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From: Carlos O. S. <co...@cn...> - 2016-11-07 15:30:59
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Dear Dmitry, as Grigori says, only with these errors it is hard to say what is going on, is there any other error message? Kind regards, Carlos Oscar On 11/07/16 13:22, Dmitry Semchonok wrote: > Dear colleagues, > > I have a problem with running > > xmipp3 - ctf_correct_wiener2d > <https://github.com/I2PC/scipion/wiki/XmippProtCTFCorrectWiener2D>: > > xmipp3 - reconstruct significant > <https://github.com/I2PC/scipion/wiki/XmippProtReconstructSignificant>: > > > I faced the following errors: > > xmipp3 - ctf_correct_wiener2d > <https://github.com/I2PC/scipion/wiki/XmippProtCTFCorrectWiener2D>: > Protocol failed: Command 'srun `which > xmipp_mpi_ctf_correct_wiener2d` -i > Runs/001129_XmippProtCTFCorrectWiener2D/input_particles.xmd -o > Runs/001129_XmippProtCTFCorrectWiener2D/corrected_ctf_particles.stk > --save_metadata_stack > Runs/001129_XmippProtCTFCorrectWiener2D/corrected_ctf_particles.xmd > --pad 2 --wc -1.0 --sampling_rate 2.24' returned non-zero exit > status 127 > > > xmipp3 - reconstruct significant > <https://github.com/I2PC/scipion/wiki/XmippProtReconstructSignificant> > Protocol failed: Command 'srun `which > xmipp_mpi_reconstruct_significant` -i > Runs/001892_XmippProtReconstructSignificant/extra/input_classes.xmd > --sym c1 --angularSampling 5.000000 --minTilt 0.000000 --maxTilt > 90.000000 --maxShift -1.000000 --dontReconstruct --angDistance > 10.000000 --useImed --odir > Runs/001892_XmippProtReconstructSignificant/tmp/iter001 --alpha0 > 0.200000 --alphaF 0.200000 --numberOfVolumes 1' returned non-zero exit > status 127 > > > > > Any suggestions? > > Thank you. > > Sincerely, > Dmitry > > > > ------------------------------------------------------------------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://biocomp.cnb.csic.es National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
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From: Carlos O. S. <co...@cn...> - 2016-11-07 15:28:46
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Dear Dmitry, in 3D -> Analysis you have multiple fscs and resolution 3D. The first one allows calculating the FSC of several volumes vs a reference including the volume alignment inside the protocol. The second one assumes that the two volumes are aligned and compare a volume vs a reference with different metrics. Kind regards, Carlos Oscar On 11/07/16 10:42, Dmitry Semchonok wrote: > Dear colleagues, > > II have 2 3D models of the same protein. > > The X-ray structure of that protein is known. > > Is there a protocol in SCIPIION to compare these 3D models, to say > where the fitting is better etc? > > Sincerely, > Dmitry > > > > > ------------------------------------------------------------------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://biocomp.cnb.csic.es National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
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From: Grigory S. <sha...@gm...> - 2016-11-07 13:09:08
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Thanks! For the ctf program it looks like you have problems with OpenMPI: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory I suggest to check if all MPI variables in scipion.config file point to correct paths (see https://github.com/I2PC/scipion/wiki/Scipion- Configuration) and run *scipion config* to make sure it doesn't show any errors For reconstruct protocol, the error is : [1;31mXMIPP_ERROR 2: Incorrect argument received [0m [1;31m [1;31mAlpha values are too large: reduce the error such that the error times the symmetry number is smaller than 1 [0m [0m [1;31mFile: software/em/xmipp/libraries/reconstruction/reconstruct_significant.cpp line: 737 [0m .. Initial significance : 0.2 Final significance : 0.2 *..* Why did you use such values? You could start with default ones: 80% and 99.5% Best regards, Grigory ------------------------------------------------------------ -------------------- Grigory Sharov, Ph.D. Institute of Genetics and Molecular and Cellular Biology Integrated Structural Biology Department (CBI) 1, rue Laurent Fries 67404 Illkirch, France tel. 03 69 48 51 00 e-mail: sh...