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From: Ipsita B. <ips...@bi...> - 2019-07-08 07:25:40
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Hi Thank you very much.. I will try that and let you know if I still have problems. Thanks and best regards, Ipsita On 8 Jul 2019, at 09:10, Jose Miguel de la Rosa Trevin <del...@gm...<mailto:del...@gm...>> wrote: Hi Ipsita, As Pablo suggested you can try to increase the java memory in the config file. Let us know if the problem persists after that change. Best, Jose Miguel On Mon, Jul 8, 2019 at 8:54 AM Pablo Conesa <pc...@cn...<mailto:pc...@cn...>> wrote: Hi, try to increase java memory setting JAVA_MAX_MEMORY = 3 In your <scipion home>/config/scipion.conf Additionally, try to prune/clean you set as soon as possible. Xmipp screening particles could be usefull to reject bad ones at the begining. El 5 jul. 2019 21:32, Ipsita Banerjee <ips...@bi...<mailto:ips...@bi...>> escribió: Dear Scipion Users, I have a dataset where I have about 2 million picked particles.. I could run relion2D classification for these particles.. However, when I click on the Analyze results button, and try to open the tab "Show classification in Scipion", I don't see anything.. When i click on the tab "show classes only", I can see the classes only.. Please, I need some help as to what I can do to continue with the processing... Thanks so much... Best regards, Ipsita _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> 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 |
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From: Jose M. de la R. T. <del...@gm...> - 2019-07-08 07:10:36
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Hi Ipsita, As Pablo suggested you can try to increase the java memory in the config file. Let us know if the problem persists after that change. Best, Jose Miguel On Mon, Jul 8, 2019 at 8:54 AM Pablo Conesa <pc...@cn...> wrote: > Hi, try to increase java memory setting > JAVA_MAX_MEMORY = 3 > > In your <scipion home>/config/scipion.conf > > Additionally, try to prune/clean you set as soon as possible. > > Xmipp screening particles could be usefull to reject bad ones at the > begining. > > > El 5 jul. 2019 21:32, Ipsita Banerjee <ips...@bi...> > escribió: > > Dear Scipion Users, > > I have a dataset where I have about 2 million picked particles.. I could > run relion2D classification for these particles.. > However, when I click on the Analyze results button, and try to open the > tab "Show classification in Scipion", I don't see anything.. > When i click on the tab "show classes only", I can see the classes only.. > Please, I need some help as to what I can do to continue with the > processing... > > Thanks so much... > > Best regards, > Ipsita > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Pablo C. <pc...@cn...> - 2019-07-08 06:54:00
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<div dir='auto'><div>Hi, try to increase java memory setting </div><div dir="auto"><span style="color: rgb(36, 41, 46); font-family: sfmono-regular, consolas, "liberation mono", menlo, courier, monospace; font-size: 12px; white-space: pre; background-color: rgb(255, 255, 255);">JAVA_MAX_MEMORY = 3</span><br><div class="gmail_extra" dir="auto"><br></div><div class="gmail_extra" dir="auto">In your <scipion home>/config/scipion.conf</div><div class="gmail_extra" dir="auto"><br></div><div class="gmail_extra" dir="auto">Additionally, try to prune/clean you set as soon as possible.</div><div class="gmail_extra" dir="auto"><br></div><div class="gmail_extra" dir="auto">Xmipp screening particles could be usefull to reject bad ones at the begining.</div><div class="gmail_extra" dir="auto"><br></div><div class="gmail_extra" dir="auto"><br><div class="gmail_quote" dir="auto">El 5 jul. 2019 21:32, Ipsita Banerjee <ips...@bi...> escribió:<br type="attribution"><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <div> <div> <div>Dear Scipion Users, <br> <br> I have a dataset where I have about 2 million picked particles.. I could run relion2D classification for these particles.. <br> However, when I click on the Analyze results button, and try to open the tab "Show classification in Scipion", I don't see anything.. <br> When i click on the tab "show classes only", I can see the classes only.. <br> Please, I need some help as to what I can do to continue with the processing... <br> <br> Thanks so much... <br> <br> Best regards, <br> Ipsita</div> <div style="margin-top:1em"></div> </div> </div> </blockquote></div><br></div></div></div> |
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From: Ipsita B. <ips...@bi...> - 2019-07-06 04:14:53
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Hi
I see this kind of error..
matplotlib.use('TkAgg')
java -Xmx2g -d64 -Djava.library.path=/pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC-CUDA/7.3.0-2.30-9.2.88/OpenMPI/3.1.1/Scipion/1.2.1/software/em/xmipp/lib -Dplugins.dir=/pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC-CUDA/7.3.0-2.30-9.2.88/OpenMPI/3.1.1/Scipion/1.2.1/software/em/xmipp/external/imagej/plugins -cp /hpc2n/eb/software/Core/Java/1.8.0_181/lib/*:/pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC-CUDA/7.3.0-2.30-9.2.88/OpenMPI/3.1.1/Scipion/1.2.1/software/em/xmipp/external/imagej/*:/pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC-CUDA/7.3.0-2.30-9.2.88/OpenMPI/3.1.1/Scipion/1.2.1/software/em/xmipp/java/lib/* xmipp.viewer.scipion.ScipionViewer -i "Runs/004703_ProtRelionClassify2D/extra/relion_it015_classes_scipion.sqlite" --render _representative._filename --labels id _size --zoom 100 --visible enabled id _size _representative._filename _rlnclassDistribution _rlnAccuracyRotations _rlnAccuracyTranslations --sortby _size desc --order enabled id _size _representative._filename _rlnclassDistribution _rlnAccuracyRotations _rlnAccuracyTranslations --scipion 42855 4703 3748
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007fb09dc69746, pid=170444, tid=0x00007fb09e7cb700
#
# JRE version: Java(TM) SE Runtime Environment (8.0_181-b13) (build 1.8.0_181-b13)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.181-b13 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C [libc.so.6+0x8b746] strlen+0x26
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /pfs/nobackup/home/s/swami63/ScipionUserData/projects/cem00264_00022_scipion_20190523/hs_err_pid170444.log
#
# If you would like to submit a bug report, please visit:
# http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
/Ipsita
On 5 Jul 2019, at 23:03, Jose Miguel de la Rosa Trevin <del...@gm...<mailto:del...@gm...>> wrote:
Dear Ipsita,
Do you see any error in the terminal after clicking "Show classification with Scipion" ??
