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From: Pablo C. <pc...@cn...> - 2018-01-15 13:51:00
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Thanks Gregory, I had a look too and that is the closest solution you can get now. Just to be more precise..... JOB_SCRIPT will have/?: ~/ScipionUserData/projects/my_project/Runs/000367_ProtRelionRefine3D/logs/job7113248.job.out ~/ScipionUserData/projects/my_project/Runs/000367_ProtRelionRefine3D/logs/job7113248.job.err Haven't run it, just guessing from the code. On 15/01/18 12:06, Gregory Sharov wrote: > Hi Daniel, > > I believe you can achieve this by using "#SBATCH -o > %_(JOB_SCRIPT)s.out -e %_(JOB_SCRIPT)s.err" > > > > 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 <tel:+44%201223%20267542> > e-mail: gs...@mr... <mailto:gs...@mr...> > > On Fri, Jan 12, 2018 at 8:39 AM, Daniel Larsson > <dan...@ic... <mailto:dan...@ic...>> wrote: > > Hi, > > I'm trying to customize my hosts.conf file for a SLURM batch > system. Currently, the .out and the .err files end up in the root > of my project directory e.g. > "~/ScipionUserData/projects/my_project/job7113248.out". I have the > SLURM variables set by: "#SBATCH -o job%%j.out -e job%%j.err". > > Instead I'd prefer if the .out and .err could go into the 'logs' > directory for the specific run together with the rest of the log > files. E.g > "~/ScipionUserData/projects/my_project/Runs/000367_ProtRelionRefine3D/logs/job7113248.out". > > Is there a way to achieve that? > > Regards, > Daniel > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > 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> > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Gregory S. <sha...@gm...> - 2018-01-15 11:06:49
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Hi Daniel, I believe you can achieve this by using "#SBATCH -o %_(JOB_SCRIPT)s.out -e %_(JOB_SCRIPT)s.err" 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 Fri, Jan 12, 2018 at 8:39 AM, Daniel Larsson <dan...@ic...> wrote: > Hi, > > I'm trying to customize my hosts.conf file for a SLURM batch system. > Currently, the .out and the .err files end up in the root of my project > directory e.g. "~/ScipionUserData/projects/my_project/job7113248.out". I > have the SLURM variables set by: "#SBATCH -o job%%j.out -e job%%j.err". > > Instead I'd prefer if the .out and .err could go into the 'logs' directory > for the specific run together with the rest of the log files. E.g > "~/ScipionUserData/projects/my_project/Runs/000367_ > ProtRelionRefine3D/logs/job7113248.out". > > Is there a way to achieve that? > > Regards, > Daniel > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Elad B. <el...@gm...> - 2018-01-12 17:04:54
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Thanks Gregory and Jose for your responses. On Fri, Jan 12, 2018 at 9:55 AM, Jose Miguel de la Rosa Trevin < del...@gm...> wrote: > Hi Elad, > > As Grigory mentioned, the facilities features are part of the normal > Scipion distribution (since that version). > You could use streaming processing also in other scenarios (not only when > acquiring data) such as long > data transfers. > > Best, > Jose Miguel > > > On Fri, Jan 12, 2018 at 9:37 AM, Gregory Sharov <sha...@gm...> > wrote: > >> Hi Elad, >> >> if I understood you correctly, there is no "special" version of scipion >> for facilities, so streaming capabilities are available from version 1.1.0+ >> >> 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, Jan 11, 2018 at 7:52 PM, Elad Binshtein <el...@gm...> wrote: >> >>> Hi, >>> Is it possible to use the streaming features is the regular version of >>> scipion? >>> >>> Thanks >>> >>> -- >>> ________________________________ >>> Elad Binshtein, Ph.D. >>> Cryo EM specialist - staff scientist >>> Center for Structure Biology (CSB) >>> MCN Room 1207 >>> Vanderbilt University >>> Nashville, TN >>> Office: +1-615-322-4671 <+1%20615-322-4671> >>> Mobile: +1-615-481-4408 <+1%20615-481-4408> >>> E-Mail: el...@gm... >>> ________________________________ >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> > -- ________________________________ Elad Binshtein, Ph.D. Cryo EM specialist - staff scientist Center for Structure Biology (CSB) MCN Room 1207 Vanderbilt University Nashville, TN Office: +1-615-322-4671 Mobile: +1-615-481-4408 E-Mail: el...@gm... ________________________________ |
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From: Pablo C. <pc...@cn...> - 2018-01-12 16:00:54
