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,

to me it looks like you have several problems:

*(scipion3) stanford@154268-2-1:~$ scipion3 installp -p
> scipion-em-reliontomo *

you should not generally run these commands inside the activated conda
environment. Also, all tomography plugins are still in beta and not
available to install this way. You should clone the github repo with a
plugin and then install it in devel mode, e.g. :
scipion3 installp -p /path/to/scipion-em-reliontomo --devel

*/usr/bin/nvidia-modprobe: unrecognized option: "-s"*

About this I really don't know. Alberto, does some xmipp installer script
use the modprobe command?

*rmdir: failed to remove 'relion-4.0': Directory not empty*

You need to update your core scipion to fix this: scipion3 update

*  129 | #error -- unsupported GNU version! gcc versions later than 8 are
> not supported!*

Here I agree with Alberto, check your cuda/gcc version. Also, I'd recommend
compiling relion outside of scipion yourself, since the default options
might not be the best for your cluster configuration.

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...

On Sat, Oct 15, 2022 at 1:51 AM Guan-Chin Su <gua...@gm...> 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 -aNo LSB modules are
> available.Distributor ID: UbuntuDescription: Ubuntu 20.04.3 LTSRelease:
> 20.04Codename: focal*
>
> *1) For reliontomo*, I get this error:
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> *(scipion3) stanford@154268-2-1:~$ scipion3 installp -p
> scipion-em-reliontomosh: 3:
> /home/stanford/miniconda3/envs/scipion3/etc/conda/deactivate.d/openjdk_deactivate.sh:
> [[: not foundsh: 9:
> /home/stanford/miniconda3/envs/scipion3/etc/conda/deactivate.d/openjdk_deactivate.sh:
> [[: not foundScipion v3.0.11 - EugeniusWARNING - The following plugins
> didn't match available plugin names:scipion-em-reliontomoYou 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-relionsh: 3:
> /home/stanford/miniconda3/envs/scipion3/etc/conda/deactivate.d/openjdk_deactivate.sh:
> [[: not foundsh: 9:
> /home/stanford/miniconda3/envs/scipion3/etc/conda/deactivate.d/openjdk_deactivate.sh:
> [[: not foundScipion v3.0.11 - EugeniusBuilding scipion-em-relion
> .../home/stanford/miniconda3/envs/scipion3/bin/python -m pip install
> scipion-em-relion==4.0.10Requirement 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-4.0cd .. &&
> 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 emptycd
> /home/stanford/path/for/scipion/scipion3/software/em/relion-4.0make -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.oIn
> 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.omake[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 1make[1]: *** [CMakeFiles/Makefile2:1471:
> src/apps/CMakeFiles/relion_jaz_gpu_util.dir/all] Error 2make: ***
> [Makefile:130: all] Error 2Traceback (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 list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

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