Hi,
> running okay with MPI = 2 but not more
> than that.
This is expected.
You have only 64 GB of memory and the input movies
are very large (K3 super-resolution).
If you are binning the movie at this step,
add "--early_binning" as the additional argument.
Best regards,
Takanori Nakane
On 2019/08/31 1:08, Nandish Kumar Khanra wrote:
> Hi Takanori,
>
>
> Thank you for your reply. It is running okay with MPI = 2 but not more
> than that.
>
>
> Size of the movie = 11520 X 8184; frame = 40;
>
> MPI = 4 and 8
>
> local (CPU) memory = 64 GB
>
>
> Thanks,
>
> Nandish
>
> ------------------------------------------------------------------------
> *From:* Takanori Nakane <[log in to unmask]>
> *Sent:* Friday, August 30, 2019 12:40:37 AM
> *To:* Nandish Kumar Khanra <[log in to unmask]>;
> [log in to unmask] <[log in to unmask]>
> *Subject:* [EXTERNAL] Re: [ccpem] Error during motion correction job in
> Relion
> Hi,
>
> We need more information.
>
> What is the size of your movies (width, height and frames),
> the number of MPI processes and the size of the local (CPU) memory?
>
> My first guess is that you ran out of memory. What if you reduce
> the number of MPI processes?
>
> Best regards,
>
> Takanori Nakane
>
> On 2019/08/30 5:16, Nandish Kumar Khanra wrote:
>> Dear all,
>>
>>
>> I am getting the following error messages when I ran the motion
>> correction job in Relion,
>>
>>
>> ‘mpirun noticed that process rank 3 with PID 0 on node localhost exited
>> on signal 9 (Killed).’
>>
>>
>> ‘Primary job terminated normally, but 1 process returned a non-zero exit
>> code. Per user-direction, the job has been aborted’
>>
>>
>> Any suggestions on how to resolve this?
>>
>>
>> Thanks,
>>
>> Nandish
>>
>>
>> ------------------------------------------------------------------------
>>
>> To unsubscribe from the CCPEM list, click the following link:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCPEM-26A-3D1&d=DwID-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=DpAiumlSV5DBIb-ActN_MUx1-7a6RRLN7Qol_bll2YM&m=UKhXfEaigcGay3TRXFUmy_wlB-Vu0k_LZCcAeO2AduI&s=l38LOWKjgycdyv4G9p4bB5HBTnKC7SgiX9W0i2TjoZQ&e=
>
>>
>
>
> ------------------------------------------------------------------------
>
> To unsubscribe from the CCPEM list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
>
########################################################################
To unsubscribe from the CCPEM list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
|