@ig... On Mon, Nov 7, 2016 at 1:51 PM, Dmitry Semchonok <sem...@gm...> wrote: > Dear Grigory, > > Please find the required files in the attachment. > > > Sincerely, > Dmitry > > 2016-11-07 13:33 GMT+01:00 Grigory Sharov <sha...@gm...>: > >> Hello Dmitry, >> >> this is not enough to see the source of error. Could you attach log files >> (run.stdout) in both cases? >> >> Best regards, >> Grigory >> >> ------------------------------------------------------------ >> -------------------- >> Grigory Sharov, Ph.D. >> Institute of Genetics and Molecular and Cellular Biology >> Integrated Structural Biology Department (CBI) >> 1, rue Laurent Fries >> 67404 Illkirch, France >> tel. 03 69 48 51 00 >> e-mail: sh...@ig... >> >> On Mon, Nov 7, 2016 at 1:22 PM, Dmitry Semchonok <sem...@gm...> >> wrote: >> >>> Dear colleagues, >>> >>> I have a problem with running >>> >>> xmipp3 - ctf_correct_wiener2d >>> <https://github.com/I2PC/scipion/wiki/XmippProtCTFCorrectWiener2D>: >>> >>> xmipp3 - reconstruct significant >>> <https://github.com/I2PC/scipion/wiki/XmippProtReconstructSignificant>: >>> >>> >>> I faced the following errors: >>> >>> xmipp3 - ctf_correct_wiener2d >>> <https://github.com/I2PC/scipion/wiki/XmippProtCTFCorrectWiener2D>: >>> Protocol failed: Command 'srun `which xmipp_mpi_ctf_correct_wiener2d` >>> -i Runs/001129_XmippProtCTFCorrectWiener2D/input_particles.xmd -o >>> Runs/001129_XmippProtCTFCorrectWiener2D/corrected_ctf_particles.stk >>> --save_metadata_stack Runs/001129_XmippProtCTFCorrec >>> tWiener2D/corrected_ctf_particles.xmd --pad 2 --wc -1.0 >>> --sampling_rate 2.24' returned non-zero exit status 127 >>> >>> >>> xmipp3 - reconstruct significant >>> <https://github.com/I2PC/scipion/wiki/XmippProtReconstructSignificant> >>> Protocol failed: Command 'srun `which xmipp_mpi_reconstruct_significant` >>> -i Runs/001892_XmippProtReconstructSignificant/extra/input_classes.xmd >>> --sym c1 --angularSampling 5.000000 --minTilt 0.000000 --maxTilt 90.000000 >>> --maxShift -1.000000 --dontReconstruct --angDistance 10.000000 --useImed >>> --odir Runs/001892_XmippProtReconstructSignificant/tmp/iter001 --alpha0 >>> 0.200000 --alphaF 0.200000 --numberOfVolumes 1' returned non-zero exit >>> status 127 >>> >>> >>> >>> >>> Any suggestions? >>> >>> Thank you. >>> >>> Sincerely, >>> Dmitry >>> >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Developer Access Program for Intel Xeon Phi Processors >>> Access to Intel Xeon Phi processor-based developer platforms. >>> With one year of Intel Parallel Studio XE. >>> Training and support from Colfax. >>> Order your platform today. http://sdm.link/xeonphi >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> >> > |
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From: Grigory S. <sha...@gm...> - 2016-11-07 12:34:02
|
Hello Dmitry, this is not enough to see the source of error. Could you attach log files (run.stdout) in both cases? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. Institute of Genetics and Molecular and Cellular Biology Integrated Structural Biology Department (CBI) 1, rue Laurent Fries 67404 Illkirch, France tel. 03 69 48 51 00 e-mail: sh...@ig... On Mon, Nov 7, 2016 at 1:22 PM, Dmitry Semchonok <sem...@gm...> wrote: > Dear colleagues, > > I have a problem with running > > xmipp3 - ctf_correct_wiener2d > <https://github.com/I2PC/scipion/wiki/XmippProtCTFCorrectWiener2D>: > > xmipp3 - reconstruct significant > <https://github.com/I2PC/scipion/wiki/XmippProtReconstructSignificant>: > > > I faced the following errors: > > xmipp3 - ctf_correct_wiener2d > <https://github.com/I2PC/scipion/wiki/XmippProtCTFCorrectWiener2D>: > Protocol failed: Command 'srun `which xmipp_mpi_ctf_correct_wiener2d` > -i Runs/001129_XmippProtCTFCorrectWiener2D/input_particles.xmd -o > Runs/001129_XmippProtCTFCorrectWiener2D/corrected_ctf_particles.stk > --save_metadata_stack Runs/001129_XmippProtCTFCorrec > tWiener2D/corrected_ctf_particles.xmd --pad 2 --wc -1.0 > --sampling_rate 2.24' returned