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As Gregory said, it is the same version, just not all protocols are "streamified", so far, for: V.1.1: Import Movies, All alignment protocols (except Xmipp ones), and CTF estimation (except xmipp ones) V.1.2.beta: Same as before, + Xmipp gain estimation, All automatic picking and extraction protocols. All the best, Pablo. On 12/01/18 15:37, Gregory Sharov wrote: > Hi Elad, > > if I understood you correctly, there is no "special" version of > scipion for facilities, so streaming capabilities are available from > version 1.1.0+ > > 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 <tel:+44%201223%20267542> > e-mail: gs...@mr... <mailto:gs...@mr...> > > On Thu, Jan 11, 2018 at 7:52 PM, Elad Binshtein <el...@gm... > <mailto:el...@gm...>> wrote: > > Hi, > Is it possible to use the streaming features is the regular > version of scipion? > > Thanks > > -- > ________________________________ > Elad Binshtein, Ph.D. > Cryo EM specialist - staff scientist > Center for Structure Biology (CSB) > MCN Room 1207 > Vanderbilt University > Nashville, TN > Office: +1-615-322-4671 <tel:+1%20615-322-4671> > Mobile: +1-615-481-4408 <tel:+1%20615-481-4408> > E-Mail: el...@gm... <mailto:el...@gm...> > ________________________________ > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > 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> > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Jose M. de la R. T. <del...@gm...> - 2018-01-12 15:55:10
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Hi Elad, As Grigory mentioned, the facilities features are part of the normal Scipion distribution (since that version). You could use streaming processing also in other scenarios (not only when acquiring data) such as long data transfers. Best, Jose Miguel On Fri, Jan 12, 2018 at 9:37 AM, Gregory Sharov <sha...@gm...> wrote: > Hi Elad, > > if I understood you correctly, there is no "special" version of scipion > for facilities, so streaming capabilities are available from version 1.1.0+ > > 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, Jan 11, 2018 at 7:52 PM, Elad Binshtein <el...@gm...> wrote: > >> Hi, >> Is it possible to use the streaming features is the regular version of >> scipion? >> >> Thanks >> >> -- >> ________________________________ >> Elad Binshtein, Ph.D. >> Cryo EM specialist - staff scientist >> Center for Structure Biology (CSB) >> MCN Room 1207 >> Vanderbilt University >> Nashville, TN >> Office: +1-615-322-4671 <+1%20615-322-4671> >> Mobile: +1-615-481-4408 <+1%20615-481-4408> >> E-Mail: el...@gm... >> ________________________________ >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Gregory S. <sha...@gm...> - 2018-01-12 14:37:53
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Hi Elad, if I understood you correctly, there is no "special" version of scipion for facilities, so streaming capabilities are available from version 1.1.0+ 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, Jan 11, 2018 at 7:52 PM, Elad Binshtein <el...@gm...> wrote: > Hi, > Is it possible to use the streaming features is the regular version of > scipion? > > Thanks > > -- > ________________________________ > Elad Binshtein, Ph.D. > Cryo EM specialist - staff scientist > Center for Structure Biology (CSB) > MCN Room 1207 > Vanderbilt University > Nashville, TN > Office: +1-615-322-4671 <+1%20615-322-4671> > Mobile: +1-615-481-4408 <+1%20615-481-4408> > E-Mail: el...@gm... > ________________________________ > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Daniel L. <dan...@ic...> - 2018-01-12 08:58:55
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Hi, I'm trying to customize my hosts.conf file for a SLURM batch system. Currently, the .out and the .err files end up in the root of my project directory e.g. "~/ScipionUserData/projects/my_project/job7113248.out". I have the SLURM variables set by: "#SBATCH -o job%%j.out -e job%%j.err". Instead I'd prefer if the .out and .err could go into the 'logs' directory for the specific run together with the rest of the log files. E.g "~/ScipionUserData/projects/my_project/Runs/000367_ProtRelionRefine3D/logs/job7113248.out". Is there a way to achieve that? Regards, Daniel |
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From: Joshua J. L. <jl...@um...> - 2018-01-12 06:18:01
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Hi Scipion Mailing list I am new to the list and am not sure how I can search old topics but I am looking for the tarball of XMIPP 2.4 . I tried downloading it from the old xmipp site but did not succeed . The one that comes with Scipion is 3.1 and I am not sure whether it will work with the old XMIPP . Where can I find the old xmipp ? Sincerly Joshua Lobo <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=icon> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=link> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> |
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From: Elad B. <el...@gm...> - 2018-01-11 19:53:02
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Hi, Is it possible to use the streaming features is the regular version of scipion? Thanks -- ________________________________ Elad Binshtein, Ph.D. Cryo EM specialist - staff scientist Center for Structure Biology (CSB) MCN Room 1207 Vanderbilt University Nashville, TN Office: +1-615-322-4671 Mobile: +1-615-481-4408 E-Mail: el...@gm... ________________________________ |
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From: Pablo C. <pc...@cn...> - 2018-01-11 11:19:35
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Dear scipion users and Em community. Since last Scipion/Xmipp release on summer 2017, we have been working on a "minor" release focusing our efforts in the streaming capabilities of Scipion. You can read more details here. <https://github.com/I2PC/scipion/wiki/Release-Notes> Note it is still a beta, so there could be some bugs. If you find any, please, please contact us. <https://github.com/I2PC/scipion/wiki/Contact-Us> If you are among those that like to be the first to try things out....this is your link: http://scipion.i2pc.es/download_form choose *V1.2.beta* All the best, Pablo Scipion/Xmipp team. |
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From: Bart <sca...@gm...> - 2017-12-22 15:25:42
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> > For 4-bit, I'd say read into uint8 and do some bit massaging (AND and shift). (ideally do it while loading, so that you don't need to effectively allocate the whole thing two/three times) And in case of UCSF, the gain reference is a NX*NY float32 image right after the agard-style extended header. You can detect its presence by seeing that NSYMBT is exactly that much (NX*NY*4) larger than NINT and NREAL would suggest. ...as far as I understand it, anyway. I've been writing a module that reads extended data for all variants that can come out of our setup, meaning FEI, UCSF, 4-bit, and SerialEM. While almost no variant marks itself, you can get suprisingly far in detection. ...though I keep on coming across new and exciting real-world deviations, so this needs more testing before it's useful to anyone else. --Bart Alewijnse @NeCEN |
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From: Pablo C. <pc...@cn...> - 2017-12-21 07:08:48
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Hi Alexander, thanks for your feedback. Could you or anyone from there help us to have it? Where are the specs? Is there any python code/module already supporting it? I've annotated this in our issue tracker. We have some other formats to support like latest dm4, so it might make sense to collect them extend our "supported data formats". Anyone missing any other "standard" format? Happy solstice! On 21/12/17 01:59, Alexander Myasnikov wrote: > I have seen that 4bit mrc format is not supported yet. Here in UCSF we > developed this format in order to avid loosing time for > compression-decompression during data collection-transfer-motion > correction and backup on tape. I was trying to build a pipeline based > on 4bit mrc, since all our microscope are collecting in this format, > but .... . > If it is not hard - can you please make this format been supported. > Thank you in advance, |
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From: Alexander M. <al...@ms...> - 2017-12-21 01:28:19
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Dear Scipion members, I have seen that 4bit mrc format is not supported yet. Here in UCSF we developed this format in order to avid loosing time for compression-decompression during data collection-transfer-motion correction and backup on tape. I was trying to build a pipeline based on 4bit mrc, since all our microscope are collecting in this format, but .... . If it is not hard - can you please make this format been supported. Thank you in advance, Alexmag |
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From: Pablo C. <pc...@cn...> - 2017-12-06 18:04:49
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Dear Somnath! I guess you've run literally what Jose said: scipion "xmipp_***" Quite often, *** means "any word or characters". just replace the 3 * with the xmipp progam you want to run. For your initial query: *scipion xmipp_**image_align* But bear in mind that any other xmipp program could be executed the same way, thus the generic, literally useless, "xmipp_***". On 05/12/17 16:36, Somnath Dutta wrote: > > Hi Jose, > > > Thank you for your help and quick reply. I am following your suggestions. > > scipion e2projectmanager.py is working fine. > > > [somnath@arjun ~]$ > /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/scipion > e2projectmanager.py > > > Scipion v1.1 (2017-06-14) Balbino > > > >>>>> python > /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/apps/pw_program.py > "e2projectmanager.py" > > ** Running command: e2projectmanager.py > > > But scipion xmipp_*** is showing the following error > > > [somnath@arjun ~]$ > /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/scipion > xmipp_*** > > > Scipion v1.1 (2017-06-14) Balbino > > > >>>>> python > /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/apps/pw_program.py > "xmipp_***" > > ** Running command: xmipp_*** > > /bin/sh: xmipp_***: command not found > > Traceback (most recent call last): > > File > "/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/apps/pw_program.py", > line 41, in <module> > > runProgram(program, params) > > File > "/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/em/__init__.py", > line 185, in runProgram > > pwutils.runJob(None, program, params, env=env) > > File > "/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/utils/process.py", > line 51, in runJob > > return runCommand(command, env, cwd) > > File > "/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/utils/process.py", > line 65, in runCommand > > check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, > env=env, cwd=cwd) > > File > "/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/software/lib/python2.7/subprocess.py", > line 540, in check_call > > raise CalledProcessError(retcode, cmd) > > subprocess.CalledProcessError: Command 'xmipp_*** ' returned non-zero > exit status 127 > > > can you please help me to resolve this problem? I mentioned in my > previous email that xmipp was working fine and opening when I used the > same terminal to install the Scipion program. > > > Thanks, > > > Best, > > Somnath > > > ------------------------------------------------------------------------ > *From:* Jose Miguel de la Rosa Trevin <del...@gm...> > *Sent:* 05 December 2017 15:39:06 > *To:* Somnath Dutta > *Cc:* sci...@li... > *Subject:* Re: [scipion-users] Scipion xmipp file not found > Hi Somnath, > > Scipion try to avoid that users need to modify their environment...so > the path and other > variables are set when you open Scipion. > > So, for easily open any other EM package, you can do it like: > > scipion xmipp_*** > scipion e2projectmanager.py > scipion relion_*** > > And so forth. > > Best, > Jose Miguel > > > On Tue, Dec 5, 2017 at 10:25 AM, Somnath Dutta <so...@ii... > <mailto:so...@ii...>> wrote: > > Hi, > > > I have installed Scipion. After finishing my installation, when I > am using the same terminal to open xmipp or eman, I can open it. > But whenever I am using a new terminal to run any GUI, like xmipp, > e2projectmanager.py ,I can't open any of these programs. It is > showing the following errors: > > > [somnath@arjun ~]$ > /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/software/em/xmipp/bin/xmipp_image_align > > /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/software/em/xmipp/bin/xmipp_image_align: > error while loading shared libraries: libXmippAlglib.so: cannot > open shared object file: No such file or directory > > > How Can I resolve this problem? Thanks in advance. > > > Thanks > > > Best, > > Somnath > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > <http://sdm.link/slashdot> > _______________________________________________ > 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> > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Somnath D. <so...@ii...> - 2017-12-05 15:37:01
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Hi Jose,
Thank you for your help and quick reply. I am following your suggestions.
scipion e2projectmanager.py is working fine.
[somnath@arjun ~]$ /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/scipion e2projectmanager.py
Scipion v1.1 (2017-06-14) Balbino
>>>>> python /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/apps/pw_program.py "e2projectmanager.py"
** Running command: e2projectmanager.py
But scipion xmipp_*** is showing the following error
[somnath@arjun ~]$ /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/scipion xmipp_***
Scipion v1.1 (2017-06-14) Balbino
>>>>> python /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/apps/pw_program.py "xmipp_***"
** Running command: xmipp_***
/bin/sh: xmipp_***: command not found
Traceback (most recent call last):
File "/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/apps/pw_program.py", line 41, in <module>
runProgram(program, params)
File "/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/em/__init__.py", line 185, in runProgram
pwutils.runJob(None, program, params, env=env)
File "/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/utils/process.py", line 51, in runJob
return runCommand(command, env, cwd)
File "/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/pyworkflow/utils/process.py", line 65, in runCommand
check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, env=env, cwd=cwd)
File "/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/software/lib/python2.7/subprocess.py", line 540, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'xmipp_*** ' returned non-zero exit status 127
can you please help me to resolve this problem? I mentioned in my previous email that xmipp was working fine and opening when I used the same terminal to install the Scipion program.
