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Hi Steve, I have one question regarding EMAN2.2 and Anaconda...I remember that I read sometime ago that you could not install eman2 as a normal conda module. Is it still like that? If yes, can you comment on the reason why it is not build as a normal Python module that one could install such as: conda install eman2 ? Thanks in advance, Best, Jose Miguel On Tue, Jun 12, 2018 at 2:13 PM Ludtke, Steven J <[log in to unmask]> wrote: > 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 > ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1