non-zero exit status 127 > > > xmipp3 - reconstruct significant > <https://github.com/I2PC/scipion/wiki/XmippProtReconstructSignificant> > Protocol failed: Command 'srun `which xmipp_mpi_reconstruct_significant` > -i Runs/001892_XmippProtReconstructSignificant/extra/input_classes.xmd > --sym c1 --angularSampling 5.000000 --minTilt 0.000000 --maxTilt 90.000000 > --maxShift -1.000000 --dontReconstruct --angDistance 10.000000 --useImed > --odir Runs/001892_XmippProtReconstructSignificant/tmp/iter001 --alpha0 > 0.200000 --alphaF 0.200000 --numberOfVolumes 1' returned non-zero exit > status 127 > > > > > Any suggestions? > > Thank you. > > Sincerely, > Dmitry > > > ------------------------------------------------------------ > ------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Dmitry S. <sem...@gm...> - 2016-11-07 12:22:08
|
Dear colleagues, I have a problem with running xmipp3 - ctf_correct_wiener2d <https://github.com/I2PC/scipion/wiki/XmippProtCTFCorrectWiener2D>: xmipp3 - reconstruct significant <https://github.com/I2PC/scipion/wiki/XmippProtReconstructSignificant>: I faced the following errors: xmipp3 - ctf_correct_wiener2d <https://github.com/I2PC/scipion/wiki/XmippProtCTFCorrectWiener2D>: Protocol failed: Command 'srun `which xmipp_mpi_ctf_correct_wiener2d` -i Runs/001129_XmippProtCTFCorrectWiener2D/input_particles.xmd -o Runs/001129_ XmippProtCTFCorrectWiener2D/corrected_ctf_particles.stk --save_metadata_stack Runs/001129_XmippProtCTFCorrectWiener2D/corrected_ctf_particles.xmd --pad 2 --wc -1.0 --sampling_rate 2.24' returned non-zero exit status 127 xmipp3 - reconstruct significant <https://github.com/I2PC/scipion/wiki/XmippProtReconstructSignificant> Protocol failed: Command 'srun `which xmipp_mpi_reconstruct_significant` -i Runs/001892_XmippProtReconstructSignificant/extra/input_classes.xmd --sym c1 --angularSampling 5.000000 --minTilt 0.000000 --maxTilt 90.000000 --maxShift -1.000000 --dontReconstruct --angDistance 10.000000 --useImed --odir Runs/001892_XmippProtReconstructSignificant/tmp/iter001 --alpha0 0.200000 --alphaF 0.200000 --numberOfVolumes 1' returned non-zero exit status 127 Any suggestions? Thank you. Sincerely, Dmitry |
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From: Grigory S. <sha...@gm...> - 2016-11-07 10:14:43
|
Hi Dmitry, if you click on question mark button for the pattern or files directory param you will see some examples. In your case you could use the following pattern: "new/grid*/*mrc" Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. Institute of Genetics and Molecular and Cellular Biology Integrated Structural Biology Department (CBI) 1, rue Laurent Fries 67404 Illkirch, France tel. 03 69 48 51 00 e-mail: sh...@ig... On Mon, Nov 7, 2016 at 11:04 AM, Dmitry Semchonok <sem...@gm...> wrote: > Dear colleagues, > > One other question - > > I have mrc files distributed in the several folders: > > FOLDER: grid1....grid2....grid3.... > > These folders are all in the folder named > > *new.* > So the files I need are lying in > > > > *FOLDER: new* > *inside* > > > *FOLDER grid 1 grid 2 grid 3 .....* > *inside* > > * mrc mrc mrc* > > > I want to add *all mrc *files that are now in *folder new* into the > *project*. > > Can I do that from the *protocol import movies*? > > Or I have to drag/copy all *.mrc the files to folder new (I'm trying to > avoid that due to huge dataset) ? > > > > Thank you > > Sincerely, > Dmitry > > > > > > > > ------------------------------------------------------------ > ------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Dmitry S. <sem...@gm...> - 2016-11-07 10:04:09
|
Dear colleagues,
One other question -
I have mrc files distributed in the several folders:
FOLDER: grid1....grid2....grid3....
These folders are all in the folder named
*new.*
So the files I need are lying in
*FOLDER: new*
*inside*
*FOLDER grid 1 grid 2 grid 3 .....*
*inside*
* mrc mrc mrc*
I want to add *all mrc *files that are now in *folder new* into the
*project*.
Can I do that from the *protocol import movies*?
Or I have to drag/copy all *.mrc the files to folder new (I'm trying to
avoid that due to huge dataset) ?
Thank you
Sincerely,
Dmitry
|
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From: Dmitry S. <sem...@gm...> - 2016-11-07 09:42:17
|
Dear colleagues, II have 2 3D models of the same protein. The X-ray structure of that protein is known. Is there a protocol in SCIPIION to compare these 3D models, to say where the fitting is better etc? Sincerely, Dmitry |
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From: Carlos O. S. <co...@cn...> - 2016-11-02 21:35:17
|
Dear Dmitry, On 11/02/16 13:33, Dmitry Semchonok wrote: > Dear colleagues, > > > Question is about *xmipp3 - reconstruct significant* > > > I have a test sample - worm Hb with *d6* type of *symmetry*. > > So in order to use *xmipp3 - reconstruct significant* protocol I have > to set the symmetry value for *c1*. This protocol accepts symmetry as one of its parameters. You may want to use it. > > Can I symmetrize the outcome volume after with xmipp3-preprocess > volume script? You can also do c1 and then symmetrize, although the result will not be the same. When you give d6 to reconstruct significant you are narrowing the search space, so there are more chances of finding the global (or at least rather good) minimum. If you use c1 in significant (when the volume is really d6), you may fall in a suboptimal value, that after symmetrization it is still suboptimal. > Whether this approach is not biased? See the discussion above. > Or for d6 type of symmetry it is initially better to run scripts like > ransac ? > Ransac can also exploit the symmetry, as significant. Kind regards, Carlos Oscar > > Thank you. > > Sincerely, > Dmitry > > > ------------------------------------------------------------------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://biocomp.cnb.csic.es National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
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From: Dmitry S. <sem...@gm...> - 2016-11-02 12:33:28
|
Dear colleagues, Question is about *xmipp3 - reconstruct significant* I have a test sample - worm Hb with *d6* type of *symmetry*. So in order to use *xmipp3 - reconstruct significant* protocol I have to set the symmetry value for *c1*. Can I symmetrize the outcome volume after with xmipp3-preprocess volume script? Whether this approach is not biased? Or for d6 type of symmetry it is initially better to run scripts like ransac ? Thank you. Sincerely, Dmitry |
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From: Grigory S. <sha...@gm...> - 2016-11-01 20:41:31
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Hi, the thing is that protocol runs with mpi=2 and 1 thread (by default in the protocol, thread number is not taken from GUI) and prints all output to console and not to run.stdout. Elad, in principle it should still run (however slowly), you could check the output in the console where you launched scipion (if it was done interactively) or the output log file from the job submission system on your cluster (if you run it on cluster). Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. Institute of Genetics and Molecular and Cellular Biology Integrated Structural Biology Department (CBI) 1, rue Laurent Fries 67404 Illkirch, France tel. 03 69 48 51 00 e-mail: sh...@ig... On Tue, Nov 1, 2016 at 9:12 PM, Carlos Oscar Sorzano <co...@cn...> wrote: > Dear Elad, > > can you send the log so that we can better see what may be happening? If > you attach a screenshot of the project, we may try to figure out the > workflow you have followed. > > Kind regards, Carlos Oscar > > On 11/01/16 17:05, Elad Binshtein wrote: > > Hi, > I'm try to go through the initial vol tutorial and in the lass step EMAN > and ransac is work good I can not run the xmipp RCT protocol (no error on > the run log just stuck on step 1/8) > any suggestion? > > Thanks > > -- > ________________________________ > Elad Binshtein, Ph.D. > Cryo EM specialist - staff scientist > Center for Structure Biology (CSB) > Vanderbilt University > Nashville, TN > Mobile: +1-615-481-4408 > E-Mail: el...@gm... > ________________________________ > > > ------------------------------------------------------------------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > -- > ------------------------------------------------------------------------ > Carlos Oscar Sánchez Sorzano e-mail: co...@cn... > Biocomputing unit http://biocomp.cnb.csic.es > National Center of Biotechnology (CSIC) > c/Darwin, 3 > Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 > 28049 MADRID (SPAIN) Fax: 34-91-585 4506 > ------------------------------------------------------------------------ > > > ------------------------------------------------------------ > ------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Carlos O. S. <co...@cn...> - 2016-11-01 20:12:53
|
Dear Elad, can you send the log so that we can better see what may be happening? If you attach a screenshot of the project, we may try to figure out the workflow you have followed. Kind regards, Carlos Oscar On 11/01/16 17:05, Elad Binshtein wrote: > Hi, > I'm try to go through the initial vol tutorial and in the lass step > EMAN and ransac is work good I can not run the xmipp RCT protocol (no > error on the run log just stuck on step 1/8) > any suggestion? > > Thanks > > -- > ________________________________ > Elad Binshtein, Ph.D. > Cryo EM specialist - staff scientist > Center for Structure Biology (CSB) > Vanderbilt University > Nashville, TN > Mobile: +1-615-481-4408 > E-Mail: el...@gm... <mailto:el...@gm...> > ________________________________ > > > ------------------------------------------------------------------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://biocomp.cnb.csic.es National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
