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From: Moustafa, I. M. <ri...@ps...> - 2020-10-28 16:25:58
|
Running "scipion3 inspect localrec" gives the following error:
Scipion v3.0.5 () devel
>>> WARNING: Image library not found!
> Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)
Plugin: localrec
>>> constants: loaded
>>> convert: loaded
>>> protocols: loaded
>>> wizards: missing
>>> viewers: loaded
>>> tests: error -> Traceback (most recent call last):
File "/usr/local/scipion/pip/scipion/install/inspect-plugins.py", line 74, in getSubmodule
m = importlib.import_module('%s.%s' % (name, subname))
File "/usr/local/miniconda/envs/.scipion3env/lib/python3.8/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 783, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/usr/local/scipion/pip/localrec/tests/__init__.py", line 27, in <module>
from .test_protocol_localized_reconstruction import (TestLocalizedReconsBase,
File "/usr/local/scipion/pip/localrec/tests/test_protocol_localized_reconstruction.py", line 37, in <module>
from xmipp3.protocols import XmippProtCreateMask3D
File "/usr/local/scipion/pip/xmipp3/protocols/__init__.py", line 50, in <module>
from .protocol_ctf_micrographs import XmippProtCTFMicrographs
File "/usr/local/scipion/pip/xmipp3/protocols/protocol_ctf_micrographs.py", line 44, in <module>
from xmipp3.base import isMdEmpty
ImportError: cannot import name 'isMdEmpty' from 'xmipp3.base' (/usr/local/scipion/pip/xmipp3/base.py)
Ibrahim
________________________________
From: Pablo Conesa <pc...@cn...>
Sent: Wednesday, October 28, 2020 2:23 AM
To: sci...@li... <sci...@li...>
Subject: Re: [scipion-users] problem installing scipion3
Despite the error, it seems localrec is installed.
What about:
./scipion3 inspect localrec
On 27/10/20 19:12, Moustafa, Ibrahim M. wrote:
scipion-em-localrec 3.0.1
--
Pablo Conesa - Madrid Scipion<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fscipion.i2pc.es%2F&data=04%7C01%7Cria2%40psu.edu%7Cbf532e8ce14541a85e1908d87b0a12e4%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C1%7C637394630482954098%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=W46ErzeEGkYXk8Ma7SO5lbA6cfarjSIk9uFY08lcJy8%3D&reserved=0> team
|
|
From: Lugmayr, W. <w.l...@uk...> - 2020-10-28 13:19:49
|
hi, i installed and compiled scipion 3.0.5-devel on a system with intel cpus. when i run now scipion on new nodes with "AMD EPYC 7402" processors the executable fails with: $ scipion3 last Scipion v3.0.5 () devel sh: line 1: 45875 Illegal instruction python -m scipion last so i do not want to have 2 versions of scipion3 but maybe compile it with intel and amd compatibility flags. how do i set these flags? cheers, wolfgang -- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Deutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 Gebäude 15 22607 Hamburg, Germany Tel.: +49 40 8998-87652 Email: wol...@cs... http://www.cssb-hamburg.de/ |
|
From: Lugmayr, W. <w.l...@uk...> - 2020-10-28 12:14:49
|
hi,
when i try the xmipp - deepemhancer protocol in scipion 3.0.5-devel i get the following error when pressing the execute button:
Pre-trained model(s) not found: deepEMhancer
Please, run 'scipion installb deepLearningToolkit' or install the scipion-em-xmipp > deepLearningToolkit package using the plugin manager.
the deepLearningToolkit is installed and the conda is there too:
/beegfs/cssb/software/em/scipion/3.0/anaconda3
/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env
/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/3DFSC
/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/cryolo-1.7.2
/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/cryoloCPU-1.7.2
/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/topaz-0.2.3
/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/xmipp_DLTK_v0.3
/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/xmipp_MicCleaner
/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/xmipp_deepEMhancer
/beegfs/cssb/software/em/scipion/3.0/devel/software/em/eman-2.31
$ ls /beegfs/cssb/software/em/scipion/3.0/devel/software/em/deepLearningToolkit
models_UPDATED_on_14_10_2020 xmipp_deepEMhancer.yml xmipp_DLTK_v0.3.yml xmipp_MicCleaner.yml
my other conda with deepemhancer runs fine with the default model location in:
$ ls /home/lugmayr/.local/share/deepEMhancerModels/production_checkpoints
deepEMhancer_highRes.hd5 deepEMhancer_masked.hd5 deepEMhancer_tightTarget.hd5 deepEMhancer_wideTarget.hd5 versions.txt
finding these files in the scipion tree gives no result.
where should the files be in the scipion directory tree?
cheers,
wolfgang
--
Universitätsklinikum Hamburg-Eppendorf (UKE)
@ Centre for Structral Systems Biology (CSSB)
@ Deutsches Elektronen-Synchrotron (DESY)
Notkestrasse 85 Gebäude 15
22607 Hamburg, Germany
Tel.: +49 40 8998-87652
Email: wol...@cs...
http://www.cssb-hamburg.de/
|
|
From: Grigory S. <sha...@gm...> - 2020-10-28 09:38:35
|
Hi Tetter, Could you try the following steps manually: 1) conda activate .scipion3env 2) cd /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07 3) rm -f xmipp.conf 4) ./xmipp config 5) ./xmipp check_config 6) ./xmipp compileAndInstall N=4 7) ln -srfn build /home/hilvertg/tetterst/software/em/xmipp If you have errors in step 4, please post it here. 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 Wed, Oct 28, 2020 at 9:00 AM Tetter Stephan <tet...@or...> wrote: > Dear all, > > > I am trying to install Scipion for single particle analysis, and more > specifically for symmetry relaxation. Unfortunately I can't seem to get the > installation to work. I am working with Ubuntu 16.04. Please be aware that > I am not a well-versed Ubuntu user. > > > I have tried installation both via the conda version and the virtualenv > version described on > https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources#fixing-fonts-in-a-conda-installation, > but they both fail eventually. (I have changed the export PATH line to > point to sr/local/cuda-9.0/bin to fit my setup.) > > > Below is what happens. Any ideas? > > > Thanks, > > > Stephan > > > hilvertg@bamf:~$ sudo apt-get install gcc g++ make libopenmpi-dev > python3-tk libfftw3-dev libhdf5-dev libtiff-dev libjpeg-dev libsqlite3-dev > openjdk-8-jdk > Reading package lists... Done > Building dependency tree > Reading state information... Done > Note, selecting 'libtiff5-dev' instead of 'libtiff-dev' > g++ is already the newest version (4:5.3.1-1ubuntu1). > gcc is already the newest version (4:5.3.1-1ubuntu1). > libfftw3-dev is already the newest version (3.3.4-2ubuntu1). > libjpeg-dev is already the newest version (8c-2ubuntu8). > make is already the newest version (4.1-6). > python3-tk is already the newest version (3.5.1-1). > libopenmpi-dev is already the newest version (1.10.2-8ubuntu1). > libsqlite3-dev is already the newest version (3.11.0-1ubuntu1.5). > libtiff5-dev is already the newest version (4.0.6-1ubuntu0.7). > openjdk-8-jdk is already the newest version (8u272-b10-0ubuntu1~16.04). > libhdf5-dev is already the newest version (1.8.16+docs-4ubuntu1.1). > 0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded. > > hilvertg@bamf:~$ export PATH=$PATH:/usr/local/cuda-9.0/bin > > > hilvertg@bamf:~$ python -m pip install --user > scipion-installerRequirement already satisfied: scipion-installer in > ./.local/lib/python2.7/site-packages (1.0.9) > Requirement already satisfied: virtualenv in > ./.local/lib/python2.7/site-packages (from scipion-installer) (20.1.0) > Requirement already satisfied: six<2,>=1.9.0 in > /usr/local/lib/python2.7/dist-packages (from virtualenv->scipion-installer) > (1.10.0) > Requirement already satisfied: appdirs<2,>=1.4.3 in > ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) > (1.4.4) > Requirement already satisfied: distlib<1,>=0.3.1 in > ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) > (0.3.1) > Requirement already satisfied: importlib-resources>=1.0; python_version < > "3.7" in ./.local/lib/python2.7/site-packages (from > virtualenv->scipion-installer) (3.2.0) > Requirement already satisfied: importlib-metadata<3,>=0.12; python_version > < "3.8" in ./.local/lib/python2.7/site-packages (from > virtualenv->scipion-installer) (2.0.0) > Requirement already satisfied: filelock<4,>=3.0.0 in > ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) > (3.0.12) > Requirement already satisfied: pathlib2<3,>=2.3.3; python_version < "3.4" > and sys_platform != "win32" in ./.local/lib/python2.7/site-packages (from > virtualenv->scipion-installer) (2.3.5) > Requirement already satisfied: typing; python_version < "3.5" in > ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; > python_version < "3.7"->virtualenv->scipion-installer) (3.7.4.3) > Requirement already satisfied: contextlib2; python_version < "3" in > ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; > python_version < "3.7"->virtualenv->scipion-installer) (0.6.0.post1) > Requirement already satisfied: zipp>=0.4; python_version < "3.8" in > ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; > python_version < "3.7"->virtualenv->scipion-installer) (1.2.0) > Requirement already satisfied: singledispatch; python_version < "3.4" in > ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; > python_version < "3.7"->virtualenv->scipion-installer) (3.4.0.3) > Requirement already satisfied: configparser>=3.5; python_version < "3" in > ./.local/lib/python2.7/site-packages (from importlib-metadata<3,>=0.12; > python_version < "3.8"->virtualenv->scipion-installer) (4.0.2) > Requirement already satisfied: scandir; python_version < "3.5" in > /usr/local/lib/python2.7/dist-packages (from pathlib2<3,>=2.3.3; > python_version < "3.4" and sys_platform != > "win32"->virtualenv->scipion-installer) (1.9.0) > > > hilvertg@bamf:~$ python3 -m scipioninstaller ~/tetterst -venv -j 4created > virtual environment CPython3.5.2.final.0-64 in 99ms > creator CPython3Posix(dest=/home/hilvertg/tetterst/.scipion3env, > clear=False, global=False) > seeder FromAppData(download=False, wheel=bundle, setuptools=bundle, > pip=bundle, via=copy, app_data_dir=/home/hilvertg/.local/share/virtualenv) > added seed packages: Pillow==7.1.2, SCons==4.0.1, bibtexparser==1.2.0, > biopython==1.76, certifi==2020.6.20, chardet==3.0.4, configparser==4.0.2, > cycler==0.10.0, future==0.18.2, idna==2.10, joblib==0.14.1, > kiwisolver==1.1.0, littleutils==0.2.2, matplotlib==3.0.3, numpy==1.18.4, > outdated==0.2.0, peppercorn==0.6, pip==20.2.4, plotter==1.3.17, > psutil==5.7.0, pyparsing==2.4.7, python_dateutil==2.8.1, requests==2.23.0, > scikit_learn==0.22.1, scipion_app==3.0.5, scipion_em==3.0.4, > scipion_em_xmipp==20.7.1, scipion_pyworkflow==3.0.5, scipy==1.4.1, > setuptools==50.3.2, six==1.15.0, urllib3==1.25.11, wheel==0.35.1 > activators > PythonActivator,FishActivator,PowerShellActivator,CShellActivator,XonshActivator,BashActivator > DEPRECATION: Python 3.5 reached the end of its life on September 13th, > 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip > 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove > support for this functionality. > Requirement already satisfied: scipion-pyworkflow in > ./.scipion3env/lib/python3.5/site-packages (3.0.5) > Requirement already satisfied: matplotlib<=3.2.2 in > ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (3.0.3) > Requirement already satisfied: psutil<=5.7.0 in > ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (5.7.0) > Requirement already satisfied: requests<=2.23.0 in > ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) > (2.23.0) > Requirement already satisfied: numpy<=1.18.4 in > ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) > (1.18.4) > Requirement already satisfied: pillow<=7.1.2 in > ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (7.1.2) > Requirement already satisfied: bibtexparser<=1.2.0 in > ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (1.2.0) > Requirement already satisfied: configparser<=5.0.0 in > ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (4.0.2) > Requirement already satisfied: cycler>=0.10 in > ./.scipion3env/lib/python3.5/site-packages (from > matplotlib<=3.2.2->scipion-pyworkflow) (0.10.0) > Requirement already satisfied: python-dateutil>=2.1 in > ./.scipion3env/lib/python3.5/site-packages (from > matplotlib<=3.2.2->scipion-pyworkflow) (2.8.1) > Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in > ./.scipion3env/lib/python3.5/site-packages (from > matplotlib<=3.2.2->scipion-pyworkflow) (2.4.7) > Requirement already satisfied: kiwisolver>=1.0.1 in > ./.scipion3env/lib/python3.5/site-packages (from > matplotlib<=3.2.2->scipion-pyworkflow) (1.1.0) > Requirement already satisfied: certifi>=2017.4.17 in > ./.scipion3env/lib/python3.5/site-packages (from > requests<=2.23.0->scipion-pyworkflow) (2020.6.20) > Requirement already satisfied: idna<3,>=2.5 in > ./.scipion3env/lib/python3.5/site-packages (from > requests<=2.23.0->scipion-pyworkflow) (2.10) > Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in > ./.scipion3env/lib/python3.5/site-packages (from > requests<=2.23.0->scipion-pyworkflow) (1.25.11) > Requirement already satisfied: chardet<4,>=3.0.2 in > ./.scipion3env/lib/python3.5/site-packages (from > requests<=2.23.0->scipion-pyworkflow) (3.0.4) > Requirement already satisfied: future>=0.16.0 in > ./.scipion3env/lib/python3.5/site-packages (from > bibtexparser<=1.2.0->scipion-pyworkflow) (0.18.2) > Requirement already satisfied: six in > ./.scipion3env/lib/python3.5/site-packages (from > cycler>=0.10->matplotlib<=3.2.2->scipion-pyworkflow) (1.15.0) > Requirement already satisfied: setuptools in > ./.scipion3env/lib/python3.5/site-packages (from > kiwisolver>=1.0.1->matplotlib<=3.2.2->scipion-pyworkflow) (50.3.2) > DEPRECATION: Python 3.5 reached the end of its life on September 13th, > 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip > 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove > support for this functionality. > Requirement