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From: Pablo C. <pc...@cn...> - 2020-08-06 13:29:04
|
Hi Hongcheng Fan, You can play with the zoom value to increase the size of the averages. This should give you bigger images and better quality. On 6/8/20 14:38, 范宏成 wrote: > Hi all, > I want to ask a simple question. Can Scipion create the selected > class2d averages pictures for publication? The linux screen capture > tool will create the picture that loses some details. Does anyone have > better ideas? > Thanks a lot > Hongcheng Fan > > > 范宏成 > m18...@16... > > <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=%E8%8C%83%E5%AE%8F%E6%88%90&uid=m18717124574%40163.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fsmfc69753e7457a6e590754a7cd5492c0d.jpg&items=%5B%22m18717124574%40163.com%22%5D> > > 签名由 网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail81> > 定制 > > > _______________________________________________ > 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: 范宏成 <187...@16...> - 2020-08-06 12:38:40
|
Hi all, I want to ask a simple question. Can Scipion create the selected class2d averages pictures for publication? The linux screen capture tool will create the picture that loses some details. Does anyone have better ideas? Thanks a lot Hongcheng Fan | | 范宏成 | | m18...@16... | 签名由网易邮箱大师定制 |
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From: 范宏成 <187...@16...> - 2020-08-03 11:58:49
|
Hi Pablo, The problem has been fixed. Thank you for your advice! Hongcheng Fan | | 范宏成 | | m18...@16... | 签名由网易邮箱大师定制 On 8/3/2020 18:49，Pablo Conesa<pc...@cn...> wrote： 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 team _______________________________________________ scipion-users mailing list sci...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - Madrid Scipion team |
|
From: Pablo C. <pc...@cn...> - 2020-08-03 10:49:41
|
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* |
|
From: 范宏成 <187...@16...> - 2020-08-03 09:23:17
|
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 |
|
From: Pablo C. <pc...@cn...> - 2020-08-03 08:33:20
|
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* |
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From: 范宏成 <187...@16...> - 2020-08-03 07:55:03
|
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 |
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From: Pablo C. <pc...@cn...> - 2020-07-28 14:21:36
|
You mean passing "-c defaults" ?
On 28/7/20 15:57, Grigory Sharov wrote:
> Great!
>
> @Pablo Conesa <mailto:pc...@cn...> I guess we should specify
> to use the defaults channel for installing xmipp libs (fftw hdf5
> libtiff openjdk) inside conda env.
>
> Best regards,
> Grigory
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
>
> MRC Laboratory of Molecular Biology,
> Francis Crick Avenue,
> Cambridge Biomedical Campus,
> Cambridge CB2 0QH, UK.
> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228>
> e-mail: gs...@mr... <mailto:gs...@mr...>
>
>
> On Tue, Jul 28, 2020 at 2:30 PM Lugmayr, Wolfgang <w.l...@uk...
> <mailto:w.l...@uk...>> wrote:
>
> hi,
>
> i made a complete first time install of scipion 3.0.0
>
> thanks the fix worked now the following way:
>
> deleted the target install dir but not the .scipion3env
> conda activate .scipion3env
> conda install hdf5 -c defaults
> python -m scipioninstaller /beegfs/cssb/software/em/scipion/3.0.0
> -j 20
> then the main project selection gui comes up with scipion3
>
> i don't know if its related but maybe it helps to find the problem:
> my ~/.condarc had conda-forge before defaults in the channels list.
>
> and the hdf5 from conda-forge reports:
>
> The following NEW packages will be INSTALLED:
> hdf5 conda-forge/linux-64::hdf5-1.10.6-nompi_h3c11f04_100
> libgfortran-ng
> conda-forge/linux-64::libgfortran-ng-7.5.0-hdf63c60_10
> CondaVerificationError: The package for hdf5 located at
> /beegfs/cssb/software/anaconda3/pkgs/hdf5-1.10.6-nompi_h3c11f04_100
> appears to be corrupted. The path 'bin/h5perf_serial' specified in
> the package manifest cannot be found.
>
> but it workd with the default channel and the following packages:
> hdf5 pkgs/main/linux-64::hdf5-1.10.6-hb1b8bf9_0
> libgfortran-ng pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0
>
> cheers,
> wolfgang
>
> ------------------------------------------------------------------------
> *From: *"Pablo Conesa" <pc...@cn...