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From: Jose M. de la R. T. <del...@gm...> - 2016-11-01 19:37:10
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Hi all, We should check the issue Grigory is pointing out. Anyway Dmitry, I think here the problem could be here that you are imported the class averages as "particles"...you should use instead "import - averages". Even if both are images, in Scipion we distinguish them conceptually. For example, you could use "averages" as input for the initial volume protocols but not particles. If this is your case, try to import averages and proceed with the reconstruct - significant protocol (or any other). Hope this helps, Jose Miguel. On Tue, Nov 1, 2016 at 8:26 PM, Grigory Sharov <sha...@gm...> wrote: > Hi, > > I believe this is a bug. It should be possible to import particles from > Xmipp/Reion/Frealign program and get both particles set and classes set. It > works, for example, for relion particle star files (after classification), > however the model.star has to be present in the same import folder. > As for the import from xmipp, if you import images.xmd after CL2D, you get > both outputParticles and outputClasses, however the representatives for > these classes are Null. This is the problem. > > Dmitry, I believe the current solution for you is to re-run xmipp cl2d > within scipion and then proceed with signficant protocol. > > Best regards, > Grigory > > ------------------------------------------------------------ > -------------------- > Grigory Sharov, Ph.D. > Institute of Genetics and Molecular and Cellular Biology > Integrated Structural Biology Department (CBI) > 1, rue Laurent Fries > 67404 Illkirch, France > tel. 03 69 48 51 00 > e-mail: sh...@ig... > > On Tue, Nov 1, 2016 at 7:32 PM, Carlos Oscar Sorzano <co...@cn...> > wrote: > >> Dear Dmitry, >> >> I'm not sure I get your question. If you work inside Scipion, calling >> reconstruct_significant should be transparent (it accepts a set of classes >> or a set of averages). Internally, it constructs a metadata that is passed >> to Xmipp. If you are coming from outside Scipion, I think you cannot create >> a set of averages or classes directly from import, but I may be wrong. >> >> Kind regards, Carlos Oscar >> >> On 11/01/16 16:17, Dmitry Semchonok wrote: >> >> Dear colleagues, >> >> I would like to run the *xmipp3 - reconstruct significant *script in >> SCIPION. >> >> I run 2D classification in xmipp. >> >> I imported images (class results) after 2D classification (*.mrcs format) >> to the SCIPION. >> >> But after importing these images - (class results) the SCIPION either >> 1. can not see them >> 2. if you export *.mrcs file with *.xml - doesn't want to run the *xmipp3 >> - reconstruct significant* script >> >> Protocol failed: Unrecognized type to create MDObject >> >> >> Could you prompt - *what* and* how* I can export from xmipp to SCIPION >> that I could run *xmipp3 - reconstruct significant *script >> >> >> Thank you. >> >> Sincerely, >> Dmitry >> >> >> >> ------------------------------------------------------------------------------ >> Developer Access Program for Intel Xeon Phi Processors >> Access to Intel Xeon Phi processor-based developer platforms. >> With one year of Intel Parallel Studio XE. >> Training and support from Colfax. >> Order your platform today. http://sdm.link/xeonphi >> >> >> >> _______________________________________________ >> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> >> -- >> ------------------------------------------------------------------------ >> Carlos Oscar Sánchez Sorzano e-mail: co...@cn... >> Biocomputing unit http://biocomp.cnb.csic.es >> National Center of Biotechnology (CSIC) >> c/Darwin, 3 >> Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 >> 28049 MADRID (SPAIN) Fax: 34-91-585 4506 >> ------------------------------------------------------------------------ >> >> >> ------------------------------------------------------------ >> ------------------ >> Developer Access Program for Intel Xeon Phi Processors >> Access to Intel Xeon Phi processor-based developer platforms. >> With one year of Intel Parallel Studio XE. >> Training and support from Colfax. >> Order your platform today. http://sdm.link/xeonphi >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> > > ------------------------------------------------------------ > ------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Grigory S. <sha...@gm...> - 2016-11-01 19:34:49
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Hi Elad, Which scipion version are you using: 1.0.1 or devel, so we could reproduce it? Do you see any errors in run.stdout? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. Institute of Genetics and Molecular and Cellular Biology Integrated Structural Biology Department (CBI) 1, rue Laurent Fries 67404 Illkirch, France tel. 03 69 48 51 00 e-mail: sh...@ig... On Tue, Nov 1, 2016 at 5:05 PM, Elad Binshtein <el...@gm...> wrote: > Hi, > I'm try to go through the initial vol tutorial and in the lass step EMAN > and ransac is work good I can not run the xmipp RCT protocol (no error on > the run log just stuck on step 1/8) > any suggestion? > > Thanks > > -- > ________________________________ > Elad Binshtein, Ph.D. > Cryo EM specialist - staff scientist > Center for Structure Biology (CSB) > Vanderbilt University > Nashville, TN > Mobile: +1-615-481-4408 > E-Mail: el...@gm... > ________________________________ > > ------------------------------------------------------------ > ------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Grigory S. <sha...@gm...> - 2016-11-01 19:26:58