Best,
Jose Miguel
On Fri, Jul 5, 2019 at 9:48 PM Ipsita Banerjee <ips...@bi...<mailto:ips...@bi...>> wrote:
Dear Scipion Users,
I have a dataset where I have about 2 million picked particles.. I could run relion2D classification for these particles..
However, when I click on the Analyze results button, and try to open the tab "Show classification in Scipion", I don't see anything..
When i click on the tab "show classes only", I can see the classes only..
Please, I need some help as to what I can do to continue with the processing...
Thanks so much...
Best regards,
Ipsita
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
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: Jose M. de la R. T. <del...@gm...> - 2019-07-05 21:03:47
|
Dear Ipsita, Do you see any error in the terminal after clicking "Show classification with Scipion" ?? Best, Jose Miguel On Fri, Jul 5, 2019 at 9:48 PM Ipsita Banerjee < ips...@bi...> wrote: > Dear Scipion Users, > > I have a dataset where I have about 2 million picked particles.. I could > run relion2D classification for these particles.. > However, when I click on the Analyze results button, and try to open the > tab "Show classification in Scipion", I don't see anything.. > When i click on the tab "show classes only", I can see the classes only.. > Please, I need some help as to what I can do to continue with the > processing... > > Thanks so much... > > Best regards, > Ipsita > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Ipsita B. <ips...@bi...> - 2019-07-05 19:47:44
|
Dear Scipion Users, I have a dataset where I have about 2 million picked particles.. I could run relion2D classification for these particles.. However, when I click on the Analyze results button, and try to open the tab "Show classification in Scipion", I don't see anything.. When i click on the tab "show classes only", I can see the classes only.. Please, I need some help as to what I can do to continue with the processing... Thanks so much... Best regards, Ipsita |
|
From: Victor M. R. A. <vr...@ib...> - 2019-07-04 16:03:16
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Hola Pablo! Muchas gracias por contestar! No soy para nada experto en SQL, tampoco en Scipion, de hecho empecé a usarlo la semana pasada con Javi Chichon allí en el CNB. Te mando el archivo en adjuntos a ver si me lo podeis recomponer. Saludos Victor El jue., 4 jul. 2019 a las 17:33, Pablo Conesa (<pc...@cn...>) escribió: > Hi Victor, we've seen this before but still do not understand how it > happens and how to prevent this. > > To fix it we need to fix your project.sqlite. > > Unless you are proficient in SQL, the best option is to send us your > project.sqlite (it should be right in your project folder at > $HOME/ScipionUserData/projects/<my project name>/project.sqlite. > > > On 4/7/19 15:59, Victor Manuel Ruiz Arroyo wrote: > > Hello, > I closed scipion and when reopened I obtained this error: > > Scipion v2.0 (2019-04-23) Diocletian >> >> >>>>> python /opt/scipion/pyworkflow/apps/pw_manager.py >> Using TensorFlow backend. >> Using TensorFlow backend. >> Traceback (most recent call last): >> File "/opt/scipion/pyworkflow/apps/pw_project.py", line 82, in <module> >> projWindow = ProjectWindow(projPath) >> File "/opt/scipion/pyworkflow/gui/project/project.py", line 125, in >> __init__ >> self.switchView(VIEW_PROTOCOLS) >> File "/opt/scipion/pyworkflow/gui/project/base.py", line 150, in >> switchView >> self.viewWidget = self.viewFuncs[newView](self.footer, self) >> File "/opt/scipion/pyworkflow/gui/project/viewprotocols.py", line 640, >> in __init__ >> c = self.createContent() >> File "/opt/scipion/pyworkflow/gui/project/viewprotocols.py", line 709, >> in createContent >> self.createRunsGraph(runsFrame) >> File "/opt/scipion/pyworkflow/gui/project/viewprotocols.py", line 1097, >> in createRunsGraph >> self.updateRunsGraph() >> File "/opt/scipion/pyworkflow/gui/project/viewprotocols.py", line 1102, >> in updateRunsGraph >> checkPids=checkPids) >> File "/opt/scipion/pyworkflow/project/project.py", line 1328, in >> getRunsGraph >> self._runsGraph = self.getGraphFromRuns(runs) >> File "/opt/scipion/pyworkflow/project/project.py", line 1346, in >> getGraphFromRuns >> for _, attr in r.iterOutputAttributes(): >> File "/opt/scipion/pyworkflow/protocol/protocol.py", line 738, in >> iterOutputAttributes >> for key, attr in iterator(): >> File "/opt/scipion/pyworkflow/protocol/protocol.py", line 750, in >> _iterOutputsNew >> attr = getattr(self, attrName) >> AttributeError: 'XmippParticlePickingAutomatic' object has no attribute >> 'outputCoordinates2' >> > > I would be very thankfull if somebody could say me how to fix the error. > > Thanks in advance > > > _______________________________________________ > 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...> - 2019-07-04 15:31:58
|
Hi Victor, we've seen this before but still do not understand how it happens and how to prevent this. To fix it we need to fix your project.sqlite. Unless you are proficient in SQL, the best option is to send us your project.sqlite (it should be right in your project folder at $HOME/ScipionUserData/projects/<my project name>/project.sqlite. On 4/7/19 15:59, Victor Manuel Ruiz Arroyo wrote: > Hello, > I closed scipion and when reopened I obtained this error: > > Scipion v2.0 (2019-04-23) Diocletian > > >>>>> python /opt/scipion/pyworkflow/apps/pw_manager.py > Using TensorFlow backend. > Using TensorFlow backend. > Traceback (most recent call last): > File "/opt/scipion/pyworkflow/apps/pw_project.py", line 82, in > <module> > projWindow = ProjectWindow(projPath) > File "/opt/scipion/pyworkflow/gui/project/project.py", line 125, > in __init__ > self.switchView(VIEW_PROTOCOLS) > File "/opt/scipion/pyworkflow/gui/project/base.py", line 150, in > switchView > self.viewWidget = self.viewFuncs[newView](self.footer, self) > File "/opt/scipion/pyworkflow/gui/project/viewprotocols.py", > line 640, in __init__ > c = self.createContent() > File "/opt/scipion/pyworkflow/gui/project/viewprotocols.py", > line 709, in createContent > self.createRunsGraph(runsFrame) > File "/opt/scipion/pyworkflow/gui/project/viewprotocols.py", > line 1097, in createRunsGraph > self.updateRunsGraph() > File "/opt/scipion/pyworkflow/gui/project/viewprotocols.py", > line 1102, in updateRunsGraph > checkPids=checkPids) > File "/opt/scipion/pyworkflow/project/project.py", line 1328, in > getRunsGraph > self._runsGraph = self.getGraphFromRuns(runs) > File "/opt/scipion/pyworkflow/project/project.py", line 1346, in > getGraphFromRuns > for _, attr in r.iterOutputAttributes(): > File "/opt/scipion/pyworkflow/protocol/protocol.py", line 738, > in iterOutputAttributes > for key, attr in iterator(): > File "/opt/scipion/pyworkflow/protocol/protocol.py", line 750, > in _iterOutputsNew > attr = getattr(self, attrName) > AttributeError: 'XmippParticlePickingAutomatic' object has no > attribute 'outputCoordinates2' > > > I would be very thankfull if somebody could say me how to fix the error. > > Thanks in advance > > > _______________________________________________ > 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: Victor M. R. A. <vr...@ib...> - 2019-07-04 14:24:01
|
Hello, I closed scipion and when reopened I obtained this error: Scipion v2.0 (2019-04-23) Diocletian > > >>>>> python /opt/scipion/pyworkflow/apps/pw_manager.py > Using TensorFlow backend. > Using TensorFlow backend. > Traceback (most recent call last): > File "/opt/scipion/pyworkflow/apps/pw_project.py", line 82, in <module> > projWindow = ProjectWindow(projPath) > File "/opt/scipion/pyworkflow/gui/project/project.py", line 125, in > __init__ > self.switchView(VIEW_PROTOCOLS) > File "/opt/scipion/pyworkflow/gui/project/base.py", line 150, in > switchView > self.viewWidget = self.viewFuncs[newView](self.footer, self) > File "/opt/scipion/pyworkflow/gui/project/viewprotocols.py", line 640, > in __init__ > c = self.createContent() > File "/opt/scipion/pyworkflow/gui/project/viewprotocols.py", line 709, > in createContent > self.createRunsGraph(runsFrame) > File "/opt/scipion/pyworkflow/gui/project/viewprotocols.py", line 1097, > in createRunsGraph > self.updateRunsGraph() > File "/opt/scipion/pyworkflow/gui/project/viewprotocols.py", line 1102, > in updateRunsGraph > checkPids=checkPids) > File "/opt/scipion/pyworkflow/project/project.py", line 1328, in > getRunsGraph > self._runsGraph = self.getGraphFromRuns(runs) > File "/opt/scipion/pyworkflow/project/project.py", line 1346, in > getGraphFromRuns > for _, attr in r.iterOutputAttributes(): > File "/opt/scipion/pyworkflow/protocol/protocol.py", line 738, in > iterOutputAttributes > for key, attr in iterator(): > File "/opt/scipion/pyworkflow/protocol/protocol.py", line 750, in > _iterOutputsNew > attr = getattr(self, attrName) > AttributeError: 'XmippParticlePickingAutomatic' object has no attribute > 'outputCoordinates2' > I would be very thankfull if somebody could say me how to fix the error. Thanks in advance |
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From: Gregory S. <sha...@gm...> - 2019-06-27 16:51:57
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yes, if you use Scipion 2.0.0 with latest relion plugin 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 267542 <+44%201223%20267542> e-mail: gs...@mr... On Thu, Jun 27, 2019 at 4:19 PM Dmitry Semchonok <sem...@gm...> wrote: > Dear colleagues, > > Is it posible to do the CTF refinement/Bayesian polishing in SCIPION? > If yes then how? > > Sincerely, > Dmitry > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry S. <sem...@gm...> - 2019-06-27 15:18:59
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Dear colleagues, Is it posible to do the CTF refinement/Bayesian polishing in SCIPION? If yes then how? Sincerely, Dmitry |
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From: Pablo C. <pc...@cn...> - 2019-06-26 16:01:00
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If you reach export particles you should be able to do "relion export particles" and will get relion star files. Alternatively, you can start a "relion extract particles", which in it's initial step will generate the star files needed by relion to do the extraction. On 26/6/19 17:44, Dmitry Semchonok wrote: > Dear Pablo, > > Yes I would like to have 1 coordinate file per micrograph. > > But also 1 file for all particles should work (I hope)\ > > > So how to do that? > > Thank you > > Sincerely, > Dmitry > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Dmitry S. <sem...@gm...> - 2019-06-26 15:44:32
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Dear Pablo, Yes I would like to have 1 coordinate file per micrograph. But also 1 file for all particles should work (I hope)\ So how to do that? Thank you Sincerely, Dmitry |
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From: Pablo C. <pc...@cn...> - 2019-06-26 12:23:15
