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

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

Dear Guan-Chin! Tomography code is not released yet.

if you are willing to betatest, I can send you a link to our slack 
workspace and you'll get more detailed instructions.

Are you using "root" to make the installation.

By default, root uses plain "sh" as default SHELL. And in the past, and 
maybe it is still there, "conda shell scripts" are not fully compatible 
with a pure sh SHELL.

Based on this: /
/

/sh: 3: 
/home/stanford/miniconda3/envs/scipion3/etc/conda/deactivate.d/openjdk_deactivate.sh: 
[[: not found/

/[[ is a bash "builtin command" not available in sh shells./

/
/

/I'd try to:/

/1.- use a non root user (which is a good practice anyway), but with 
privileges on the Scipion installation folder and conda ones./

/2.- change default shell to bash? --> 
https://unix.stackexchange.com/questions/663130/how-to-set-bash-default-shell-for-the-root-user
/

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
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

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