I keep getting set fault on a specific dataset with RELION 1.2b7. i don't understand what's happening.It had been running fine with a previous version of relion (1.1). The images have been normalized with relion_preprocess.
Expectation iteration 1
3.82/9.13 min .........................~~(,_,"> exp_thisparticle_sumweight= 0 [oo]
exp_part_id= 11894exp_iimage=6
mic_id= 717 mymodel.scale_correction[mic_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
1.6e-05
4.2e-05
0.00011
0.0001
7.3e-05
6.9e-05
6.8e-05
7.1e-05
6.9e-05
7e-05
.
.
.
0
0
0
0
wsum_model.pdf_direction[exp_ipart]=
3.95/9.18 min .........................~~(,_,">[node82:31096] *** Process received signal ***
[node82:31096] Signal: Segmentation fault (11)
[node82:31096] Signal code: Address not mapped (1)
[node82:31096] Failing at address: 0xae47000
[node82:31096] [ 0] /lib64/libpthread.so.0 [0x7f4323b25b30]
[node82:31096] [ 1] /guam.raid.cluster.software//relion-1.2b7/lib/librelion-1.2.so.1(_ZlsIdERSoS0_RK13MultidimArrayIT_E+0x8a) [0x7f432593627a]
[node82:31096] [ 2] /guam.raid.cluster.software//relion-1.2b7/lib/librelion-1.2.so.1(_ZN11MlOptimiser37convertAllSquaredDifferencesToWeightsEv+0x188b) [0x7f43259cdf4b]
[node82:31096] [ 3] /guam.raid.cluster.software//relion-1.2b7/lib/librelion-1.2.so.1(_ZN11MlOptimiser24expectationSomeParticlesEll+0x20c) [0x7f43259cef3c]
[node82:31096] [ 4] /guam.raid.cluster.software//relion-1.2b7/lib/librelion-1.2.so.1(_ZN14MlOptimiserMpi11expectationEv+0x1135) [0x7f4325a28cd5]
[node82:31096] [ 5] /guam.raid.cluster.software//relion-1.2b7/lib/librelion-1.2.so.1(_ZN14MlOptimiserMpi7iterateEv+0x70) [0x7f4325a34050]
[node82:31096] [ 6] /guam.raid.cluster.software//relion-1.2b7/bin/relion_refine_mpi(main+0x47) [0x40a2e7]
[node82:31096] [ 7] /lib64/libc.so.6(__libc_start_main+0xe6) [0x7f43237dc436]
[node82:31096] [ 8] /guam.raid.cluster.software//relion-1.2b7/bin/relion_refine_mpi(__gxx_personality_v0+0x139) [0x40a1a9]
[node82:31096] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 18 with PID 31096 on node node82 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
--
Amedee des Georges
Frank lab
Howard Hughes Medical Institute
Dept. of Biochemistry and Molecular Biophysics
650 W 168th St, P&S Black Building room 221
New York, NY 10032
(T) 212 305-9527
(F) 212 305-9500
(E) [log in to unmask]
http://franklab.cpmc.columbia.edu