already satisfied: scipion-app in > ./.scipion3env/lib/python3.5/site-packages (3.0.5) > Requirement already satisfied: outdated==0.2.0 in > ./.scipion3env/lib/python3.5/site-packages (from scipion-app) (0.2.0) > Requirement already satisfied: scipion-em in > ./.scipion3env/lib/python3.5/site-packages (from scipion-app) (3.0.4) > Requirement already satisfied: littleutils in > ./.scipion3env/lib/python3.5/site-packages (from > outdated==0.2.0->scipion-app) (0.2.2) > Requirement already satisfied: requests in > ./.scipion3env/lib/python3.5/site-packages (from > outdated==0.2.0->scipion-app) (2.23.0) > Requirement already satisfied: scipion-pyworkflow in > ./.scipion3env/lib/python3.5/site-packages (from scipion-em->scipion-app) > (3.0.5) > Requirement already satisfied: biopython==1.76 in > ./.scipion3env/lib/python3.5/site-packages (from scipion-em->scipion-app) > (1.76) > Requirement already satisfied: idna<3,>=2.5 in > ./.scipion3env/lib/python3.5/site-packages (from > requests->outdated==0.2.0->scipion-app) (2.10) > Requirement already satisfied: chardet<4,>=3.0.2 in > ./.scipion3env/lib/python3.5/site-packages (from > requests->outdated==0.2.0->scipion-app) (3.0.4) > Requirement already satisfied: certifi>=2017.4.17 in > ./.scipion3env/lib/python3.5/site-packages (from > requests->outdated==0.2.0->scipion-app) (2020.6.20) > Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in > ./.scipion3env/lib/python3.5/site-packages (from > requests->outdated==0.2.0->scipion-app) (1.25.11) > Requirement already satisfied: matplotlib<=3.2.2 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow->scipion-em->scipion-app) (3.0.3) > Requirement already satisfied: configparser<=5.0.0 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow->scipion-em->scipion-app) (4.0.2) > Requirement already satisfied: numpy<=1.18.4 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow->scipion-em->scipion-app) (1.18.4) > Requirement already satisfied: pillow<=7.1.2 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow->scipion-em->scipion-app) (7.1.2) > Requirement already satisfied: bibtexparser<=1.2.0 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow->scipion-em->scipion-app) (1.2.0) > Requirement already satisfied: psutil<=5.7.0 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow->scipion-em->scipion-app) (5.7.0) > Requirement already satisfied: cycler>=0.10 in > ./.scipion3env/lib/python3.5/site-packages (from > matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (0.10.0) > Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in > ./.scipion3env/lib/python3.5/site-packages (from > matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.4.7) > Requirement already satisfied: python-dateutil>=2.1 in > ./.scipion3env/lib/python3.5/site-packages (from > matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.8.1) > Requirement already satisfied: kiwisolver>=1.0.1 in > ./.scipion3env/lib/python3.5/site-packages (from > matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.1.0) > Requirement already satisfied: future>=0.16.0 in > ./.scipion3env/lib/python3.5/site-packages (from > bibtexparser<=1.2.0->scipion-pyworkflow->scipion-em->scipion-app) (0.18.2) > Requirement already satisfied: six in > ./.scipion3env/lib/python3.5/site-packages (from > cycler>=0.10->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) > (1.15.0) > Requirement already satisfied: setuptools in > ./.scipion3env/lib/python3.5/site-packages (from > kiwisolver>=1.0.1->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) > (50.3.2) > Scipion v3.0.5 () devel > > >>> WARNING: Image library not found! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin > manager window) > > > Building scipion-em-xmipp ... > /home/hilvertg/tetterst/.scipion3env/bin/python -m pip install > scipion-em-xmipp==20.7.1 > DEPRECATION: Python 3.5 reached the end of its life on September 13th, > 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip > 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove > support for this functionality. > Requirement already satisfied: scipion-em-xmipp==20.7.1 in > ./.scipion3env/lib/python3.5/site-packages (20.7.1) > Requirement already satisfied: joblib in > ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) > (0.14.1) > Requirement already satisfied: peppercorn in > ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) > (0.6) > Requirement already satisfied: plotter in > ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) > (1.3.17) > Requirement already satisfied: scons in > ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) > (4.0.1) > Requirement already satisfied: scikit-learn==0.22.1 in > ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) > (0.22.1) > Requirement already satisfied: setuptools in > ./.scipion3env/lib/python3.5/site-packages (from > scons->scipion-em-xmipp==20.7.1) (50.3.2) > Requirement already satisfied: scipy>=0.17.0 in > ./.scipion3env/lib/python3.5/site-packages (from > scikit-learn==0.22.1->scipion-em-xmipp==20.7.1) (1.4.1) > Requirement already satisfied: numpy>=1.11.0 in > ./.scipion3env/lib/python3.5/site-packages (from > scikit-learn==0.22.1->scipion-em-xmipp==20.7.1) (1.18.4) > Done (0.36 seconds) > Building xmippSrc-3.20.07 ... > Skipping command: wget -nv -c -O > /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz > mv -v /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz.part > /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz > All targets exist. > Skipping command: tar -xf xmippSrc-v3.20.07.tgz > All targets exist. > cd /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07 > cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp > compileAndInstall N=4 && ln -srfn build > /home/hilvertg/tetterst/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null > Traceback (most recent call last): > File "./xmipp", line 1753, in <module> > XMIPP_SCRIPT_VERSION = getScriptVersion() > File "./xmipp", line 1718, in getScriptVersion > return lastCommit[0].strip() > IndexError: list index out of range > Traceback (most recent call last): > File > "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/__main__.py", > line 453, in <module> > main() > File > "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/__main__.py", > line 296, in main > installPluginMethods() > File > "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/install_plugin.py", > line 231, in installPluginMethods > plugin.installBin({'args': ['-j', numberProcessor]}) > File > "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", > line 220, in execute > command.execute() > File > "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", > line 161, in execute > "running '%s')" % (t, cmd)) > AssertionError: target > '/home/hilvertg/tetterst/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && ./xmipp > check_config && ./xmipp compileAndInstall N=4 && ln -srfn build > /home/hilvertg/tetterst/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null') > Error at main: target > '/home/hilvertg/tetterst/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && ./xmipp > check_config && ./xmipp compileAndInstall N=4 && ln -srfn build > /home/hilvertg/tetterst/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null') > > Something went wrong running: > cd /home/hilvertg/tetterst && > /usr/bin/python3 -m virtualenv --python=python3 .scipion3env && > . /home/hilvertg/tetterst/.scipion3env/bin/activate && > cd /home/hilvertg/tetterst && > mkdir -p software/lib && > mkdir -p software/bindings && > mkdir -p software/em && > export SCIPION_HOME=/home/hilvertg/tetterst && > pip install scipion-pyworkflow && > pip install scipion-app && > python -m scipion installp -p scipion-em-xmipp -j 4 > Installation cancelled. > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Pablo C. <pc...@cn...> - 2020-10-28 09:36:14
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Sorry, Smith, some how your email got stuck. It is not mandatory to use GPU, but many software integrated does need GPU. On 17/10/20 11:57, Smith Lee via scipion-users wrote: > Dear All, > > It said "Scipion can be installed using conda or virtualenv". Here I > ask, is using GPU mandatory for install and running Scipion v3.0? > > I am looking forward to getting your reply. > > Best wishes, > > Smith > > > > _______________________________________________ > 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: Grigory S. <sha...@gm...> - 2020-10-28 09:20:58
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Hi Tiru, It looks like a problem with MPI. What happens if you run: mpirun -np 2 echo 'test'? 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 Wed, Oct 28, 2020 at 9:00 AM Tiru Hcu <tir...@gm...> wrote: > Hi, > I am trying to install Scipion3 on my CPU laptop, unfortunately I couldn't > succeed. Please can you guide me to installation. I have conda 4.8. > Thank you and best regards > Tiru > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Jose M. de la R. T. <del...@gm...> - 2020-10-28 09:05:01
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Hi Smith, GPU is not mandatory. If you don't have GPU, then you can't use GPU programs. Best, Jose Miguel On Wed, Oct 28, 2020 at 10:00 AM Smith Lee via scipion-users < sci...@li...> wrote: > Dear All, > > It said "Scipion can be installed using conda or virtualenv". Here I ask, > is using GPU mandatory for install and running Scipion v3.0? > > I am looking forward to getting your reply. > > Best wishes, > > Smith > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Tetter S. <tet...@or...> - 2020-10-28 08:07:00
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Dear all, I am trying to install Scipion for single particle analysis, and more specifically for symmetry relaxation. Unfortunately I can't seem to get the installation to work. I am working with Ubuntu 16.04. Please be aware that I am not a well-versed Ubuntu user. I have tried installation both via the conda version and the virtualenv version described on https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources#fixing-fonts-in-a-conda-installation, but they both fail eventually. (I have changed the export PATH line to point to sr/local/cuda-9.0/bin to fit my setup.) Below is what happens. Any ideas? Thanks, Stephan hilvertg@bamf:~$ sudo apt-get install gcc g++ make libopenmpi-dev python3-tk libfftw3-dev libhdf5-dev libtiff-dev libjpeg-dev libsqlite3-dev openjdk-8-jdk Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'libtiff5-dev' instead of 'libtiff-dev' g++ is already the newest version (4:5.3.1-1ubuntu1). gcc is already the newest version (4:5.3.1-1ubuntu1). libfftw3-dev is already the newest version (3.3.4-2ubuntu1). libjpeg-dev is already the newest version (8c-2ubuntu8). make is already the newest version (4.1-6). python3-tk is already the newest version (3.5.1-1). libopenmpi-dev is already the newest version (1.10.2-8ubuntu1). libsqlite3-dev is already the newest version (3.11.0-1ubuntu1.5). libtiff5-dev is already the newest version (4.0.6-1ubuntu0.7). openjdk-8-jdk is already the newest version (8u272-b10-0ubuntu1~16.04). libhdf5-dev is already the newest version (1.8.16+docs-4ubuntu1.1). 0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded. hilvertg@bamf:~$ export PATH=$PATH:/usr/local/cuda-9.0/bin hilvertg@bamf:~$ python -m pip install --user scipion-installerRequirement already satisfied: scipion-installer in ./.local/lib/python2.7/site-packages (1.0.9) Requirement already satisfied: virtualenv in ./.local/lib/python2.7/site-packages (from scipion-installer) (20.1.0) Requirement already satisfied: six<2,>=1.9.0 in /usr/local/lib/python2.7/dist-packages (from virtualenv->scipion-installer) (1.10.0) Requirement already satisfied: appdirs<2,>=1.4.3 in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (1.4.4) Requirement already satisfied: distlib<1,>=0.3.1 in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (0.3.1) Requirement already satisfied: importlib-resources>=1.0; python_version < "3.7" in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (3.2.0) Requirement already satisfied: importlib-metadata<3,>=0.12; python_version < "3.8" in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (2.0.0) Requirement already satisfied: filelock<4,>=3.0.0 in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (3.0.12) Requirement already satisfied: pathlib2<3,>=2.3.3; python_version < "3.4" and sys_platform != "win32" in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (2.3.5) Requirement already satisfied: typing; python_version < "3.5" in ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; python_version < "3.7"->virtualenv->scipion-installer) (3.7.4.3) Requirement already satisfied: contextlib2; python_version < "3" in ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; python_version < "3.7"->virtualenv->scipion-installer) (0.6.0.post1) Requirement already satisfied: zipp>=0.4; python_version < "3.8" in ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; python_version < "3.7"->virtualenv->scipion-installer) (1.2.0) Requirement already satisfied: singledispatch; python_version < "3.4" in ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; python_version < "3.7"->virtualenv->scipion-installer) (3.4.0.3) Requirement already satisfied: configparser>=3.5; python_version < "3" in ./.local/lib/python2.7/site-packages (from importlib-metadata<3,>=0.12; python_version < "3.8"->virtualenv->scipion-installer) (4.0.2) Requirement already satisfied: scandir; python_version < "3.5" in /usr/local/lib/python2.7/dist-packages (from pathlib2<3,>=2.3.3; python_version < "3.4" and sys_platform != "win32"->virtualenv->scipion-installer) (1.9.0) hilvertg@bamf:~$ python3 -m scipioninstaller ~/tetterst -venv -j 4created virtual environment CPython3.5.2.final.0-64 in 99ms creator CPython3Posix(dest=/home/hilvertg/tetterst/.scipion3env, clear=False, global=False) seeder FromAppData(download=False, wheel=bundle, setuptools=bundle, pip=bundle, via=copy, app_data_dir=/home/hilvertg/.local/share/virtualenv) added seed packages: Pillow==7.1.2, SCons==4.0.1, bibtexparser==1.2.0, biopython==1.76, certifi==2020.6.20, chardet==3.0.4, configparser==4.0.2, cycler==0.10.0, future==0.18.2, idna==2.10, joblib==0.14.1, kiwisolver==1.1.0, littleutils==0.2.2, matplotlib==3.0.3, numpy==1.18.4, outdated==0.2.0, peppercorn==0.6, pip==20.2.4, plotter==1.3.17, psutil==5.7.0, pyparsing==2.4.7, python_dateutil==2.8.1, requests==2.23.0, scikit_learn==0.22.1, scipion_app==3.0.5, scipion_em==3.0.4, scipion_em_xmipp==20.7.1, scipion_pyworkflow==3.0.5, scipy==1.4.1, setuptools==50.3.2, six==1.15.0, urllib3==1.25.11, wheel==0.35.1 activators PythonActivator,FishActivator,PowerShellActivator,CShellActivator,XonshActivator,BashActivator DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality. Requirement already satisfied: scipion-pyworkflow in ./.scipion3env/lib/python3.5/site-packages (3.0.5) Requirement already satisfied: matplotlib<=3.2.2 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (3.0.3) Requirement already satisfied: psutil<=5.7.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (5.7.0) Requirement already satisfied: requests<=2.23.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (2.23.0) Requirement already satisfied: numpy<=1.18.4 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (1.18.4) Requirement already satisfied: pillow<=7.1.2 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (7.1.2) Requirement already satisfied: bibtexparser<=1.2.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (1.2.0) Requirement already satisfied: configparser<=5.0.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (4.0.2) Requirement already satisfied: cycler>=0.10 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (0.10.0) Requirement already satisfied: python-dateutil>=2.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.8.1) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.4.7) Requirement already satisfied: kiwisolver>=1.0.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (1.1.0) Requirement already satisfied: certifi>=2017.4.17 in ./.scipion3env/lib/python3.5/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2020.6.20) Requirement already satisfied: idna<3,>=2.5 in ./.scipion3env/lib/python3.5/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2.10) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in ./.scipion3env/lib/python3.5/site-packages (from requests<=2.23.0->scipion-pyworkflow) (1.25.11) Requirement already satisfied: chardet<4,>=3.0.2 in ./.scipion3env/lib/python3.5/site-packages (from requests<=2.23.0->scipion-pyworkflow) (3.0.4) Requirement already satisfied: future>=0.16.0 in ./.scipion3env/lib/python3.5/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow) (0.18.2) Requirement already satisfied: six in ./.scipion3env/lib/python3.5/site-packages (from cycler>=0.10->matplotlib<=3.2.2->scipion-pyworkflow) (1.15.0) Requirement already satisfied: setuptools in ./.scipion3env/lib/python3.5/site-packages (from kiwisolver>=1.0.1->matplotlib<=3.2.2->scipion-pyworkflow) (50.3.2) DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality. Requirement already satisfied: scipion-app in ./.scipion3env/lib/python3.5/site-packages (3.0.5) Requirement already satisfied: outdated==0.2.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-app) (0.2.0) Requirement already satisfied: scipion-em in ./.scipion3env/lib/python3.5/site-packages (from scipion-app) (3.0.4) Requirement already satisfied: littleutils in ./.scipion3env/lib/python3.5/site-packages (from outdated==0.2.0->scipion-app) (0.2.2) Requirement already satisfied: requests in ./.scipion3env/lib/python3.5/site-packages (from outdated==0.2.0->scipion-app) (2.23.0) Requirement already satisfied: scipion-pyworkflow in ./.scipion3env/lib/python3.5/site-packages (from scipion-em->scipion-app) (3.0.5) Requirement already satisfied: biopython==1.76 in ./.scipion3env/lib/python3.5/site-packages (from scipion-em->scipion-app) (1.76) Requirement already satisfied: idna<3,>=2.5 in ./.scipion3env/lib/python3.5/site-packages (from requests->outdated==0.2.0->scipion-app) (2.10) Requirement already satisfied: chardet<4,>=3.0.2 in ./.scipion3env/lib/python3.5/site-packages (from requests->outdated==0.2.0->scipion-app) (3.0.4) Requirement already satisfied: certifi>=2017.4.17 in ./.scipion3env/lib/python3.5/site-packages (from requests->outdated==0.2.0->scipion-app) (2020.6.20) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in ./.scipion3env/lib/python3.5/site-packages (from requests->outdated==0.2.0->scipion-app) (1.25.11) Requirement already satisfied: matplotlib<=3.2.2 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (3.0.3) Requirement already satisfied: configparser<=5.0.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (4.0.2) Requirement already satisfied: numpy<=1.18.4 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.18.4) Requirement already satisfied: pillow<=7.1.2 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (7.1.2) Requirement already satisfied: bibtexparser<=1.2.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.2.0) Requirement already satisfied: psutil<=5.7.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (5.7.0) Requirement already satisfied: cycler>=0.10 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (0.10.0) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.4.7) Requirement already satisfied: python-dateutil>=2.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.8.1) Requirement already satisfied: kiwisolver>=1.0.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.1.0) Requirement already satisfied: future>=0.16.0 in ./.scipion3env/lib/python3.5/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow->scipion-em->scipion-app) (0.18.2) Requirement already satisfied: six in ./.scipion3env/lib/python3.5/site-packages (from cycler>=0.10->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.15.0) Requirement already satisfied: setuptools in ./.scipion3env/lib/python3.5/site-packages (from kiwisolver>=1.0.1->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (50.3.2) Scipion v3.0.5 () devel >>> WARNING: Image library not found! > Please install Xmipp to get full functionality. (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) Building scipion-em-xmipp ... /home/hilvertg/tetterst/.scipion3env/bin/python -m pip install scipion-em-xmipp==20.7.1 DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality. Requirement already satisfied: scipion-em-xmipp==20.7.1 in ./.scipion3env/lib/python3.5/site-packages (20.7.1) Requirement already satisfied: joblib in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (0.14.1) Requirement already satisfied: peppercorn in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (0.6) Requirement already satisfied: plotter in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (1.3.17) Requirement already satisfied: scons in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (4.0.1) Requirement already satisfied: scikit-learn==0.22.1 in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (0.22.1) Requirement already satisfied: setuptools in ./.scipion3env/lib/python3.5/site-packages (from scons->scipion-em-xmipp==20.7.1) (50.3.2) Requirement already satisfied: scipy>=0.17.0 in ./.scipion3env/lib/python3.5/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7.1) (1.4.1) Requirement already satisfied: numpy>=1.11.0 in ./.scipion3env/lib/python3.5/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7.1) (1.18.4) Done (0.36 seconds) Building xmippSrc-3.20.07 ... Skipping command: wget -nv -c -O /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz mv -v /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz.part /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz All targets exist. Skipping command: tar -xf xmippSrc-v3.20.07.tgz All targets exist. cd /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07 cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srfn build /home/hilvertg/tetterst/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null Traceback (most recent call last): File "./xmipp", line 1753, in <module> XMIPP_SCRIPT_VERSION = getScriptVersion() File "./xmipp", line 1718, in getScriptVersion return lastCommit[0].strip() IndexError: list index out of range Traceback (most recent call last): File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/__main__.py", line 453, in <module> main() File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/__main__.py", line 296, in main installPluginMethods() File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods plugin.installBin({'args': ['-j', numberProcessor]}) File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", line 220, in execute command.execute() File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", line 161, in execute "running '%s')" % (t, cmd)) AssertionError: target '/home/hilvertg/tetterst/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srfn build /home/hilvertg/tetterst/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') Error at main: target '/home/hilvertg/tetterst/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srfn build /home/hilvertg/tetterst/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') Something went wrong running: cd /home/hilvertg/tetterst && /usr/bin/python3 -m virtualenv --python=python3 .scipion3env && . /home/hilvertg/tetterst/.scipion3env/bin/activate && cd /home/hilvertg/tetterst && mkdir -p software/lib && mkdir -p software/bindings && mkdir -p software/em && export SCIPION_HOME=/home/hilvertg/tetterst && pip install scipion-pyworkflow && pip install scipion-app && python -m scipion installp -p scipion-em-xmipp -j 4 Installation cancelled. |
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From: Pablo C. <pc...@cn...> - 2020-10-28 06:23:50
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Despite the error, it seems localrec is installed. What about: ./scipion3 inspect localrec On 27/10/20 19:12, Moustafa, Ibrahim M. wrote: > scipion-em-localrec 3.0.1 -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Moustafa, I. M. <ri...@ps...> - 2020-10-27 18:46:10
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That is what I get:
Scipion v3.0.5 () devel
Package Version
------------------- ---------
appdirs 1.4.4
bibtexparser 1.2.0
biopython 1.76
brotlipy 0.7.0
certifi 2020.6.20
cffi 1.14.3
chardet 3.0.4
configparser 5.0.0
cryptography 3.1.1
cycler 0.10.0
distlib 0.3.1
emtable 0.0.7
filelock 3.0.12
future 0.18.2
idna 2.10
importlib-metadata 2.0.0
joblib 0.17.0
kiwisolver 1.2.0
littleutils 0.2.2
matplotlib 3.2.2
mrcfile 1.1.2
numpy 1.19.2
opencv-python 4.4.0.44
outdated 0.2.0
peppercorn 0.6
Pillow 7.1.2
pip 20.2.4
plotter 1.3.17
psutil 5.7.0
pycparser 2.20
pyOpenSSL 19.1.0
pyparsing 2.4.7
PySocks 1.7.1
python-dateutil 2.8.1
requests 2.23.0
scikit-learn 0.22.1
scipion-app 3.0.5
scipion-em 3.0.4
scipion-em-eman2 3.1.1
scipion-em-localrec 3.0.1
scipion-em-locscale 3.0.2
scipion-em-relion 3.0.0b3
scipion-em-tomo 3.0.6
scipion-em-xmipp 20.7.1
scipion-em-xmipp2 3.0.0
scipion-installer 1.0.9
scipion-pyworkflow 3.0.5
scipy 1.5.3
SCons 4.0.1
setuptools 50.3.2
six 1.15.0
urllib3 1.25.11
virtualenv 20.0.35
wheel 0.35.1zipp 3.3.1
Ibrahim
________________________________
From: Pablo Conesa <pc...@cn...>
Sent: Tuesday, October 27, 2020 1:26 PM
To: sci...@li... <sci...@li...>
Subject: Re: [scipion-users] problem installing scipion3
ummm,
what does give you:
scipion3 python -m pip list ?
On 27/10/20 17:23, Moustafa, Ibrahim M. wrote:
I can confirm that I have permission on the environment folder.
I also checked to see if installation goes to HOME/.local but nothing related to scipion there.
Ibrahim
________________________________
From: Pablo Conesa <pc...@cn...><mailto:pc...@cn...>
Sent: Tuesday, October 27, 2020 4:55 AM
To: sci...@li...<mailto:sci...@li...> <sci...@li...><mailto:sci...@li...>
Subject: Re: [scipion-users] problem installing scipion3
I meant ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em*
But I can see that environment lacks all scipion packages.
I'm guessing you do not have permission on the environment folder and all goes to you HOME/.local installation.
If I'm right non of the plugins installation should work cause we do not expect not having permissions on the environment.
Could you please verify this case?
ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages
Will list who owns that folder.
On 27/10/20 8:29, Moustafa, Ibrahim M. wrote:
ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em
gives nothing.
The following packages exist in
ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/
brotli
brotlipy-0.7.0-py3.8.egg-info
certifi
certifi-2020.6.20-py3.8.egg-info
cffi
cffi-1.14.3.dist-info
_cffi_backend.cpython-38-x86_64-linux-gnu.so
chardet
chardet-3.0.4.dist-info
cryptography
cryptography-3.1.1.dist-info
_distutils_hack
distutils-precedence.pth
easy_install.py
idna
idna-2.10.dist-info
OpenSSL
pip
pip-20.2.4-py3.8.egg-info
pkg_resources
__pycache__
pycparser
pycparser-2.20.dist-info
pyOpenSSL-19.1.0.dist-info
PySocks-1.7.1.dist-info
README.txt
requests
requests-2.24.0.dist-info
SConse--(71%)
scons-3.1.2-py3.8.egg-info
setuptools
setuptools-50.3.0.post20201006-py3.8.egg-info
six-1.15.0.dist-info
six.py
sockshandler.py
socks.py
urllib3
urllib3-1.25.11.dist-info
wheel
wheel-0.35.1-py3.6.egg-info
Ibrahim
________________________________
From: pc...@cn...<mailto:pc...@cn...> <pc...@cn...><mailto:pc...@cn...>
Sent: Tuesday, October 27, 2020 2:18 AM
To: Mailing list for Scipion users <sci...@li...><mailto:sci...@li...>
Subject: Re: [scipion-users] problem installing scipion3
What gives you:
ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_ em_
El 26 oct. 2020 17:57, "Moustafa, Ibrahim M." <ri...@ps...><mailto:ri...@ps...> escribió:
Hi Pablo,
Thanks for your reply.
I tried your suggestions and I got the following error:
==================================================================================
Scipion v3.0.5 () devel
Building scipion-em-localrec ...
/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1
Collecting scipion-em-localrec==3.0.1
Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
Installing collected packages: scipion-em-localrec
Successfully installed scipion-em-localrec-3.0.1
Traceback (most recent call last):
File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module>
main()
File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main
installPluginMethods()
File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethod s
installed = plugin.installPipModule(version=pluginVersion)
File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule
environment.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute
command.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_ em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip in stall scipion-em-localrec==3.0.1')
Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_e m_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip ins tall scipion-em-localrec==3.0.1')
==================================================================================
Any idea to fix this?
Thanks for help.
Ibrahim
________________________________
From: pc...@cn...<mailto:pc...@cn...> <pc...@cn...><mailto:pc...@cn...>
Sent: Saturday, October 24, 2020 11:56 PM
To: Mailing list for Scipion users <sci...@li...><mailto:sci...@li...>
Cc: Carnegie, Mike Scott <mz...@ps...><mailto:mz...@ps...>
Subject: Re: [scipion-users] problem installing scipion3
Hi, I'm sorry about you poor experience installing the plugin
Can you try:
scipion3 python -m pip uninstall scipion-em-localrec
And then:
scipion3 installs -p scipion-em-localrec
?
Then we can also check what is wrong with bumpy.
All the best, Pablo.
El 24 oct. 2020 2:12, "Moustafa, Ibrahim M." <ri...@ps...><mailto:ri...@ps...> escribió:
Dear All,
We are having so much trouble installing Scipion 3. We thought it went through installation but then it complained about xmipp because of conflict between numpy-1.19.1 (installed with OpenCV) and numpy-1.18.4 (installed from pip). None of the plugins seem to be properly installed when we tried, although it showed "Successfully Finished' in the log!
Trying to install localrec-em showed the following error:
===========================================================================================
>scipion3 installp -p scipion-em-localrec
/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1
Collecting scipion-em-localrec==3.0.1
Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
Installing collected packages: scipion-em-localrec
Successfully installed scipion-em-localrec-3.0.1
WARNING: Target directory /usr/local/scipion/pip/scipion_em_localrec-3.0.1.dist-info already exists. Specify --upgrade to force replacement.
WARNING: Target directory /usr/local/scipion/pip/localrec already exists. Specify --upgrade to force replacement.
Traceback (most recent call last):
File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module>
main()
File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main
installPluginMethods()
File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethods
installed = plugin.installPipModule(version=pluginVersion)
File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule
environment.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute
command.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')
Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')
==================================================================================
Not sure what we are doing wrong! It would be appreciated if someone can share a "clear" protocol of how to properly install Scipion 3 along with plugins. We are mostly interested in
localrec plugin.
P.S. we are using py3.8 from miniconda
Appreciate your help,
Ibrahim
Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
Millennium Science Complex
University Park
State College, PA16802
Phone: (814) 863 5940
Fax: (814) 865 7927
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7C60fcd9d7e1464670fe4308d87a9d8a01%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637394164338323767%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=a2tbboP7oT54mj9a50c%2B%2BdkqOjTJnAvdQziAdF%2FTLVg%3D&reserved=0>
--
Pablo Conesa - Madrid Scipion<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fscipion.i2pc.es%2F&data=04%7C01%7Cria2%40psu.edu%7C60fcd9d7e1464670fe4308d87a9d8a01%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637394164338333762%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=gf%2FyR2OiniQV8mMkXJXqpwCQCGFsF%2BbmDCLRSC61XXk%3D&reserved=0> team
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7C60fcd9d7e1464670fe4308d87a9d8a01%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637394164338343758%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ysbbhtTOAy00BSkxu7uaLkDKwEI07lX%2Bi%2FOfxvMXTSw%3D&reserved=0>
--
Pablo Conesa - Madrid Scipion<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fscipion.i2pc.es%2F&data=04%7C01%7Cria2%40psu.edu%7C60fcd9d7e1464670fe4308d87a9d8a01%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637394164338343758%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=JGzc0%2BJ7plYhrhbirjrmUhM9cHGpz3jwm2Zbm8nqbC0%3D&reserved=0> team
|
|
From: Pablo C. <pc...@cn...> - 2020-10-27 17:26:55
|
ummm,
what does give you:
scipion3 python -m pip list ?
On 27/10/20 17:23, Moustafa, Ibrahim M. wrote:
> I can confirm that I have permission on the environment folder.
> I also checked to see if installation goes to HOME/.local but nothing
> related to scipion there.
>
> Ibrahim
>
>
> ------------------------------------------------------------------------
> *From:* Pablo Conesa <pc...@cn...>
> *Sent:* Tuesday, October 27, 2020 4:55 AM
> *To:* sci...@li...
> <sci...@li...>
> *Subject:* Re: [scipion-users] problem installing scipion3
>
> I meant ls -l
> /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em*
>
>
> But I can see that environment lacks all scipion packages.
>
>
> I'm guessing you do not have permission on the environment folder and
> all goes to you HOME/.local installation.
>
>
> If I'm right non of the plugins installation should work cause we do
> not expect not having permissions on the environment.
>
>
> Could you please verify this case?
>
>
> ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages
>
>
> Will list who owns that folder.
>
>
> On 27/10/20 8:29, Moustafa, Ibrahim M. wrote:
>> ls -l
>> /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em
>>
>> gives nothing.
>>
>> The following packages exist in
>> ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/
>>
>> brotli
>> brotlipy-0.7.0-py3.8.egg-info
>> certifi
>> certifi-2020.6.20-py3.8.egg-info
>> cffi
>> cffi-1.14.3.dist-info
>> _cffi_backend.cpython-38-x86_64-linux-gnu.so
>> chardet
>> chardet-3.0.4.dist-info
>> cryptography
>> cryptography-3.1.1.dist-info
>> _distutils_hack
>> distutils-precedence.pth
>> easy_install.py
>> idna
>> idna-2.10.dist-info
>> OpenSSL
>> pip
>> pip-20.2.4-py3.8.egg-info
>> pkg_resources
>> __pycache__
>> pycparser
>> pycparser-2.20.dist-info
>> pyOpenSSL-19.1.0.dist-info
>> PySocks-1.7.1.dist-info
>> README.txt
>> requests
>> requests-2.24.0.dist-info
>> SConse--(71%)
>> scons-3.1.2-py3.8.egg-info
>> setuptools
>> setuptools-50.3.0.post20201006-py3.8.egg-info
>> six-1.15.0.dist-info
>> six.py
>> sockshandler.py
>> socks.py
>> urllib3
>> urllib3-1.25.11.dist-info
>> wheel
>> wheel-0.35.1-py3.6.egg-info
>>
>> Ibrahim
>> ------------------------------------------------------------------------
>> *From:* pc...@cn... <mailto:pc...@cn...>
>> <pc...@cn...> <mailto:pc...@cn...>
>> *Sent:* Tuesday, October 27, 2020 2:18 AM
>> *To:* Mailing list for Scipion users
>> <sci...@li...>
>> <mailto:sci...@li...>
>> *Subject:* Re: [scipion-users] problem installing scipion3
>> What gives you:
>>
>> ls -l
>> /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_
>> em_
>>
>> El 26 oct. 2020 17:57, "Moustafa, Ibrahim M." <ri...@ps...>
>> <mailto:ri...@ps...> escribió:
>>
>> Hi Pablo,
>>
>> Thanks for your reply.
>>
>> I tried your suggestions and I got the following error:
>>
>> ==================================================================================
>> Scipion v3.0.5 () devel
>> Building scipion-em-localrec ...
>> /usr/local/miniconda/envs/.scipion3env/bin/python -m pip install
>> scipion-em-localrec==3.0.1
>> Collecting scipion-em-localrec==3.0.1
>> Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
>> Installing collected packages: scipion-em-localrec
>> Successfully installed scipion-em-localrec-3.0.1
>> Traceback (most recent call last):
>> File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in
>> <module>
>> main()
>> File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in
>> main
>> installPluginMethods()
>> File
>> "/usr/local/scipion/pip/scipion/install/install_plugin.py", line
>> 229, in installPluginMethod s
>> installed = plugin.installPipModule(version=pluginVersion)
>> File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py",
>> line 152, in installPipModule
>> environment.execute()
>> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
>> 748, in execute
>> self._executeTargets(targetList)
>> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
>> 690, in _executeTargets
>> tgt.execute()
>> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
>> 220, in execute
>> command.execute()
>> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
>> 160, in execute
>> assert glob(t), ("target '%s' not built (after "
>> AssertionError: target
>> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_
>> em_localrec*' not built (after running
>> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip in
>> stall scipion-em-localrec==3.0.1')
>> Error at main: target
>> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_e
>> m_localrec*' not built (after running
>> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip ins
>> tall scipion-em-localrec==3.0.1')
>>
>> ==================================================================================
>>
>> Any idea to fix this?
>>
>> Thanks for help.
>> Ibrahim
>> ------------------------------------------------------------------------
>> *From:* pc...@cn... <mailto:pc...@cn...>
>> <pc...@cn...> <mailto:pc...@cn...>
>> *Sent:* Saturday, October 24, 2020 11:56 PM
>> *To:* Mailing list for Scipion users
>> <sci...@li...>
>> <mailto:sci...@li...>
>> *Cc:* Carnegie, Mike Scott <mz...@ps...> <mailto:mz...@ps...>
>> *Subject:* Re: [scipion-users] problem installing scipion3
>> Hi, I'm sorry about you poor experience installing the plugin
>>
>> Can you try:
>>
>> scipion3 python -m pip uninstall scipion-em-localrec
>>
>> And then:
>>
>> scipion3 installs -p scipion-em-localrec
>>
>> ?
>> Then we can also check what is wrong with bumpy.
>>
>> All the best, Pablo.
>>
>> El 24 oct. 2020 2:12, "Moustafa, Ibrahim M." <ri...@ps...>
>> <mailto:ri...@ps...> escribió:
>>
>> Dear All,
>>
>> We are having so much trouble installing Scipion 3. We
>> thought it went through installation but then it complained
>> about xmipp because of conflict between numpy-1.19.1
>> (installed with OpenCV) and numpy-1.18.4 (installed from
>> pip). None of the plugins seem to be properly installed when
>> we tried, although it showed "Successfully Finished' in the log!
>>
>> Trying to install localrec-em showed the following error:
>>
>> ===========================================================================================
>> >scipion3 installp -p scipion-em-localrec
>> /usr/local/miniconda/envs/.scipion3env/bin/python -m pip
>> install scipion-em-localrec==3.0.1
>> Collecting scipion-em-localrec==3.0.1
>> Using cached scipion_em_localrec-3.0.1-py3-none-any.whl
>> (530 kB)
>> Installing collected packages: scipion-em-localrec
>> Successfully installed scipion-em-localrec-3.0.1
>> WARNING: Target directory
>> /usr/local/scipion/pip/scipion_em_localrec-3.0.1.dist-info
>> already exists. Specify --upgrade to force replacement.
>> WARNING: Target directory /usr/local/scipion/pip/localrec
>> already exists. Specify --upgrade to force replacement.
>> Traceback (most recent call last):
>> File "/usr/local/scipion/pip/scipion/__main__.py", line
>> 453, in <module>
>> main()
>> File "/usr/local/scipion/pip/scipion/__main__.py", line
>> 296, in main
>> installPluginMethods()
>> File
>> "/usr/local/scipion/pip/scipion/install/install_plugin.py",
>> line 229, in installPluginMethods
>> installed = plugin.installPipModule(version=pluginVersion)
>> File
>> "/usr/local/scipion/pip/scipion/install/plugin_funcs.py",
>> line 152, in installPipModule
>> environment.execute()
>> File "/usr/local/scipion/pip/scipion/install/funcs.py",
>> line 748, in execute
>> self._executeTargets(targetList)
>> File "/usr/local/scipion/pip/scipion/install/funcs.py",
>> line 690, in _executeTargets
>> tgt.execute()
>> File "/usr/local/scipion/pip/scipion/install/funcs.py",
>> line 220, in execute
>> command.execute()
>> File "/usr/local/scipion/pip/scipion/install/funcs.py",
>> line 160, in execute
>> assert glob(t), ("target '%s' not built (after "
>> AssertionError: target
>> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*'
>> not built (after running
>> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip
>> install scipion-em-localrec==3.0.1')
>> Error at main: target
>> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*'
>> not built (after running
>> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip
>> install scipion-em-localrec==3.0.1')
>> ==================================================================================
>>
>> Not sure what we are doing wrong! It would be appreciated
>> if someone can share a "clear" protocol of how to properly
>> install Scipion 3 along with plugins. We are mostly
>> interested in
>> localrec plugin.