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Hi, I believe this is a bug. It should be possible to import particles from Xmipp/Reion/Frealign program and get both particles set and classes set. It works, for example, for relion particle star files (after classification), however the model.star has to be present in the same import folder. As for the import from xmipp, if you import images.xmd after CL2D, you get both outputParticles and outputClasses, however the representatives for these classes are Null. This is the problem. Dmitry, I believe the current solution for you is to re-run xmipp cl2d within scipion and then proceed with signficant protocol. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. Institute of Genetics and Molecular and Cellular Biology Integrated Structural Biology Department (CBI) 1, rue Laurent Fries 67404 Illkirch, France tel. 03 69 48 51 00 e-mail: sh...@ig... On Tue, Nov 1, 2016 at 7:32 PM, Carlos Oscar Sorzano <co...@cn...> wrote: > Dear Dmitry, > > I'm not sure I get your question. If you work inside Scipion, calling > reconstruct_significant should be transparent (it accepts a set of classes > or a set of averages). Internally, it constructs a metadata that is passed > to Xmipp. If you are coming from outside Scipion, I think you cannot create > a set of averages or classes directly from import, but I may be wrong. > > Kind regards, Carlos Oscar > > On 11/01/16 16:17, Dmitry Semchonok wrote: > > Dear colleagues, > > I would like to run the *xmipp3 - reconstruct significant *script in > SCIPION. > > I run 2D classification in xmipp. > > I imported images (class results) after 2D classification (*.mrcs format) > to the SCIPION. > > But after importing these images - (class results) the SCIPION either > 1. can not see them > 2. if you export *.mrcs file with *.xml - doesn't want to run the *xmipp3 > - reconstruct significant* script > > Protocol failed: Unrecognized type to create MDObject > > > Could you prompt - *what* and* how* I can export from xmipp to SCIPION > that I could run *xmipp3 - reconstruct significant *script > > > Thank you. > > Sincerely, > Dmitry > > > > ------------------------------------------------------------------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > -- > ------------------------------------------------------------------------ > Carlos Oscar Sánchez Sorzano e-mail: co...@cn... > Biocomputing unit http://biocomp.cnb.csic.es > National Center of Biotechnology (CSIC) > c/Darwin, 3 > Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 > 28049 MADRID (SPAIN) Fax: 34-91-585 4506 > ------------------------------------------------------------------------ > > > ------------------------------------------------------------ > ------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Carlos O. S. <co...@cn...> - 2016-11-01 18:33:07
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Dear Dmitry, I'm not sure I get your question. If you work inside Scipion, calling reconstruct_significant should be transparent (it accepts a set of classes or a set of averages). Internally, it constructs a metadata that is passed to Xmipp. If you are coming from outside Scipion, I think you cannot create a set of averages or classes directly from import, but I may be wrong. Kind regards, Carlos Oscar On 11/01/16 16:17, Dmitry Semchonok wrote: > Dear colleagues, > > I would like to run the *xmipp3 - reconstruct significant *script in > SCIPION. > > I run 2D classification in xmipp. > > I imported images (class results) after 2D classification (*.mrcs > format) to the SCIPION. > > But after importing these images - (class results) the SCIPION either > 1. can not see them > 2. if you export *.mrcs file with *.xml - doesn't want to run the > *xmipp3 - reconstruct significant* script > > Protocol failed: Unrecognized type to create MDObject > > > Could you prompt - *what* and*how* I can export from xmipp to SCIPION > that I could run *xmipp3 - reconstruct significant *script > > > Thank you. > > Sincerely, > Dmitry > > > > ------------------------------------------------------------------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://biocomp.cnb.csic.es National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
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From: Elad B. <el...@gm...> - 2016-11-01 16:05:24
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Hi, I'm try to go through the initial vol tutorial and in the lass step EMAN and ransac is work good I can not run the xmipp RCT protocol (no error on the run log just stuck on step 1/8) any suggestion? Thanks -- ________________________________ Elad Binshtein, Ph.D. Cryo EM specialist - staff scientist Center for Structure Biology (CSB) Vanderbilt University Nashville, TN Mobile: +1-615-481-4408 E-Mail: el...@gm... ________________________________ |
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From: Dmitry S. <sem...@gm...> - 2016-11-01 15:17:38
