Re: [scipion-users] Problems with plugin installation: xmipp, relion, reliontomo

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Hello Guan-Chin,

About Relion and Xmipp issue: looks like an issue with OpenJDK, it is 
trying to manage the environment deactivation but cannot. Also there is 
a problem with nvidia: which version of CUDA do you have? check the 
CUDA-gcc compatibility. <https://gist.github.com/ax3l/9489132>

On 15/10/22 2:50, Guan-Chin Su wrote:
> Dear all,
>
> We seem to have successfully created a Scipion3 environment and 
> installation on a couple computers in the Chiu lab at Stanford but I 
> am now running into errors when I try to install plugins (I have tried 
> relion, reliontomo and xmipp so far).
>
> The OS on the workstation I am using now is the following:
> /(scipion3) stanford@154268-2-1:~$ lsb_release -a
> No LSB modules are available.
> Distributor ID: Ubuntu
> Description: *Ubuntu 20.04.3 LTS*
> Release: 20.04
> Codename: focal/
>
> *1) For reliontomo*, I get this error:
>
> /(scipion3) stanford@154268-2-1:~$ *scipion3 installp -p 
> scipion-em-reliontomo*
> sh: 3: 
> /home/stanford/miniconda3/envs/scipion3/etc/conda/deactivate.d/openjdk_deactivate.sh: 
> [[: not found
> sh: 9: 
> /home/stanford/miniconda3/envs/scipion3/etc/conda/deactivate.d/openjdk_deactivate.sh: 
> [[: not found
> Scipion v3.0.11 - Eugenius
> *WARNING - The following plugins didn't match available plugin names:
> scipion-em-reliontomo*
> You can see the list of available plugins with the following command:
> scipion installp --help/
>
>
> *For xmipp I get this error:*
>
> /(scipion3) stanford@154268-2-1:~$ scipion3 installp -p scipion-em-xmipp
> /
> /sh: 3: 
> /home/stanford/miniconda3/envs/scipion3/etc/conda/deactivate.d/openjdk_deactivate.sh: 
> [[: not found/
> /sh: 9: 
> /home/stanford/miniconda3/envs/scipion3/etc/conda/deactivate.d/openjdk_deactivate.sh: 
> [[: not found/
> /Scipion v3.0.11 - Eugenius/
> //usr/bin/nvidia-modprobe: unrecognized option: "-s"/
> /
> /
> /ERROR: Invalid commandline, please run `/usr/bin/nvidia-modprobe 
> --help` for usage information./
> /
> /
> //usr/bin/nvidia-modprobe: unrecognized option: "-s"/
> /
> /
> /ERROR: Invalid commandline, please run `/usr/bin/nvidia-modprobe 
> --help` for usage information./
> /
> /
> /Building scipion-em-xmipp .../
> //home/stanford/miniconda3/envs/scipion3/bin/python -m pip install 
> scipion-em-xmipp==22.7.0/
> /Requirement already satisfied: scipion-em-xmipp==22.7.0 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (22.7.0)/
> /Requirement already satisfied: peppercorn in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-em-xmipp==22.7.0) (0.6)/
> /Requirement already satisfied: PyWavelets in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-em-xmipp==22.7.0) (1.4.1)/
> /Requirement already satisfied: scikit-learn==0.22.1 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-em-xmipp==22.7.0) (0.22.1)/
> /Requirement already satisfied: scons in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-em-xmipp==22.7.0) (4.4.0)/
> /Requirement already satisfied: joblib in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-em-xmipp==22.7.0) (1.2.0)/
> /Requirement already satisfied: plotter in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-em-xmipp==22.7.0) (1.3.19)/
> /Requirement already satisfied: scipy>=0.17.0 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scikit-learn==0.22.1->scipion-em-xmipp==22.7.0) (1.8.1)/
> /Requirement already satisfied: numpy>=1.11.0 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scikit-learn==0.22.1->scipion-em-xmipp==22.7.0) (1.18.4)/
> /Requirement already satisfied: setuptools in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scons->scipion-em-xmipp==22.7.0) (63.4.1)/
> /Done (0.56 seconds)/
> //usr/bin/nvidia-modprobe: unrecognized option: "-s"/
> /
> /
> /ERROR: Invalid commandline, please run `/usr/bin/nvidia-modprobe 
> --help` for usage information./
> /
> /
> //usr/bin/nvidia-modprobe: unrecognized option: "-s"/
> /
> /
> /ERROR: Invalid commandline, please run `/usr/bin/nvidia-modprobe 
