could use python -c ‘import sys; print(sys.path)’ to print out the directories where python will search for modules. Is it different between root and user? >> For me, it includes …/python3.8/site-packages , which contains scipioninstaller, and I think that eventually leads to it finding scipion3. I can’t tell exactly where the module referred to as “scipion” is located, but specifying its directory in PYTHONPATH could solve it? >> >> Otherwise, potentially the directory where the scipion module is found has permissions that deny user access, and need chmod? >> >> Hope it doesn’t take too many more knots before it’s working! >> Teige >> >> >>> On 2 Jun 2021, at 22:50, Morgan Beeby <m....@im... <mailto:m....@im...>> wrote: >>> >>> Dear all, >>> >>> I wondered if anyone could help point me in the direction of installing scipion3 for all users on a machine (ultimately for cluster install for all users)? I seem to be tying myself in knots with what seems to be a trivial install. >>> >>> As root, I am doing the following to install on Linux Mint 20 (after insuring all prequisite libraries are installed): >>> pip install scipion-installer >>> python -m scipioninstaller /usr/local/bin/scipion3 -venv -j 4 >>> Then as user: >>> alias scipion3=/usr/local/bin/scipion3/scipion3 >>> scipion3 >>> But I get an error: >>> >>> /usr/bin/python: No module named scipion >>> (it runs ok for root) >>> >>> It seems like this should just work, but after hours of playing around, I've had no success, and I cannot find anything on multiuser installs on linux. >>> >>> thanks, >>> >>> Morgan >>> >>> >>> -- >>> Dr Morgan Beeby >>> Department of Life Sciences >>> c/o Department of Chemistry Stores >>> Imperial College London >>> Frankland Road >>> London, SW7 2AZ >>> United Kingdom >>> >>> Office: +44 (0)20 7594 5251 >>> Web : www.beebylab.org <> >>> >>> ~ ~ ~ >>> >>> Schedule a meeting with me: https://go.oncehub.com/MorganBeeby <https://go.oncehub.com/MorganBeeby> >>> >>> ~ ~ ~ >>> >>> Drop in office hours, no appointment necessary, over the next 7 days: >>> >>> (Teams link <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NzA4MjI4OGItZmYwOC00Yjk5LThkMzQtNmU1MGI1YjJkYTZh%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) 12:30pm - 1:00pm (Europe/London), Wednesday 02 Jun >>> (Teams link <https://teams.microsoft.com/l/meetup-join/19%3ameeting_OTExZWZhZjctYjdhNC00YmZmLTg3MmUtYzc5NjE1NDkzNWI2%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) 1:15pm - 1:45pm (Europe/London), Monday 07 Jun >>> (Teams link <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NWZlNGZmYzMtMWJjZS00M2Q4LWFhNGQtNTdlYmE2YTFmZjc4%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) 1:15pm - 1:45pm (Europe/London), Tuesday 08 Jun >>> >>> Full schedule and links: http://www.beebylab.org/contact/ <http://www.beebylab.org/contact/> >>> _______________________________________________ >>> 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> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Pablo C. <pc...@cn...> - 2021-06-03 09:19:15
|
All seems to be around what Grigory and Teige are saying. I'm curious about what is going on there and learn how to do that setup with virtualenv. If you like, I'm available for a shared desktop session to find out, and later document how to do that setup. -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* On 3/6/21 10:54, Grigory Sharov wrote: > I think you should have a folder > /usr/local/bin/scipion3/.venv/scipion3 where the venv is located.. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Thu, Jun 3, 2021 at 9:52 AM Teige Matthews-Palmer > <tei...@gm... <mailto:tei...@gm...>> wrote: > > Hi Morgan, > > I installed scipion3 and its packages a while ago and remember it > was a bit tricky/fussy on Centos7 too. > > Just some ideas, it seems like user’s python is not searching the > directory where the scipion module is, or permissions stop it from > finding the module? > > The scipion launcher /usr/local/scipion3/scipion3 starts with the > shebang #!