>>
>> P.S. we are using py3.8 from miniconda
>>
>> Appreciate your help,
>> Ibrahim
>>
>> Ibrahim M.Moustafa, Ph.D.
>> Pennsylvania State University
>> Biochemistry & Molecular Biology Dept.
>> Millennium Science Complex
>> University Park
>> State College, PA16802
>>
>> Phone: (814) 863 5940
>> Fax: (814) 865 7927
>>
>>
>>
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li... <mailto:sci...@li...>
>> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7C774807a890214593e17a08d87a5624dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637393857703415521%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=PvC4Bn6CISvDINVVQkd%2F782qbuzD%2FRKoewGp1ha3EXI%3D&reserved=0>
> --
> Pablo Conesa - *Madrid Scipion
> <https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fscipion.i2pc.es%2F&data=04%7C01%7Cria2%40psu.edu%7C774807a890214593e17a08d87a5624dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637393857703425518%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=dZ4Xg%2FwlTSxgvhTYugEHUKXjd4Y%2FY5h2Hth%2BG3Iwj9Q%3D&reserved=0>
> team*
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Moustafa, I. M. <ri...@ps...> - 2020-10-27 16:23:55
|
I can confirm that I have permission on the environment folder.
I also checked to see if installation goes to HOME/.local but nothing related to scipion there.
Ibrahim
________________________________
From: Pablo Conesa <pc...@cn...>
Sent: Tuesday, October 27, 2020 4:55 AM
To: sci...@li... <sci...@li...>
Subject: Re: [scipion-users] problem installing scipion3
I meant ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em*
But I can see that environment lacks all scipion packages.
I'm guessing you do not have permission on the environment folder and all goes to you HOME/.local installation.
If I'm right non of the plugins installation should work cause we do not expect not having permissions on the environment.
Could you please verify this case?
ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages
Will list who owns that folder.
On 27/10/20 8:29, Moustafa, Ibrahim M. wrote:
ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em
gives nothing.
The following packages exist in
ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/
brotli
brotlipy-0.7.0-py3.8.egg-info
certifi
certifi-2020.6.20-py3.8.egg-info
cffi
cffi-1.14.3.dist-info
_cffi_backend.cpython-38-x86_64-linux-gnu.so
chardet
chardet-3.0.4.dist-info
cryptography
cryptography-3.1.1.dist-info
_distutils_hack
distutils-precedence.pth
easy_install.py
idna
idna-2.10.dist-info
OpenSSL
pip
pip-20.2.4-py3.8.egg-info
pkg_resources
__pycache__
pycparser
pycparser-2.20.dist-info
pyOpenSSL-19.1.0.dist-info
PySocks-1.7.1.dist-info
README.txt
requests
requests-2.24.0.dist-info
SConse--(71%)
scons-3.1.2-py3.8.egg-info
setuptools
setuptools-50.3.0.post20201006-py3.8.egg-info
six-1.15.0.dist-info
six.py
sockshandler.py
socks.py
urllib3
urllib3-1.25.11.dist-info
wheel
wheel-0.35.1-py3.6.egg-info
Ibrahim
________________________________
From: pc...@cn...<mailto:pc...@cn...> <pc...@cn...><mailto:pc...@cn...>
Sent: Tuesday, October 27, 2020 2:18 AM
To: Mailing list for Scipion users <sci...@li...><mailto:sci...@li...>
Subject: Re: [scipion-users] problem installing scipion3
What gives you:
ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_ em_
El 26 oct. 2020 17:57, "Moustafa, Ibrahim M." <ri...@ps...><mailto:ri...@ps...> escribió:
Hi Pablo,
Thanks for your reply.
I tried your suggestions and I got the following error:
==================================================================================
Scipion v3.0.5 () devel
Building scipion-em-localrec ...
/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1
Collecting scipion-em-localrec==3.0.1
Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
Installing collected packages: scipion-em-localrec
Successfully installed scipion-em-localrec-3.0.1
Traceback (most recent call last):
File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module>
main()
File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main
installPluginMethods()
File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethod s
installed = plugin.installPipModule(version=pluginVersion)
File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule
environment.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute
command.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_ em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip in stall scipion-em-localrec==3.0.1')
Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_e m_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip ins tall scipion-em-localrec==3.0.1')
==================================================================================
Any idea to fix this?
Thanks for help.
Ibrahim
________________________________
From: pc...@cn...<mailto:pc...@cn...> <pc...@cn...><mailto:pc...@cn...>
Sent: Saturday, October 24, 2020 11:56 PM
To: Mailing list for Scipion users <sci...@li...><mailto:sci...@li...>
Cc: Carnegie, Mike Scott <mz...@ps...><mailto:mz...@ps...>
Subject: Re: [scipion-users] problem installing scipion3
Hi, I'm sorry about you poor experience installing the plugin
Can you try:
scipion3 python -m pip uninstall scipion-em-localrec
And then:
scipion3 installs -p scipion-em-localrec
?
Then we can also check what is wrong with bumpy.
All the best, Pablo.
El 24 oct. 2020 2:12, "Moustafa, Ibrahim M." <ri...@ps...><mailto:ri...@ps...> escribió:
Dear All,
We are having so much trouble installing Scipion 3. We thought it went through installation but then it complained about xmipp because of conflict between numpy-1.19.1 (installed with OpenCV) and numpy-1.18.4 (installed from pip). None of the plugins seem to be properly installed when we tried, although it showed "Successfully Finished' in the log!
Trying to install localrec-em showed the following error:
===========================================================================================
>scipion3 installp -p scipion-em-localrec
/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1
Collecting scipion-em-localrec==3.0.1
Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
Installing collected packages: scipion-em-localrec
Successfully installed scipion-em-localrec-3.0.1
WARNING: Target directory /usr/local/scipion/pip/scipion_em_localrec-3.0.1.dist-info already exists. Specify --upgrade to force replacement.
WARNING: Target directory /usr/local/scipion/pip/localrec already exists. Specify --upgrade to force replacement.
Traceback (most recent call last):
File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module>
main()
File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main
installPluginMethods()
File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethods
installed = plugin.installPipModule(version=pluginVersion)
File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule
environment.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute
command.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')
Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')
==================================================================================
Not sure what we are doing wrong! It would be appreciated if someone can share a "clear" protocol of how to properly install Scipion 3 along with plugins. We are mostly interested in
localrec plugin.
P.S. we are using py3.8 from miniconda
Appreciate your help,
Ibrahim
Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
Millennium Science Complex
University Park
State College, PA16802
Phone: (814) 863 5940
Fax: (814) 865 7927
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7C774807a890214593e17a08d87a5624dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637393857703415521%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=PvC4Bn6CISvDINVVQkd%2F782qbuzD%2FRKoewGp1ha3EXI%3D&reserved=0>
--
Pablo Conesa - Madrid Scipion<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fscipion.i2pc.es%2F&data=04%7C01%7Cria2%40psu.edu%7C774807a890214593e17a08d87a5624dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637393857703425518%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=dZ4Xg%2FwlTSxgvhTYugEHUKXjd4Y%2FY5h2Hth%2BG3Iwj9Q%3D&reserved=0> team
|
|
From: Pablo C. <pc...@cn...> - 2020-10-27 08:55:51
|
I meant ls -l
/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em*
But I can see that environment lacks all scipion packages.
I'm guessing you do not have permission on the environment folder and
all goes to you HOME/.local installation.
If I'm right non of the plugins installation should work cause we do not
expect not having permissions on the environment.
Could you please verify this case?
ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages
Will list who owns that folder.
On 27/10/20 8:29, Moustafa, Ibrahim M. wrote:
> ls -l
> /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em
>
> gives nothing.
>
> The following packages exist in
> ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/
>
> brotli
> brotlipy-0.7.0-py3.8.egg-info
> certifi
> certifi-2020.6.20-py3.8.egg-info
> cffi
> cffi-1.14.3.dist-info
> _cffi_backend.cpython-38-x86_64-linux-gnu.so
> chardet
> chardet-3.0.4.dist-info
> cryptography
> cryptography-3.1.1.dist-info
> _distutils_hack
> distutils-precedence.pth
> easy_install.py
> idna
> idna-2.10.dist-info
> OpenSSL
> pip
> pip-20.2.4-py3.8.egg-info
> pkg_resources
> __pycache__
> pycparser
> pycparser-2.20.dist-info
> pyOpenSSL-19.1.0.dist-info
> PySocks-1.7.1.dist-info
> README.txt
> requests
> requests-2.24.0.dist-info
> SConse--(71%)
> scons-3.1.2-py3.8.egg-info
> setuptools
> setuptools-50.3.0.post20201006-py3.8.egg-info
> six-1.15.0.dist-info
> six.py
> sockshandler.py
> socks.py
> urllib3
> urllib3-1.25.11.dist-info
> wheel
> wheel-0.35.1-py3.6.egg-info
>
> Ibrahim
> ------------------------------------------------------------------------
> *From:* pc...@cn... <pc...@cn...>
> *Sent:* Tuesday, October 27, 2020 2:18 AM
> *To:* Mailing list for Scipion users <sci...@li...>
> *Subject:* Re: [scipion-users] problem installing scipion3
> What gives you:
>
> ls -l
> /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_
> em_
>
> El 26 oct. 2020 17:57, "Moustafa, Ibrahim M." <ri...@ps...> escribió:
>
> Hi Pablo,
>
> Thanks for your reply.
>
> I tried your suggestions and I got the following error:
>
> ==================================================================================
> Scipion v3.0.5 () devel
> Building scipion-em-localrec ...
> /usr/local/miniconda/envs/.scipion3env/bin/python -m pip install
> scipion-em-localrec==3.0.1
> Collecting scipion-em-localrec==3.0.1
> Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
> Installing collected packages: scipion-em-localrec
> Successfully installed scipion-em-localrec-3.0.1
> Traceback (most recent call last):
> File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in
> <module>
> main()
> File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main
> installPluginMethods()
> File "/usr/local/scipion/pip/scipion/install/install_plugin.py",
> line 229, in installPluginMethod s
> installed = plugin.installPipModule(version=pluginVersion)
> File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py",
> line 152, in installPipModule
> environment.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 748, in execute
> self._executeTargets(targetList)
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 690, in _executeTargets
> tgt.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 220, in execute
> command.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 160, in execute
> assert glob(t), ("target '%s' not built (after "
> AssertionError: target
> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_
> em_localrec*' not built (after running
> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip in
> stall scipion-em-localrec==3.0.1')
> Error at main: target
> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_e
> m_localrec*' not built (after running
> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip ins
> tall scipion-em-localrec==3.0.1')
>
> ==================================================================================
>
> Any idea to fix this?
>
> Thanks for help.
> Ibrahim
> ------------------------------------------------------------------------
> *From:* pc...@cn... <pc...@cn...>
> *Sent:* Saturday, October 24, 2020 11:56 PM
> *To:* Mailing list for Scipion users
> <sci...@li...>
> *Cc:* Carnegie, Mike Scott <mz...@ps...>
> *Subject:* Re: [scipion-users] problem installing scipion3
> Hi, I'm sorry about you poor experience installing the plugin
>
> Can you try:
>
> scipion3 python -m pip uninstall scipion-em-localrec
>
> And then:
>
> scipion3 installs -p scipion-em-localrec
>
> ?
> Then we can also check what is wrong with bumpy.
>
> All the best, Pablo.
>
> El 24 oct. 2020 2:12, "Moustafa, Ibrahim M." <ri...@ps...> escribió:
>
> Dear All,
>
> We are having so much trouble installing Scipion 3. We
> thought it went through installation but then it complained
> about xmipp because of conflict between numpy-1.19.1
> (installed with OpenCV) and numpy-1.18.4 (installed from pip).
> None of the plugins seem to be properly installed when we
> tried, although it showed "Successfully Finished' in the log!
>
> Trying to install localrec-em showed the following error:
>
> ===========================================================================================
> >scipion3 installp -p scipion-em-localrec
> /usr/local/miniconda/envs/.scipion3env/bin/python -m pip
> install scipion-em-localrec==3.0.1
> Collecting scipion-em-localrec==3.0.1
> Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
> Installing collected packages: scipion-em-localrec
> Successfully installed scipion-em-localrec-3.0.1
> WARNING: Target directory
> /usr/local/scipion/pip/scipion_em_localrec-3.0.1.dist-info
> already exists. Specify --upgrade to force replacement.
> WARNING: Target directory /usr/local/scipion/pip/localrec
> already exists. Specify --upgrade to force replacement.
> Traceback (most recent call last):
> File "/usr/local/scipion/pip/scipion/__main__.py", line 453,
> in <module>
> main()
> File "/usr/local/scipion/pip/scipion/__main__.py", line 296,
> in main
> installPluginMethods()
> File
> "/usr/local/scipion/pip/scipion/install/install_plugin.py",
> line 229, in installPluginMethods
> installed = plugin.installPipModule(version=pluginVersion)
> File
> "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line
> 152, in installPipModule
> environment.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 748, in execute
> self._executeTargets(targetList)
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 690, in _executeTargets
> tgt.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 220, in execute
> command.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 160, in execute
> assert glob(t), ("target '%s' not built (after "
> AssertionError: target
> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*'
> not built (after running
> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip
> install scipion-em-localrec==3.0.1')
> Error at main: target
> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*'
> not built (after running
> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip
> install scipion-em-localrec==3.0.1')
> ==================================================================================
>
> Not sure what we are doing wrong! It would be appreciated
> if someone can share a "clear" protocol of how to properly
> install Scipion 3 along with plugins. We are mostly interested in
> localrec plugin.
>
> P.S. we are using py3.8 from miniconda
>
> Appreciate your help,
> Ibrahim
>
> Ibrahim M.Moustafa, Ph.D.
> Pennsylvania State University
> Biochemistry & Molecular Biology Dept.
> Millennium Science Complex
> University Park
> State College, PA16802
>
> Phone: (814) 863 5940
> Fax: (814) 865 7927
>
>
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Pablo C. <pc...@cn...> - 2020-10-27 08:46:14
|
One more thing! Do you have write permissions in
/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages ?
On 27/10/20 7:18, pc...@cn... wrote:
> What gives you:
>
> ls -l
> /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_
> em_
>
> El 26 oct. 2020 17:57, "Moustafa, Ibrahim M." <ri...@ps...> escribió:
>
> Hi Pablo,
>
> Thanks for your reply.
>
> I tried your suggestions and I got the following error:
>
> ==================================================================================
> Scipion v3.0.5 () devel
> Building scipion-em-localrec ...
> /usr/local/miniconda/envs/.scipion3env/bin/python -m pip install
> scipion-em-localrec==3.0.1
> Collecting scipion-em-localrec==3.0.1
> Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
> Installing collected packages: scipion-em-localrec
> Successfully installed scipion-em-localrec-3.0.1
> Traceback (most recent call last):
> File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in
> <module>
> main()
> File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main
> installPluginMethods()
> File "/usr/local/scipion/pip/scipion/install/install_plugin.py",
> line 229, in installPluginMethod s
> installed = plugin.installPipModule(version=pluginVersion)
> File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py",
> line 152, in installPipModule
> environment.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 748, in execute
> self._executeTargets(targetList)
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 690, in _executeTargets
> tgt.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 220, in execute
> command.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 160, in execute
> assert glob(t), ("target '%s' not built (after "
> AssertionError: target
> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_
> em_localrec*' not built (after running
> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip in stall
> scipion-em-localrec==3.0.1')
> Error at main: target
> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_e
> m_localrec*' not built (after running
> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip ins tall
> scipion-em-localrec==3.0.1')
>
> ==================================================================================
>
> Any idea to fix this?
>
> Thanks for help.
> Ibrahim
> ------------------------------------------------------------------------
> *From:* pc...@cn... <pc...@cn...>
> *Sent:* Saturday, October 24, 2020 11:56 PM
> *To:* Mailing list for Scipion users
> <sci...@li...>
> *Cc:* Carnegie, Mike Scott <mz...@ps...>
> *Subject:* Re: [scipion-users] problem installing scipion3
> Hi, I'm sorry about you poor experience installing the plugin
>
> Can you try:
>
> scipion3 python -m pip uninstall scipion-em-localrec
>
> And then:
>
> scipion3 installs -p scipion-em-localrec
>
> ?
> Then we can also check what is wrong with bumpy.
>
> All the best, Pablo.
>
> El 24 oct. 2020 2:12, "Moustafa, Ibrahim M." <ri...@ps...> escribió:
>
> Dear All,
>
> We are having so much trouble installing Scipion 3. We
> thought it went through installation but then it complained
> about xmipp because of conflict between numpy-1.19.1
> (installed with OpenCV) and numpy-1.18.4 (installed from pip).
> None of the plugins seem to be properly installed when we
> tried, although it showed "Successfully Finished' in the log!
>
> Trying to install localrec-em showed the following error:
>
> ===========================================================================================
> >scipion3 installp -p scipion-em-localrec
> /usr/local/miniconda/envs/.scipion3env/bin/python -m pip
> install scipion-em-localrec==3.0.1
> Collecting scipion-em-localrec==3.0.1
> Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
> Installing collected packages: scipion-em-localrec
> Successfully installed scipion-em-localrec-3.0.1
> WARNING: Target directory
> /usr/local/scipion/pip/scipion_em_localrec-3.0.1.dist-info
> already exists. Specify --upgrade to force replacement.
> WARNING: Target directory /usr/local/scipion/pip/localrec
> already exists. Specify --upgrade to force replacement.
> Traceback (most recent call last):
> File "/usr/local/scipion/pip/scipion/__main__.py", line 453,
> in <module>
> main()
> File "/usr/local/scipion/pip/scipion/__main__.py", line 296,
> in main
> installPluginMethods()
> File
> "/usr/local/scipion/pip/scipion/install/install_plugin.py",
> line 229, in installPluginMethods
> installed = plugin.installPipModule(version=pluginVersion)
> File
> "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line
> 152, in installPipModule
> environment.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 748, in execute
> self._executeTargets(targetList)
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 690, in _executeTargets
> tgt.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 220, in execute
> command.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 160, in execute
> assert glob(t), ("target '%s' not built (after "
> AssertionError: target
> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*'
> not built (after running
> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip
> install scipion-em-localrec==3.0.1')
> Error at main: target
> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*'
> not built (after running
> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip
> install scipion-em-localrec==3.0.1')
> ==================================================================================
>
> Not sure what we are doing wrong! It would be appreciated
> if someone can share a "clear" protocol of how to properly
> install Scipion 3 along with plugins. We are mostly interested in
> localrec plugin.
>
> P.S. we are using py3.8 from miniconda
>
> Appreciate your help,
> Ibrahim
>
> Ibrahim M.Moustafa, Ph.D.
> Pennsylvania State University
> Biochemistry & Molecular Biology Dept.
> Millennium Science Complex
> University Park
> State College, PA16802
>
> Phone: (814) 863 5940
> Fax: (814) 865 7927
>
>
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Moustafa, I. M. <ri...@ps...> - 2020-10-27 07:29:21
|
ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em
gives nothing.
The following packages exist in
ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/
brotli
brotlipy-0.7.0-py3.8.egg-info
certifi
certifi-2020.6.20-py3.8.egg-info
cffi
cffi-1.14.3.dist-info
_cffi_backend.cpython-38-x86_64-linux-gnu.so
chardet
chardet-3.0.4.dist-info
cryptography
cryptography-3.1.1.dist-info
_distutils_hack
distutils-precedence.pth
easy_install.py
idna
idna-2.10.dist-info
OpenSSL
pip
pip-20.2.4-py3.8.egg-info
pkg_resources
__pycache__
pycparser
pycparser-2.20.dist-info
pyOpenSSL-19.1.0.dist-info
PySocks-1.7.1.dist-info
README.txt
requests
requests-2.24.0.dist-info
SConse--(71%)
scons-3.1.2-py3.8.egg-info
setuptools
setuptools-50.3.0.post20201006-py3.8.egg-info
six-1.15.0.dist-info
six.py
sockshandler.py
socks.py
urllib3
urllib3-1.25.11.dist-info
wheel
wheel-0.35.1-py3.6.egg-info
Ibrahim
________________________________
From: pc...@cn... <pc...@cn...>
Sent: Tuesday, October 27, 2020 2:18 AM
To: Mailing list for Scipion users <sci...@li...>
Subject: Re: [scipion-users] problem installing scipion3
What gives you:
ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_ em_
El 26 oct. 2020 17:57, "Moustafa, Ibrahim M." <ri...@ps...> escribió:
Hi Pablo,
Thanks for your reply.
I tried your suggestions and I got the following error:
==================================================================================
Scipion v3.0.5 () devel
Building scipion-em-localrec ...
/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1
Collecting scipion-em-localrec==3.0.1
Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
Installing collected packages: scipion-em-localrec
Successfully installed scipion-em-localrec-3.0.1
Traceback (most recent call last):
File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module>
main()
File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main
installPluginMethods()
File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethod s
installed = plugin.installPipModule(version=pluginVersion)
File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule
environment.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute
command.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_ em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip in stall scipion-em-localrec==3.0.1')
Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_e m_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip ins tall scipion-em-localrec==3.0.1')
==================================================================================
Any idea to fix this?
Thanks for help.
Ibrahim
________________________________
From: pc...@cn... <pc...@cn...>
Sent: Saturday, October 24, 2020 11:56 PM
To: Mailing list for Scipion users <sci...@li...>
Cc: Carnegie, Mike Scott <mz...@ps...>
Subject: Re: [scipion-users] problem installing scipion3
Hi, I'm sorry about you poor experience installing the plugin
Can you try:
scipion3 python -m pip uninstall scipion-em-localrec
And then:
scipion3 installs -p scipion-em-localrec
?
Then we can also check what is wrong with bumpy.
All the best, Pablo.
El 24 oct. 2020 2:12, "Moustafa, Ibrahim M." <ri...@ps...> escribió:
Dear All,
We are having so much trouble installing Scipion 3. We thought it went through installation but then it complained about xmipp because of conflict between numpy-1.19.1 (installed with OpenCV) and numpy-1.18.4 (installed from pip). None of the plugins seem to be properly installed when we tried, although it showed "Successfully Finished' in the log!
Trying to install localrec-em showed the following error:
===========================================================================================
>scipion3 installp -p scipion-em-localrec
/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1
Collecting scipion-em-localrec==3.0.1
Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
Installing collected packages: scipion-em-localrec
Successfully installed scipion-em-localrec-3.0.1
WARNING: Target directory /usr/local/scipion/pip/scipion_em_localrec-3.0.1.dist-info already exists. Specify --upgrade to force replacement.
WARNING: Target directory /usr/local/scipion/pip/localrec already exists. Specify --upgrade to force replacement.
Traceback (most recent call last):
File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module>
main()
File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main
installPluginMethods()
File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethods
installed = plugin.installPipModule(version=pluginVersion)
File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule
environment.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute
command.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')
Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')
==================================================================================
Not sure what we are doing wrong! It would be appreciated if someone can share a "clear" protocol of how to properly install Scipion 3 along with plugins. We are mostly interested in
localrec plugin.
