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
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