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Re: [scipion-users] Scipion3-install-3Dfsc
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From: Pablo C. <pc...@cn...> - 2020-08-03 10:49:41
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Maybe manually will work?: cd /home/fanhc/scipion3/software/em/fsc3D-3.0 eval "$(/home/fanhc/anaconda3/bin/conda shell.bash hook)" conda env create -f environment.yml touch IS_INSTALLED On 3/8/20 11:22, 范宏成 wrote: > Hi Pablo > I actviated the conda and reinstalled 3dfsc. The output is: > plugin.log > 00001: Found existing installation: scipion-em-fsc3d 3.0.5 > 00002: Uninstalling scipion-em-fsc3d-3.0.5: > 00003: Successfully uninstalled scipion-em-fsc3d-3.0.5 > 00004: Removing fsc3D-3.0 binaries... > 00005: Binary fsc3D-3.0 has been uninstalled successfully > 00006: Removing scipion-em-fsc3d plugin... > 00007: Processing > /home/fanhc/.cache/pip/wheels/d2/6a/3d/d8105cfbfb2f44c0c79b496cc6f3aa2f9bb2ae6a1a85790608/scipion_em_fsc3d-3.0.5-py3-none-any.whl > 00008: Requirement already satisfied: scipion-em in > ./.scipion3env/lib/python3.6/site-packages (from > scipion-em-fsc3d==3.0.5) (3.0.0) > 00009: Requirement already satisfied: biopython==1.76 in > ./.scipion3env/lib/python3.6/site-packages (from > scipion-em->scipion-em-fsc3d==3.0.5) (1.76) > 00010: Requirement already satisfied: scipion-pyworkflow in > ./.scipion3env/lib/python3.6/site-packages (from > scipion-em->scipion-em-fsc3d==3.0.5) (3.0.0a10) > 00011: Requirement already satisfied: numpy in > ./.scipion3env/lib/python3.6/site-packages (from > biopython==1.76->scipion-em->scipion-em-fsc3d==3.0.5) (1.18.5) > 00012: Requirement already satisfied: psutil in > ./.scipion3env/lib/python3.6/site-packages (from > scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (5.7.0) > 00013: Requirement already satisfied: pillow in > ./.scipion3env/lib/python3.6/site-packages (from > scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (7.1.2) > 00014: Requirement already satisfied: matplotlib in > ./.scipion3env/lib/python3.6/site-packages (from > scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (3.2.2) > 00015: Requirement already satisfied: requests in > ./.scipion3env/lib/python3.6/site-packages (from > scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (2.24.0) > 00016: Requirement already satisfied: configparser in > ./.scipion3env/lib/python3.6/site-packages (from > scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (5.0.0) > 00017: Requirement already satisfied: bibtexparser in > ./.scipion3env/lib/python3.6/site-packages (from > scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (1.2.0) > 00018: Requirement already satisfied: cycler>=0.10 in > ./.scipion3env/lib/python3.6/site-packages (from > matplotlib->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) > (0.10.0) > 00019: Requirement already satisfied: > pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in > ./.scipion3env/lib/python3.6/site-packages (from > matplotlib->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) > (2.4.7) > 00020: Requirement already satisfied: python-dateutil>=2.1 in > ./.scipion3env/lib/python3.6/site-packages (from > matplotlib->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) > (2.8.1) > 00021: Requirement already satisfied: kiwisolver>=1.0.1 in > ./.scipion3env/lib/python3.6/site-packages (from > matplotlib->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) > (1.2.0) > 00022: Requirement already satisfied: certifi>=2017.4.17 in > ./.scipion3env/lib/python3.6/site-packages (from > requests->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) > (2020.4.5.2) > 00023: Requirement already satisfied: idna<3,>=2.5 in > ./.scipion3env/lib/python3.6/site-packages (from > requests->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (2.9) > 00024: Requirement already satisfied: > urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in > ./.scipion3env/lib/python3.6/site-packages (from > requests->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) > (1.25.9) > 00025: Requirement already satisfied: chardet<4,>=3.0.2 in > ./.scipion3env/lib/python3.6/site-packages (from > requests->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (3.0.4) > 00026: Requirement already satisfied: future>=0.16.0 in > ./.scipion3env/lib/python3.6/site-packages (from > bibtexparser->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) > (0.18.2) > 00027: Requirement already satisfied: six in > ./.scipion3env/lib/python3.6/site-packages (from > cycler>=0.10->matplotlib->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) > (1.15.0) > 00028: Installing collected packages: scipion-em-fsc3d > 00029: Successfully installed scipion-em-fsc3d-3.0.5 > 00030: Collecting package metadata (repodata.json): ...working... > 00031: done > 00032: Solving environment: ...working... 00033: done > 00034: 2020-08-03 05:18:21,794 INFO: Error executing the operation: > install scipion-em-fsc3d > 00035: install scipion-em-fsc3d==3.0.5 > 00036: Done (1.25 seconds) > 00037: Building fsc3D-3.0 ... > 00038: Skipping command: wget -nv -c -O > /home/fanhc/scipion3/software/em/fsc3D-3.0.tgz.part > https://github.com/azazellochg/fsc3D/archive/3.0.tar.gz > 00039: mv -v /home/fanhc/scipion3/software/em/fsc3D-3.0.tgz.part > /home/fanhc/scipion3/software/em/fsc3D-3.0.tgz > 00040: All targets exist. > 00041: cd /home/fanhc/scipion3/software/em > 00042: tar -xf fsc3D-3.0.tgz > 00043: cd /home/fanhc/scipion3/software/em/fsc3D-3.0 > 00044: eval "$(/home/fanhc/anaconda3/bin/conda shell.bash > hook)"&&conda env create -f environment.yml &&touch IS_INSTALLED > > plugin.err > 00001: WARNING: You are using pip version 20.1.1; however, version > 20.2 is available. > 00002: You should consider upgrading via the > '/home/fanhc/scipion3/.scipion3env/bin/python -m pip install --upgrade > pip' command. > 00003: /bin/sh: line 80: 22608 Segmentation fault (core dumped) > "$CONDA_EXE" $_CE_M $_CE_CONDA "$cmd" "$@" > 00004: 2020-08-03 05:18:21,794 ERROR: Error executing the > operation: install scipion-em-fsc3d > > Hongcheng Fan > > > > > > 在 2020-08-03 16:33:06，"Pablo Conesa" <pc...@cn...> 写道： > > Hi, you need to tell scipion how to activate conda. > > I've got this in my config file (SCIPION_HOME/config/scipion.conf) > > --------------------------scipin-conf ----------------------- > > [PLUGINS] > CONDA_ACTIVATION_CMD = eval "$(/extra/miniconda3/bin/conda > shell.bash hook)" > > ---------------------------------------------------------------- > > > You will need to modify the path. Please note that this will not > under tcsh/csh shells. > > > On 3/8/20 9:54, 范宏成 wrote: >> Hi all, >> When I installed the 3dfsc in scipion3 plugin >> manager,(cenos7,anaconda3,cuda10.1) I faced some errors. See the >> following: >> plugin.log >> 00001: Found existing installation: scipion-em-fsc3d 3.0.5 >> 00002: Uninstalling scipion-em-fsc3d-3.0.5: >> 00003: Successfully uninstalled scipion-em-fsc3d-3.0.5 >> 00004: Removing fsc3D-3.0 binaries... >> 00005: Binary fsc3D-3.0 has been uninstalled successfully >> 00006: Removing scipion-em-fsc3d plugin... >> 00007: Processing >> /home/fanhc/.cache/pip/wheels/d2/6a/3d/d8105cfbfb2f44c0c79b496cc6f3aa2f9bb2ae6a1a85790608/scipion_em_fsc3d-3.0.5-py3-none-any.whl >> 00008: Requirement already satisfied: scipion-em in >> ./.scipion3env/lib/python3.6/site-packages (from >> scipion-em-fsc3d==3.0.5) (3.0.0) >> 00009: Requirement already satisfied: biopython==1.76 in >> ./.scipion3env/lib/python3.6/site-packages (from >> scipion-em->scipion-em-fsc3d==3.0.5) (1.76) >> 00010: Requirement already satisfied: scipion-pyworkflow in >> ./.scipion3env/lib/python3.6/site-packages (from >> scipion-em->scipion-em-fsc3d==3.0.5) (3.0.0a10) >> 00011: Requirement already satisfied: numpy in >> ./.scipion3env/lib/python3.6/site-packages (from >> biopython==1.76->scipion-em->scipion-em-fsc3d==3.0.5) (1.18.5) >> 00012: Requirement already satisfied: bibtexparser in >> ./.scipion3env/lib/python3.6/site-packages (from >> scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (1.2.0) >> 00013: Requirement already satisfied: pillow in >> ./.scipion3env/lib/python3.6/site-packages (from >> scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (7.1.2) >> 00014: Requirement already satisfied: psutil in >> ./.scipion3env/lib/python3.6/site-packages (from >> scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (5.7.0) >> 00015: Requirement already satisfied: requests in >> ./.scipion3env/lib/python3.6/site-packages (from >> scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (2.24.0) >> 00016: Requirement already satisfied: configparser in >> ./.scipion3env/lib/python3.6/site-packages (from >> scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (5.0.0) >> 00017: Requirement already satisfied: matplotlib in >> ./.scipion3env/lib/python3.6/site-packages (from >> scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (3.2.2) >> 00018: Requirement already satisfied: future>=0.16.0 in >> ./.scipion3env/lib/python3.6/site-packages (from >> bibtexparser->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) >> (0.18.2) >> 00019: Requirement already satisfied: pyparsing>=2.0.3 in >> ./.scipion3env/lib/python3.6/site-packages (from >> bibtexparser->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) >> (2.4.7) >> 00020: Requirement already satisfied: idna<3,>=2.5 in >> ./.scipion3env/lib/python3.6/site-packages (from >> requests->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) >> (2.9) >> 00021: Requirement already satisfied: chardet<4,>=3.0.2 in >> ./.scipion3env/lib/python3.6/site-packages (from >> requests->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) >> (3.0.4) >> 00022: Requirement already satisfied: certifi>=2017.4.17 in >> ./.scipion3env/lib/python3.6/site-packages (from >> requests->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) >> (2020.4.5.2) >> 00023: Requirement already satisfied: >> urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in >> ./.scipion3env/lib/python3.6/site-packages (from >> requests->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) >> (1.25.9) >> 00024: Requirement already satisfied: kiwisolver>=1.0.1 in >> ./.scipion3env/lib/python3.6/site-packages (from >> matplotlib->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) >> (1.2.0) >> 00025: Requirement already satisfied: python-dateutil>=2.1 in >> ./.scipion3env/lib/python3.6/site-packages (from >> matplotlib->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) >> (2.8.1) >> 00026: Requirement already satisfied: cycler>=0.10 in >> ./.scipion3env/lib/python3.6/site-packages (from >> matplotlib->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) >> (0.10.0) >> 00027: Requirement already satisfied: six>=1.5 in >> ./.scipion3env/lib/python3.6/site-packages (from >> python-dateutil>=2.1->matplotlib->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) >> (1.15.0) >> 00028: Installing collected packages: scipion-em-fsc3d >> 00029: Successfully installed scipion-em-fsc3d-3.0.5 >> 00030: Collecting package metadata (repodata.json): >> ...working... 00031: done >> 00032: Solving environment: ...working... 00033: done >> 00034: 2020-08-03 03:48:21,120 INFO: Error executing the >> operation: install scipion-em-fsc3d >> 00035: install scipion-em-fsc3d==3.0.5 >> 00036: Done (1.26 seconds) >> 00037: WARNING!!: CONDA_ACTIVATION_CMD variable not defined. >> Relying on conda being in the PATH >> 00038: Building fsc3D-3.0 ... >> 00039: Skipping command: wget -nv -c -O >> /home/fanhc/scipion3/software/em/fsc3D-3.0.tgz.part >> https://github.com/azazellochg/fsc3D/archive/3.0.tar.gz >> 00040: mv -v >> /home/fanhc/scipion3/software/em/fsc3D-3.0.tgz.part >> /home/fanhc/scipion3/software/em/fsc3D-3.0.tgz >> 00041: All targets exist. >> 00042: cd /home/fanhc/scipion3/software/em >> 00043: tar -xf fsc3D-3.0.tgz >> 00044: cd /home/fanhc/scipion3/software/em/fsc3D-3.0 >> 00045: conda env create -f environment.yml &&touch IS_INSTALLED >> >> plugin.er00001: WARNING: You are using pip version 20.1.1; >> however, version 20.2 is available. >> 00002: You should consider upgrading via the >> '/home/fanhc/scipion3/.scipion3env/bin/python -m pip install >> --upgrade pip' command. >> 00003: /bin/sh: line 1: 17742 Segmentation fault (core dumped) >> conda env create -f environment.yml >> 00004: 2020-08-03 03:48:21,120 ERROR: Error executing the >> operation: install scipion-em-fsc3d >> >> How to fix it? Thank you! >> Hongcheng Fan >> >> >> >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