/usr/bin/env python3, which should invoke the default > python3 of the user’s environment. I don’t think this would be the > issue, but maybe user has a different default python binary? > > Or, you could use /python -c ‘import sys; print(sys.path)’/ to > print out the directories where python will search for modules. Is > it different between root and user? > For me, it includes …/python3.8/site-packages , which contains > scipioninstaller, and I think that eventually leads to it finding > scipion3. I can’t tell exactly where the module referred to as > “scipion” is located, but specifying its directory in PYTHONPATH > could solve it? > > Otherwise, potentially the directory where the scipion module is > found has permissions that deny user access, and need chmod? > > Hope it doesn’t take too many more knots before it’s working! > Teige > > >> On 2 Jun 2021, at 22:50, Morgan Beeby <m....@im... >> <mailto:m....@im...>> wrote: >> >> Dear all, >> >> I wondered if anyone could help point me in the direction of >> installing scipion3 for all users on a machine (ultimately for >> cluster install for all users)? I seem to be tying myself in >> knots with what seems to be a trivial install. >> >> As root, I am doing the following to install on Linux Mint 20 >> (after insuring all prequisite libraries are installed): >> >> * >> pip install scipion-installer >> * >> python -m scipioninstaller /usr/local/bin/scipion3 -venv -j 4 >> >> Then as user: >> >> * alias scipion3=/usr/local/bin/scipion3/scipion3 >> * scipion3 >> >> But I get an error: >> >> * /usr/bin/python: No module named scipion >> >> (it runs ok for root) >> >> It seems like this should just work, but after hours of playing >> around, I've had no success, and I cannot find anything on >> multiuser installs on linux. >> >> thanks, >> >> Morgan >> >> >> -- >> Dr Morgan Beeby >> Department of Life Sciences >> c/o Department of Chemistry Stores >> Imperial College London >> Frankland Road >> London, SW7 2AZ >> United Kingdom >> >> Office: +44 (0)20 7594 5251 >> Web : www.beebylab.org >> >> ~ ~ ~ >> >> Schedule a meeting with me: https://go.oncehub.com/MorganBeeby >> <https://go.oncehub.com/MorganBeeby> >> >> ~ ~ ~ >> >> Drop in office hours, no appointment necessary, over the next 7 days: >> >> (Teams link >> <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NzA4MjI4OGItZmYwOC00Yjk5LThkMzQtNmU1MGI1YjJkYTZh%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) >> 12:30pm - 1:00pm (Europe/London), Wednesday 02 Jun >> (Teams link >> <https://teams.microsoft.com/l/meetup-join/19%3ameeting_OTExZWZhZjctYjdhNC00YmZmLTg3MmUtYzc5NjE1NDkzNWI2%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) >> 1:15pm - 1:45pm (Europe/London), Monday 07 Jun >> (Teams link >> <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NWZlNGZmYzMtMWJjZS00M2Q4LWFhNGQtNTdlYmE2YTFmZjc4%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) >> 1:15pm - 1:45pm (Europe/London), Tuesday 08 Jun >> >> Full schedule and links: http://www.beebylab.org/contact/ >> <http://www.beebylab.org/contact/> >> _______________________________________________ >> 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> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users ** |
|
From: Teige Matthews-P. <tei...@gm...> - 2021-06-03 09:14:42
|
That sounds probably right! On my install the module called scipion is found in …/scipion3/.scipion3env/bin/scipion , it and everything alongside it are owned by root and 755 permission and it works fine (I think it’s a venv install - at least I know I wanted to avoid miniconda). Good luck Teige > On 3 Jun 2021, at 17:54, Grigory Sharov <sha...@gm...> wrote: > > I think you should have a folder /usr/local/bin/scipion3/.venv/scipion3 where the venv is located.. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Thu, Jun 3, 2021 at 9:52 AM Teige Matthews-Palmer <tei...@gm... <mailto:tei...@gm...>> wrote: > Hi Morgan, > > I installed scipion3 and its packages a while ago and remember it was a bit tricky/fussy on Centos7 too. > > Just some ideas, it seems like user’s python is not searching the directory where the scipion module is, or permissions stop it from finding the module? > > The scipion launcher /usr/local/scipion3/scipion3 starts with the shebang #!