Thanks,
Best,
Somnath
________________________________
From: Jose Miguel de la Rosa Trevin <del...@gm...>
Sent: 05 December 2017 15:39:06
To: Somnath Dutta
Cc: sci...@li...
Subject: Re: [scipion-users] Scipion xmipp file not found
Hi Somnath,
Scipion try to avoid that users need to modify their environment...so the path and other
variables are set when you open Scipion.
So, for easily open any other EM package, you can do it like:
scipion xmipp_***
scipion e2projectmanager.py
scipion relion_***
And so forth.
Best,
Jose Miguel
On Tue, Dec 5, 2017 at 10:25 AM, Somnath Dutta <so...@ii...<mailto:so...@ii...>> wrote:
Hi,
I have installed Scipion. After finishing my installation, when I am using the same terminal to open xmipp or eman, I can open it. But whenever I am using a new terminal to run any GUI, like xmipp, e2projectmanager.py , I can't open any of these programs. It is showing the following errors:
[somnath@arjun ~]$ /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/software/em/xmipp/bin/xmipp_image_align
/home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/software/em/xmipp/bin/xmipp_image_align: error while loading shared libraries: libXmippAlglib.so: cannot open shared object file: No such file or directory
How Can I resolve this problem? Thanks in advance.
Thanks
Best,
Somnath
------------------------------------------------------------------------------
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|
|
From: Jose M. de la R. T. <del...@gm...> - 2017-12-05 10:09:14
|
Hi Somnath, Scipion try to avoid that users need to modify their environment...so the path and other variables are set when you open Scipion. So, for easily open any other EM package, you can do it like: scipion xmipp_*** scipion e2projectmanager.py scipion relion_*** And so forth. Best, Jose Miguel On Tue, Dec 5, 2017 at 10:25 AM, Somnath Dutta <so...@ii...> wrote: > Hi, > > > I have installed Scipion. After finishing my installation, when I am > using the same terminal to open xmipp or eman, I can open it. But whenever > I am using a new terminal to run any GUI, like xmipp, e2projectmanager.py > , I can't open any of these programs. It is showing the following errors: > > > [somnath@arjun ~]$ /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0. > 1/scipion/software/em/xmipp/bin/xmipp_image_align > > /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0. > 1/scipion/software/em/xmipp/bin/xmipp_image_align: error while loading > shared libraries: libXmippAlglib.so: cannot open shared object file: No > such file or directory > > > How Can I resolve this problem? Thanks in advance. > > > Thanks > > > Best, > > Somnath > > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Somnath D. <so...@ii...> - 2017-12-05 10:00:07
|
Hi, I have installed Scipion. After finishing my installation, when I am using the same terminal to open xmipp or eman, I can open it. But whenever I am using a new terminal to run any GUI, like xmipp, e2projectmanager.py , I can't open any of these programs. It is showing the following errors: [somnath@arjun ~]$ /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/software/em/xmipp/bin/xmipp_image_align /home/GroupMisc/GroupSD/somnath/Software/SCIPION/1.0.1/scipion/software/em/xmipp/bin/xmipp_image_align: error while loading shared libraries: libXmippAlglib.so: cannot open shared object file: No such file or directory How Can I resolve this problem? Thanks in advance. Thanks Best, Somnath |
|
From: Roberto M. <ro...@cn...> - 2017-11-30 08:35:49
|
Hi,
Modify file: pyworkflow/object.py
replace class String by:
class String(Scalar):
"""String object. """
DATETIME_FORMAT = "%Y-%m-%d %H:%M:%S"
FS = ".%f" # Fento seconds
def _convertValue(self, value):
return str(value)
def empty(self):
""" Return true if None or len == 0 """
if not self.hasValue():
return True
return len(self.get().strip()) == 0
def datetime(self, formatStr=None, fs=True):
""" Get the datetime from the string value.