P.S. we are using py3.8 from miniconda
Appreciate your help,
Ibrahim
Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
Millennium Science Complex
University Park
State College, PA16802
Phone: (814) 863 5940
Fax: (814) 865 7927
|
|
From: <pc...@cn...> - 2020-10-27 06:25:08
|
<div dir='auto'>What gives you:<div dir="auto"><br></div><div dir="auto">ls -l <span style="font-family: calibri, arial, helvetica, sans-serif; font-size: 16px;">/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_ em_</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">El 26 oct. 2020 17:57, "Moustafa, Ibrahim M." <ri...@ps...> escribió:<br type="attribution" /><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Hi Pablo,</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Thanks for your reply.</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> I tried your suggestions and I got the following error:</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> ==================================================================================</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Scipion v3.0.5 () devel <div>Building scipion-em-localrec ...</div> <div>/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1</div> <div>Collecting scipion-em-localrec==3.0.1</div> <div> Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)</div> <div>Installing collected packages: scipion-em-localrec</div> <div>Successfully installed scipion-em-localrec-3.0.1</div> <div>Traceback (most recent call last):</div> <div> File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module></div> <div> main()</div> <div> File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main</div> <div> installPluginMethods()</div> <div> File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethod s</div> <div> installed = plugin.installPipModule(version=pluginVersion)</div> <div> File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule</div> <div> environment.execute()</div> <div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute</div> <div> self._executeTargets(targetList)</div> <div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets</div> <div> tgt.execute()</div> <div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute</div> <div> command.execute()</div> <div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute</div> <div> assert glob(t), ("target '%s' not built (after "</div> <div>AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_ em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip in stall scipion-em-localrec==3.0.1')</div> <div>Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_e m_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip ins tall scipion-em-localrec==3.0.1')</div> <br /> ==================================================================================</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Any idea to fix this?</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Thanks for help.</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Ibrahim</div> <div></div> <hr style="display:inline-block;width:98%" /> <div dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> pconesa@cnb.csic.es <pconesa@cnb.csic.es><br /> <b>Sent:</b> Saturday, October 24, 2020 11:56 PM<br /> <b>To:</b> Mailing list for Scipion users <scipion-users@lists.sourceforge.net><br /> <b>Cc:</b> Carnegie, Mike Scott <mzc5001@psu.edu><br /> <b>Subject:</b> Re: [scipion-users] problem installing scipion3</font> <div> </div> </div> <div> <div dir="auto"> <div>Hi, I'm sorry about you poor experience installing the plugin <div dir="auto"><br /> </div> <div dir="auto">Can you try:</div> <div dir="auto"><br /> </div> <div dir="auto">scipion3 python -m pip uninstall scipion-em-localrec</div> <div dir="auto"><br /> </div> <div dir="auto">And then:</div> <div dir="auto"><br /> </div> <div dir="auto">scipion3 installs -p scipion-em-localrec</div> <br /> <div dir="auto">?</div> <div dir="auto">Then we can also check what is wrong with bumpy.</div> <div dir="auto"><br /> </div> <div dir="auto">All the best, Pablo.</div> <div><br /> <div>El 24 oct. 2020 2:12, "Moustafa, Ibrahim M." <ria2@psu.edu> escribió:<br type="attribution" /> <blockquote style="margin:0 0 0 0.8ex;border-left:1px #ccc solid;padding-left:1ex"> <div dir="ltr"> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Dear All,</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> We are having so much trouble installing Scipion 3. We thought it went through installation but then it complained about xmipp because of conflict between numpy-1.19.1 (installed with OpenCV) and numpy-1.18.4 (installed from pip). None of the plugins seem to be properly installed when we tried, although it showed "Successfully Finished' in the log!</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Trying to install localrec-em showed the following error:</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> ===========================================================================================</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> >scipion3 installp -p scipion-em-localrec</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> /usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1 <div>Collecting scipion-em-localrec==3.0.1</div> <div> Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)</div> <div>Installing collected packages: scipion-em-localrec</div> <div>Successfully installed scipion-em-localrec-3.0.1</div> <div>WARNING: Target directory /usr/local/scipion/pip/scipion_em_localrec-3.0.1.dist-info already exists. Specify --upgrade to force replacement.</div> <div>WARNING: Target directory /usr/local/scipion/pip/localrec already exists. Specify --upgrade to force replacement.</div> <div>Traceback (most recent call last):</div> <div> File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module></div> <div> main()</div> <div> File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main</div> <div> installPluginMethods()</div> <div> File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethods</div> <div> installed = plugin.installPipModule(version=pluginVersion)</div> <div> File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule</div> <div> environment.execute()</div> <div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute</div> <div> self._executeTargets(targetList)</div> <div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets</div> <div> tgt.execute()</div> <div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute</div> <div> command.execute()</div> <div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute</div> <div> assert glob(t), ("target '%s' not built (after "</div> <div>AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')</div> Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')<br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> ==================================================================================</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Not sure what we are doing wrong! It would be appreciated if someone can share a "clear" protocol of how to properly install Scipion 3 along with plugins. We are mostly interested in </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> localrec plugin.</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> P.S. we are using py3.8 from miniconda</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Appreciate your help,</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Ibrahim</div> <div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div> <div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <div style="color:rgb( 34 , 34 , 34 );font-family:'arial' , 'helvetica' , sans-serif;font-size:small;background-color:rgb( 255 , 255 , 255 )"> <span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Ibrahim M.Moustafa, Ph.D.</span><br /> <span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Pennsylvania State University</span><br /> </div> <div style="color:rgb( 34 , 34 , 34 );font-family:'arial' , 'helvetica' , sans-serif;font-size:small;background-color:rgb( 255 , 255 , 255 )"> <span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Biochemistry & Molecular Biology Dept.</span></div> <div style="color:rgb( 34 , 34 , 34 );font-family:'arial' , 'helvetica' , sans-serif;font-size:small;background-color:rgb( 255 , 255 , 255 )"> <span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Millennium Science Complex </span><br /> <span style="font-family:'comic sans ms' , 'chalkboard' , cursive">University Park</span><br /> <span style="font-family:'comic sans ms' , 'chalkboard' , cursive">State College, PA16802</span><br /> <br /> <span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Phone: (814) 863 5940</span><br /> <span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Fax: (814) 865 7927</span></div> <br /> </div> </div> </div> </div> </div> </blockquote> </div> <br /> </div> </div> </div> </div> </div> </blockquote></div><br></div> |
|
From: Moustafa, I. M. <ri...@ps...> - 2020-10-26 19:32:12
|
Hi Pablo,
Thanks for your reply.
I tried your suggestions and I got the following error:
==================================================================================
Scipion v3.0.5 () devel
Building scipion-em-localrec ...
/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1
Collecting scipion-em-localrec==3.0.1
Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
Installing collected packages: scipion-em-localrec
Successfully installed scipion-em-localrec-3.0.1
Traceback (most recent call last):
File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module>
main()
File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main
installPluginMethods()
File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethod s
installed = plugin.installPipModule(version=pluginVersion)
File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule
environment.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute
command.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_ em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip in stall scipion-em-localrec==3.0.1')
Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_e m_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip ins tall scipion-em-localrec==3.0.1')
==================================================================================
Any idea to fix this?
Thanks for help.
Ibrahim
________________________________
From: pc...@cn... <pc...@cn...>
Sent: Saturday, October 24, 2020 11:56 PM
To: Mailing list for Scipion users <sci...@li...>
Cc: Carnegie, Mike Scott <mz...@ps...>
Subject: Re: [scipion-users] problem installing scipion3
Hi, I'm sorry about you poor experience installing the plugin
Can you try:
scipion3 python -m pip uninstall scipion-em-localrec
And then:
scipion3 installs -p scipion-em-localrec
?
Then we can also check what is wrong with bumpy.
All the best, Pablo.
El 24 oct. 2020 2:12, "Moustafa, Ibrahim M." <ri...@ps...> escribió:
Dear All,
We are having so much trouble installing Scipion 3. We thought it went through installation but then it complained about xmipp because of conflict between numpy-1.19.1 (installed with OpenCV) and numpy-1.18.4 (installed from pip). None of the plugins seem to be properly installed when we tried, although it showed "Successfully Finished' in the log!
Trying to install localrec-em showed the following error:
===========================================================================================
>scipion3 installp -p scipion-em-localrec
/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1
Collecting scipion-em-localrec==3.0.1
Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
Installing collected packages: scipion-em-localrec
Successfully installed scipion-em-localrec-3.0.1
WARNING: Target directory /usr/local/scipion/pip/scipion_em_localrec-3.0.1.dist-info already exists. Specify --upgrade to force replacement.
WARNING: Target directory /usr/local/scipion/pip/localrec already exists. Specify --upgrade to force replacement.
Traceback (most recent call last):
File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module>
main()
File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main
installPluginMethods()
File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethods
installed = plugin.installPipModule(version=pluginVersion)
File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule
environment.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute
command.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')
Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')
==================================================================================
Not sure what we are doing wrong! It would be appreciated if someone can share a "clear" protocol of how to properly install Scipion 3 along with plugins. We are mostly interested in
localrec plugin.
P.S. we are using py3.8 from miniconda
Appreciate your help,
Ibrahim
Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
Millennium Science Complex
University Park
State College, PA16802
Phone: (814) 863 5940
Fax: (814) 865 7927
|
|
From: <pc...@cn...> - 2020-10-25 03:56:59
|
<div dir='auto'><div>Hi, I'm sorry about you poor experience installing the plugin<div dir="auto"><br></div><div dir="auto">Can you try:</div><div dir="auto"><br></div><div dir="auto">scipion3 python -m pip uninstall scipion-em-localrec</div><div dir="auto"><br></div><div dir="auto">And then:</div><div dir="auto"><br></div><div dir="auto">scipion3 installs -p scipion-em-localrec</div><br><div class="gmail_extra" dir="auto">?</div><div class="gmail_extra" dir="auto">Then we can also check what is wrong with bumpy.</div><div class="gmail_extra" dir="auto"><br></div><div class="gmail_extra" dir="auto">All the best, Pablo.</div><div class="gmail_extra"><br><div class="gmail_quote">El 24 oct. 2020 2:12, "Moustafa, Ibrahim M." <ri...@ps...> escribió:<br type="attribution"><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
Dear All,</div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
<br>
</div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
We are having so much trouble installing Scipion 3. We thought it went through installation but then it complained about xmipp because of conflict between numpy-1.19.1 (installed with OpenCV) and numpy-1.18.4 (installed from pip). None of the plugins seem
to be properly installed when we tried, although it showed "Successfully Finished' in the log!</div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
<br>
</div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
Trying to install localrec-em showed the following error:</div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
<br>
</div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
===========================================================================================</div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
>scipion3 installp -p scipion-em-localrec</div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1
<div>Collecting scipion-em-localrec==3.0.1</div>
<div> Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)</div>
<div>Installing collected packages: scipion-em-localrec</div>
<div>Successfully installed scipion-em-localrec-3.0.1</div>
<div>WARNING: Target directory /usr/local/scipion/pip/scipion_em_localrec-3.0.1.dist-info already exists. Specify --upgrade to force replacement.</div>
<div>WARNING: Target directory /usr/local/scipion/pip/localrec already exists. Specify --upgrade to force replacement.</div>
<div>Traceback (most recent call last):</div>
<div> File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module></div>
<div> main()</div>
<div> File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main</div>
<div> installPluginMethods()</div>
<div> File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethods</div>
<div> installed = plugin.installPipModule(version=pluginVersion)</div>
<div> File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule</div>
<div> environment.execute()</div>
<div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute</div>
<div> self._executeTargets(targetList)</div>
<div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets</div>
<div> tgt.execute()</div>
<div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute</div>
<div> command.execute()</div>
<div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute</div>
<div> assert glob(t), ("target '%s' not built (after "</div>
<div>AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')</div>
Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')<br>
</div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
==================================================================================</div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
<br>
</div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
Not sure what we are doing wrong! It would be appreciated if someone can share a "clear" protocol of how to properly install Scipion 3 along with plugins. We are mostly interested in </div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
localrec plugin.</div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
<br>
</div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
P.S. we are using py3.8 from miniconda</div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
<br>
</div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
Appreciate your help,</div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
Ibrahim</div>
<div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
<br>
</div>
<div>
<div>
<div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )">
<div style="color:rgb( 34 , 34 , 34 );font-family:'arial' , 'helvetica' , sans-serif;font-size:small;background-color:rgb( 255 , 255 , 255 )">
<span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Ibrahim M.Moustafa, Ph.D.</span><br>
<span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Pennsylvania State University</span><br>
</div>
<div style="color:rgb( 34 , 34 , 34 );font-family:'arial' , 'helvetica' , sans-serif;font-size:small;background-color:rgb( 255 , 255 , 255 )">
<span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Biochemistry & Molecular Biology Dept.</span></div>
<div style="color:rgb( 34 , 34 , 34 );font-family:'arial' , 'helvetica' , sans-serif;font-size:small;background-color:rgb( 255 , 255 , 255 )">
<span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Millennium Science Complex </span><br>
<span style="font-family:'comic sans ms' , 'chalkboard' , cursive">University Park</span><br>
<span style="font-family:'comic sans ms' , 'chalkboard' , cursive">State College, PA16802</span><br>
<br>
<span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Phone: (814) 863 5940</span><br>
<span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Fax: (814) 865 7927</span></div>
<br>
</div>
</div>
</div>
</div>
</div>
</blockquote></div><br></div></div></div> |
|
From: Moustafa, I. M. <ri...@ps...> - 2020-10-24 00:27:17
|
Dear All,
We are having so much trouble installing Scipion 3. We thought it went through installation but then it complained about xmipp because of conflict between numpy-1.19.1 (installed with OpenCV) and numpy-1.18.4 (installed from pip). None of the plugins seem to be properly installed when we tried, although it showed "Successfully Finished' in the log!
Trying to install localrec-em showed the following error:
===========================================================================================
>scipion3 installp -p scipion-em-localrec
/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1
Collecting scipion-em-localrec==3.0.1
Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
Installing collected packages: scipion-em-localrec
Successfully installed scipion-em-localrec-3.0.1
WARNING: Target directory /usr/local/scipion/pip/scipion_em_localrec-3.0.1.dist-info already exists. Specify --upgrade to force replacement.
WARNING: Target directory /usr/local/scipion/pip/localrec already exists. Specify --upgrade to force replacement.
Traceback (most recent call last):
File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module>
main()
File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main
installPluginMethods()
File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethods
installed = plugin.installPipModule(version=pluginVersion)
File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule
environment.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute
command.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')
Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')
==================================================================================
Not sure what we are doing wrong! It would be appreciated if someone can share a "clear" protocol of how to properly install Scipion 3 along with plugins. We are mostly interested in
localrec plugin.