/usr/bin/env python3, which should invoke the default python3 of the user’s environment. I don’t think this would be the issue, but maybe user has a different default python binary? > > Or, you could use python -c ‘import sys; print(sys.path)’ to print out the directories where python will search for modules. Is it different between root and user? > For me, it includes …/python3.8/site-packages , which contains scipioninstaller, and I think that eventually leads to it finding scipion3. I can’t tell exactly where the module referred to as “scipion” is located, but specifying its directory in PYTHONPATH could solve it? > > Otherwise, potentially the directory where the scipion module is found has permissions that deny user access, and need chmod? > > Hope it doesn’t take too many more knots before it’s working! > Teige > > >> On 2 Jun 2021, at 22:50, Morgan Beeby <m....@im... <mailto:m....@im...>> wrote: >> >> Dear all, >> >> I wondered if anyone could help point me in the direction of installing scipion3 for all users on a machine (ultimately for cluster install for all users)? I seem to be tying myself in knots with what seems to be a trivial install. >> >> As root, I am doing the following to install on Linux Mint 20 (after insuring all prequisite libraries are installed): >> pip install scipion-installer >> python -m scipioninstaller /usr/local/bin/scipion3 -venv -j 4 >> Then as user: >> alias scipion3=/usr/local/bin/scipion3/scipion3 >> scipion3 >> But I get an error: >> >> /usr/bin/python: No module named scipion >> (it runs ok for root) >> >> It seems like this should just work, but after hours of playing around, I've had no success, and I cannot find anything on multiuser installs on linux. >> >> thanks, >> >> Morgan >> >> >> -- >> Dr Morgan Beeby >> Department of Life Sciences >> c/o Department of Chemistry Stores >> Imperial College London >> Frankland Road >> London, SW7 2AZ >> United Kingdom >> >> Office: +44 (0)20 7594 5251 >> Web : www.beebylab.org <> >> >> ~ ~ ~ >> >> Schedule a meeting with me: https://go.oncehub.com/MorganBeeby <https://go.oncehub.com/MorganBeeby> >> >> ~ ~ ~ >> >> Drop in office hours, no appointment necessary, over the next 7 days: >> >> (Teams link <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NzA4MjI4OGItZmYwOC00Yjk5LThkMzQtNmU1MGI1YjJkYTZh%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) 12:30pm - 1:00pm (Europe/London), Wednesday 02 Jun >> (Teams link <https://teams.microsoft.com/l/meetup-join/19%3ameeting_OTExZWZhZjctYjdhNC00YmZmLTg3MmUtYzc5NjE1NDkzNWI2%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) 1:15pm - 1:45pm (Europe/London), Monday 07 Jun >> (Teams link <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NWZlNGZmYzMtMWJjZS00M2Q4LWFhNGQtNTdlYmE2YTFmZjc4%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) 1:15pm - 1:45pm (Europe/London), Tuesday 08 Jun >> >> Full schedule and links: http://www.beebylab.org/contact/ <http://www.beebylab.org/contact/> >> _______________________________________________ >> 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> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Grigory S. <sha...@gm...> - 2021-06-03 08:55:21
|
I think you should have a folder /usr/local/bin/scipion3/.venv/scipion3 where the venv is located.. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Jun 3, 2021 at 9:52 AM Teige Matthews-Palmer <tei...@gm...> wrote: > Hi Morgan, > > I installed scipion3 and its packages a while ago and remember it was a > bit tricky/fussy on Centos7 too. > > Just some ideas, it seems like user’s python is not searching the > directory where the scipion module is, or permissions stop it from finding > the module? > > The scipion launcher /usr/local/scipion3/scipion3 starts with the shebang > #!/usr/bin/env python3, which should invoke the default python3 of the > user’s environment. I don’t think this would be the issue, but maybe user > has a different default python binary? > > Or, you could use *python -c ‘import sys; print(sys.path)’* to print out > the directories where python will search for modules. Is it different > between root and user? > For me, it includes …/python3.8/site-packages , which contains > scipioninstaller, and I think that eventually leads to it finding scipion3. > I can’t tell exactly where the module referred to as “scipion” is located, > but specifying its directory in PYTHONPATH could solve it? > > Otherwise, potentially the directory where the scipion module is found has > permissions that deny user access, and need chmod? > > Hope it doesn’t take too many more knots before it’s working! > Teige > > > On 2 Jun 2021, at 22:50, Morgan Beeby <m....