> --help` for usage information./
>
>
> *For relion I get this error:*
>
> /(scipion3) stanford@154268-2-1:~$ scipion3 installp -p scipion-em-relion
> sh: 3: 
> /home/stanford/miniconda3/envs/scipion3/etc/conda/deactivate.d/openjdk_deactivate.sh: 
> [[: not found
> sh: 9: 
> /home/stanford/miniconda3/envs/scipion3/etc/conda/deactivate.d/openjdk_deactivate.sh: 
> [[: not found
> Scipion v3.0.11 - Eugenius
> Building scipion-em-relion ...
> /home/stanford/miniconda3/envs/scipion3/bin/python -m pip install 
> scipion-em-relion==4.0.10
> Requirement already satisfied: scipion-em-relion==4.0.10 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (4.0.10)
> Requirement already satisfied: emtable>=0.0.14 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-em-relion==4.0.10) (0.0.14)
> Requirement already satisfied: scipion-em in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-em-relion==4.0.10) (3.0.22)
> Requirement already satisfied: scipion-pyworkflow>=3.0.15 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-em->scipion-em-relion==4.0.10) (3.0.25)
> Requirement already satisfied: tifffile in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-em->scipion-em-relion==4.0.10) (2021.11.2)
> Requirement already satisfied: biopython==1.76 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-em->scipion-em-relion==4.0.10) (1.76)
> Requirement already satisfied: scipy<=1.8.1 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-em->scipion-em-relion==4.0.10) (1.8.1)
> Requirement already satisfied: numpy in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> biopython==1.76->scipion-em->scipion-em-relion==4.0.10) (1.18.4)
> Requirement already satisfied: configparser<=5.0.2 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) (5.0.2)
> Requirement already satisfied: requests<=2.25.1 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) 
> (2.25.1)
> Requirement already satisfied: tkcolorpicker<=2.1.3 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) (2.1.3)
> Requirement already satisfied: psutil<=5.8.0 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) (5.8.0)
> Requirement already satisfied: pillow<=8.2.0 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) (8.2.0)
> Requirement already satisfied: mpi4py<=3.0.3 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) (3.0.3)
> Requirement already satisfied: bibtexparser<=1.2.0 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) (1.2.0)
> Requirement already satisfied: matplotlib==3.2.2 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) (3.2.2)
> Requirement already satisfied: 
> pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) 
> (3.0.9)
> Requirement already satisfied: cycler>=0.10 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) 
> (0.11.0)
> Requirement already satisfied: kiwisolver>=1.0.1 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) 
> (1.4.4)
> Requirement already satisfied: python-dateutil>=2.1 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) 
> (2.8.2)
> Requirement already satisfied: future>=0.16.0 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) 
> (0.18.2)
> Requirement already satisfied: chardet<5,>=3.0.2 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) 
> (4.0.0)
> Requirement already satisfied: idna<3,>=2.5 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) 
> (2.10)
> Requirement already satisfied: urllib3<1.27,>=1.21.1 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) 
> (1.26.12)
> Requirement already satisfied: certifi>=2017.4.17 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) 
> (2022.9.14)
> Requirement already satisfied: six>=1.5 in 
> ./miniconda3/envs/scipion3/lib/python3.8/site-packages (from 
> python-dateutil>=2.1->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-relion==4.0.10) 
> (1.16.0)
> Done (0.63 seconds)
> Building relion-4.0 ...
>   Skipping command: wget -nv -c -O 
> /home/stanford/path/for/scipion/scipion3/software/em/void.tgz.part 
> http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz
> mv -v 
> /home/stanford/path/for/scipion/scipion3/software/em/void.tgz.part 