> <mailto:pc...@cn...>>
> *To: *"Mailing list for Scipion users"
> <sci...@li...
> <mailto:sci...@li...>>
> *Sent: *Tuesday, 28 July, 2020 13:58:41
> *Subject: *Re: [scipion-users] scipion 3.0.0 / xmippSrc-v3.20.07b1
> / HDF5 linking error
>
> Hi wolfgang,
>
> it seems the installer went for a conda installation
> ("/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib")
>
> xmipp installation, at the beginning should detect the the conda
> environment and trigger the installation of the hdf5 lib and others.
>
> I'm right now realizing the output log of the installation is not
> kept..probably something to do.
>
> Do you, by any change kept the output log of the installation. Or
> maybe triggering the installation again will work to check if
> xmipp was detecting the "conda mode" and trigger
>
>
> One thing you can do is:
>
> 1.- conda activate .scipion3env
>
> 2.- conda install hdf5
>
> 3.- scipion3 installb xmippSrc
>
>
> If other libraries are missing repeat adapting step 2.
>
> It would be great to learn why is not doing this xmipp itself.
>
>
> On 28/7/20 11:21, Lugmayr, Wolfgang wrote:
>
> hi,
>
> i tried to install the (unreleased) scipion3 and came to a hdf5 linking error (full log at end of mail):
>
> /beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
> Some error occurred during the compilation of 'xmipp' ('bin/xmipp_mpi_reconstruct_fourier_accel').
>
> my conda environment contains hdf5
> $ conda list | grep hdf5
> hdf5 1.10.4 hb1b8bf9_0
> but the hidden .scipion3env does not contain one.
>
> do i need the latest hdf5 1.12.0 or is this a buildscript problem?
>
> cheers,
> wolfgang
>
>
>
>
> mpicxx -o lib/libXmippParallelCuda.so -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs -L -shared libraries/parallel_adapt_cuda/mpi_reconstruct_fourier_gpu.os -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp -lXmippInterfaceCuda -lXmippCuda -lcudart -lcufft -lnvidia-ml -lcuFFTAdvisor
> mpicxx -o lib/libXmippParallel.so -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -shared libraries/parallel/mpi_angular_accuracy_pca.os libraries/parallel/mpi_angular_class_average.os libraries/parallel/mpi_angular_continuous_assign.os libraries/parallel/mpi_angular_project_library.os libraries/parallel/mpi_angular_projection_matching.os libraries/parallel/mpi_angular_sph_alignment.os libraries/parallel/mpi_classify_CL2D.os libraries/parallel/mpi_classify_CL2D_core_analysis.os libraries/parallel/mpi_classify_CLTomo_prog.os libraries/parallel/mpi_classify_FTTRI.os libraries/parallel/mpi_image_rotational_pca.os libraries/parallel/mpi_image_sort.os libraries/parallel/mpi_ml_align2d.os libraries/parallel/mpi_multireference_aligneability.os libraries/parallel/mpi_nma_alignment.os libraries/parallel/mpi_nma_alignment_vol.os libraries/parallel/mpi_performance_test.os libraries/parallel/mpi_project_XR.os libraries/parallel/mpi_reconstruct_admm.os libraries/parallel/mpi_reconstruct_art.os libraries/parallel/mpi_reconstruct_fourier.os libraries/parallel/mpi_reconstruct_fourier_accel.os libraries/parallel/mpi_reconstruct_significant.os libraries/parallel/mpi_reconstruct_wbp.os libraries/parallel/mpi_run.os libraries/parallel/mpi_transform_adjust_image_grey_levels.os libraries/parallel/mpi_validation_nontilt.os libraries/parallel/mpi_volumeset_align.os libraries/parallel/xmipp_mpi.os -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp -lpython3.8
> mpicxx -o bin/xmipp_mpi_reconstruct_fourier_accel applications/programs/mpi_reconstruct_fourier_accel/mpi_reconstruct_fourier_accel_main.o -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -L/beegfs/cssb/software/devel/gcc/8.4.0/lib64 -L/beegfs/cssb/software/devel/mpc/1.0.3/lib -L/beegfs/cssb/software/devel/mpfr/3.1.4/lib -L/beegfs/cssb/software/devel/hwloc/2.1.0/lib -L/beegfs/cssb/software/devel/ucx/1.8.0/lib -L/beegfs/cssb/software/devel/openmpi/4.0.3/lib -L/usr/local/cuda-10.1/lib64 -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore -lXmippParallel
> lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
> lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
> /beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
> collect2: error: ld returned 1 exit status
> scons: *** [bin/xmipp_mpi_reconstruct_fourier_accel] Error 1
> scons: building terminated because of errors.
