Dear Samir,
Make sure that relion was compiled with the same MPI installation (mpich?)
as the one you are using to run it with. This sounds trivial, but on many
systems it is not. For example, imagic (and other programmes) may come
with their own MPI and "hijack" your system installed one. Commands like
"which mpirun" in the shell where you execute relion should help.
HTH,
S
> Hi Scheres,
> Thanks for replay, I download relion again, after rebooting the computer.
> I got less errors than before. I run the gui, so far ctf and extracting
> particles worked fine. However I got this error while doing 2d
> classification:
>
> Here is the command that I run:
>
> Executing: mpirun -n 8 `which relion_refine_mpi` --o Class2D/run1 --i
> ./particles.star --particle_diameter 350 --angpix 1.45 --iter 25
> --tau2_fudge 2 --flatten_solvent --K 10 --oversampling 1 --psi_step 10
> --offset_range 30 --offset_step 2 --norm --scal
>
> And here is the error :
>
> Executing: mpirun -n 8 `which relion_refine_mpi` --o Class2D/run1 --i
> ./particles.star --particle_diameter 350 --angpix 1.45 --iter 25
> --tau2_fudge 2 --flatten_solvent --K 10 --oversampling 1 --psi_step 10
> --offset_range 10 --offset_step 2 --norm --scale --j 1 &
> /home/sb/Programs/relion-1.2/bin/relion_refine_mpi: symbol lookup error:
> /usr/lib/libmpich.so.3: undefined symbol: MPL_env2str
> /home/sb/Programs/relion-1.2/bin/relion_refine_mpi: symbol lookup error:
> /usr/lib/libmpich.so.3: undefined symbol: MPL_env2str
> /home/sb/Programs/relion-1.2/bin/relion_refine_mpi: symbol lookup error:
> /usr/lib/libmpich.so.3: undefined symbol: MPL_env2str
> /home/sb/Programs/relion-1.2/bin/relion_refine_mpi: symbol lookup error:
> /usr/lib/libmpich.so.3: undefined symbol: MPL_env2str
> /home/sb/Programs/relion-1.2/bin/relion_refine_mpi: symbol lookup error:
> /usr/lib/libmpich.so.3: undefined symbol: MPL_env2str
> /home/sb/Programs/relion-1.2/bin/relion_refine_mpi: symbol lookup error:
> /usr/lib/libmpich.so.3: undefined symbol: MPL_env2str
> /home/sb/Programs/relion-1.2/bin/relion_refine_mpi: symbol lookup error:
> /usr/lib/libmpich.so.3: undefined symbol: MPL_env2str
> /home/sb/Programs/relion-1.2/bin/relion_refine_mpi: symbol lookup error:
> /usr/lib/libmpich.so.3: undefined symbol: MPL_env2str
> --------------------------------------------------------------------------
> mpirun noticed that the job aborted, but has no info as to the process
> that caused that situation.
>
> Any help will be appreciated.
> Thank you
> Cheers,
> Samir
>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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