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

[Joshua J. L. <jl...@um...>]

Hi  Dr.Ferrer

It seems like  you are running out of memory on your cards . What is the
box size ? .Also you might want to give an odd number of MPI because one
will always become a master an the rest
will be slaves

Sincerely
Joshua Lobo

On Mon, Jan 22, 2018 at 11:46 AM, Montserrat Fabrega Ferrer <
mf...@ib...> wrote:

> 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/libreli
> on_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
>
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