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Dear colleagues, I would like to run the *xmipp3 - reconstruct significant *script in SCIPION. I run 2D classification in xmipp. I imported images (class results) after 2D classification (*.mrcs format) to the SCIPION. But after importing these images - (class results) the SCIPION either 1. can not see them 2. if you export *.mrcs file with *.xml - doesn't want to run the *xmipp3 - reconstruct significant* script Protocol failed: Unrecognized type to create MDObject Could you prompt - *what* and* how* I can export from xmipp to SCIPION that I could run *xmipp3 - reconstruct significant *script Thank you. Sincerely, Dmitry |
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From: Jose M. de la R. T. <del...@gm...> - 2016-10-28 07:46:22
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Dear Yashar, Unfortunately, the 'Localized Reconstruction' integrated into Scipion is only in the development branch, which is planned to be released as a new version for beginning of next year. The version installed via SBGrid is the previous release v1.0.1. You will you need to install the development branch for that, take a look at: https://github.com/I2PC/scipion/wiki/How-to-Install and let us know if you have any trouble. Apart from that, the error you are having, probably is related to the configuration file at the user level, at ~/.config/scipion/scipion.conf. Can you try to run scipion config and check if fix that error? Bests, Jose Miguel On Thu, Oct 27, 2016 at 3:34 PM, Yashar Sadian <sa...@em...> wrote: > Hi > I am trying to run the localized reconstruction protocol by Ilca et al, > 2015 which uses scipion but I receive the following error: > -bash-4.1$ scipion > Error: No section: 'PACKAGES' > Please check the configuration file > /g/sbgrid/programs/x86_64-linux/scipion/1.0.1/config/scipion.conf and > try again. > -bash-4.1$ cd /g/sbgrid/programs/x86_64-linux/scipion/1.0.1/config/ > > could you please tell me what exactly I need to do to troubleshoot? > > -- > Best, > Yashar Sadian > > > Christoph Mueller's group > Structural and computational Biology Unit > European Molecular Biology Laboratory (EMBL) > Meyerhofstrasse 1 > 69117 Heidelberg, Germany > > Phone: 0049-6221-387-8496 > Email: sa...@em... > > > ------------------------------------------------------------ > ------------------ > The Command Line: Reinvented for Modern Developers > Did the resurgence of CLI tooling catch you by surprise? > Reconnect with the command line and become more productive. > Learn the new .NET and ASP.NET CLI. Get your free copy! > http://sdm.link/telerik > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Yashar S. <sa...@em...> - 2016-10-27 13:34:12
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Hi I am trying to run the localized reconstruction protocol by Ilca et al, 2015 which uses scipion but I receive the following error: -bash-4.1$ scipion Error: No section: 'PACKAGES' Please check the configuration file /g/sbgrid/programs/x86_64-linux/scipion/1.0.1/config/scipion.conf and try again. -bash-4.1$ cd /g/sbgrid/programs/x86_64-linux/scipion/1.0.1/config/ could you please tell me what exactly I need to do to troubleshoot? -- Best, Yashar Sadian Christoph Mueller's group Structural and computational Biology Unit European Molecular Biology Laboratory (EMBL) Meyerhofstrasse 1 69117 Heidelberg, Germany Phone: 0049-6221-387-8496 Email: sa...@em... |
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From: Jose M. de la R. T. <del...@gm...> - 2016-10-25 08:48:45
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Dear Dmitry, There is a protocol that does exactly what you want. It is: extract-coordinates. As input, you should provide a SetOfParticles (usually the 'good' ones, after screening, classification, subset, etc) and a SetOfMicrographs. The ouput will be a SetOfCoordinates....you can even visualize them as a normal picking job. You do not need to take care about different in the pixel size (due to possible downsampling), the coordinates will be scaled properly. After that you can proceed to a normal particles-extraction step and get the new set of particles. Hope this helps, Jose Miguel. On Tue, Oct 25, 2016 at 10:43 AM, Dmitry Semchonok <sem...@gm...> wrote: > Dear colleagues, > > I have the good set of particles. > > I want extract the original micrographs that contain these set of > particles. > > Is there a tool in the SCIPION to do that? > > > Thank you. > > Sincerely, > Dmitry > > ------------------------------------------------------------ > ------------------ > The Command Line: Reinvented for Modern Developers > Did the resurgence of CLI tooling catch you by surprise? > Reconnect with the command line and become more productive. > Learn the new .NET and ASP.NET CLI. Get your free copy! > http://sdm.link/telerik > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Dmitry S. <sem...@gm...> - 2016-10-25 08:43:41
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Dear colleagues, I have the good set of particles. I want extract the original micrographs that contain these set of particles. Is there a tool in the SCIPION to do that? Thank you. Sincerely, Dmitry |
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From: Jose M. de la R. T. <del...@gm...> - 2016-10-17 09:20:43
