Hi,
Probably this issue is related to
https://github.com/3dem/relion/issues/473 and
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCPEM;4363c392.1905.
We have just got a locally reproducible case of this bug and
started investigation. I will post here when the bug fix is ready.
Best regards,
Takanori Nakane
On 2019/06/17 19:25, Dieter Blaas wrote:
> Dear colleagues,
>
> running 3D classification without alignment worked fine until
> iteration 8 with about 4 hours per iteration. I killed the 9th iteration
> after about 10 hours as it did not show any output. I then continued the
> run but the same is happening again.
>
> It has been running now over night, again without producing any
> meaningful output. See below. The 12 cpus run with about 100 % but,
> according to 'top' use little RAM (~ 4% each). Nevertheless, 'free'
> shows that 267 GB (out of 512 GB) are being used. I already had such a
> case some time ago and posted it but did not receive any hint. Does
> anybody know what is happening here and how to avoid it? I believed that
> it would go away with version 3.0 but apparently not!
>
> Thanks for help, bw Dieter
>
> Reading in optimiser.star ...
> === RELION MPI setup ===
> + Number of MPI processes = 12
> + Number of threads per MPI process = 4
> + Total number of threads therefore = 48
> + Master (0) runs on host = dorothy4.msp.univie.ac.at
> + Slave 1 runs on host = dorothy4.msp.univie.ac.at
> + Slave 2 runs on host = dorothy4.msp.univie.ac.at
> + Slave 3 runs on host = dorothy4.msp.univie.ac.at
> + Slave 4 runs on host = dorothy4.msp.univie.ac.at
> + Slave 5 runs on host = dorothy4.msp.univie.ac.at
> + Slave 6 runs on host = dorothy4.msp.univie.ac.at
> + Slave 7 runs on host = dorothy4.msp.univie.ac.at
> + Slave 8 runs on host = dorothy4.msp.univie.ac.at
> + Slave 9 runs on host = dorothy4.msp.univie.ac.at
> + Slave 10 runs on host = dorothy4.msp.univie.ac.at
> + Slave 11 runs on host = dorothy4.msp.univie.ac.at
> =================
> Running CPU instructions in double precision.
>
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max F. Perutz Laboratories
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,
> Tel: 0043 1 4277 61630,
> Fax: 0043 1 4277 9616,
> e-mail: [log in to unmask]
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