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Re: [scipion-users] Scipion3-install-3Dfsc
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From: 范宏成 <187...@16...> - 2020-08-03 09:23:17
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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 team |
