Hi Tat,
It would be best to avoid the older nodes, and run only 1 or 2 MPI jobs 
on each newer node, with 12 or 6 threads (-j) each, respectively.
HTH,
S
On 07/16/2014 02:16 PM, Tat Cheung Cheng wrote:
> Hi Dr Scheres,
>
> Sorry to say that I am still a little confused here. Please allow me 
> to be a little more specific here.
> I ran refinement on a 12 node cluster, the older half of the 12 nodes 
> is with 8 cores each, ~1.5 Gb memory per core, while the newer half is 
> with 12 cores each, ~2.4Gb per core. Originally I ran the job with j 
> -8,  and the estimated memory may exceed the capacity on the older 
> nodes, and that may caused the abort.
>
> Estimated memory for expectation step  > 8.70496 Gb
>
> Estimated memory for maximization step > 15.3861 Gb
>
>
> I think what I can do here is to use a lower -j, or limit the job to 
> the newer nodes with more memory. So my question here is which way do 
> you think is a better/more efficient way to run?
>
> Thanks very much again.
>
>
> Best Regards,
>
> Tat
>
>
>
>
> On Tue, Jul 15, 2014 at 3:29 AM, Sjors Scheres 
> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
>     Hi Tat,
>     1: RELION will only include the resolution shells it deems
>     necessary in
>     the 2D/3D refinement/classification. This is normal.
>     2: You run out of RAM. Are you running a single MPI node and multiple
>     threads on each 48Gb node? If you run multiple MPI nodes, each of them
>     will replicate the RAM. Threads share the same RAM. See Wiki for more
>     details.
>     HTH, S
>     > Hi Dr Scheres,
>     >
>     > I have collected some data recently, and I am using Relion for 2D
>     > classification, 3D classification and refinement. But there are some
>     > questions that puzzle me.
>     >
>     > 1.  In 2D and 3D classification, it seems the signal
>     (rlnSsnrMap) drops to
>     > zero beyond resolution 8.0A in every class in 2D classification
>     and 8.6A
>     > in 3D classification, no matter how many particles in the class (an
>     > example is shown below), but I have set --strict_highres_exp 6
>     in both
>     > run. I wonder is it a feature of Relion to use 8.0A/8.6A as a
>     cutoff for
>     > 2D/3D classification or is there some problem with my original data.
>     >
>     >           47     0.122396     8.170213     0.001602     0.000000
>     > 1.123953e-08 9.000828e-12 2.063652e-05
>     >           48     0.125000     8.000000     0.001286     0.000000
>     > 1.555068e-08 9.999181e-12 6.504905e-06
>     >           49     0.127604     7.836735     0.000000     0.000000
>     > 0.000000     0.000000     0.000000
>     >
>     >
>     > 2.  In Refinement, the program somehow aborts at the final stage
>     when
>     > calculating the gold-standard FSC. The error log says
>     >
>     > Allocate: No space left
>     > File: ./src/multidim_array.h line: 962
>     >
>     > And I increase the max memory (to 48Gb) for the run, but the
>     program says
>     >  Estimated memory for expectation step  > 8.64817 Gb, available
>     memory =
>     > 48 Gb.
>     >  Estimated memory for maximization step > 15.3861 Gb, available
>     memory =
>     > 48 Gb
>     >
>     > I thought 48Gb should be more than enough, but it still aborts
>     there. I
>     > wonder is the memory I allowed too little for the job? or is there
>     > something else I should change.
>     >
>     > Thanks very much
>     >
>     > Best Regards,
>     > Tat
>     >
>
>
>     --
>     Sjors Scheres
>     MRC Laboratory of Molecular Biology
>     Francis Crick Avenue, Cambridge Biomedical Campus
>     Cambridge CB2 0QH, U.K.
>     tel: +44 (0)1223 267061 <tel:%2B44%20%280%291223%20267061>
>     http://www2.mrc-lmb.cam.ac.uk/groups/scheres
>
>

-- 
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