[scipion-users] Relion auto-refine error in Scipion

[Montserrat F. F. <mf...@ib...>]

Hi,

I am trying to run a Relion auto-refine in Scipion v1.1 (2017-06-14)
Balbino. The Relion version is 2.0.3. However, I get the error I copy
below. Does anybody have any suggestion that would help?

Thank you very much in advance,

Montserrat Fabrega

00001:   RUNNING PROTOCOL -----------------
00002:             PID: 10237
00003:         Scipion: v1.1 (2017-06-14) Balbino
00004:      currentDir: /gpfs/projects/irb12/irb12336/
ScipionUserData/projects/Titan
00005:      workingDir: Runs/011639_ProtRelionRefine3D
00006:         runMode: Continue
00007:             MPI: 4
00008:         threads: 4
00009:   len(steps) 3 len(prevSteps) 0
00010:    Starting at step: 1
00011:    Running steps
00012:   STARTED: convertInputStep, step 1
00013:     2018-01-22 00:13:40.523885
00014:   Converting set from 'Runs/011589_ProtUserSubSet/particles.sqlite'
into 'Runs/011639_ProtRelionRefine3D/input_particles.star'
00015:   FINISHED: convertInputStep, step 1
00016:     2018-01-22 00:13:45.845200
00017:   STARTED: runRelionStep, step 2
00018:     2018-01-22 00:13:45.860738
00019:   srun  `which relion_refine_mpi` --gpu  --low_resol_join_halves 40
--pool 3 --auto_local_healpix_order 4 --angpix 1.04
--dont_combine_weights_via_disc  --ref
Runs/011639_ProtRelionRefine3D/tmp/proposedVolume00003.mrc
--scale  --offset_range 5.0 --ini_high 60.0 --offset_step 2.0
--healpix_order 2 --auto_refine  --ctf  --oversampling 1
--split_random_halves  --o Runs/011639_ProtRelionRefine3D/extra/relion --i
Runs/011639_ProtRelionRefine3D/input_particles.star --zero_mask  --norm
--firstiter_cc  --sym c12 --flatten_solvent  --particle_diameter 228.8  --j
4
00020:    === RELION MPI setup ===
00021:    + Number of MPI processes             = 4
00022:    + Number of threads per MPI process  = 4
00023:    + Total number of threads therefore  = 16
00024:    + Master  (0) runs on host            = nvb36
00025:    + Slave     1 runs on host            = nvb36
00026:    + Slave     2 runs on host            = nvb36
00027:    + Slave     3 runs on host            = nvb36
00028:    =================
00029:    uniqueHost nvb36 has 3 ranks.
00030:   GPU-ids not specified for this rank, threads will automatically be
mapped to available devices.
00031:    Thread 0 on slave 1 mapped to device 0
00032:    Thread 1 on slave 1 mapped to device 0
00033:    Thread 2 on slave 1 mapped to device 0
00034:    Thread 3 on slave 1 mapped to device 1
00035:   GPU-ids not specified for this rank, threads will automatically be
mapped to available devices.
00036:    Thread 0 on slave 2 mapped to device 1
00037:    Thread 1 on slave 2 mapped to device 1
00038:    Thread 2 on slave 2 mapped to device 2
00039:    Thread 3 on slave 2 mapped to device 2
00040:   GPU-ids not specified for this rank, threads will automatically be
mapped to available devices.
00041:    Thread 0 on slave 3 mapped to device 2
00042:    Thread 1 on slave 3 mapped to device 3
00043:    Thread 2 on slave 3 mapped to device 3
00044:    Thread 3 on slave 3 mapped to device 3
00045:   Device 1 on nvb36 is split between 2 slaves
00046:   Device 2 on nvb36 is split between 2 slaves
00047:   [nvb36:10305] *** Process received signal ***
00048:   [nvb36:10305] Signal: Segmentation fault (11)
00049:   [nvb36:10305] Signal code: Address not mapped (1)
00050:   [nvb36:10305] Failing at address: 0x2802b08
00051:   [nvb36:10305] [ 0] /lib64/libpthread.so.0() [0x358740f790]
00052:   [nvb36:10305] [ 1] /opt/mpi/bullxmpi/1.2.9.1/lib/
libmpi.so.1(opal_memory_ptmalloc2_free+0x26)
<http://1.2.9.1/lib/libmpi.so.1%28opal_memory_ptmalloc2_free+0x26%29>
[0x2ac8aeb94046]
00053:   [nvb36:10305] [ 2] /apps/RELION/2.0.3/lib/librelion_lib.so(_
ZN14MlOptimiserMpi10initialiseEv+0x115f) [0x2ac8a7491f0f]
00054:   [nvb36:10305] [ 3]
/apps/RELION/2.0.3/bin/relion_refine_mpi(main+0x218)
[0x4052c8]
00055:   [nvb36:10305] [ 4] /lib64/libc.so.6(__libc_start_main+0xfd)
[0x3586c1ed5d]
00056:   [nvb36:10305] [ 5] /apps/RELION/2.0.3/bin/relion_refine_mpi()
[0x404fe9]
00057:   [nvb36:10305] *** End of error message ***
00058:   srun: error: nvb36: task 0: Segmentation fault