Params:
formatStr: if is None, use the default DATETIME_FORMAT.
fs: Use femto seconds or not, only when format=None
"""
if formatStr is None:
try:
formatStr = self.DATETIME_FORMAT
if fs:
formatStr += self.FS
datetime = dt.datetime.strptime(self._objValue, formatStr)
except Exception as ex:
# Maybe the %f (femtoseconds) is not working
# let's try to format without it
datetime = dt.datetime.strptime(self._objValue,
self.DATETIME_FORMAT)
else:
datetime = dt.datetime.strptime(self._objValue, formatStr)
return datetime
Hope this helps
On Wed, Nov 29, 2017 at 10:35 AM, Dmitry A. Semchonok
<sem...@gm...> wrote:
> Dear colleagues,
>
> It is probably the common error when you use 2 different rely on versions
>
> Is there an easy fix for that?
>
>
> time data '2017-11-03 23:17:36' does not match format '%Y-%m-%d %H:%M:%S.%f'
>
>
> Thank you!
>
>
> Sincerely,
>
> Dmitry
>
>
>
>
>
|
|
From: Joseph L. <ly...@mb...> - 2017-11-30 07:17:13
|
Hi all, Thanks for the speedy reply. In Aarhus, we are using version 1.1 (Balbino). Best, Joe ________________________________ From: Jose Miguel de la Rosa Trevin <del...@gm...> Sent: 30 November 2017 08:07 To: Gregory Sharov Cc: Joseph Lyons; sci...@li... Subject: Re: [scipion-users] Particle extraction from a dataset filtered based on CTF Hi Joe, I remember this was discussed during the EM course at Copenhagen recently. For sure the proposed way of Grigory will work, but your workflow is very common and I think it make sense allow this case without the extra step of the subset protocol. We will review this and get back to you. As Grigory pointed out, it would be good to know which version are you using. Best, Jose Miguel On Thu, Nov 30, 2017 at 12:44 AM, Gregory Sharov <sha...@gm...<mailto:sha...@gm...>> wrote: Hi Joe, just to be sure: which Scipion version are you using? One of the ways to to this is to use scipion subset protocol with intersection option: 1) first input will be your all dose-weighted mics (full set) 2) second input will be a set of mics (small one) This will get you a dose-weighted subset of mics that you can use for particle extraction (provide there either CTF subset or full CTF set, it should work both ways). 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<tel:+44%201223%20267542> e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Nov 29, 2017 at 8:58 PM, Joseph Lyons <ly...@mb...<mailto:ly...@mb...>> wrote: Hi all, I have a data set comprised of dose-weighted and non-dose-weighted micrographs. CTF estimation was performed on the non-dose-weighted group and I have selected a set of micrographs from this set based on CTF. ? The problem arises when I want to extract particles from the dose weighted set and assign the CTF from the smaller set to this process. When I use the smaller CTF set - it complains of missing CTF based on micName or micId. I was told that this would just allow particle extraction from the micrographs common to both the DW and CTF sets. Am I missing something? Best, Joe ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ 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...> - 2017-11-30 07:07:43
|
Hi Joe, I remember this was discussed during the EM course at Copenhagen recently. For sure the proposed way of Grigory will work, but your workflow is very common and I think it make sense allow this case without the extra step of the subset protocol. We will review this and get back to you. As Grigory pointed out, it would be good to know which version are you using. Best, Jose Miguel On Thu, Nov 30, 2017 at 12:44 AM, Gregory Sharov <sha...@gm...> wrote: > Hi Joe, > > just to be sure: which Scipion version are you using? > > One of the ways to to this is to use scipion subset protocol with > intersection option: > > 1) first input will be your all dose-weighted mics (full set) > 2) second input will be a set of mics (small one) > > This will get you a dose-weighted subset of mics that you can use for > particle extraction (provide there either CTF subset or full CTF set, it > should work both ways). > > 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 Wed, Nov 29, 2017 at 8:58 PM, Joseph Lyons <ly...@mb...> wrote: > >> Hi all, >> >> >> I have a data set comprised of dose-weighted and non-dose-weighted >> micrographs. CTF estimation was performed on the non-dose-weighted group >> and I have selected a set of micrographs from this set based on CTF. >> >> >> The problem arises when I want to extract particles from the dose >> weighted set and assign the CTF from the smaller set to this process. >> >> >> When I use the smaller CTF set - it complains of missing CTF based on >> micName or micId. I was told that this would just allow particle extraction >> from the micrographs common to both the DW and CTF sets. Am I missing >> something? >> >> >> Best, >> >> >> Joe >> >> >> >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Gregory S. <sha...@gm...> - 2017-11-29 23:44:45
