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 2018

CCPEM June 2018

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Setting up a Linux Box with Cuda for EM

From:

Chris Richardson <[log in to unmask]>

Reply-To:

Chris Richardson <[log in to unmask]>

Date:

Tue, 12 Jun 2018 09:36:44 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (1 lines)

On the subject of conflicting libraries and dependencies, I recommend the use of environment modules.

       http://modules.sourceforge.net

We use modules and have multiple versions of fftw and openmpi installed for software that is picky about what it requires.  Using modules also allows you to have several versions of a package installed, which is handy if you want to reproduce work done with an earlier version of Relion, Spider, and so on. 

As an example, to use the latest version of Relion you might type (or have set up in your bashrc/cshrc)

  module load openmpi/2.0.1 relion/2.1.0

If you want to revert to an older version of relion for some reason, it’s as simple as

  module unload relion
  module load relion/2.0.3

As mentioned by Benoit, using Anaconda environments to encapsulate python software helps a lot with python package issues.

Regards,

Chris
-- 
Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk
 
 
 

On 12/06/2018, 09:28, "Collaborative Computational Project in Electron cryo-Microscopy on behalf of Clemens Grimm" <[log in to unmask] on behalf of [log in to unmask]> wrote:

    Dear All,
    
    we are currently setting up a Linux machine with two Nvidia cards and  
    Cuda for Relion2 and Eman2, CCPEM etc.
    
    After several tries with the current versions of CentOS 7 and Ubuntu  
    and recent versions of the Cuda toolbox (9.2, 9.1), we had to find out  
    that there are various dependencies and incompatibilities of what  
    binaries are available for the different Cuda versions, what can be  
    installed alongside and what Cuda versions enable a successful  
    compilation in particular of Relion2.
    
    Another problem we ran into was that the EMAN2 installation interferes  
    with the compilation of Relion2 by installing conflicting  FFTW  
    libraries.
    
    The Liao lab has published a very helpful and comprehensive protocol  
    to setup a linux box under Ubuntu 14. However, this distribution will  
    reach its end of life in less than a year.
    
    It would be great if colleagues would be willing to share their  
    current configuration and experiences as of what Linux distribution  
    and what Cuda version(s) they use with the different software  
    packages, and whether different Cuda versions can be used successfully  
    alongside.
    
    Thanks,
    Clemens
    
    --------------------------------------------------
    Dr. Clemens Grimm
    Institut für Biochemie
    Biozentrum der Universität Würzburg
    Am Hubland
    D-97074 Würzburg
    Germany
    e-mail: [log in to unmask]
    phone : +49 0931 31 84031
    -------------------------------------------------
    
    ########################################################################
    
    To unsubscribe from the CCPEM list, click the following link:
    https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
    


The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
 
 
######################################################################## 
 
To unsubscribe from the CCPEM list, click the following link: 
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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

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