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Dmitry, do you want 1 star file per micrograph? On 26/6/19 11:47, Dmitry A. Semchonok wrote: > Dear colleagues, > > > I would like to extract the coordinates form the set of picked > particles to have 1 coordinate file per image. > > > I tried Scipion extract file protocol but it doesn't have the files of > the coordinates in the folder. > > > Any suggestions? > > > Thank you. > > > Sincerely, > Dmitry > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Dmitry A. S. <sem...@gm...> - 2019-06-26 09:47:04
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Dear colleagues, I would like to extract the coordinates form the set of picked particles to have 1 coordinate file per image. I tried Scipion extract file protocol but it doesn't have the files of the coordinates in the folder. Any suggestions? Thank you. Sincerely, Dmitry |
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From: Pablo C. <pc...@cn...> - 2019-06-14 13:07:45
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Great! On 13/6/19 15:22, Wood, Katie wrote: > > Thank you Laura and Pablo, > > I have checked my config file and for both eman2 and chimera my > version numbers were wrong. I have corrected it now and rebooted > scipion, and chimera and eman2 work now! Thanks for your help! > > Best wishes, > > Katherine > > *From: *Laura <lde...@cn...> > *Reply-To: *Mailing list for Scipion users > <sci...@li...> > *Date: *Thursday, 13 June 2019 at 14:12 > *To: *"sci...@li..." > <sci...@li...> > *Subject: *Re: [scipion-users] eman2 and chimera issues > > Hi Katherine, > > it seems that you are trying to use eman-2.12 while scipion > automatically installs 2.21. > > Could you check your environmental variables opening the plugin > manager and then Configuration/Variables on the top menu? > > For instance I have: > > cid:par...@cn... > > If you are using eman 2.12 you should add the variable with your > version either on your $HOME/.config/scipion/scipion.conf file or on > the scipion one (scipion_path/config/scipion.conf) > > Regarding chimera, check that whatever is on CHIMERA_HOME variable exists. > > any doubt just ask > > best regards > > Laura > > On 13/6/19 13:10, Wood, Katie wrote: > > Hello, > > I’m having some problems using the eman2 programs in scipion. I > put in all the variables the easy refine program asks me for but I > end up with the following error whenever I try to execute the program: > > /Missing Variables: / > > /EMAN2DIR: /home/u1666362/software/scipion/software/em/eman-2.12/ > > // > > I get the same error when trying to run a different eman2 program, > but it doesn't happen for relion or xmipp, so I’m assuming I need > to alter something eman2 related. I was wondering if anyone knew > how to fix this? I couldn't find any answers on the mailing list > so far. > > Also when I try to use the chimera viewer for 3D volumes it says I > haven’t installed the chimera plugin, however, I have installed > the plugin so I don’t know what to do to fix this either. I do > have chimera installed though on my pc (not the plugin from > scipion, so have two chimeras essentially) which works and was > there before I installed scipion. Do I need to uninstall that? > > Thanks in advance! > > Best wishes, > > Katherine Wood > > > > > _______________________________________________ > > scipion-users mailing list > > sci...@li... <mailto:sci...@li...> > > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Arshad, R. <r.a...@ru...> - 2019-06-14 08:42:13
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Dear All, I want to improve local resolution of core part of cryo-EM structure, as it shows flexibility at periphery. I am trying masked 3D classification and auto-refinement in relion using a mask generated from pdb (added in 'reference mask' tab). Unfortunately, the structure gets distorted at refinement step. Should I include an extra step between 3D alignment and auto-refinement? Moreover, I would also like to try signal subtraction from flexible part of 3D map. Can somebody explain the correct way to do it in scipion? Thanks in advance. Best regards, Rameez Arshad -- Rameez Arshad, PhD student | Electron Microscopy Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 7, 9747 AG, Groningen, The Netherlands +31 50 363 4378 |
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From: Wood, K. <K.W...@wa...> - 2019-06-13 13:54:57
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Thank you Laura and Pablo, I have checked my config file and for both eman2 and chimera my version numbers were wrong. I have corrected it now and rebooted scipion, and chimera and eman2 work now! Thanks for your help! Best wishes, Katherine From: Laura <lde...@cn...> Reply-To: Mailing list for Scipion users <sci...@li...> Date: Thursday, 13 June 2019 at 14:12 To: "sci...@li..." <sci...@li...> Subject: Re: [scipion-users] eman2 and chimera issues Hi Katherine, it seems that you are trying to use eman-2.12 while scipion automatically installs 2.21. Could you check your environmental variables opening the plugin manager and then Configuration/Variables on the top menu? For instance I have: [cid:par...@cn...] If you are using eman 2.12 you should add the variable with your version either on your $HOME/.config/scipion/scipion.conf file or on the scipion one (scipion_path/config/scipion.conf) Regarding chimera, check that whatever is on CHIMERA_HOME variable exists. any doubt just ask best regards Laura On 13/6/19 13:10, Wood, Katie wrote: Hello, I’m having some problems using the eman2 programs in scipion. I put in all the variables the easy refine program asks me for but I end up with the following error whenever I try to execute the program: Missing Variables: EMAN2DIR: /home/u1666362/software/scipion/software/em/eman-2.12 I get the same error when trying to run a different eman2 program, but it doesn't happen for relion or xmipp, so I’m assuming I need to alter something eman2 related. I was wondering if anyone knew how to fix this? I couldn't find any answers on the mailing list so far. Also when I try to use the chimera viewer for 3D volumes it says I haven’t installed the chimera plugin, however, I have installed the plugin so I don’t know what to do to fix this either. I do have chimera installed though on my pc (not the plugin from scipion, so have two chimeras essentially) which works and was there before I installed scipion. Do I need to uninstall that? Thanks in advance! Best wishes, Katherine Wood _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Laura <lde...@cn...> - 2019-06-13 13:10:40
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Hi Katherine, it seems that you are trying to use eman-2.12 while scipion automatically installs 2.21. Could you check your environmental variables opening the plugin manager and then Configuration/Variables on the top menu? For instance I have: If you are using eman 2.12 you should add the variable with your version either on your $HOME/.config/scipion/scipion.conf file or on the scipion one (scipion_path/config/scipion.conf) Regarding chimera, check that whatever is on CHIMERA_HOME variable exists. any doubt just ask best regards Laura On 13/6/19 13:10, Wood, Katie wrote: > > Hello, > > I’m having some problems using the eman2 programs in scipion. I put in > all the variables the easy refine program asks me for but I end up > with the following error whenever I try to execute the program: > > /Missing Variables: / > > /EMAN2DIR: /home/u1666362/software/scipion/software/em/eman-2.12/ > > // > > I get the same error when trying to run a different eman2 program, but > it doesn't happen for relion or xmipp, so I’m assuming I need to alter > something eman2 related. I was wondering if anyone knew how to fix > this? I couldn't find any answers on the mailing list so far. > > Also when I try to use the chimera viewer for 3D volumes it says I > haven’t installed the chimera plugin, however, I have installed the > plugin so I don’t know what to do to fix this either. I do have > chimera installed though on my pc (not the plugin from scipion, so > have two chimeras essentially) which works and was there before I > installed scipion. Do I need to uninstall that? > > Thanks in advance! > > Best wishes, > > Katherine Wood > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Pablo C. <pc...@cn...> - 2019-06-13 13:08:20
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<div dir='auto'>Hi, you are probably using previous version of scipion config. Could you send the content of your $HOME/.config/scipion/scipion.conf?<div dir="auto"><br></div><div dir="auto">You might be pointing to Eman 2.12 but probably have 2.21 installed.</div><div dir="auto"><br></div><div dir="auto">If so you can:</div><div dir="auto">A. Move away the config file and make a fresh one ("scipion config" will generate it)</div><div dir="auto">B. Edit the existing config file to point to the installed version of Eman..</div><div dir="auto">C. Install Eman 2.12</div><div dir="auto"><br></div><div dir="auto">Cheers, Pablo.</div></div><div class="gmail_extra"><br><div class="gmail_quote">El 13 jun. 2019 13:10, "Wood, Katie" <K.W...@wa...> escribió:<br type="attribution" /><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>
<div>
<p><span style="font-size:11pt">Hello,</span></p>
<p><span style="font-size:11pt"> </span></p>
<p><span style="font-size:11pt">I’m having some problems using the eman2 programs in scipion. I put in all the variables the easy refine program asks me for but I end up with the following error whenever I try to execute the program:</span></p>
<p><span style="font-size:11pt"> </span></p>
<p><i><span style="font-size:11pt">Missing Variables: </span></i></p>
<p><i><span style="font-size:11pt">EMAN2DIR: /home/u1666362/software/scipion/software/em/eman-2.12</span></i></p>
<p><i><span style="font-size:11pt"> </span></i></p>
<p><span style="font-size:11pt">I get the same error when trying to run a different eman2 program, but it doesn't happen for relion or xmipp, so I’m assuming I need to alter something eman2 related. I was wondering if anyone knew how to
fix this? I couldn't find any answers on the mailing list so far.</span></p>
<p><span style="font-size:11pt"> </span></p>
<p><span style="font-size:11pt">Also when I try to use the chimera viewer for 3D volumes it says I haven’t installed the chimera plugin, however, I have installed the plugin so I don’t know what to do to fix this either. I do have chimera
installed though on my pc (not the plugin from scipion, so have two chimeras essentially) which works and was there before I installed scipion. Do I need to uninstall that?</span></p>
<p><span style="font-size:11pt"> </span></p>
<p><span style="font-size:11pt">Thanks in advance!</span></p>
<p><span style="font-size:11pt"> </span></p>
<p><span style="font-size:11pt">Best wishes,</span></p>
<p><span style="font-size:11pt"> </span></p>
<p><span style="font-size:11pt">Katherine Wood</span></p>