|
Hi Joe, just to be sure: which Scipion version are you using? One of the ways to to this is to use scipion subset protocol with intersection option: 1) first input will be your all dose-weighted mics (full set) 2) second input will be a set of mics (small one) This will get you a dose-weighted subset of mics that you can use for particle extraction (provide there either CTF subset or full CTF set, it should work both ways). 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 Wed, Nov 29, 2017 at 8:58 PM, Joseph Lyons <ly...@mb...> wrote: > Hi all, > > > I have a data set comprised of dose-weighted and non-dose-weighted > micrographs. CTF estimation was performed on the non-dose-weighted group > and I have selected a set of micrographs from this set based on CTF. > > > The problem arises when I want to extract particles from the dose weighted > set and assign the CTF from the smaller set to this process. > > > When I use the smaller CTF set - it complains of missing CTF based on > micName or micId. I was told that this would just allow particle extraction > from the micrographs common to both the DW and CTF sets. Am I missing > something? > > > Best, > > > Joe > > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Joseph L. <ly...@mb...> - 2017-11-29 21:31:12
|
Hi all, I have a data set comprised of dose-weighted and non-dose-weighted micrographs. CTF estimation was performed on the non-dose-weighted group and I have selected a set of micrographs from this set based on CTF. ? The problem arises when I want to extract particles from the dose weighted set and assign the CTF from the smaller set to this process. When I use the smaller CTF set - it complains of missing CTF based on micName or micId. I was told that this would just allow particle extraction from the micrographs common to both the DW and CTF sets. Am I missing something? Best, Joe |
|
From: Pablo C. <pc...@cn...> - 2017-11-29 11:07:01
|
Hi Dmitry....aren't you subscribed to the user list, I replied to you on the same day you've sent a similar question. Please read bellow. On 29/11/17 10:35, Dmitry A. Semchonok wrote: > Dear colleagues, > > It is probably the common error when you use 2 different rely on versions > > Is there an easy fix for that? > > > time data '2017-11-03 23:17:36' does not match format '%Y-%m-%d > %H:%M:%S.%f' > > > Thank you! > > > Sincerely, > > Dmitry > -------- Forwarded Message -------- Subject: Re: [scipion-users] fix for___%Y-%m-%d %H:%M:%S.% Date: Wed, 22 Nov 2017 16:13:31 +0100 From: Pablo Conesa <pc...@cn...> To: sci...@li... Hi Dmitry, latest code seems to be compatible with latest release.: https://github.com/I2PC/scipion/blob/release-1.1.facilities-devel/pyworkflow/object.py#L653 Master version is here <https://github.com/I2PC/scipion/blob/master/pyworkflow/object.py#L653> I would carefully try to make your "master" version datetime method look like the recent one. Can I ask why you are switching versions? Let us know how it goes. All the best, Pablo. On 22/11/17 09:44, D.A. Semchonok wrote: > Dear colleagues, > > Is there an easy fix for such an error that occur when you switch > between the SCIPION versions? > > *time data '2017-11-03 23:17:36' does not match format '%Y-%m-%d > %H:%M:%S.%*f' > > Thank you! > > Sincerely, > Dmitry > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org!http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Dmitry A. S. <sem...@gm...> - 2017-11-29 09:35:12
|
Dear colleagues, It is probably the common error when you use 2 different rely on versions Is there an easy fix for that? time data '2017-11-03 23:17:36' does not match format '%Y-%m-%d %H:%M:%S.%f' Thank you! Sincerely, Dmitry |
|
From: Pablo C. <pc...@cn...> - 2017-11-22 15:48:14
|
Hi Dmitry, latest code seems to be compatible with latest release.: https://github.com/I2PC/scipion/blob/release-1.1.facilities-devel/pyworkflow/object.py#L653 Master version is here <https://github.com/I2PC/scipion/blob/master/pyworkflow/object.py#L653> I would carefully try to make your "master" version datetime method look like the recent one. Can I ask why you are switching versions? Let us know how it goes. All the best, Pablo. On 22/11/17 09:44, D.A. Semchonok wrote: > Dear colleagues, > > Is there an easy fix for such an error that occur when you switch > between the SCIPION versions? > > *time data '2017-11-03 23:17:36' does not match format '%Y-%m-%d > %H:%M:%S.%*f' > > Thank you! > > Sincerely, > Dmitry > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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