Hi all,
We tried to install Relion 1.4 in a RHEL 6 system which was built with a
minimal interface as a file server and thus incomplete development tools
and X system. The install failed due to missing X libraries. After yum
group install of X and development tools, it still does not work. I wonder
whether some of you might have had similar experiences and what other X
libraries are missing. Thanks.
Qiu-Xing
On 5/3/16, 10:37 AM, "Collaborative Computational Project in Electron
cryo-Microscopy on behalf of Sjors Scheres" <[log in to unmask] on
behalf of [log in to unmask]> 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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