</div>
</div>
</blockquote></div><br></div> |
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From: Wood, K. <K.W...@wa...> - 2019-06-13 12:43:24
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Hello, I’m having some problems using the eman2 programs in scipion. I put in all the variables the easy refine program asks me for but I end up with the following error whenever I try to execute the program: Missing Variables: EMAN2DIR: /home/u1666362/software/scipion/software/em/eman-2.12 I get the same error when trying to run a different eman2 program, but it doesn't happen for relion or xmipp, so I’m assuming I need to alter something eman2 related. I was wondering if anyone knew how to fix this? I couldn't find any answers on the mailing list so far. Also when I try to use the chimera viewer for 3D volumes it says I haven’t installed the chimera plugin, however, I have installed the plugin so I don’t know what to do to fix this either. I do have chimera installed though on my pc (not the plugin from scipion, so have two chimeras essentially) which works and was there before I installed scipion. Do I need to uninstall that? Thanks in advance! Best wishes, Katherine Wood |
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From: Lugmayr, W. <w.l...@uk...> - 2019-06-13 09:22:49
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hi david, sorry it took a while to try your tip. now i have a python problem: cmake -DWITH_FFMPEG=OFF -DWITH_CUDA:BOOL=ON-DWITH_LIBV4L=ON-DWITH_V4L=OFF -DCMAKE_INSTALL_PREFIX:PATH=/beegfs/cssb/software/em/scipion/2.0/software . > /beegfs/cssb/software/em/scipion/2.0/software/log/opencv_cmake.log 2>&1 Error: target '/beegfs/cssb/software/em/scipion/2.0/software/tmp/opencv-2.4.13/Makefile' not built (after running 'cmake -DWITH_FFMPEG=OFF -DWITH_CUDA:BOOL=ON-DWITH_LIBV4L=ON-DWITH_V4L=OFF -DCMAKE_INSTALL_PREFIX:PATH=/beegfs/cssb/software/em/scipion/2.0/software . > /beegfs/cssb/software/em/scipion/2.0/software/log/opencv_cmake.log 2>&1') the lines in the log are: -- Could NOT find PythonLibs: Found unsuitable version "2.7.5", but required is exact version "2.7.15" (found /lib64/libpython2.7.so) : -- Python: -- Interpreter: /beegfs/cssb/software/em/scipion/2.0/software/bin/python2 (ver 2.7.15) -- Libraries: /lib64/libpython2.7.so (ver 2.7.5) -- numpy: /beegfs/cssb/software/em/scipion/2.0/software/lib/python2.7/site-packages/numpy/core/include (ver 1.14.1) -- packages path: lib/python2.7/site-packages so if i do in a new login terminal: $ ldd /beegfs/cssb/software/em/scipion/2.0/software/bin/python2 libpython2.7.so.1.0 => /lib64/libpython2.7.so.1.0 (0x00002b49812b3000) i also made an environment module to set the LD_LIBRARY_PATH to the right location and then: $ ldd /beegfs/cssb/software/em/scipion/2.0/software/bin/python2 libpython2.7.so.1.0 => /beegfs/cssb/software/em/scipion/2.0/software/lib/libpython2.7.so.1.0 (0x00002afad38b5000) but the scipion install seems to ignore these LD_LIBRARY_PATH cheers, wolfgang From: "David Maluenda" <dma...@cn...> To: "Mailing list for Scipion users" <sci...@li...> Sent: Wednesday, 29 May, 2019 10:40:48 Subject: Re: [scipion-users] OpenCV not found for Xmipp Hi David, Wolfgang and Scipion users, Regarding the first question of why the openCV code of Xmipp is not compailing when OpenCV is in a alternate location, Xmipp needs the headers files of OpenCV to compile that part of the code, thus you must have installed the devel version of the OpenCV package and, also, the include folder of the openCV must be seeable during the compilation time. Regarding the libtiff versions fight, yes Scipion has libtiff5, then if other libtiff is used to compile the system's openCV, it will fail. Both issues might be fixed by installing OpenCV inside Scipion via $ cd $SCIPION_HOME $ ./scipion install opencv -j N where N is the number of processors (take into account that this installation takes a while, thus the bigger N is better). NOTE: Regarding the OpenCV inside Scipion, we have using the OpenCV-v2.4.13 by default and we have checked that it works fine for Centos7 and Ubuntu16. However, for Ubuntu 18, we have observed that the OpenCV-v3.4.1 should be used. Therefore, if you use Ubuntu18, you should edit the $SCIPION_HOME/config/scipion.conf in such a way that OPENCV_VER=3.4.1 and then install opencv using the command above (this only works if Scipion is installed from sources, not from binaries). Finally, just to note that OpenCV is used by Xmipp only for two non critical protocols (Optical Alignment and Enric -former Volume Homogenizer-). Therefore, if you don't need this two protocols and it still not working even with the hints pointed out above, the OpenCV code in Xmipp can be ignored by editing $SCIPION_HOME/config/scipion.conf in such a way that OPENCV=False and, then, trying to compile Xmipp again. I hope tht it will help and my appologies for the late reply. Thanks for reporting! [ http://ucm.es/ ] _____ Dr. David Maluenda Niubó [ mailto:dma...@cn... | dma...@cn... ] - (+34) 619 029 310 [ http://www.cnb.csic.es/ | CSIC - Centro Nacional de Biotecnología ] [ http://biocomputingunit.es/ | BioComputing Unit ] This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. On Tue, May 28, 2019 at 6:12 PM Hoover, David (NIH/CIT) [E] via scipion-users < [ mailto:sci...@li... | sci...