@im...> wrote: > > Dear all, > > I wondered if anyone could help point me in the direction of installing > scipion3 for all users on a machine (ultimately for cluster install for all > users)? I seem to be tying myself in knots with what seems to be a trivial > install. > > As root, I am doing the following to install on Linux Mint 20 (after > insuring all prequisite libraries are installed): > > - pip install scipion-installer > - python -m scipioninstaller /usr/local/bin/scipion3 -venv -j 4 > > Then as user: > > - alias scipion3=/usr/local/bin/scipion3/scipion3 > - scipion3 > > But I get an error: > > - /usr/bin/python: No module named scipion > > (it runs ok for root) > It seems like this should just work, but after hours of playing around, > I've had no success, and I cannot find anything on multiuser installs on > linux. > > thanks, > > Morgan > > > -- > Dr Morgan Beeby > Department of Life Sciences > c/o Department of Chemistry Stores > Imperial College London > Frankland Road > London, SW7 2AZ > United Kingdom > > Office: +44 (0)20 7594 5251 > Web : www.beebylab.org > > ~ ~ ~ > > Schedule a meeting with me: https://go.oncehub.com/MorganBeeby > > ~ ~ ~ > > Drop in office hours, no appointment necessary, over the next 7 days: > > (Teams link > <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NzA4MjI4OGItZmYwOC00Yjk5LThkMzQtNmU1MGI1YjJkYTZh%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) > 12:30pm - 1:00pm (Europe/London), Wednesday 02 Jun > (Teams link > <https://teams.microsoft.com/l/meetup-join/19%3ameeting_OTExZWZhZjctYjdhNC00YmZmLTg3MmUtYzc5NjE1NDkzNWI2%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) > 1:15pm - 1:45pm (Europe/London), Monday 07 Jun > (Teams link > <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NWZlNGZmYzMtMWJjZS00M2Q4LWFhNGQtNTdlYmE2YTFmZjc4%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) > 1:15pm - 1:45pm (Europe/London), Tuesday 08 Jun > > Full schedule and links: http://www.beebylab.org/contact/ > _______________________________________________ > 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: Grigory S. <sha...@gm...> - 2021-06-03 08:53:10
|
Hi Morgan, I have never used venv but I suspect the folder with it is owned by root and other users have no permissions Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Jun 3, 2021 at 8:40 AM Morgan Beeby <m....@im...> wrote: > Dear all, > > I wondered if anyone could help point me in the direction of installing > scipion3 for all users on a machine (ultimately for cluster install for all > users)? I seem to be tying myself in knots with what seems to be a trivial > install. > > As root, I am doing the following to install on Linux Mint 20 (after > insuring all prequisite libraries are installed): > > - pip install scipion-installer > - python -m scipioninstaller /usr/local/bin/scipion3 -venv -j 4 > > Then as user: > > - alias scipion3=/usr/local/bin/scipion3/scipion3 > - scipion3 > > But I get an error: > > - /usr/bin/python: No module named scipion > > (it runs ok for root) > It seems like this should just work, but after hours of playing around, > I've had no success, and I cannot find anything on multiuser installs on > linux. > > thanks, > > Morgan > > > -- > Dr Morgan Beeby > Department of Life Sciences > c/o Department of Chemistry Stores > Imperial College London > Frankland Road > London, SW7 2AZ > United Kingdom > > Office: +44 (0)20 7594 5251 > Web : www.beebylab.org > > ~ ~ ~ > > Schedule a meeting with me: https://go.oncehub.com/MorganBeeby > > ~ ~ ~ > > Drop in office hours, no appointment necessary, over the next 7 days: > > (Teams link > <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NzA4MjI4OGItZmYwOC00Yjk5LThkMzQtNmU1MGI1YjJkYTZh%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) > 12:30pm - 1:00pm (Europe/London), Wednesday 02 Jun > (Teams link > <https://teams.microsoft.com/l/meetup-join/19%3ameeting_OTExZWZhZjctYjdhNC00YmZmLTg3MmUtYzc5NjE1NDkzNWI2%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) > 1:15pm - 1:45pm (Europe/London), Monday 07 Jun > (Teams link > <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NWZlNGZmYzMtMWJjZS00M2Q4LWFhNGQtNTdlYmE2YTFmZjc4%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) > 1:15pm - 1:45pm (Europe/London), Tuesday 08 Jun > > Full schedule and links: http://www.beebylab.org/contact/ > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Teige Matthews-P. <tei...@gm...> - 2021-06-03 08:52:33
