JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for CCPEM Archives


CCPEM Archives

CCPEM Archives


CCPEM@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

CCPEM Home

CCPEM Home

CCPEM  June 2014

CCPEM June 2014

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: relion_refine_mpi, threads and hostfile

From:

Sjors Scheres <[log in to unmask]>

Reply-To:

Sjors Scheres <[log in to unmask]>

Date:

Fri, 13 Jun 2014 11:27:25 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (33 lines)

Dear Ambroise,

Thank you for your feedback to the list!

I completely agree with you that this may be a tricky thing to achieve 
on some clusters. However, it has nothing to do with relion code in 
itself: it would be exactly the same for any MPI programme (e.g. a 
hello-world one you would write yourself). It is a consequence of how 
the MPI standard is implemented, and how it communicates with your job 
allocation system (i.e. queue). It is not an easy problem, as the 
hardware for parallel computing is extremely diverse.

Best,
Sjors

On 06/13/2014 10:20 AM, Ambroise Desfosses wrote:
> Dear Sjors, dear all,
>
> thanks for your anwers. It appeared that the problem mainly came from the way our cluster system (LSF) was setting up the environment for MPI (which I guess relion somehow parses as well ?). We managed to finally reserve the right amount of cpus and providing the correct list of host to mpirun by playing with internal LSF environment variables related to MPI usage.
> What may be useful for a general use of Relion on various cluster systems would be to know how exactly Relion reads the MPI environment and make use of it to distribute the master and the slaves jobs. Also, it appeared relatively difficult to set up the parralelization in a way that several mpi jobs end up on the same host, which can be useful for hosts with many cpus. We have e.g. 80 cpus machines, and there it seems that using 80 threads is way too much for most of our Relion's usage, therefore it could be nice to send e.g. 4 mpijobs with 20 threads each on those machines. We found kind of a solution for this, but very specific to our cluster and not ideal at all.
> Again, thanks for your help, and for users working on a LSF cluster, do not hesitate to contact me if questions/other suggestions.
>
> Cheers,
> Ambroise Desfosses

-- 
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

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

March 2024
February 2024
January 2024
December 2023
November 2023
October 2023
September 2023
August 2023
July 2023
June 2023
May 2023
April 2023
March 2023
February 2023
January 2023
December 2022
November 2022
October 2022
September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

For help and support help@jisc.ac.uk

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager