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From: Mohamad H. <moh...@so...> - 2022-11-03 14:48:45
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Hello Helder, Have you taken a look at the host configuration here ( [ https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/host-configuration.html | https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/host-configuration.html ] )? Best of luck, Mohamad From: "Helder Veras Ribeiro Filho" <hel...@ln...> To: sci...@li... Sent: Wednesday, November 2, 2022 5:07:53 PM Subject: [scipion-users] scipion - singularity - HPC Hello scipion group! I'm trying to launch Scipion from a singularity container in an HPC with the slurm as a scheduler. The container works fine and I'm able to execute Scipion routines correctly without using a queue. The problem is when I try to send Scipion jobs using the queue in the Scipion interface. I suppose that it is a slurm/singularity configuration problem. Could anyone who was successful in sending jobs to queue from a singularity launched scipion help me with some tips? Best, Helder Helder Veras Ribeiro Filho, PhD Brazilian Biosciences National Laboratory - LNBio Brazilian Center for Research in Energy and Materials - CNPEM 10,000 Giuseppe Maximo Scolfaro St. Campinas, SP - Brazil 13083-100 +55 (19) 3512-1255 Aviso Legal: Esta mensagem e seus anexos podem conter informações confidenciais e/ou de uso restrito. Observe atentamente seu conteúdo e considere eventual consulta ao remetente antes de copiá-la, divulgá-la ou distribuí-la. Se você recebeu esta mensagem por engano, por favor avise o remetente e apague-a imediatamente. Disclaimer: This email and its attachments may contain confidential and/or privileged information. Observe its content carefully and consider possible querying to the sender before copying, disclosing or distributing it. If you have received this email by mistake, please notify the sender and delete it immediately. _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Helder V. R. F. <hel...@ln...> - 2022-11-02 16:23:44
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Hello scipion group! I'm trying to launch Scipion from a singularity container in an HPC with the slurm as a scheduler. The container works fine and I'm able to execute Scipion routines correctly without using a queue. The problem is when I try to send Scipion jobs using the queue in the Scipion interface. I suppose that it is a slurm/singularity configuration problem. Could anyone who was successful in sending jobs to queue from a singularity launched scipion help me with some tips? Best, Helder Helder Veras Ribeiro Filho, PhD Brazilian Biosciences National Laboratory - LNBio Brazilian Center for Research in Energy and Materials - CNPEM 10,000 Giuseppe Maximo Scolfaro St. Campinas, SP - Brazil 13083-100 +55(19) 3512-1255 Aviso Legal: Esta mensagem e seus anexos podem conter informações confidenciais e/ou de uso restrito. Observe atentamente seu conteúdo e considere eventual consulta ao remetente antes de copiá-la, divulgá-la ou distribuí-la. Se você recebeu esta mensagem por engano, por favor avise o remetente e apague-a imediatamente. Disclaimer: This email and its attachments may contain confidential and/or privileged information. Observe its content carefully and consider possible querying to the sender before copying, disclosing or distributing it. If you have received this email by mistake, please notify the sender and delete it immediately. |
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From: Carlos O. S. <co...@cn...> - 2022-10-24 10:34:57
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Dear Colleagues, The Registration for the “*Instruct course on Cryo-Electron Tomography Image Processing. Madrid, December 13 – 16, 2022* ” is now open: http://i2pc.es/instruct-course-on-cryo-electron-tomography-image-processing-madrid-december-13-16-2022/ The course aims at providing a comprehensive overview of the whole image processing pipeline in Electron Tomography (ET) from the movie alignment of the tilt series, 3D reconstruction of the tomogram, particle identification, and subtomogram averaging, *all inside Scipion integration framework*. The course is aimed at researchers of all levels wanting to adopt electron microscopy as one of the tools at their disposal for elucidating biological structures. Registration will be open until *_November 14, 2022_*. You can fill your registration at: https://forms.gle/kjiv2pqSFWUXTkXX7 With best Regards I2PC Team ========================================================================= Blanca E. Benitez National Center for Biotechnology - CSIC Biocomputing Unit/ I2PC Phone: +34 91 585 4922 CSIC ext: 432178 Email: bl...@cn... |
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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 > |
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From: Guan-Chin Su <gua...@gm...> - 2022-10-20 02:30:12
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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: > > > > > > > > > *(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 |
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From: Guan-Chin Su <gua...@gm...> - 2022-10-20 02:10:15
