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:

"Ludtke, Steven J" <[log in to unmask]>

Reply-To:

Ludtke, Steven J

Date:

Tue, 12 Jun 2018 12:13:31 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (1 lines)

I would add that there is no longer a very good reason to build EMAN2 yourself. The binaries we provide now are pretty well optimized for modern Cpu/Gpu. Regardless, since EMAN2 now uses anaconda as a base, the only environment variable you should use with it is PATH. It should find its libraries itself, so it should not interfere with anything else, unless its an executable. If it does all you have to do is pull it out of path. You should not be setting LD_LIBRARY_PATH or anything else. 
 
Sent from my iPhone 
 
> On Jun 12, 2018, at 5:36 AM, Chris Richardson <[log in to unmask]> wrote: 
>  
> On the subject of conflicting libraries and dependencies, I recommend the use of environment modules. 
>  
>       https://urldefense.proofpoint.com/v2/url?u=http-3A__modules.sourceforge.net&d=DwIGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=GWA2IF6nkq8sZMXHpp1Xpg&m=xbbHeT_4e_9YPejFrgtnAFuywgCsQkjMrmYbU3-2VLw&s=3Ptn1EsjSOyiTFRVkgVNrJ5sLsvOeHdJXzAD9gOg_Ls&e= 
>  
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCPEM-26A-3D1&d=DwIGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=GWA2IF6nkq8sZMXHpp1Xpg&m=xbbHeT_4e_9YPejFrgtnAFuywgCsQkjMrmYbU3-2VLw&s=kFkXPwFTVkkKVhveiYcOnK6AcPDF0GV5Gf0U8i2wMUs&e= 
>  
>  
>  
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCPEM-26A-3D1&d=DwIGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=GWA2IF6nkq8sZMXHpp1Xpg&m=xbbHeT_4e_9YPejFrgtnAFuywgCsQkjMrmYbU3-2VLw&s=kFkXPwFTVkkKVhveiYcOnK6AcPDF0GV5Gf0U8i2wMUs&e= 
 
######################################################################## 
 
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

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

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