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Re: [scipion-users] Problems with plugin installation: xmipp, relion, reliontomo
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From: Grigory S. <sha...@gm...> - 2022-10-20 08:04:04
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Hi Guan-Chin, I suggest we first fix your core scipion installation. I'll send you an invitation link to our Slack channel, I hope you can join so we can fix this faster than exchanging emails. 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 Thu, Oct 20, 2022 at 3:30 AM Guan-Chin Su <gua...@gm...> wrote: > 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: >> >> >> >> >> >> >> >> >> *(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 >> <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 > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