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Dear Grigory, Thank you for the advice! I have tried to compile relion directly but also get lots of errors. The scipion team presented to our group a couple of months ago and it seemed like a great tool to avoid installation issues with individual packages. This is my gcc version: *stanford@154268-2-1:~/scipion_reliontomo_src$ gcc --versiongcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0Copyright (C) 2019 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.* I have cloned the github for scipion-em-reliontomo and tried to install it in --devel mode without my scipion3 environment activated and after updating my base scipion3. I still get this error: *stanford@154268-2-1:~/scipion_reliontomo_src$ scipion3 installp -p /home/stanford/scipion_reliontomo_src/scipion-em-reliontomo/ --devel* *Scipion v3.0.12 - EugeniusBuilding scipion-em-reliontomo .../home/stanford/miniconda3/envs/scipion3/bin/python -m pip install -e /home/stanford/scipion_reliontomo_src/scipion-em-reliontomo/Obtaining file:///home/stanford/scipion_reliontomo_src/scipion-em-reliontomo Preparing metadata (setup.py) ... error error: subprocess-exited-with-error × python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [10 lines of output] Traceback (most recent call last): File "<string>", line 2, in <module> File "<pip-setuptools-caller>", line 34, in <module> File "/home/stanford/scipion_reliontomo_src/scipion-em-reliontomo/setup.py", line 37, in <module> from reliontomo import __version__ File "/home/stanford/scipion_reliontomo_src/scipion-em-reliontomo/reliontomo/__init__.py", line 27, in <module> from reliontomo.constants import RELIONTOMO_HOME, RELIONTOMO_DEFAULT, RELION, RELIONTOMO_CUDA_LIB, V4_0 File "/home/stanford/scipion_reliontomo_src/scipion-em-reliontomo/reliontomo/constants.py", line 28, in <module> from tomo.constants import BOTTOM_LEFT_CORNER ModuleNotFoundError: No module named 'tomo' [end of output] note: This error originates from a subprocess, and is likely not a problem with pip.error: metadata-generation-failed× Encountered error while generating package metadata.╰─> See above for output.note: This is an issue with the package mentioned above, not pip.hint: See above for details.target '/home/stanford/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion-em-reliontomo*' not built (after running '/home/stanford/miniconda3/envs/scipion3/bin/python -m pip install -e /home/stanford/scipion_reliontomo_src/scipion-em-reliontomo/')stanford@154268-2-1:~/scipion_reliontomo_src$ * Thank you so much for your advice. Regards, Guan-Chin . On Tue, Oct 18, 2022 at 1:37 AM Grigory Sharov <sha...@gm...> wrote: > 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: >> >> >> >> >> >> >> >> >> *(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:* >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> *(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 >> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > -- 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 |
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From: Pablo C. <pc...@cn...> - 2022-10-18 09:27:02
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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* |
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From: Alberto G. M. <alb...@cn...> - 2022-10-18 08:54:47
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Xmipp has no this dependency and the installer does not use it. On 18/10/22 10:37, Grigory Sharov wrote: > > About this I really don't know. Alberto, does some xmipp installer > script use the modprobe command? -- Alberto García Mena National Center for Biotechnology - CSIC Facility software support & Xmipp team @ Biocomputing Unit / I2PC |
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From: Grigory S. <sha...@gm...> - 2022-10-18 08:37:34
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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: > > > > > > > > > *(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:* > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *(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 > |
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From: Alberto G. M. <alb...@cn...> - 2022-10-18 08:19:30
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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 |
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From: Guan-Chin Su <gua...@gm...> - 2022-10-15 00:51:22
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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: *(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:* *(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 |
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From: Yunior C. F. R. <cfo...@cn...> - 2022-10-06 10:37:55
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Hi all, As you may have seen, a new version of cryoSPARC (v4.0.0) has been released. This version, at the moment, is incompatible with our plugin. I strongly recommend that you do not update cryoSPARC. The plugin will not work correctly. On the other hand, when you want to downgrade to return to the previous version, it is possible that there is a problem with the database. I am working to make the plugin compatible with this version as soon as possible. Cheers, Yun |
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From: HONG Z. <hz...@wi...> - 2022-09-19 15:30:15
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Thank you so much Alberto. It works with the mask:D I like the result better than ResMap and monoRes. Best, Hong > On Sep 19, 2022, at 3:23 AM, Alberto Garcia Mena <alb...@cn...> wrote: > > Hi Hong, > > Thanks for write us. This protocol needs a binary mask to run. > > Please include it and tell us if works fine. > > BR > > On 19/9/22 1:04, HONG ZHAN via scipion-users wrote: >> Dear Scipion user group, >> >> I installed Xmipp3 and deep learning toolkit however, after I import the volume then call the local deepres, I had this error as below: >> >> >> 00001: Traceback (most recent call last): >> 00002: File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 202, in run >> 00003: self._run() >> 00004: File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 253, in _run >> 00005: resultFiles = self._runFunc() >> 00006: File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 249, in _runFunc >> 00007: return self._func(*self._args) >> 00008: File "/home/hong/scipion-em-xmipp/xmipp3/protocols/protocol_resolution_deepres.py", line 144, in convertInputStep >> 00009: self.maskFn = self.Mask.get().getFileName() >> 00010: AttributeError: 'NoneType' object has no attribute 'getFileName' >> 00011: Protocol failed: 'NoneType' object has no attribute ‘getFileName' >> >> However, MonoRes works fine. Any tips to overcome this error? >> >> Thanks, >> Hong >> _______________________________________________ >> 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 > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Alberto G. M. <alb...@cn...> - 2022-09-19 08:24:17
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Hi Hong, Thanks for write us. This protocol needs a binary mask to run. Please include it and tell us if works fine. BR On 19/9/22 1:04, HONG ZHAN via scipion-users wrote: > Dear Scipion user group, > > I installed Xmipp3 and deep learning toolkit however, after I import the volume then call the local deepres, I had this error as below: > > > 00001: Traceback (most recent call last): > 00002: File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 202, in run > 00003: self._run() > 00004: File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 253, in _run > 00005: resultFiles = self._runFunc() > 00006: File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 249, in _runFunc > 00007: return self._func(*self._args) > 00008: File "/home/hong/scipion-em-xmipp/xmipp3/protocols/protocol_resolution_deepres.py", line 144, in convertInputStep > 00009: self.maskFn = self.Mask.get().getFileName() > 00010: AttributeError: 'NoneType' object has no attribute 'getFileName' > 00011: Protocol failed: 'NoneType' object has no attribute ‘getFileName' > > However, MonoRes works fine. Any tips to overcome this error? > > Thanks, > Hong > _______________________________________________ > 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 |
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From: HONG Z. <hz...@wi...> - 2022-09-18 23:04:55
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Dear Scipion user group, I installed Xmipp3 and deep learning toolkit however, after I import the volume then call the local deepres, I had this error as below: 00001: Traceback (most recent call last): 00002: File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 202, in run 00003: self._run() 00004: File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 253, in _run 00005: resultFiles = self._runFunc() 00006: File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 249, in _runFunc 00007: return self._func(*self._args) 00008: File "/home/hong/scipion-em-xmipp/xmipp3/protocols/protocol_resolution_deepres.py", line 144, in convertInputStep 00009: self.maskFn = self.Mask.get().getFileName() 00010: AttributeError: 'NoneType' object has no attribute 'getFileName' 00011: Protocol failed: 'NoneType' object has no attribute ‘getFileName' However, MonoRes works fine. Any tips to overcome this error? Thanks, Hong |
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From: Alberto G. M. <alb...@cn...> - 2022-09-09 08:02:21
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Please for Xmipp installation visit: https://github.com/I2PC/xmipp/wiki/Installing-Xmipp-on-Ubuntu-22.04https://github.com/I2PC/xmipp/wiki/Installing-Xmipp-on-Ubuntu-22.04 <https://github.com/I2PC/xmipp/wiki/Installing-Xmipp-on-Ubuntu-22.04> On 9/9/22 9:46, Pablo Conesa wrote: > > Hi Matt, I've asked colleagues and this is what I've found: > > It is possible to install. Scipion (all python code) should have no > problem. Xmipp companion should work, "as long as you stick to GCC 10 > or 11". > > I think what is not possible is to use some binaries (gctf and > gAutomatch) that have not been updated to recent cudas and recent GPUs > are not compatible with old cudas. (I've asked developer about this > and wasn't clear if the were going to update them or "open the code") ;-( > > > Several people here are using it without problems. Not sure though if > they are usinf xmipp devel version or production one. > > Maybe someone from Xmipp team can comment more precisely about this. > > > On 8/9/22 20:12, Matt Harrington via scipion-users wrote: >> Has Scipion been fully tested on Ubuntu 22.04? I believe there were >> issues when 22.04 was first released, but it's been out for a while now. >> >> Matt >> > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > _______________________________________________ > 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 |
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From: Pablo C. <pc...@cn...> - 2022-09-09 07:47:05
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Hi Matt, I've asked colleagues and this is what I've found: It is possible to install. Scipion (all python code) should have no problem. Xmipp companion should work, "as long as you stick to GCC 10 or 11". I think what is not possible is to use some binaries (gctf and gAutomatch) that have not been updated to recent cudas and recent GPUs are not compatible with old cudas. (I've asked developer about this and wasn't clear if the were going to update them or "open the code") ;-( Several people here are using it without problems. Not sure though if they are usinf xmipp devel version or production one. Maybe someone from Xmipp team can comment more precisely about this. On 8/9/22 20:12, Matt Harrington via scipion-users wrote: > Has Scipion been fully tested on Ubuntu 22.04? I believe there were > issues when 22.04 was first released, but it's been out for a while now. > > Matt > -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Matt H. <ma...@ms...> - 2022-09-08 18:36:56
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Has Scipion been fully tested on Ubuntu 22.04? I believe there were issues when 22.04 was first released, but it's been out for a while now. Matt |
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From: Anastasina, M. <mar...@he...> - 2022-08-29 15:43:49
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Pablo — I suppose the first case could be the problem then, as the quota is not exceeded. I managed to overcome the issue by breaking the dataset in several smaller ones and it worked smoothly.
Grigory — I see, thank you for the explanation.
And thank you both for spending time to help with mom question, I do appreciate that!
Have a nice evening,
Maria
On 29. Aug 2022, at 18.23, Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> wrote:
Hi,
Yes, you could increase the number of threads and batch size as well. Despite the fact that ctffind4 cant process multiple mics at once, it can reduce the overhead and calls to update the database.
E.g. if you have 30000 mics and submit a job with 24 threads and batch size = 24, then you will have 30000/24=1250 batches (protocol steps), each batch will run 24 mics in parallel (since 24 threads will run 24 ctffind jobs for each single micrograph)
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<tel:+44%201223%20267228>
e-mail: gs...@mr...<mailto:gs...@mr...>
On Mon, Aug 29, 2022 at 4:12 PM Pablo Conesa <pc...@cn...<mailto:pc...@cn...>> wrote:
Thanks Maria!
I can see 2 cases here:
Either your cluster filesystem is busy and can't cope with "high demands" (this is kindof our fault) of Scipion needs to write data in sqlite.
Or I've seen this message recently also when quota is exceeded. As a cluster user you may have a quota. It may worth trying to check it.
On 29/8/22 14:50, Anastasina, Maria wrote:
Hi Pablo and Grigory,
Thank you so much for kindly helping me to figure out the issue!
I run the job on a cluster requesting 1 node with 1 MPI and 2 threads (reading your comments I suppose generally I should try more threads for faster calculation, right?). Aligned micrographs were ready before launching CTFFind4, so I did not use streaming and left the corresponding tab unchanged (= sleep when waiting 0 sec, batch size 1).
As I am running the job on a HPC cluster, I assume filesystem should not be an issue?
Strangely, the run.stderr file is empty (literally zero bytes), so nothing useful to attach here. The run.stdout file is very big as the number of micrographs is so large, but I copy its header and the problematic part below in case it is useful.
Best regards,
Maria
Hostname: r18g05.bullx
PID: 39966
pyworkflow: 3.0.16
plugin: cistem
plugin v: 3.1.0
currentDir: /scratch/project_2004278/ScipionUserData/projects/immTBEV
workingDir: Runs/097922_CistemProtCTFFind
runMode: Continue
MPI: 1
threads: 2
Starting at step: 1
Running steps
ESC[35mSTARTEDESC[0m: estimateCtfStep, step 1, time 2022-08-18 12:25:28.707054
Estimating CTF of micrograph: 1
Estimating CTF of micrograph: 35874
^[[32m /appl/soft/math/scipion/3.0.7/software/em/cistem-1.0.0-beta/ctffind << eof > Runs/097922_CistemProtCTFFind/extra/GridSquare_17902459_Data_FoilHole_$
Runs/097922_CistemProtCTFFind/tmp/mic_035874/GridSquare_17902459_Data_FoilHole_17908572_Data_17904056_17904058_20220320_195052_fractions_aligned_mic_DW.mrc
Runs/097922_CistemProtCTFFind/extra/GridSquare_17902459_Data_FoilHole_17908572_Data_17904056_17904058_20220320_195052_fractions_aligned_mic_DW_ctf.mrc
1.104100
300.000000
2.700000
0.100000
512
36.800000
2.570000
5000.000000
40000.000000
200.000000
no
no
yes
100.000000
no
no
eof
^[[0m
Error trying to update output of protocol, tries=1
Error trying to update output of protocol, tries=2
Error trying to update output of protocol, tries=3
Error trying to update output of protocol, tries=4
Traceback (most recent call last):
File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 470, in __tryUpdateOutputSet
outputSet.write() # Write to commit changes
File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/object.py", line 1165, in write
self._getMapper().commit()
File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/mapper/sqlite.py", line 762, in commit
self.db.commit()
sqlite3.OperationalError: database is locked
On 29. Aug 2022, at 13.42, Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> wrote:
Hi Maria,
Pablo is correct here. Could you please tell is what number of threads/mpi you used and also what parameters you set on streaming tab. Are you running the job on a cluster? Maybe you can attach here run.stderr?
Grigory
On Mon, Aug 29, 2022, 11:17 Pablo Conesa <pc...@cn...<mailto:pc...@cn...>> wrote:
Thank you Maria!
The error you are reporting may be unrelated with "CTFFind4 in Scipion".
“sqlite3.OperationalError: database is locked"
Is related, probably to concurrency. There are several factors that may cause this.
threads: If you specify a high number of threads, many of them will process at the same time CTFs. This is desirable and we have made the effort to enable as many threads as available, but if this happens reducing the threads may help.
streaming: Streaming processing implied many active protocols that favors concurrency.
filesystem: A slow filesystem (e.g.: network filesystem mounted over a a slow ethernet connection) may provide locks.
In theory, CTFfind and many others, should cope nicely with large datasets, or at least is being doing this for a long time without any issue. This may be a specific issue.
On 29/8/22 9:07, Anastasina, Maria wrote:
Dear Scipion users,
I’m get an unexpected error when running CTFFind4 in Scipion 3.0.8 on a large (50K) set of micrographs. The protocol fails after processing about 70 % of micrographs with the error: “sqlite3.OperationalError: database is locked”.
Sometimes re-launching in continuation mode helps to process few more micrographs, but the protocol will eventually fail again with the same error. Breaking the data set in smaller chunks (about 10K micrographs each) helps and the protocol ran in the same conditions succeeds for all the micrographs.
I wonder does this indicate that CTFFind4 has problems handling large datasets and should be used on smaller datasets? Or is there possibly another problem that I am not noticing? I’m not attaching run.stdout as it is pretty large (31MB), if need I can upload it to eg grdive.
Thank you,
Maria
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es/> team
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es/> team
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Grigory S. <sha...@gm...> - 2022-08-29 15:24:04
|
Hi, Yes, you could increase the number of threads and batch size as well. Despite the fact that ctffind4 cant process multiple mics at once, it can reduce the overhead and calls to update the database. E.g. if you have 30000 mics and submit a job with 24 threads and batch size = 24, then you will have 30000/24=1250 batches (protocol steps), each batch will run 24 mics in parallel (since 24 threads will run 24 ctffind jobs for each single micrograph) 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 Mon, Aug 29, 2022 at 4:12 PM Pablo Conesa <pc...@cn...> wrote: > Thanks Maria! > > I can see 2 cases here: > > Either your cluster filesystem is busy and can't cope with "high demands" > (this is kindof our fault) of Scipion needs to write data in sqlite. > > Or I've seen this message recently also when quota is exceeded. As a > cluster user you may have a quota. It may worth trying to check it. > > > On 29/8/22 14:50, Anastasina, Maria wrote: > > Hi Pablo and Grigory, > > Thank you so much for kindly helping me to figure out the issue! > > I run the job on a cluster requesting 1 node with 1 MPI and 2 threads > (reading your comments I suppose generally I should try more threads for > faster calculation, right?). Aligned micrographs were ready before > launching CTFFind4, so I did not use streaming and left the corresponding > tab unchanged (= sleep when waiting 0 sec, batch size 1). > > As I am running the job on a HPC cluster, I assume filesystem should not > be an issue? > > Strangely, the run.stderr file is empty (literally zero bytes), so nothing > useful to attach here. The run.stdout file is very big as the number of > micrographs is so large, but I copy its header and the problematic part > below in case it is useful. > > Best regards, > Maria > > Hostname: r18g05.bullx > PID: 39966 > pyworkflow: 3.0.16 > plugin: cistem > plugin v: 3.1.0 > currentDir: /scratch/project_2004278/ScipionUserData/projects/immTBEV > workingDir: Runs/097922_CistemProtCTFFind > runMode: Continue > MPI: 1 > threads: 2 > Starting at step: 1 > Running steps > ESC[35mSTARTEDESC[0m: estimateCtfStep, step 1, time 2022-08-18 > 12:25:28.707054 > Estimating CTF of micrograph: 1 > > Estimating CTF of micrograph: 35874 > ^[[32m > /appl/soft/math/scipion/3.0.7/software/em/cistem-1.0.0-beta/ctffind << > eof > > Runs/097922_CistemProtCTFFind/extra/GridSquare_17902459_Data_FoilHole_$ > > Runs/097922_CistemProtCTFFind/tmp/mic_035874/GridSquare_17902459_Data_FoilHole_17908572_Data_17904056_17904058_20220320_195052_fractions_aligned_mic_DW.mrc > > Runs/097922_CistemProtCTFFind/extra/GridSquare_17902459_Data_FoilHole_17908572_Data_17904056_17904058_20220320_195052_fractions_aligned_mic_DW_ctf.mrc > 1.104100 > 300.000000 > 2.700000 > 0.100000 > 512 > 36.800000 > 2.570000 > 5000.000000 > 40000.000000 > 200.000000 > no > no > yes > 100.000000 > no > no > eof > > ^[[0m > Error trying to update output of protocol, tries=1 > Error trying to update output of protocol, tries=2 > Error trying to update output of protocol, tries=3 > Error trying to update output of protocol, tries=4 > Traceback (most recent call last): > File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 470, in __tryUpdateOutputSet > outputSet.write() # Write to commit changes > File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/object.py", > line 1165, in write > self._getMapper().commit() > File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/mapper/sqlite.py", > line 762, in commit > self.db.commit() > sqlite3.OperationalError: database is locked > > On 29. Aug 2022, at 13.42, Grigory Sharov <sha...@gm...> > wrote: > > Hi Maria, > > Pablo is correct here. Could you please tell is what number of threads/mpi > you used and also what parameters you set on streaming tab. Are you running > the job on a cluster? Maybe you can attach here run.stderr? > > Grigory > > On Mon, Aug 29, 2022, 11:17 Pablo Conesa <pc...@cn...> wrote: > >> Thank you Maria! >> >> The error you are reporting may be unrelated with "CTFFind4 in Scipion". >> >> “sqlite3.OperationalError: database is locked" >> >> Is related, probably to concurrency. There are several factors that may >> cause this. >> >> *threads*: If you specify a high number of threads, many of them will >> process at the same time CTFs. This is desirable and we have made the >> effort to enable as many threads as available, but if this happens >> reducing the threads may help. >> >> *streaming*: Streaming processing implied many active protocols that >> favors concurrency. >> >> *filesystem*: A slow filesystem (e.g.: network filesystem mounted over a >> a slow ethernet connection) may provide locks. >> >> In theory, CTFfind and many others, should cope nicely with large >> datasets, or at least is being doing this for a long time without any >> issue. This may be a specific issue. >> >> On 29/8/22 9:07, Anastasina, Maria wrote: >> >> Dear Scipion users, >> >> I’m get an unexpected error when running CTFFind4 in Scipion 3.0.8 on a large (50K) set of micrographs. The protocol fails after processing about 70 % of micrographs with the error: “sqlite3.OperationalError: database is locked”. >> >> Sometimes re-launching in continuation mode helps to process few more micrographs, but the protocol will eventually fail again with the same error. Breaking the data set in smaller chunks (about 10K micrographs each) helps and the protocol ran in the same conditions succeeds for all the micrographs. >> >> I wonder does this indicate that CTFFind4 has problems handling large datasets and should be used on smaller datasets? Or is there possibly another problem that I am not noticing? I’m not attaching run.stdout as it is pretty large (31MB), if need I can upload it to eg grdive. >> >> Thank you, >> Maria >> >> >> >> >> _______________________________________________ >> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> -- >> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es/> team* >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Pablo C. <pc...@cn...> - 2022-08-29 15:10:35
|
Thanks Maria! I can see 2 cases here: Either your cluster filesystem is busy and can't cope with "high demands" (this is kindof our fault) of Scipion needs to write data in sqlite. Or I've seen this message recently also when quota is exceeded. As a cluster user you may have a quota. It may worth trying to check it. On 29/8/22 14:50, Anastasina, Maria wrote: > Hi Pablo and Grigory, > > Thank you so much for kindly helping me to figure out the issue! > > I run the job on a cluster requesting 1 node with 1 MPI and 2 threads > (reading your comments I suppose generally I should try more threads > for faster calculation, right?). Aligned micrographs were ready before > launching CTFFind4, so I did not use streaming and left the > corresponding tab unchanged (= sleep when waiting 0 sec, batch size 1). > > As I am running the job on a HPC cluster, I assume filesystem should > not be an issue? > > Strangely, the run.stderr file is empty (literally zero bytes), so > nothing useful to attach here. The run.stdout file is very big as the > number of micrographs is so large, but I copy its header and the > problematic part below in case it is useful. > > Best regards, > Maria > > Hostname: r18g05.bullx > PID: 39966 > pyworkflow: 3.0.16 > plugin: cistem > plugin v: 3.1.0 > currentDir: /scratch/project_2004278/ScipionUserData/projects/immTBEV > workingDir: Runs/097922_CistemProtCTFFind > runMode: Continue > MPI: 1 > threads: 2 > Starting at step: 1 > Running steps > ESC[35mSTARTEDESC[0m: estimateCtfStep, step 1, time 2022-08-18 > 12:25:28.707054 > Estimating CTF of micrograph: 1 > > Estimating CTF of micrograph: 35874 > ^[[32m > /appl/soft/math/scipion/3.0.7/software/em/cistem-1.0.0-beta/ctffind > << eof > > Runs/097922_CistemProtCTFFind/extra/GridSquare_17902459_Data_FoilHole_$ > Runs/097922_CistemProtCTFFind/tmp/mic_035874/GridSquare_17902459_Data_FoilHole_17908572_Data_17904056_17904058_20220320_195052_fractions_aligned_mic_DW.mrc > Runs/097922_CistemProtCTFFind/extra/GridSquare_17902459_Data_FoilHole_17908572_Data_17904056_17904058_20220320_195052_fractions_aligned_mic_DW_ctf.mrc > 1.104100 > 300.000000 > 2.700000 > 0.100000 > 512 > 36.800000 > 2.570000 > 5000.000000 > 40000.000000 > 200.000000 > no > no > yes > 100.000000 > no > no > eof > > ^[[0m > Error trying to update output of protocol, tries=1 > Error trying to update output of protocol, tries=2 > Error trying to update output of protocol, tries=3 > Error trying to update output of protocol, tries=4 > Traceback (most recent call last): > File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 470, in __tryUpdateOutputSet > outputSet.write() # Write to commit changes > File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/object.py", > line 1165, in write > self._getMapper().commit() > File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/mapper/sqlite.py", > line 762, in commit > self.db.commit() > sqlite3.OperationalError: database is locked > >> On 29. Aug 2022, at 13.42, Grigory Sharov <sha...@gm...> >> wrote: >> >> Hi Maria, >> >> Pablo is correct here. Could you please tell is what number of >> threads/mpi you used and also what parameters you set on streaming >> tab. Are you running the job on a cluster? Maybe you can attach here >> run.stderr? >> >> Grigory >> >> On Mon, Aug 29, 2022, 11:17 Pablo Conesa <pc...@cn...> wrote: >> >> Thank you Maria! >> >> The error you are reporting may be unrelated with "CTFFind4 in >> Scipion". >> >> “sqlite3.OperationalError: database is locked" >> >> Is related, probably to concurrency. There are several factors >> that may cause this. >> >> *threads*: If you specify a high number of threads, many of them >> will process at the same time CTFs. This is desirable and we have >> made the effort to enable as many threads as available, but if >> this happens reducing the threads may help. >> >> *streaming*: Streaming processing implied many active protocols >> that favors concurrency. >> >> *filesystem*: A slow filesystem (e.g.: network filesystem mounted >> over a a slow ethernet connection) may provide locks. >> >> In theory, CTFfind and many others, should cope nicely with large >> datasets, or at least is being doing this for a long time without >> any issue. This may be a specific issue. >> >> On 29/8/22 9:07, Anastasina, Maria wrote: >>> Dear Scipion users, >>> >>> I’m get an unexpected error when running CTFFind4 in Scipion 3.0.8 on a large (50K) set of micrographs. The protocol fails after processing about 70 % of micrographs with the error: “sqlite3.OperationalError: database is locked”. >>> >>> Sometimes re-launching in continuation mode helps to process few more micrographs, but the protocol will eventually fail again with the same error. Breaking the data set in smaller chunks (about 10K micrographs each) helps and the protocol ran in the same conditions succeeds for all the micrographs. >>> >>> I wonder does this indicate that CTFFind4 has problems handling large datasets and should be used on smaller datasets? Or is there possibly another problem that I am not noticing? I’m not attaching run.stdout as it is pretty large (31MB), if need I can upload it to eg grdive. >>> >>> Thank you, >>> Maria >>> >>> >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >> -- >> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es/> team* >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Anastasina, M. <mar...@he...> - 2022-08-29 13:06:52
|
Hi Pablo and Grigory,
Thank you so much for kindly helping me to figure out the issue!
I run the job on a cluster requesting 1 node with 1 MPI and 2 threads (reading your comments I suppose generally I should try more threads for faster calculation, right?). Aligned micrographs were ready before launching CTFFind4, so I did not use streaming and left the corresponding tab unchanged (= sleep when waiting 0 sec, batch size 1).
As I am running the job on a HPC cluster, I assume filesystem should not be an issue?
Strangely, the run.stderr file is empty (literally zero bytes), so nothing useful to attach here. The run.stdout file is very big as the number of micrographs is so large, but I copy its header and the problematic part below in case it is useful.
Best regards,
Maria
Hostname: r18g05.bullx
PID: 39966
pyworkflow: 3.0.16
plugin: cistem
plugin v: 3.1.0
currentDir: /scratch/project_2004278/ScipionUserData/projects/immTBEV
workingDir: Runs/097922_CistemProtCTFFind
runMode: Continue
MPI: 1
threads: 2
Starting at step: 1
Running steps
ESC[35mSTARTEDESC[0m: estimateCtfStep, step 1, time 2022-08-18 12:25:28.707054
Estimating CTF of micrograph: 1
Estimating CTF of micrograph: 35874
^[[32m /appl/soft/math/scipion/3.0.7/software/em/cistem-1.0.0-beta/ctffind << eof > Runs/097922_CistemProtCTFFind/extra/GridSquare_17902459_Data_FoilHole_$
Runs/097922_CistemProtCTFFind/tmp/mic_035874/GridSquare_17902459_Data_FoilHole_17908572_Data_17904056_17904058_20220320_195052_fractions_aligned_mic_DW.mrc
Runs/097922_CistemProtCTFFind/extra/GridSquare_17902459_Data_FoilHole_17908572_Data_17904056_17904058_20220320_195052_fractions_aligned_mic_DW_ctf.mrc
1.104100
300.000000
2.700000
0.100000
512
36.800000
2.570000
5000.000000
40000.000000
200.000000
no
no
yes
100.000000
no
no
eof
^[[0m
Error trying to update output of protocol, tries=1
Error trying to update output of protocol, tries=2
Error trying to update output of protocol, tries=3
Error trying to update output of protocol, tries=4
Traceback (most recent call last):
File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 470, in __tryUpdateOutputSet
outputSet.write() # Write to commit changes
File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/object.py", line 1165, in write
self._getMapper().commit()
File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/mapper/sqlite.py", line 762, in commit
self.db.commit()
sqlite3.OperationalError: database is locked
On 29. Aug 2022, at 13.42, Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> wrote:
Hi Maria,
Pablo is correct here. Could you please tell is what number of threads/mpi you used and also what parameters you set on streaming tab. Are you running the job on a cluster? Maybe you can attach here run.stderr?
Grigory
On Mon, Aug 29, 2022, 11:17 Pablo Conesa <pc...@cn...<mailto:pc...@cn...>> wrote:
Thank you Maria!
The error you are reporting may be unrelated with "CTFFind4 in Scipion".
“sqlite3.OperationalError: database is locked"
Is related, probably to concurrency. There are several factors that may cause this.
threads: If you specify a high number of threads, many of them will process at the same time CTFs. This is desirable and we have made the effort to enable as many threads as available, but if this happens reducing the threads may help.
streaming: Streaming processing implied many active protocols that favors concurrency.
filesystem: A slow filesystem (e.g.: network filesystem mounted over a a slow ethernet connection) may provide locks.
In theory, CTFfind and many others, should cope nicely with large datasets, or at least is being doing this for a long time without any issue. This may be a specific issue.