> /home/stanford/path/for/scipion/scipion3/software/em/void.tgz
>   All targets exist.
>   Skipping command: mkdir 
> /home/stanford/path/for/scipion/scipion3/software/em/relion-4.0
>   All targets exist.
>   Skipping command: tar -xf void.tgz -C relion-4.0
>   All targets exist.
> cd /home/stanford/path/for/scipion/scipion3/software/em/relion-4.0
> cd .. && rmdir relion-4.0 && git clone 
> https://github.com/3dem/relion.git relion-4.0 && cd relion-4.0 && git 
> checkout ver4.0 && cmake -DCMAKE_INSTALL_PREFIX=./ .
> rmdir: failed to remove 'relion-4.0': Directory not empty
> cd /home/stanford/path/for/scipion/scipion3/software/em/relion-4.0
> make -j 1
> [  0%] Built target copy_scripts
> [  2%] Built target class_ranker_model_file
> [  3%] Built target OWN_FLTK
> [  4%] Building NVCC (Device) object 
> src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/relion_jaz_gpu_util_generated_test00.cu.o
> In file included from /usr/local/cuda/include/cuda_runtime.h:83,
>                  from <command-line>:
> */usr/local/cuda/include/crt/host_config.h:129:2: error: #error -- 
> unsupported GNU version! gcc versions later than 8 are not supported!*
>   129 | #error -- unsupported GNU version! gcc versions later than 8 
> are not supported!
>       |  ^~~~~
> CMake Error at 
> relion_jaz_gpu_util_generated_test00.cu.o.Release.cmake:220 (message):
>   Error generating
> /home/stanford/path/for/scipion/scipion3/software/em/relion-4.0/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/./relion_jaz_gpu_util_generated_test00.cu.o
>
>
> make[2]: *** 
> [src/apps/CMakeFiles/relion_jaz_gpu_util.dir/build.make:72: 
> src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/relion_jaz_gpu_util_generated_test00.cu.o] 
> Error 1
> make[1]: *** [CMakeFiles/Makefile2:1471: 
> src/apps/CMakeFiles/relion_jaz_gpu_util.dir/all] Error 2
> make: *** [Makefile:130: all] Error 2
> Traceback (most recent call last):
>   File 
> "/home/stanford/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", 
> line 495, in <module>
>     main()
>   File 
> "/home/stanford/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", 
> line 309, in main
>     installPluginMethods()
>   File 
> "/home/stanford/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", 
> line 233, in installPluginMethods
>     plugin.installBin({'args': ['-j', numberProcessor]})
>   File 
> "/home/stanford/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", 
> line 166, in installBin
>     environment.execute()
>   File 
> "/home/stanford/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", 
> line 750, in execute
>     self._executeTargets(targetList)
>   File 
> "/home/stanford/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", 
> line 692, in _executeTargets
>     tgt.execute()
>   File 
> "/home/stanford/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", 
> line 216, in execute
>     command.execute()
>   File 
> "/home/stanford/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", 
> line 156, in execute
>     assert glob(t), ("target '%s' not built (after "
> AssertionError: target 
> '/home/stanford/path/for/scipion/scipion3/software/em/relion-4.0/bin/relion_refine' 
> not built (after running 'make -j 1')
> Error at main: target 
> '/home/stanford/path/for/scipion/scipion3/software/em/relion-4.0/bin/relion_refine' 
> not built (after running 'make -j 1')
> /
>
> Any help would be greatly appreciated.
>
> Best,
> Guan-Chin
> --
>
> Guan-Chin Su, Ph.D.
> Postdoctoral fellow
> Department of Bioengineering
> Stanford University
> Phone:(650)495-4548
> Email: gua...@ga... <mailto:Email%3Ag...@ga...>; 
> gcsu@ <mailto:dod...@gm...>stanford. <http://stanford.com>edu
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

-- 
Alberto García Mena
National Center for Biotechnology - CSIC
Facility software support & Xmipp team @ Biocomputing Unit / I2PC

Re: [scipion-users] Problems with plugin installation: xmipp, relion, reliontomo

Image processing framework to integrate EM software packages.

Re: [scipion-users] Problems with plugin installation: xmipp, relion, reliontomo