>
> Some error occurred during the compilation of 'xmipp' ('bin/xmipp_mpi_reconstruct_fourier_accel').
>
> Traceback (most recent call last):
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 443, in <module>
> main()
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 287, in main
> installPluginMethods()
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods
> plugin.installBin({'args': ['-j', numberProcessor]})
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
> environment.execute()
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
> self._executeTargets(targetList)
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
> tgt.execute()
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 220, in execute
> command.execute()
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 160, in execute
> assert glob(t), ("target '%s' not built (after "
> AssertionError: target '/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmip
>
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> <mailto:sci...@li...>
> https://lists.sourceforge.net/lists/listinfo/scipion-users
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> <mailto:sci...@li...>
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Grigory S. <sha...@gm...> - 2020-07-28 13:57:47
|
Great!
@Pablo Conesa <pc...@cn...> I guess we should specify to use the
defaults channel for installing xmipp libs (fftw hdf5 libtiff openjdk)
inside conda env.
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 Tue, Jul 28, 2020 at 2:30 PM Lugmayr, Wolfgang <w.l...@uk...> wrote:
> hi,
>
> i made a complete first time install of scipion 3.0.0
>
> thanks the fix worked now the following way:
>
> deleted the target install dir but not the .scipion3env
> conda activate .scipion3env
> conda install hdf5 -c defaults
> python -m scipioninstaller /beegfs/cssb/software/em/scipion/3.0.0 -j 20
> then the main project selection gui comes up with scipion3
>
> i don't know if its related but maybe it helps to find the problem:
> my ~/.condarc had conda-forge before defaults in the channels list.
>
> and the hdf5 from conda-forge reports:
>
> The following NEW packages will be INSTALLED:
> hdf5 conda-forge/linux-64::hdf5-1.10.6-nompi_h3c11f04_100
> libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.5.0-hdf63c60_10
> CondaVerificationError: The package for hdf5 located at
> /beegfs/cssb/software/anaconda3/pkgs/hdf5-1.10.6-nompi_h3c11f04_100
> appears to be corrupted. The path 'bin/h5perf_serial' specified in the
> package manifest cannot be found.
>
> but it workd with the default channel and the following packages:
> hdf5 pkgs/main/linux-64::hdf5-1.10.6-hb1b8bf9_0
> libgfortran-ng pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0
>
> cheers,
> wolfgang
>
> ------------------------------
> *From: *"Pablo Conesa" <pc...@cn...>
> *To: *"Mailing list for Scipion users" <
> sci...@li...>
> *Sent: *Tuesday, 28 July, 2020 13:58:41
> *Subject: *Re: [scipion-users] scipion 3.0.0 / xmippSrc-v3.20.07b1 / HDF5
> linking error
>
> Hi wolfgang,
>
> it seems the installer went for a conda installation
> ("/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib")
>
> xmipp installation, at the beginning should detect the the conda
> environment and trigger the installation of the hdf5 lib and others.
>
> I'm right now realizing the output log of the installation is not
> kept..probably something to do.
>
> Do you, by any change kept the output log of the installation. Or maybe
> triggering the installation again will work to check if xmipp was detecting
> the "conda mode" and trigger
>
>
> One thing you can do is:
>
> 1.- conda activate .scipion3env
>
> 2.- conda install hdf5
>
> 3.- scipion3 installb xmippSrc
>
>
> If other libraries are missing repeat adapting step 2.
>
> It would be great to learn why is not doing this xmipp itself.
>
>
> On 28/7/20 11:21, Lugmayr, Wolfgang wrote:
>
> hi,
>
> i tried to install the (unreleased) scipion3 and came to a hdf5 linking error (full log at end of mail):
>
> /beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
> Some error occurred during the compilation of 'xmipp' ('bin/xmipp_mpi_reconstruct_fourier_accel').
>
> my conda environment contains hdf5
> $ conda list | grep hdf5
> hdf5 1.10.4 hb1b8bf9_0
> but the hidden .scipion3env does not contain one.
