Hi Mani,
Not sure. Perhaps you could try the tutorial data set, or some other
small data set that you know will work, to test whether there is
something wrong with your computer setup.
HTH,
Sjors
On 05/06/2016 08:52 AM, Manikandan KARUPPASAMY wrote:
> Hi Sjors,
>
> I did try without --scratchdir and used only
> --dont_combine_weights_via_disc .
>
> Still the run stucks at 'noise spectra estimation'
>
> Anything else to look in?
>
> with kind regards
>
> Mani.
>
> On 2016-05-03 16:37, Sjors Scheres wrote:
>> Hi Mani,
>> Perhaps you could try without --scratchdi? Or use the option not to
>> combine data thru the disk?
>> HTH,
>> Sjors
>> On 05/03/2016 02:52 PM, Manikandan KARUPPASAMY wrote:
>>> Hi All,
>>>
>>> I am running a 2D classification in Relion 1.4 as below using slurm.
>>>
>>> $salloc -n 96 mpirun `which relion_refine_mpi` --o all/Class2D/run2
>>> --i all.star --particle_diameter 360 --angpix 1.38 --ctf --iter 50
>>> --tau2_fudge 2 --K 200 --flatten_solvent --zero_mask
>>> --strict_highres_exp 5 --oversampling 1 --psi_step 10 --offset_range
>>> 12 --offset_step 2 --norm --scale --j 1 --memory_per_thread 2
>>> --scratchdir /emdata4/scratch_4relion/
>>>
>>> The program runs for ~30 mins and writes the optimiser file but not
>>> *mrcs . It does not give any error message and just hangs forever
>>> until you kill the job.
>>>
>>>
>>> -rw-r--r-- 1 mkaruppa users 51M May 3 14:51
>>> all/Class2D/run2_it000_data.star
>>> -rw-r--r-- 1 mkaruppa users 4.0K May 3 15:25
>>> all/Class2D/run2_it000_optimiser.star
>>> -rw-r--r-- 1 mkaruppa users 0 May 3 15:25
>>> all/Class2D/run2_it000_classes.mrcs
>>>
>>> The data set is ~110k particles of 320 box size.
>>>
>>> Please help.
>>>
>>> with kind regards
>>>
>>> Mani.
>
--
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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