P.S. we are using py3.8 from miniconda
Appreciate your help,
Ibrahim
Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
Millennium Science Complex
University Park
State College, PA16802
Phone: (814) 863 5940
Fax: (814) 865 7927
|
|
From: Moustafa, I. M. <ri...@ps...> - 2020-10-24 00:12:05
|
Dear All, We just installed Scipion3 and now trying to install plugins through the plugin manager. For deepLearningToolKit plugin, it went through compiling and stuck at "Downloading pre-trained models...". Not sure if it is progressing or something wrong with the installation; waited over 2 hrs and still showing the same message! Any idea how to fix this? check the downloads? Thanks in advance for your help. Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. Millennium Science Complex University Park State College, PA16802 Phone: (814) 863 5940 Fax: (814) 865 7927 |
|
From: Pablo C. <pc...@cn...> - 2020-10-20 15:48:50
|
wow! good to know it can be fast with 10GB (not available in some machines) On 20/10/20 17:26, Dmitry Semchonok wrote: > Thank you Pablo - I put 10 Gb and it opened immediately! > > Kind regards, > Dmitry > > >> On 20. Oct 2020, at 17:05, Pablo Conesa <pc...@cn... >> <mailto:pc...@cn...>> wrote: >> >> Try to increase the memory using the config file and giving more >> memory to JAVA: >> >> JAVA_MAX_MEMORY = 3 >> >> Note: units are in GB --> 3 equals 3GB of RAM >> >> I've seen the viewer coping with 8M particles but taking ages to >> load, so if there is no error, wait! >> >> >> Another option would be to use "split set" to split the set in >> smaller ones and review them and then join. >> >> >> Cheers! >> >> >> On 20/10/20 16:52, Dmitry Semchonok wrote: >>> One more small question — >>> >>> >>> I have 5 000 000 particles and java fails while opening the result >>> of relion 2D. >>> >>> Any idea how to get the classes/particles that I want? >>> >>> Thank you! >>> >>> >>> Sincerely, >>> Dmitry >>> >>> >>> ERROR loading project: scratch >>> Project database not found at >>> '/home/user/Data/ScipionUserData/projects/scratch/project.sqlite' >>> >>> java -Xmx2g -d64 >>> -Djava.library.path=/usr/local/scipion/software/em/xmipp/lib >>> -Dplugins.dir=/usr/local/scipion/software/em/xmipp/bindings/java/imagej/plugins >>> -cp >>> /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.242.b08-0.el7_7.x86_64/lib/*:/usr/local/scipion/software/em/xmipp/bindings/java/imagej/*:/usr/local/scipion/software/em/xmipp/bindings/java/lib/* >>> xmipp.viewer.scipion.ScipionViewer -i >>> "Runs/001802_ProtRelionClassify2D/classes2D.sqlite" --render >>> _representative._filename --labels id _size --zoom 152 --visible >>> enabled id _size _representative._filename _rlnclassDistribution >>> _rlnAccuracyRotations _rlnAccuracyTranslations --sortby _size desc >>> --order enabled id _size _representative._filename >>> _rlnclassDistribution _rlnAccuracyRotations _rlnAccuracyTranslations >>> --scipion 57898 1802 1712 >>> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space >>> at java.util.Arrays.copyOfRange(Arrays.java:3664) >>> at java.lang.String.<init>(String.java:207) >>> at java.lang.String.toUpperCase(String.java:2810) >>> at java.lang.String.toUpperCase(String.java:2833) >>> at org.sqlite.RS.findColumn(RS.java:163) >>> at org.sqlite.RS.getInt(RS.java:527) >>> at >>> xmipp.viewer.scipion.ScipionMetaData.loadValues(ScipionMetaData.java:207) >>> at >>> xmipp.viewer.scipion.ScipionMetaData.loadData(ScipionMetaData.java:151) >>> at xmipp.viewer.scipion.ScipionMetaData.<init>(ScipionMetaData.java:91) >>> at xmipp.viewer.scipion.ScipionMetaData.<init>(ScipionMetaData.java:68) >>> at >>> xmipp.viewer.windows.ImagesWindowFactory.openScipionMetadata(ImagesWindowFactory.java:223) >>> at xmipp.viewer.scipion.ScipionViewer.openFile(ScipionViewer.java:71) >>> at xmipp.viewer.scipion.ScipionViewer.main(ScipionViewer.java:52) >>> >>> >>> >>> _______________________________________________ >>> 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... >> <mailto: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: Dmitry S. <Sem...@gm...> - 2020-10-20 15:26:37
|
Thank you Pablo - I put 10 Gb and it opened immediately! Kind regards, Dmitry > On 20. Oct 2020, at 17:05, Pablo Conesa <pc...@cn...> wrote: > > Try to increase the memory using the config file and giving more memory to JAVA: > > JAVA_MAX_MEMORY = 3 > > Note: units are in GB --> 3 equals 3GB of RAM > > I've seen the viewer coping with 8M particles but taking ages to load, so if there is no error, wait! > > > > Another option would be to use "split set" to split the set in smaller ones and review them and then join. > > > > Cheers! > > > > On 20/10/20 16:52, Dmitry Semchonok wrote: >> One more small question — >> >> >> I have 5 000 000 particles and java fails while opening the result of relion 2D. >> >> Any idea how to get the classes/particles that I want? >> >> Thank you! >> >> >> Sincerely, >> Dmitry >> >> >> ERROR loading project: scratch >> Project database not found at '/home/user/Data/ScipionUserData/projects/scratch/project.sqlite' >> >> java -Xmx2g -d64 -Djava.library.path=/usr/local/scipion/software/em/xmipp/lib -Dplugins.dir=/usr/local/scipion/software/em/xmipp/bindings/java/imagej/plugins -cp /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.242.b08-0.el7_7.x86_64/lib/*:/usr/local/scipion/software/em/xmipp/bindings/java/imagej/*:/usr/local/scipion/software/em/xmipp/bindings/java/lib/* xmipp.viewer.scipion.ScipionViewer -i "Runs/001802_ProtRelionClassify2D/classes2D.sqlite" --render _representative._filename --labels id _size --zoom 152 --visible enabled id _size _representative._filename _rlnclassDistribution _rlnAccuracyRotations _rlnAccuracyTranslations --sortby _size desc --order enabled id _size _representative._filename _rlnclassDistribution _rlnAccuracyRotations _rlnAccuracyTranslations --scipion 57898 1802 1712 >> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space >> at java.util.Arrays.copyOfRange(Arrays.java:3664) >> at java.lang.String.<init>(String.java:207) >> at java.lang.String.toUpperCase(String.java:2810) >> at java.lang.String.toUpperCase(String.java:2833) >> at org.sqlite.RS.findColumn(RS.java:163) >> at org.sqlite.RS.getInt(RS.java:527) >> at xmipp.viewer.scipion.ScipionMetaData.loadValues(ScipionMetaData.java:207) >> at xmipp.viewer.scipion.ScipionMetaData.loadData(ScipionMetaData.java:151) >> at xmipp.viewer.scipion.ScipionMetaData.<init>(ScipionMetaData.java:91) >> at xmipp.viewer.scipion.ScipionMetaData.<init>(ScipionMetaData.java:68) >> at xmipp.viewer.windows.ImagesWindowFactory.openScipionMetadata(ImagesWindowFactory.java:223) >> at xmipp.viewer.scipion.ScipionViewer.openFile(ScipionViewer.java:71) >> at xmipp.viewer.scipion.ScipionViewer.main(ScipionViewer.java:52) >> >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users <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...> - 2020-10-20 15:05:31
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Try to increase the memory using the config file and giving more memory to JAVA: JAVA_MAX_MEMORY = 3 Note: units are in GB --> 3 equals 3GB of RAM I've seen the viewer coping with 8M particles but taking ages to load, so if there is no error, wait! Another option would be to use "split set" to split the set in smaller ones and review them and then join. Cheers! On 20/10/20 16:52, Dmitry Semchonok wrote: > One more small question — > > > I have 5 000 000 particles and java fails while opening the result of > relion 2D. > > Any idea how to get the classes/particles that I want? > > Thank you! > > > Sincerely, > Dmitry > > > ERROR loading project: scratch > Project database not found at > '/home/user/Data/ScipionUserData/projects/scratch/project.sqlite' > > java -Xmx2g -d64 > -Djava.library.path=/usr/local/scipion/software/em/xmipp/lib > -Dplugins.dir=/usr/local/scipion/software/em/xmipp/bindings/java/imagej/plugins > -cp > /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.242.b08-0.el7_7.x86_64/lib/*:/usr/local/scipion/software/em/xmipp/bindings/java/imagej/*:/usr/local/scipion/software/em/xmipp/bindings/java/lib/* > xmipp.viewer.scipion.ScipionViewer -i > "Runs/001802_ProtRelionClassify2D/classes2D.sqlite" --render > _representative._filename --labels id _size --zoom 152 --visible > enabled id _size _representative._filename _rlnclassDistribution > _rlnAccuracyRotations _rlnAccuracyTranslations --sortby _size desc > --order enabled id _size _representative._filename > _rlnclassDistribution _rlnAccuracyRotations _rlnAccuracyTranslations > --scipion 57898 1802 1712 > Exception in thread "main" java.lang.OutOfMemoryError: Java heap space > at java.util.Arrays.copyOfRange(Arrays.java:3664) > at java.lang.String.<init>(String.java:207) > at java.lang.String.toUpperCase(String.java:2810) > at java.lang.String.toUpperCase(String.java:2833) > at org.sqlite.RS.findColumn(RS.java:163) > at org.sqlite.RS.getInt(RS.java:527) > at > xmipp.viewer.scipion.ScipionMetaData.loadValues(ScipionMetaData.java:207) > at xmipp.viewer.scipion.ScipionMetaData.loadData(ScipionMetaData.java:151) > at xmipp.viewer.scipion.ScipionMetaData.<init>(ScipionMetaData.java:91) > at xmipp.viewer.scipion.ScipionMetaData.<init>(ScipionMetaData.java:68) > at > xmipp.viewer.windows.ImagesWindowFactory.openScipionMetadata(ImagesWindowFactory.java:223) > at xmipp.viewer.scipion.ScipionViewer.openFile(ScipionViewer.java:71) > at xmipp.viewer.scipion.ScipionViewer.main(ScipionViewer.java:52) > > > > _______________________________________________ > 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: Dmitry S. <Sem...@gm...> - 2020-10-20 14:52:45
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One more small question — I have 5 000 000 particles and java fails while opening the result of relion 2D. Any idea how to get the classes/particles that I want? Thank you! Sincerely, Dmitry ERROR loading project: scratch Project database not found at '/home/user/Data/ScipionUserData/projects/scratch/project.sqlite' java -Xmx2g -d64 -Djava.library.path=/usr/local/scipion/software/em/xmipp/lib -Dplugins.dir=/usr/local/scipion/software/em/xmipp/bindings/java/imagej/plugins -cp /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.242.b08-0.el7_7.x86_64/lib/*:/usr/local/scipion/software/em/xmipp/bindings/java/imagej/*:/usr/local/scipion/software/em/xmipp/bindings/java/lib/* xmipp.viewer.scipion.ScipionViewer -i "Runs/001802_ProtRelionClassify2D/classes2D.sqlite" --render _representative._filename --labels id _size --zoom 152 --visible enabled id _size _representative._filename _rlnclassDistribution _rlnAccuracyRotations _rlnAccuracyTranslations --sortby _size desc --order enabled id _size _representative._filename _rlnclassDistribution _rlnAccuracyRotations _rlnAccuracyTranslations --scipion 57898 1802 1712 Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at java.util.Arrays.copyOfRange(Arrays.java:3664) at java.lang.String.<init>(String.java:207) at java.lang.String.toUpperCase(String.java:2810) at java.lang.String.toUpperCase(String.java:2833) at org.sqlite.RS.findColumn(RS.java:163) at org.sqlite.RS.getInt(RS.java:527) at xmipp.viewer.scipion.ScipionMetaData.loadValues(ScipionMetaData.java:207) at xmipp.viewer.scipion.ScipionMetaData.loadData(ScipionMetaData.java:151) at xmipp.viewer.scipion.ScipionMetaData.<init>(ScipionMetaData.java:91) at xmipp.viewer.scipion.ScipionMetaData.<init>(ScipionMetaData.java:68) at xmipp.viewer.windows.ImagesWindowFactory.openScipionMetadata(ImagesWindowFactory.java:223) at xmipp.viewer.scipion.ScipionViewer.openFile(ScipionViewer.java:71) at xmipp.viewer.scipion.ScipionViewer.main(ScipionViewer.java:52) |
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From: Pablo C. <pc...@cn...> - 2020-10-20 14:49:03
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Yes that is the idea, I'll ask others to put some presentations there. Keep the link! On 20/10/20 16:41, Dmitry Semchonok wrote: > Thank you, Pablo — I have an access and I see your nice presentations! > > If happens some other contributions it will be very educational not > only for me but for the community :) > > Sincerely, > Dmitry > > >> On 20. Oct 2020, at 15:33, Pablo Conesa <pc...@cn... >> <mailto:pc...@cn...>> wrote: >> >> Ok, let's do this. >> >> I've created a "public" folder where anyone should be able to access >> (read only) >> >> https://drive.google.com/drive/folders/1Ued4tMRW31LIepNtcHPoCuVOuMQgXvpj?usp=sharing >> >> I've put some of my recent presentations (none of them will suit you). >> >> But other's might be able to add more. >> >> >> Can you access them? >> >> >> On 20/10/20 15:29, Dmitry Semchonok wrote: >>> Dear Pablo, >>> >>> I am looking for the presentation(s) that includes some theory about >>> image formation, image processing workflow and correspondent steps >>> in the SCIPION. >>> >>> Kind regards, >>> Dmitry >>> >>> >>>> On 20. Oct 2020, at 15:26, Pablo Conesa <pc...@cn... >>>> <mailto:pc...@cn...>> wrote: >>>> >>>> Hi Dmitry! >>>> >>>> We have lots of them but nothing nothing or a few publicly >>>> available (for no special reason). >>>> >>>> What are you exactly looking for? >>>> >>>> On 20/10/20 14:01, Dmitry Semchonok wrote: >>>>> >>>>> Dear colleagues, >>>>> >>>>> >>>>> Small question – >>>>> >>>>> is there a place where I can find the presentations about image >>>>> processing steps in SCIPION (preferably in *pptx format)? >>>>> >>>>> >>>>> Sincerely, >>>>> >>>>> Dmitry >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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... >>>> <mailto: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* >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto: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* |
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