>
> do i need the latest hdf5 1.12.0 or is this a buildscript problem?
>
> cheers,
> wolfgang
>
>
>
>
> mpicxx -o lib/libXmippParallelCuda.so -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs -L -shared libraries/parallel_adapt_cuda/mpi_reconstruct_fourier_gpu.os -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp -lXmippInterfaceCuda -lXmippCuda -lcudart -lcufft -lnvidia-ml -lcuFFTAdvisor
> mpicxx -o lib/libXmippParallel.so -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -shared libraries/parallel/mpi_angular_accuracy_pca.os libraries/parallel/mpi_angular_class_average.os libraries/parallel/mpi_angular_continuous_assign.os libraries/parallel/mpi_angular_project_library.os libraries/parallel/mpi_angular_projection_matching.os libraries/parallel/mpi_angular_sph_alignment.os libraries/parallel/mpi_classify_CL2D.os libraries/parallel/mpi_classify_CL2D_core_analysis.os libraries/parallel/mpi_classify_CLTomo_prog.os libraries/parallel/mpi_classify_FTTRI.os libraries/parallel/mpi_image_rotational_pca.os libraries/parallel/mpi_image_sort.os libraries/parallel/mpi_ml_align2d.os libraries/parallel/mpi_multireference_aligneability.os libraries/parallel/mpi_nma_alignment.os libraries/parallel/mpi_nma_alignment_vol.os libraries/parallel/mpi_performance_test.os libraries/parallel/mpi_project_XR.os libraries/parallel/mpi_reconstruct_admm.os libraries/parallel/mpi_reconstruct_art.os libraries/parallel/mpi_reconstruct_fourier.os libraries/parallel/mpi_reconstruct_fourier_accel.os libraries/parallel/mpi_reconstruct_significant.os libraries/parallel/mpi_reconstruct_wbp.os libraries/parallel/mpi_run.os libraries/parallel/mpi_transform_adjust_image_grey_levels.os libraries/parallel/mpi_validation_nontilt.os libraries/parallel/mpi_volumeset_align.os libraries/parallel/xmipp_mpi.os -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp -lpython3.8
> mpicxx -o bin/xmipp_mpi_reconstruct_fourier_accel applications/programs/mpi_reconstruct_fourier_accel/mpi_reconstruct_fourier_accel_main.o -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -L/beegfs/cssb/software/devel/gcc/8.4.0/lib64 -L/beegfs/cssb/software/devel/mpc/1.0.3/lib -L/beegfs/cssb/software/devel/mpfr/3.1.4/lib -L/beegfs/cssb/software/devel/hwloc/2.1.0/lib -L/beegfs/cssb/software/devel/ucx/1.8.0/lib -L/beegfs/cssb/software/devel/openmpi/4.0.3/lib -L/usr/local/cuda-10.1/lib64 -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore -lXmippParallel
> lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
> lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
> /beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
> collect2: error: ld returned 1 exit status
> scons: *** [bin/xmipp_mpi_reconstruct_fourier_accel] Error 1
> scons: building terminated because of errors.
>
> Some error occurred during the compilation of 'xmipp' ('bin/xmipp_mpi_reconstruct_fourier_accel').
>
> Traceback (most recent call last):
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 443, in <module>
> main()
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 287, in main
> installPluginMethods()
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods
> plugin.installBin({'args': ['-j', numberProcessor]})
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
> environment.execute()
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
> self._executeTargets(targetList)
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
> tgt.execute()
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 220, in execute
> command.execute()
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 160, in execute
> assert glob(t), ("target '%s' not built (after "
> AssertionError: target '/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmip
>
>
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: Lugmayr, W. <w.l...@uk...> - 2020-07-28 13:30:19
|
hi,
i made a complete first time install of scipion 3.0.0
thanks the fix worked now the following way:
deleted the target install dir but not the .scipion3env
conda activate .scipion3env
conda install hdf5 -c defaults
python -m scipioninstaller /beegfs/cssb/software/em/scipion/3.0.0 -j 20
then the main project selection gui comes up with scipion3
i don't know if its related but maybe it helps to find the problem:
my ~/.condarc had conda-forge before defaults in the channels list.
