Is it reproducible, i.e. will it happen at the same point if you run it
again? I don't think you're doing anything wrong on the command line.
S
> Hi Sjors,
>
> I was trying to run a 3D classification without any alignments (
> --skip_align), but it crashed. Any idea why?
>
> mpirun -n 12 relion_refine_mpi --o Class3D/run1 --i input.star
> --particle_diameter 80 --angpix 1.35 --ref 3d.mrc --firstiter_cc
> --ini_high
> 20 --iter 25 --tau2_fudge 4 --flatten_solvent --zero_mask --ctf --sym C1
> --K 5 --skip_align --oversampling 1 --norm --scale --j 4
>
> === RELION MPI setup ===
> + Number of MPI processes = 12
> + Number of threads per MPI process = 4
> + Total number of threads therefore = 48
> + Master (0) runs on host = umbongo.strubi.ox.ac.uk
> + Slave 1 runs on host = umbongo.strubi.ox.ac.uk
> + Slave 2 runs on host = umbongo.strubi.ox.ac.uk
> + Slave 3 runs on host = umbongo.strubi.ox.ac.uk
> + Slave 4 runs on host = umbongo.strubi.ox.ac.uk
> + Slave 5 runs on host = umbongo.strubi.ox.ac.uk
> + Slave 6 runs on host = umbongo.strubi.ox.ac.uk
> + Slave 7 runs on host = umbongo.strubi.ox.ac.uk
> + Slave 8 runs on host = umbongo.strubi.ox.ac.uk
> + Slave 9 runs on host = umbongo.strubi.ox.ac.uk
> + Slave 10 runs on host = umbongo.strubi.ox.ac.uk
> + Slave 11 runs on host = umbongo.strubi.ox.ac.uk
> =================
> Estimating initial noise spectra
> 6.44/6.44 hrs
> ............................................................~~(,_,">
> CurrentResolution= 19.2857 Angstroms, which requires orientationSampling
> of at least 25.7143 degrees for a particle of diameter 80 Angstroms
> Oversampling= 0 NrHiddenVariableSamplingPoints= 5
> OrientationalSampling= 15 NrOrientations= 1
> TranslationalSampling= 2 NrTranslations= 1
> =============================
> Estimated memory for expectation step > 0.128429 Gb, available memory =
> 8
> Gb.
> Estimated memory for maximization step > 0.0102344 Gb, available memory =
> 8 Gb.
> Expectation iteration 1 of 25
> 000/??? sec
> ~~(,_,"> [oo]***
> glibc detected *** relion_refine_mpi: double free or corruption (fasttop):
> 0x00002ace90f56ff0 ***
> ======= Backtrace: =========
> /lib64/libc.so.6[0x36a2076166]
> /raid/44/juha/apps/relion-1.3/lib/librelion-1.3.so.1(_ZN8Matrix1DIdE14coreDeallocateEv+0x17)[0x2ace2605a3d7]
> /raid/44/juha/apps/relion-1.3/lib/librelion-1.3.so.1(_ZN15HealpixSampling17setOneTranslationE8Matrix1DIdE+0x34)[0x2ace260ac214]
> /raid/44/juha/apps/relion-1.3/lib/librelion-1.3.so.1(_ZN11MlOptimiser35doThreadGetFourierTransformsAndCtfsEi+0x3d66)[0x2ace26112fb6]
> /raid/44/juha/apps/relion-1.3/lib/librelion-1.3.so.1(_Z11_threadMainPv+0x1d)[0x2ace26123f0d]
> /lib64/libpthread.so.0[0x36a24079d1]
> /lib64/libc.so.6(clone+0x6d)[0x36a20e8b5d]
>
> ....
> [umbongo:84156] Signal: Aborted (6)
> [umbongo:84156] Signal code: (-6)
> [umbongo:84156] [ 0] /lib64/libpthread.so.0() [0x36a240f710]
> [umbongo:84156] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x36a2032925]
> [umbongo:84156] [ 2] /lib64/libc.so.6(abort+0x175) [0x36a2034105]
> [umbongo:84156] [ 3] /lib64/libc.so.6() [0x36a2070837]
> [umbongo:84156] [ 4] /lib64/libc.so.6() [0x36a2076166]
> [umbongo:84156] [ 5]
> /raid/44/juha/apps/relion-1.3/lib/librelion-1.3.so.1(_ZN8Matrix1DIdE14coreDeallocateEv+0x17)
> [0x2b23874c53d7]
> [umbongo:84156] [ 6]
> /raid/44/juha/apps/relion-1.3/lib/librelion-1.3.so.1(_ZN15HealpixSampling17setOneTranslationE8Matrix1DIdE+0x34)
> [0x2b2387517214]
> [umbongo:84156] [ 7]
> /raid/44/juha/apps/relion-1.3/lib/librelion-1.3.so.1(_ZN11MlOptimiser35doThreadGetFourierTransformsAndCtfsEi+0x3d66)
> [0x2b238757dfb6]
> [umbongo:84156] [ 8]
> /raid/44/juha/apps/relion-1.3/lib/librelion-1.3.so.1(_Z11_threadMainPv+0x1d)
> [0x2b238758ef0d]
> [umbongo:84156] [ 9] /lib64/libpthread.so.0() [0x36a24079d1]
> [umbongo:84156] [10] /lib64/libc.so.6(clone+0x6d) [0x36a20e8b5d]
> [umbongo:84156] *** End of error message ***
>
> Best
> Juha
>
--
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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