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CCPEM  June 2018

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Subject:

Re: Setting up a Linux Box with Cuda for EM

From:

Benoît Zuber <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Tue, 12 Jun 2018 09:16:41 +0000

Content-Type:

text/plain

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text/plain (1 lines)

Dear Clemens, 
 
To avoid conflicts between EMAN2 and other programs, you can follow instructions to install EMAN2 from source in an anaconda environment.  
http://blake.bcm.edu/emanwiki/EMAN2/BUILD_SYSTEM_ANACONDA 
 
For the CUDA problems, yes this is a pain. There is a workaround. You can use different cuda versions for different packages. You can compile relion with whatever recent cuda version you like. This would be the cuda version that you source in your bashrc. Now for other binaries that require a specific cuda version (e.g. motioncor2) you make a script that sets the script environment to this cuda version and runs the binary of interest.  
 
For example we made a script called MotionCor2.sh: 
 
------ 
#!/bin/bash 
LD_LIBRARY_PATH=/usr/local/cuda-9.1/lib64:$LD_LIBRARY_PATH /usr/local/bin/MotionCor2_Cuda9.1_v1.0.5 "$@" 
------- 
 
And we use it so: 
./MotionCor2.sh [OPTIONS] 
 
All the variables ("OPTIONS") that you pass to the script are passed further to the executable by "$@" 
(see https://stackoverflow.com/a/5163260/448521 ) 
 
Then instead of pointing to MotionCor2 executable in relion, you point to your script. 
 
Hope this helps 
 
Benoit 
 
 
 
Le 12.06.18 10:40, « Collaborative Computational Project in Electron cryo-Microscopy au nom de Clemens Grimm » <[log in to unmask] au nom de [log in to unmask]> a écrit : 
 
    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 
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