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

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Dear Pablo,

I would be happy to betatest.

I followed the instructions here:
https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html,
only used sudo when instructed to.

I noticed the line to install gcc v 8, but it seems like my workstation
uses gcc v 9.4 by default,

I can confirm gcc-8 is successfully installed:

*stanford@154268-2-1:~/scipion_reliontomo_src$ gcc-8 --versiongcc-8 (Ubuntu
8.4.0-3ubuntu2) 8.4.0Copyright (C) 2018 Free Software Foundation, Inc.This
is free software; see the source for copying conditions.  There is
NOwarranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.*

But how do I tell the workstation to use v 8.4 instead of the default 9.4
and is there a risk that this change could break my machine or other
software?

By the way, I am trying this on my personal workstation, from a non-root
username ("Stanford"), running Ubuntu 20, not a cluster.

I think my default shell was already bash but just in case I ran:

*stanford@154268-2-1:~/scipion_reliontomo_src$ chsh -s /bin/bash stanford*

I do not seem to be able to change the default shell for root but maybe
this should not matter if I do not run the installation command as root.

Thank you for your help,

Regards,

Guan-Chin

On Tue, Oct 18, 2022 at 2:26 AM Pablo Conesa <pc...@cn...> wrote:

> 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
> <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:
>
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> *(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:*
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> *(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
> <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
> <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... <Email%3Ag...@ga...>; gcsu@
> <dod...@gm...>stanford. <http://stanford.com>edu
>
>
>
> _______________________________________________
> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>

-- 

Guan-Chin Su, Ph.D.
Postdoctoral fellow
Department of Bioengineering
Stanford University
Phone:(650)495-4548
Email: gua...@ga... <Email%3Ag...@ga...>; gcsu@
<dod...@gm...>stanford. <http://stanford.com>edu

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