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I2PC / scipion

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)
http://scipion.i2pc.es
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2D classification failure #2079

Closed PatriciaGD closed 4 years ago

PatriciaGD commented 4 years ago

Hi,

When I tried to run a 2D classification using Xmpp3 or Relion it always fail. I get these error messages:

00020: 2020-05-12 08:33:39,725 ERROR: Protocol failed: Command 'mpirun -np 2 which xmipp_mpi_classify_CL2D -i Runs/002332_XmippProtCL2D/tmp/input_particles.xmd --odir Runs/002332_XmippProtCL2D/extra --oroot level --nref 50 --iter 25 --distance correlation --classicalMultiref --nref0 4' returned non-zero exit status 1

or

00093: Protocol failed: Command 'mpirun -np 8 which relion_refine_mpi --gpu --tau2_fudge 2 --scale --dont_combine_weights_via_disc --iter 25 --norm --psi_step 10.0 --ctf --offset_range 5.0 --oversampling 1 --pool 3 --scratch_dir /scratch/tmp-pg --o Runs/001440_ProtRelionClassify2D/extra/relion --i Runs/001440_ProtRelionClassify2D/input_particles.star --particle_diameter 304.5 --K 20 --ctf_phase_flipped --flatten_solvent --zero_mask --offset_step 2.0 --angpix 1.05 --j 1' returned non-zero exit status 1

I have tried downscaling the particles and also using different amounts of MPIs but it keeps falling. I am using Scipion v2.0 (2019-04-23) Diocletian.

Many thanks in advance!

Best regards, Patricia Gil

azazellochg commented 4 years ago

Hello @PatriciaGD let's start from basic checks. Could you please run 'scipion run mpirun -np 3 hostname' command and post the output here?

PatriciaGD commented 4 years ago

Hi, This is all I got:
Sorry! You were supposed to get help about: opal_init:startup:internal-failure But I couldn't open the help file: /usr/lib64/openmpi-2.0.1/share/openmpi/help-opal-runtime.txt: No such file or directory. Sorry!

Many thanks for the quick answer! Patricia Gil

azazellochg commented 4 years ago

OK, so mpi is not configured properly for scipion. Could you please verify that all MPI* vars are set properly in the configuration file, as described here: https://scipion-em.github.io/docs/docs/scipion-modes/scipion-configuration.html

Also you could run 'mpirun -np 3 hostname' outside of scipion to make sure your system mpi works.

PatriciaGD commented 4 years ago

It doesn´t run: command not found I can imagine that the problem is the system mpi configuration. What could be the solution? I can´t install anything myself but I can report the problem to the IT technician. Also, I am working on another server via ssh.

azazellochg commented 4 years ago

Yes, since there can be many different options, I would consult the IT person responsible for the server on how to use mpi.

On Tue, May 12, 2020, 09:29 PatriciaGD notifications@github.com wrote:

It doesn´t run: command not found I can imagine that the problem is the system mpi configuration. What could be the solution? I can´t install anything myself but I can report the problem to the IT technician. Also, I am working on another server via ssh.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/I2PC/scipion/issues/2079#issuecomment-627194805, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABVBPJSPESHMFOX5MVDNMDTRRECHVANCNFSM4M6SSX3A .

PatriciaGD commented 4 years ago

Ok, many thanks for your help.