Hi Jian,
Not sure. Apparently, somehow the stdout and stderr buffers fill up.
Couldn't you redirect those to files on the disk using your job submission
script? I have never seen this (but have also no experience with sgi
compilers).
HTH,
S
> Dear Sjors,
>
> We managed to compile Relion with SGI mpi compiler on our cluster.
> During the test-run on tutorial data, the 2D classification finished all
> fine, but the 3D classification gives error after first round. DO you
> have any suggestion?
>
> Thanks and Regards,
> Jian
>
> ========================================================
> ========================================================
> + Slave 10 runs on host = kahuna
> + Slave 11 runs on host = kahuna
> =================
> MlOptimiser::initialiseGeneral: WARNING modifying pixel size from 1 to
> 3.54 based on magnification information in the input STAR file
> Estimating initial noise spectra
> 2/ 2 sec
> ............................................................~~(,_,">
> CurrentResolution= 59 Angstroms, which requires orientationSampling of
> at least 32.7273 degrees for a particle of diameter 200 Angstroms
> Oversampling= 0 NrHiddenVariableSamplingPoints= 387072
> OrientationalSampling= 15 NrOrientations= 4608
> TranslationalSampling= 2 NrTranslations= 21
> =============================
> Oversampling= 1 NrHiddenVariableSamplingPoints= 12386304
> OrientationalSampling= 7.5 NrOrientations= 36864
> TranslationalSampling= 1 NrTranslations= 84
> =============================
> Estimated memory for expectation step > 0.861024 Gb, available memory
> = 24 Gb.
> Estimated memory for maximization step > 0.0102344 Gb, available
> memory = 24 Gb.
> Expectation iteration 1 of 25
> 10.95/10.95 min
> ............................................................~~(,_,">
> Maximization ...
> 2/ 2 sec
> ............................................................~~(,_,">
> Estimating accuracies in the orientational assignment ...
> MPT ERROR: STDOUT or STDERR buffer exhausted.
> MPI: Set MPI_UNBUFFERED_STDIO or output no more than about 8192 characters
> MPI: between newlines.
>
> ========================================================
> ========================================================
>
--
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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