|
Hi Morgan, I installed scipion3 and its packages a while ago and remember it was a bit tricky/fussy on Centos7 too. Just some ideas, it seems like user’s python is not searching the directory where the scipion module is, or permissions stop it from finding the module? The scipion launcher /usr/local/scipion3/scipion3 starts with the shebang #!/usr/bin/env python3, which should invoke the default python3 of the user’s environment. I don’t think this would be the issue, but maybe user has a different default python binary? Or, you could use python -c ‘import sys; print(sys.path)’ to print out the directories where python will search for modules. Is it different between root and user? For me, it includes …/python3.8/site-packages , which contains scipioninstaller, and I think that eventually leads to it finding scipion3. I can’t tell exactly where the module referred to as “scipion” is located, but specifying its directory in PYTHONPATH could solve it? Otherwise, potentially the directory where the scipion module is found has permissions that deny user access, and need chmod? Hope it doesn’t take too many more knots before it’s working! Teige > On 2 Jun 2021, at 22:50, Morgan Beeby <m....@im...> wrote: > > Dear all, > > I wondered if anyone could help point me in the direction of installing scipion3 for all users on a machine (ultimately for cluster install for all users)? I seem to be tying myself in knots with what seems to be a trivial install. > > As root, I am doing the following to install on Linux Mint 20 (after insuring all prequisite libraries are installed): > pip install scipion-installer > python -m scipioninstaller /usr/local/bin/scipion3 -venv -j 4 > Then as user: > alias scipion3=/usr/local/bin/scipion3/scipion3 > scipion3 > But I get an error: > > /usr/bin/python: No module named scipion > (it runs ok for root) > > It seems like this should just work, but after hours of playing around, I've had no success, and I cannot find anything on multiuser installs on linux. > > thanks, > > Morgan > > > -- > Dr Morgan Beeby > Department of Life Sciences > c/o Department of Chemistry Stores > Imperial College London > Frankland Road > London, SW7 2AZ > United Kingdom > > Office: +44 (0)20 7594 5251 > Web : www.beebylab.org <x-msg://36/www.beebylab.org> > > ~ ~ ~ > > Schedule a meeting with me: https://go.oncehub.com/MorganBeeby <https://go.oncehub.com/MorganBeeby> > > ~ ~ ~ > > Drop in office hours, no appointment necessary, over the next 7 days: > > (Teams link <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NzA4MjI4OGItZmYwOC00Yjk5LThkMzQtNmU1MGI1YjJkYTZh%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) 12:30pm - 1:00pm (Europe/London), Wednesday 02 Jun > (Teams link <https://teams.microsoft.com/l/meetup-join/19%3ameeting_OTExZWZhZjctYjdhNC00YmZmLTg3MmUtYzc5NjE1NDkzNWI2%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) 1:15pm - 1:45pm (Europe/London), Monday 07 Jun > (Teams link <https://teams.microsoft.com/l/meetup-join/19%3ameeting_NWZlNGZmYzMtMWJjZS00M2Q4LWFhNGQtNTdlYmE2YTFmZjc4%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>) 1:15pm - 1:45pm (Europe/London), Tuesday 08 Jun > > Full schedule and links: http://www.beebylab.org/contact/ <http://www.beebylab.org/contact/> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Morgan B. <m....@im...> - 2021-06-02 14:17:49
|
Dear all,
I wondered if anyone could help point me in the direction of installing
scipion3 for all users on a machine (ultimately for cluster install for
all users)? I seem to be tying myself in knots with what seems to be a
trivial install.