On 29/8/22 9:07, Anastasina, Maria wrote:
Dear Scipion users,
I’m get an unexpected error when running CTFFind4 in Scipion 3.0.8 on a large (50K) set of micrographs. The protocol fails after processing about 70 % of micrographs with the error: “sqlite3.OperationalError: database is locked”.
Sometimes re-launching in continuation mode helps to process few more micrographs, but the protocol will eventually fail again with the same error. Breaking the data set in smaller chunks (about 10K micrographs each) helps and the protocol ran in the same conditions succeeds for all the micrographs.
I wonder does this indicate that CTFFind4 has problems handling large datasets and should be used on smaller datasets? Or is there possibly another problem that I am not noticing? I’m not attaching run.stdout as it is pretty large (31MB), if need I can upload it to eg grdive.
Thank you,
Maria
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es/> team
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Grigory S. <sha...@gm...> - 2022-08-29 10:43:11
|
Hi Maria, Pablo is correct here. Could you please tell is what number of threads/mpi you used and also what parameters you set on streaming tab. Are you running the job on a cluster? Maybe you can attach here run.stderr? Grigory On Mon, Aug 29, 2022, 11:17 Pablo Conesa <pc...@cn...> wrote: > Thank you Maria! > > The error you are reporting may be unrelated with "CTFFind4 in Scipion". > > “sqlite3.OperationalError: database is locked" > > Is related, probably to concurrency. There are several factors that may > cause this. > > *threads*: If you specify a high number of threads, many of them will > process at the same time CTFs. This is desirable and we have made the > effort to enable as many threads as available, but if this happens > reducing the threads may help. > > *streaming*: Streaming processing implied many active protocols that > favors concurrency. > > *filesystem*: A slow filesystem (e.g.: network filesystem mounted over a > a slow ethernet connection) may provide locks. > > In theory, CTFfind and many others, should cope nicely with large > datasets, or at least is being doing this for a long time without any > issue. This may be a specific issue. > > On 29/8/22 9:07, Anastasina, Maria wrote: > > Dear Scipion users, > > I’m get an unexpected error when running CTFFind4 in Scipion 3.0.8 on a large (50K) set of micrographs. The protocol fails after processing about 70 % of micrographs with the error: “sqlite3.OperationalError: database is locked”. > > Sometimes re-launching in continuation mode helps to process few more micrographs, but the protocol will eventually fail again with the same error. Breaking the data set in smaller chunks (about 10K micrographs each) helps and the protocol ran in the same conditions succeeds for all the micrographs. > > I wonder does this indicate that CTFFind4 has problems handling large datasets and should be used on smaller datasets? Or is there possibly another problem that I am not noticing? I’m not attaching run.stdout as it is pretty large (31MB), if need I can upload it to eg grdive. > > Thank you, > Maria > > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Pablo C. <pc...@cn...> - 2022-08-29 10:17:17
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Thank you Maria! The error you are reporting may be unrelated with "CTFFind4 in Scipion". “sqlite3.OperationalError: database is locked" Is related, probably to concurrency. There are several factors that may cause this. *threads*: If you specify a high number of threads, many of them will process at the same time CTFs. This is desirable and we have made the effort to enable as many threads as available, but if this happens reducing the threads may help. *streaming*: Streaming processing implied many active protocols that favors concurrency. *filesystem*: A slow filesystem (e.g.: network filesystem mounted over a a slow ethernet connection) may provide locks. In theory, CTFfind and many others, should cope nicely with large datasets, or at least is being doing this for a long time without any issue. This may be a specific issue. On 29/8/22 9:07, Anastasina, Maria wrote: > Dear Scipion users, > > I’m get an unexpected error when running CTFFind4 in Scipion 3.0.8 on a large (50K) set of micrographs. The protocol fails after processing about 70 % of micrographs with the error: “sqlite3.OperationalError: database is locked”. > > Sometimes re-launching in continuation mode helps to process few more micrographs, but the protocol will eventually fail again with the same error. Breaking the data set in smaller chunks (about 10K micrographs each) helps and the protocol ran in the same conditions succeeds for all the micrographs. > > I wonder does this indicate that CTFFind4 has problems handling large datasets and should be used on smaller datasets? Or is there possibly another problem that I am not noticing? I’m not attaching run.stdout as it is pretty large (31MB), if need I can upload it to eg grdive. > > Thank you, > Maria > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Anastasina, M. <mar...@he...> - 2022-08-29 09:41:55
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Dear Scipion users, I’m get an unexpected error when running CTFFind4 in Scipion 3.0.8 on a large (50K) set of micrographs. The protocol fails after processing about 70 % of micrographs with the error: “sqlite3.OperationalError: database is locked”. Sometimes re-launching in continuation mode helps to process few more micrographs, but the protocol will eventually fail again with the same error. Breaking the data set in smaller chunks (about 10K micrographs each) helps and the protocol ran in the same conditions succeeds for all the micrographs. I wonder does this indicate that CTFFind4 has problems handling large datasets and should be used on smaller datasets? Or is there possibly another problem that I am not noticing? I’m not attaching run.stdout as it is pretty large (31MB), if need I can upload it to eg grdive. Thank you, Maria |
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