@li... ] > wrote: No. I've been attempting to compile Xmipp from source, but that is even harder. David Hoover HPC @ NIH On 5/27/2019 11:28 AM, Pablo Conesa wrote: > Hi David! Have we ever replied to you with a solution? > > On 23/5/19 17:09, Hoover, David (NIH/CIT) [E] via scipion-users wrote: >> Hi, >> >> I recently installed Scipion 2.0 and all the plugins, and attempted to run the tutorials. We have OpenCV installed in an alternate location, and I make it available by setting $PATH and $LD_LIBRARY_PATH. I keep getting complaints that it is not installed, and that I should fix this and reinstall Xmipp. >> >> How does Xmipp know where OpenCV is? Can I set a configuration somewhere stating where it is located? >> >> David Hoover >> HPC @ NIH >> >> >> _______________________________________________ >> scipion-users mailing list >> [ mailto:sci...@li... | sci...@li... ] >> [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] > > > _______________________________________________ > scipion-users mailing list > [ mailto:sci...@li... | sci...@li... ] > [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | 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 |
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From: Hoover, D. (NIH/C. [E] <hoo...@hp...> - 2019-05-30 15:36:47
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On 5/30/2019 4:32 AM, Pablo Conesa wrote: > > On 29/5/19 16:52, Hoover, David (NIH/CIT) [E] via scipion-users wrote: >> Is there a way of compiling fftw within Scipion as well? We have fftw installed in an alternate location, and the Scipion compilation mechanism does not accept CFLAGS or CXXFLAGS. > > I would try this: > > 1.- move all libfftw3* under <scipion-home>/software/lib > > 2.- ln -s <path to your libfftw3.so> <scipion-home>/software/lib/ > > This way scipion will not try to install it's own fftw3 lib. > > You might need to recompile xmipp (may be not). Relion uses it's own fftw3, unless you also have your own installation. I found it much simpler and reliable to recompile opencv, fftw3 and fftw3f within scipion. Yes, this entails compiling Xmipp from source, and yes it takes boatloads of time (about 3 hours on 32 cpus), but it is worth it for sanity's sake. At least the compilation does not fail at the very end with some bizarre linker error... As for Relion, I can always recompile that outside of Scipion. > > Looking at the code.....exporting CFLAGS or CXXFLAGS should also work but couldn't find any confirmation in the make or make install log files. Not sure about this. > This does NOT work. When you compile from source within Scipion a setup config file is generated (at least for Xmipp, in software/em/xmippSrc-v3.19.04/xmipp.conf) that overrides any preset environment variables. I couldn't find a way of inheriting CCFLAGS or CXXFLAGS without hacking the code. Allowing additional variables (LD_LIBRARY_PATH, LIBRARY_PATH, C_INCLUDE_PATH) might be a good enhancement for those of us who have multiple versions of core libraries available in a multiuser environment. > Cheers, Pablo > > Madrid Scipion team |
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From: Pablo C. <pc...@cn...> - 2019-05-30 08:32:45
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On 29/5/19 16:52, Hoover, David (NIH/CIT) [E] via scipion-users wrote: > Is there a way of compiling fftw within Scipion as well? We have fftw installed in an alternate location, and the Scipion compilation mechanism does not accept CFLAGS or CXXFLAGS. I would try this: 1.- move all libfftw3* under <scipion-home>/software/lib 2.- ln -s <path to your libfftw3.so> <scipion-home>/software/lib/ This way scipion will not try to install it's own fftw3 lib. You might need to recompile xmipp (may be not). Relion uses it's own fftw3, unless you also have your own installation. Looking at the code.....exporting CFLAGS or CXXFLAGS should also work but couldn't find any confirmation in the make or make install log files. Not sure about this. Cheers, Pablo Madrid Scipion team > > David Hoover > HPC @ NIH > > On 5/29/2019 4:40 AM, David Maluenda wrote: >> Hi David, Wolfgang and Scipion users, >> >> Regarding the first question of why the openCV code of Xmipp is not compailing when OpenCV is in a alternate location, Xmipp needs the headers files of OpenCV to compile that part of the code, thus you must have installed the devel version of the OpenCV package and, also, the include folder of the openCV must be seeable during the compilation time. >> >> Regarding the libtiff versions fight, yes Scipion has libtiff5, then if other libtiff is used to compile the system's openCV, it will fail. >> >> Both issues might be fixed by installing OpenCV inside Scipion via >> >> $ cd $SCIPION_HOME >> $ ./scipion install opencv -j N >> >> where N is the number of processors (take into account that this installation takes a while, thus the bigger N is better). >> >> NOTE: Regarding the OpenCV inside Scipion, we have using the OpenCV-v2.4.13 by default and we have checked that it works fine for Centos7 and Ubuntu16. However, for Ubuntu 18, we have observed that the OpenCV-v3.4.1 should be used. Therefore, if you use Ubuntu18, you should edit the$SCIPION_HOME/config/scipion.conf in such a way that OPENCV_VER=3.4.1 and then install opencv using the command above (this only works if Scipion is installed from sources, not from binaries). >> >> >> Finally, just to note that OpenCV is used by Xmipp only for two non critical protocols (Optical Alignment and Enric -former Volume Homogenizer-). Therefore, if you don't need this two protocols and it still not working even with the hints pointed out above, the OpenCV code in Xmipp can be ignored by editing $SCIPION_HOME/config/scipion.conf in such a way that OPENCV=False and, then, trying to compile Xmipp again. >> >> >> I hope tht it will help and my appologies for the late reply. >> >> >> Thanks for reporting! >> >> <http://ucm.es/> >> *_____ >> Dr. David Maluenda Niubó* >> dma...@cn... <mailto:dma...@cn...> - (+34) 619 029 310 >> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es> >> BioComputing Unit <http://biocomputingunit.es/> >> >> This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. >> >> >> >> On Tue, May 28, 2019 at 6:12 PM Hoover, David (NIH/CIT) [E] via scipion-users <sci...@li... <mailto:sci...@li...>> wrote: >> >> No. I've been attempting to compile Xmipp from source, but that is even harder. >> >> David Hoover >> HPC @ NIH >> >> On 5/27/2019 11:28 AM, Pablo Conesa wrote: >> > Hi David! Have we ever replied to you with a solution? >> > >> > On 23/5/19 17:09, Hoover, David (NIH/CIT) [E] via scipion-users wrote: >> >> Hi, >> >> >> >> I recently installed Scipion 2.0 and all the plugins, and attempted to run the tutorials. We have OpenCV installed in an alternate location, and I make it available by setting $PATH and $LD_LIBRARY_PATH. I keep getting complaints that it is not installed, and that I should fix this and reinstall Xmipp. >> >> >> >> How does Xmipp know where OpenCV is? Can I set a configuration somewhere stating where it is located? >> >> >> >> David Hoover >> >> HPC @ NIH >> >> >> >> >> >> _______________________________________________ >> >> scipion-users mailing list >> >> sci...@li... <mailto:sci...@li...> >> >> 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 >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Hoover, D. (NIH/C. [E] <hoo...@hp...> - 2019-05-29 14:54:50
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Is there a way of compiling fftw within Scipion as well? We have fftw installed in an alternate location, and the Scipion compilation mechanism does not accept CFLAGS or CXXFLAGS. David Hoover HPC @ NIH On 5/29/2019 4:40 AM, David Maluenda wrote: > Hi David, Wolfgang and Scipion users, > > Regarding the first question of why the openCV code of Xmipp is not compailing when OpenCV is in a alternate location, Xmipp needs the headers files of OpenCV to compile that part of the code, thus you must have installed the devel version of the OpenCV package and, also, the include folder of the openCV must be seeable during the compilation time. > > Regarding the libtiff versions fight, yes Scipion has libtiff5, then if other libtiff is used to compile the system's openCV, it will fail. > > Both issues might be fixed by installing OpenCV inside Scipion via > > $ cd $SCIPION_HOME > $ ./scipion install opencv -j N > > where N is the number of processors (take into account that this installation takes a while, thus the bigger N is better). > > NOTE: Regarding the OpenCV inside Scipion, we have using the OpenCV-v2.4.13 by default and we have checked that it works fine for Centos7 and Ubuntu16. However, for Ubuntu 18, we have observed that the OpenCV-v3.4.1 should be used. Therefore, if you use Ubuntu18, you should edit the$SCIPION_HOME/config/scipion.conf in such a way that OPENCV_VER=3.4.1 and then install opencv using the command above (this only works if Scipion is installed from sources, not from binaries). > > > Finally, just to note that OpenCV is used by Xmipp only for two non critical protocols (Optical Alignment and Enric -former Volume Homogenizer-). Therefore, if you don't need this two protocols and it still not working even with the hints pointed out above, the OpenCV code in Xmipp can be ignored by editing $SCIPION_HOME/config/scipion.conf in such a way that OPENCV=False and, then, trying to compile Xmipp again. > > > I hope tht it will help and my appologies for the late reply. > > > Thanks for reporting! > > <http://ucm.es/> > *_____ > Dr. David Maluenda Niubó* > dma...@cn... <mailto:dma...@cn...> - (+34) 619 029 310 > CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es> > BioComputing Unit <http://biocomputingunit.es/> > > This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. > > > > On Tue, May 28, 2019 at 6:12 PM Hoover, David (NIH/CIT) [E] via scipion-users <sci...@li... <mailto:sci...@li...>> wrote: > > No. I've been attempting to compile Xmipp from source, but that is even harder. > > David Hoover > HPC @ NIH > > On 5/27/2019 11:28 AM, Pablo Conesa wrote: > > Hi David! Have we ever replied to you with a solution? > > > > On 23/5/19 17:09, Hoover, David (NIH/CIT) [E] via scipion-users wrote: > >> Hi, > >> > >> I recently installed Scipion 2.0 and all the plugins, and attempted to run the tutorials. We have OpenCV installed in an alternate location, and I make it available by setting $PATH and $LD_LIBRARY_PATH. I keep getting complaints that it is not installed, and that I should fix this and reinstall Xmipp. > >> > >> How does Xmipp know where OpenCV is? Can I set a configuration somewhere stating where it is located? > >> > >> David Hoover > >> HPC @ NIH > >> > >> > >> _______________________________________________ > >> scipion-users mailing list > >> sci...@li... <mailto:sci...@li...> > >> 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 > > > > _______________________________________________ > scipion-users mailing list > sci...@li... <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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