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Hi, As Grigory mentioned, you need to modify the scipion/config/scipion.conf to set correctly the path to MPI and JAVA variables. Take a look in the wiki page: https://github.com/I2PC/scipion/wiki/How-to-Install and https://github.com/I2PC/scipion/wiki/Scipion-Configuration. Bests, Jose Miguel. On Mon, Oct 17, 2016 at 10:46 AM, Grigory Sharov <sha...@gm...> wrote: > Hi, > > you have to modify all these variables so they would point to the correct > path. > > Best regards, > Grigory > > ------------------------------------------------------------ > -------------------- > Grigory Sharov, Ph.D. > Institute of Genetics and Molecular and Cellular Biology > Integrated Structural Biology Department (CBI) > 1, rue Laurent Fries > 67404 Illkirch, France > tel. 03 69 48 51 00 > e-mail: sh...@ig... > > On Mon, Oct 17, 2016 at 8:36 AM, Subhomoi Borkotoky <sub...@gm... > > wrote: > >> Hi, >> >> While configuring the scipion on my desktop (Ubuntu 14.04, 64bit), I am >> getting the following error. I am not sure what to change in the >> "scipion.conf" file. I am attaching the screenshots and conf file. Please >> suggest. >> >> " Path to MPI_LIBDIR (/usr/lib64/mpi/gcc/openmpi/lib) should exist but >> it doesn't. >> Path to MPI_INCLUDE (/usr/lib64/mpi/gcc/openmpi/include) should exist >> but it doesn't. >> Path to MPI_BINDIR (/usr/lib64/mpi/gcc/openmpi/bin) should exist but >> it doesn't. >> Path to JAVA_HOME (/usr/lib64/jvm/java-1.7.0-openjdk-1.7.0) should >> exist but it doesn't. >> Path to JAVA_BINDIR (/usr/lib64/jvm/java-1.7.0-openjdk-1.7.0/bin) >> should exist but it doesn't. >> Cannot find file: /usr/lib64/jvm/java-1.7.0-openjdk-1.7.0/bin/java >> Cannot find file: /usr/lib64/jvm/java-1.7.0-openjdk-1.7.0/bin/javac >> Cannot find file: /usr/lib64/jvm/java-1.7.0-openjdk-1.7.0/bin/jar >> Cannot find file: /usr/lib64/mpi/gcc/openmpi/bin/mpicc >> Cannot find file: /usr/lib64/mpi/gcc/openmpi/bin/mpiCC >> Cannot find file: /usr/lib64/mpi/gcc/openmpi/bin/mpiCC >> Cannot find file: /usr/lib64/mpi/gcc/openmpi/include/mpi.h" >> >> >> >> -- >> Yours Sincerely, >> -------------------------- >> SUBHOMOI BORKOTOKY, >> Centre for Bioinformatics >> Pondicherry University >> Pondicherry,INDIA. >> >> Alternate Email: sub...@ma... >> >> >> >> ------------------------------------------------------------ >> ------------------ >> 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: Grigory S. <sha...@gm...> - 2016-10-17 08:47:10
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Hi, you have to modify all these variables so they would point to the correct path. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. Institute of Genetics and Molecular and Cellular Biology Integrated Structural Biology Department (CBI) 1, rue Laurent Fries 67404 Illkirch, France tel. 03 69 48 51 00 e-mail: sh...@ig... On Mon, Oct 17, 2016 at 8:36 AM, Subhomoi Borkotoky <sub...@gm...> wrote: > Hi, > > While configuring the scipion on my desktop (Ubuntu 14.04, 64bit), I am > getting the following error. I am not sure what to change in the > "scipion.conf" file. I am attaching the screenshots and conf file. Please > suggest. > > " Path to MPI_LIBDIR (/usr/lib64/mpi/gcc/openmpi/lib) should exist but it > doesn't. > Path to MPI_INCLUDE (/usr/lib64/mpi/gcc/openmpi/include) should exist > but it doesn't. > Path to MPI_BINDIR (/usr/lib64/mpi/gcc/openmpi/bin) should exist but it > doesn't. > Path to JAVA_HOME (/usr/lib64/jvm/java-1.7.0-openjdk-1.7.0) should > exist but it doesn't. > Path to JAVA_BINDIR (/usr/lib64/jvm/java-1.7.0-openjdk-1.7.0/bin) > should exist but it doesn't. > Cannot find file: /usr/lib64/jvm/java-1.7.0-openjdk-1.7.0/bin/java > Cannot find file: /usr/lib64/jvm/java-1.7.0-openjdk-1.7.0/bin/javac > Cannot find file: /usr/lib64/jvm/java-1.7.0-openjdk-1.7.0/bin/jar > Cannot find file: /usr/lib64/mpi/gcc/openmpi/bin/mpicc > Cannot find file: /usr/lib64/mpi/gcc/openmpi/bin/mpiCC > Cannot find file: /usr/lib64/mpi/gcc/openmpi/bin/mpiCC > Cannot find file: /usr/lib64/mpi/gcc/openmpi/include/mpi.h" > > > > -- > Yours Sincerely, > -------------------------- > SUBHOMOI BORKOTOKY, > Centre for Bioinformatics > Pondicherry University > Pondicherry,INDIA. > > Alternate Email: sub...@ma... > > > > ------------------------------------------------------------ > ------------------ > 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: Subhomoi B. <sub...@gm...> - 2016-10-17 06:37:34
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Hi, While configuring the scipion on my desktop (Ubuntu 14.04, 64bit), I am getting the following error. I am not sure what to change in the "scipion.conf" file. I am attaching the screenshots and conf file. Please suggest. " Path to MPI_LIBDIR (/usr/lib64/mpi/gcc/openmpi/lib) should exist but it doesn't. Path to MPI_INCLUDE (/usr/lib64/mpi/gcc/openmpi/include) should exist but it doesn't. Path to MPI_BINDIR (/usr/lib64/mpi/gcc/openmpi/bin) should exist but it doesn't. Path to JAVA_HOME (/usr/lib64/jvm/java-1.7.0-openjdk-1.7.0) should exist but it doesn't. Path to JAVA_BINDIR (/usr/lib64/jvm/java-1.7.0-openjdk-1.7.0/bin) should exist but it doesn't. Cannot find file: /usr/lib64/jvm/java-1.7.0-openjdk-1.7.0/bin/java Cannot find file: /usr/lib64/jvm/java-1.7.0-openjdk-1.7.0/bin/javac Cannot find file: /usr/lib64/jvm/java-1.7.0-openjdk-1.7.0/bin/jar Cannot find file: /usr/lib64/mpi/gcc/openmpi/bin/mpicc Cannot find file: /usr/lib64/mpi/gcc/openmpi/bin/mpiCC Cannot find file: /usr/lib64/mpi/gcc/openmpi/bin/mpiCC Cannot find file: /usr/lib64/mpi/gcc/openmpi/include/mpi.h" -- Yours Sincerely, -------------------------- SUBHOMOI BORKOTOKY, Centre for Bioinformatics Pondicherry University Pondicherry,INDIA. Alternate Email: sub...@ma... |
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