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Re: [scipion-users] warnings about missing plugins and CONDA
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From: Pablo C. <pc...@cn...> - 2019-11-05 09:58:48
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Hi Daniel. CUDA variable is there just for Xmipp. It will not affect Relion compilation or others. I recommend you to leave CUDA to True, xmipp has a movie correlation method in GPU and they are porting other method to GPU. You can set OPENCV=False if you hit compilation errors. On 1/11/19 11:22, Daniel Larsson wrote: > > >> On 2019-11-01, at 11:14, Daniel Larsson <dan...@ic... >> <mailto:dan...@ic...>> wrote: >> >> >> >>> On 2019-10-31, at 11:32, Pablo Conesa <pc...@CN... >>> <mailto:pc...@CN...>> wrote: >>> >>> Hi Daniel, >>> >>> About XMIPP: >>> >>> You probably have the plugin (python code that wrapps xmipp) but not >>> the actual xmipp. >>> >>> Try scipion installb >>> >>> I'm getting: >>> >>> xmippBin_Centos 3.19.04 [ ] >>> xmippBin_Debian 3.19.04 [ ] >>> xmippSrc 3.19.04 [X] >>> >>> First ones are compiled xmipp for Centos and Debian. >>> >>> 3rd are sources and will require compiling xmipp, but probably safer >>> in terms of dependencies. >>> >>> >> Running "scipion installb" revealed that I indeed do not have xmipp >> installed. I did not realize that you could drill down for Xmipp in >> the Plugin Manager GUI. When I tried installing xmippSrc, it turns >> out that I have a too old g++ compiler (needs 4.8 or later). I guess >> that is why I did not get xmipp in the first place. Now I figured out >> how to use g++ version 7.3.1, but run into problems with missing >> opencv headers. I don't think I will need such features and wondering >> how I should customize my installation to run with "--no-opencv". >> Where should I edit? > > Ok, found the OPENCV = True/False flag in config/scipion.conf thanks > to some googling: > https://sourceforge.net/p/scipion/mailman/message/36738786/ > > Also while digging around in the scipion.conf file, I realized that I > have CUDA = False. I guess I should remove all plugins and recompile > them with the CUDA = True if I want Relion with CUDA, right? > >>> >>> About CONDA_ACTIVATION_CMD: >>> >>> Some plugins, (in your case sphire) require to have conda installed. >>> Conda installation ask you to "add itself" to the shell so you have >>> conda in the PATH. >>> >>> When doing so, python calls, in some cases are messed up due to >>> having conda and its python exposed in the terminal. >>> >>> We recommend not to have conda initialized in the terminal and tell >>> scipion how to activate conda using the variable "CONDA_ACTIVATION_CMD" >>> >>> >>> In my case I got this in the <Scipion-home>/config/scipion.conf >>> under BUILD section: >>> >>> CONDA_ACTIVATION_CMD = eval "$(/extra/miniconda3/bin/conda >>> shell.bash hook)" >>> >>> NOTE: Conda usually tells you that command. >>> seehttps://github.com/scipion-em/scipion-em-sphire#cryolo-integration >>> >> Ok. I don't think there is Conda available. I'll uninstall >> Sphire/cryolo for the time being. >> >>> >>> About Locascale: Locscale plugin has a dependency to Eman plugin, >>> try to install eman plugin: >>> >>> scipion installp -p scipion-em-eman2 >>> >> Ok. Fixed that! >> >>> >>> >>> >>> On 31/10/19 10:55, Daniel Larsson wrote: >>>> So I just installed Scipion 2.0 on a CentOS cluster and installed some plugins using the Plugin Manger and get some warnings. First, I installed Xmipp, but I stil get a warning about missing Xmipp binaries when I start Scipion. I ran the scipion installp --help --checkUpdates command (see below for the output). There are also warnings about locscale and eman2/PyQt4. And what is the CONDA warning about? Any suggestions? >>>> >>>> Regards, >>>> Daniel >>>> >>>> >>>> >>>> >>>> >>>>> scipion installp --help --checkUpdates >>>> Scipion v2.0 (2019-04-23) Diocletian >>>> >>>>>>>>> python /home/larsson/software/scipion_v2.0/pyworkflow/install/install-plugin.py /home/larsson/software/scipion_v2.0/scipion installp --help --checkUpdates >>>> >>> WARNING: Xmipp binaries not found. Ghost active.....BOOOOOO! >>>> > Please install Xmipp to get full functionality. >>>> (Configuration->Plugins->scipion-em-xmipp in Scipion manager window) >>>> >>>> > error when importing from eman2: No module named PyQt4 >>>> Called by /home/larsson/software/scipion_v2.0/software/lib/python2.7/site-packages/locscale/constants.py, line 34 >>>> Check the plugin manager (Configuration->Plugins in Scipion manager window) >>>> or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, >>>> it could be a versions compatibility issue. >>>> >>>> Warning: couldn't find Plugin for scipion-em-locscale >>>> Dirname: locscale >>>> WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH >>>> usage: /home/larsson/software/scipion_v2.0/scipion installp [-h] [--noBin] [-p pluginName [pipVersion ...]] >>>> >>>> optional arguments: >>>> -h, --help show help >>>> --noBin Optional flag to install plugins only as a python module, >>>> without installing the plugin binaries. This will affect >>>> all plugins specified in the command. >>>> --checkUpdates Optional flag to check which plugins have new releases. >>>> -p pluginName [pluginVersion ...], --plugin pluginName [pluginVersion ...] >>>> - pluginName: the name of the plugin to install from the list >>>> of available plugins shown below. >>>> - pluginVersion: (optional) pip version to install. If not specified, >>>> will install the latest compatible with current Scipion. >>>> --devel Optional flag to indicate that we will pass install sources instead >>>> of pip names. Sources might be local paths or git urls. With local >>>> paths, will do pip install -e (editable mode). It is expected to find >>>> the plugin name in the basename of the path or in the repo name. >>>> (i.e. it needs to match the one specified in setup.py). E.g: >>>> scipion installp -p path/to/pluginName --devel >>>> scipion installp -phttps://github.com/someOrg/pluginName.git --devel >>>> -j j Number of CPUs to use for compilation >>>> >>>> Example: /home/larsson/software/scipion_v2.0/scipion installp -p scipion-em-grigoriefflab 1.0.1 -p scipion-em-relion -p scipion-em-eman2 >>>> >>>> Available plugins: ([ ] not installed, [X] seems already installed) >>>> >>>> scipion-em-appion 1.0.2 [X] >>>> scipion-em-atomstructutils 1.0.7 [X] >>>> scipion-em-atsas 1.0.6 [X] >>>> scipion-em-bamfordlab [ ] >>>> scipion-em-bsoft 1.0.3 [X] >>>> scipion-em-ccp4 1.0.12 [X] >>>> scipion-em-chimera 1.0.2 [X] >>>> scipion-em-cryoef 1.0.5 [X] >>>> scipion-em-cryomethods [ ] >>>> scipion-em-cryosparc2 1.0.7 [X] >>>> scipion-em-eman2 [ ] >>>> scipion-em-empiar 1.0.3 [X] >>>> scipion-em-emxlib [ ] >>>> scipion-em-esrf [ ] >>>> scipion-em-gautomatch 1.0.7 [X] >>>> scipion-em-gctf 1.0.7 [X] >>>> scipion-em-grigoriefflab 1.0.6 [X] >>>> scipion-em-imagic [ ] >>>> scipion-em-ispyb [ ] >>>> scipion-em-localrec 2.0 [X] >>>> scipion-em-locscale 1.0.5 [X] >>>> scipion-em-motioncorr 1.0.4 [X] >>>> scipion-em-nysbc [ ] >>>> scipion-em-phenix [ ] >>>> scipion-em-powerfit [ ] >>>> scipion-em-relion 1.0.7 [X] >>>> scipion-em-resmap 1.0.5 [X] >>>> scipion-em-simple [ ] >>>> scipion-em-sphire 1.2.9 [X] >>>> scipion-em-spider [ ] >>>> scipion-em-topaz [ ] >>>> scipion-em-xmipp 19.4.3 [X] >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här:http://www.uu.se/om-uu/dataskydd-personuppgifter/ >>>> >>>> E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here:http://www.uu.se/en/about-uu/data-protection-policy >>>> >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> -- >>> Pablo Conesa -*MadridScipion <http://scipion.i2pc.es/>team* >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> <mailto:sci...@li...> >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