As root, I am doing the following to install on Linux Mint 20 (after
insuring all prequisite libraries are installed):
*
pip install scipion-installer
*
python -m scipioninstaller /usr/local/bin/scipion3 -venv -j 4
Then as user:
* alias scipion3=/usr/local/bin/scipion3/scipion3
* scipion3
But I get an error:
* /usr/bin/python: No module named scipion
(it runs ok for root)
It seems like this should just work, but after hours of playing around,
I've had no success, and I cannot find anything on multiuser installs on
linux.
thanks,
Morgan
--
Dr Morgan Beeby
Department of Life Sciences
c/o Department of Chemistry Stores
Imperial College London
Frankland Road
London, SW7 2AZ
United Kingdom
Office: +44 (0)20 7594 5251
Web : www.beebylab.org <www.beebylab.org>
~ ~ ~
Schedule a meeting with me: https://go.oncehub.com/MorganBeeby
<https://go.oncehub.com/MorganBeeby>
~ ~ ~
Drop in office hours, no appointment necessary, over the next 7 days:
(Teams link
<https://teams.microsoft.com/l/meetup-join/19%3ameeting_NzA4MjI4OGItZmYwOC00Yjk5LThkMzQtNmU1MGI1YjJkYTZh%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>)
12:30pm - 1:00pm (Europe/London), Wednesday 02 Jun
(Teams link
<https://teams.microsoft.com/l/meetup-join/19%3ameeting_OTExZWZhZjctYjdhNC00YmZmLTg3MmUtYzc5NjE1NDkzNWI2%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>)
1:15pm - 1:45pm (Europe/London), Monday 07 Jun
(Teams link
<https://teams.microsoft.com/l/meetup-join/19%3ameeting_NWZlNGZmYzMtMWJjZS00M2Q4LWFhNGQtNTdlYmE2YTFmZjc4%40thread.v2/0?context=%7b%22Tid%22%3a%222b897507-ee8c-4575-830b-4f8267c3d307%22%2c%22Oid%22%3a%22ecb94a12-de34-4549-a7a5-083198e59504%22%7d>)
1:15pm - 1:45pm (Europe/London), Tuesday 08 Jun
Full schedule and links: http://www.beebylab.org/contact/
<http://www.beebylab.org/contact/>
|
|
From: khaja f. t. <kha...@gm...> - 2021-05-31 23:58:12
|
Thanks for this information. On Mon, 31 May 2021, 8:31 pm Grigory Sharov, <sha...@gm...> wrote: > Hi, > > I believe the web tools have been deprecated quite a while ago. You'd have > to install Scipion on your PC. > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Mon, May 31, 2021 at 3:50 PM khaja faisal tarique < > kha...@gm...> wrote: > >> Hi >> >> I am trying to use Resmap and Monores using scipion web tools My Res Map >> using the following link but the webpage is not working. Am I >> doing something wrong? >> >> Link: <http://scipion.cnb.csic.es/m/myresmap> >> http://scipion.cnb.csic.es/m/myresmap >> >> >> Best Regards >> -- >> Faisal Tarique Khaja >> Research Associate >> Indian Institute of Science >> Bangalore, India >> _______________________________________________ >> 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: Grigory S. <sha...@gm...> - 2021-05-31 15:01:32
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Hi, I believe the web tools have been deprecated quite a while ago. You'd have to install Scipion on your PC. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Mon, May 31, 2021 at 3:50 PM khaja faisal tarique < kha...@gm...> wrote: > Hi > > I am trying to use Resmap and Monores using scipion web tools My Res Map > using the following link but the webpage is not working. Am I > doing something wrong? > > Link: <http://scipion.cnb.csic.es/m/myresmap> > http://scipion.cnb.csic.es/m/myresmap > > > Best Regards > -- > Faisal Tarique Khaja > Research Associate > Indian Institute of Science > Bangalore, India > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: khaja f. t. <kha...@gm...> - 2021-05-31 14:50:31
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Hi I am trying to use Resmap and Monores using scipion web tools My Res Map using the following link but the webpage is not working. Am I doing something wrong? Link: <http://scipion.cnb.csic.es/m/myresmap> http://scipion.cnb.csic.es/m/myresmap Best Regards -- Faisal Tarique Khaja Research Associate Indian Institute of Science Bangalore, India |
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