and the hdf5 from conda-forge reports:
The following NEW packages will be INSTALLED:
hdf5 conda-forge/linux-64::hdf5-1.10.6-nompi_h3c11f04_100
libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.5.0-hdf63c60_10
CondaVerificationError: The package for hdf5 located at /beegfs/cssb/software/anaconda3/pkgs/hdf5-1.10.6-nompi_h3c11f04_100
appears to be corrupted. The path 'bin/h5perf_serial' specified in the package manifest cannot be found.
but it workd with the default channel and the following packages:
hdf5 pkgs/main/linux-64::hdf5-1.10.6-hb1b8bf9_0
libgfortran-ng pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0
cheers,
wolfgang
From: "Pablo Conesa" <pc...@cn...>
To: "Mailing list for Scipion users" <sci...@li...>
Sent: Tuesday, 28 July, 2020 13:58:41
Subject: Re: [scipion-users] scipion 3.0.0 / xmippSrc-v3.20.07b1 / HDF5 linking error
Hi wolfgang,
it seems the installer went for a conda installation ("/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib")
xmipp installation, at the beginning should detect the the conda environment and trigger the installation of the hdf5 lib and others.
I'm right now realizing the output log of the installation is not kept..probably something to do.
Do you, by any change kept the output log of the installation. Or maybe triggering the installation again will work to check if xmipp was detecting the "conda mode" and trigger
One thing you can do is:
1.- conda activate .scipion3env
2.- conda install hdf5
3.- scipion3 installb xmippSrc
If other libraries are missing repeat adapting step 2.
It would be great to learn why is not doing this xmipp itself.
On 28/7/20 11:21, Lugmayr, Wolfgang wrote:
hi,
i tried to install the (unreleased) scipion3 and came to a hdf5 linking error (full log at end of mail):
/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
Some error occurred during the compilation of 'xmipp' ('bin/xmipp_mpi_reconstruct_fourier_accel').
my conda environment contains hdf5
$ conda list | grep hdf5
hdf5 1.10.4 hb1b8bf9_0
but the hidden .scipion3env does not contain one.
do i need the latest hdf5 1.12.0 or is this a buildscript problem?
cheers,
wolfgang
mpicxx -o lib/libXmippParallelCuda.so -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs -L -shared libraries/parallel_adapt_cuda/mpi_reconstruct_fourier_gpu.os -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp -lXmippInterfaceCuda -lXmippCuda -lcudart -lcufft -lnvidia-ml -lcuFFTAdvisor
mpicxx -o lib/libXmippParallel.so -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -shared libraries/parallel/mpi_angular_accuracy_pca.os libraries/parallel/mpi_angular_class_average.os libraries/parallel/mpi_angular_continuous_assign.os libraries/parallel/mpi_angular_project_library.os libraries/parallel/mpi_angular_projection_matching.os libraries/parallel/mpi_angular_sph_alignment.os libraries/parallel/mpi_classify_CL2D.os libraries/parallel/mpi_classify_CL2D_core_analysis.os libraries/parallel/mpi_classify_CLTomo_prog.os libraries/parallel/mpi_classify_FTTRI.os libraries/parallel/mpi_image_rotational_pca.os libraries/parallel/mpi_image_sort.os libraries/parallel/mpi_ml_align2d.os libraries/parallel/mpi_multireference_aligneability.os libraries/parallel/mpi_nma_alignment.os libraries/parallel/mpi_nma_alignment_vol.os libraries/parallel/mpi_performance_test.os libraries/parallel/mpi_project_XR.os libraries/parallel/mpi_reconstruct_admm.os libraries/parallel/mpi_reconstruct_art.os libraries/parallel/mpi_reconstruct_fourier.os libraries/parallel/mpi_reconstruct_fourier_accel.os libraries/parallel/mpi_reconstruct_significant.os libraries/parallel/mpi_reconstruct_wbp.os libraries/parallel/mpi_run.os libraries/parallel/mpi_transform_adjust_image_grey_levels.os libraries/parallel/mpi_validation_nontilt.os libraries/parallel/mpi_volumeset_align.os libraries/parallel/xmipp_mpi.os -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp -lpython3.8
mpicxx -o bin/xmipp_mpi_reconstruct_fourier_accel applications/programs/mpi_reconstruct_fourier_accel/mpi_reconstruct_fourier_accel_main.o -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -L/beegfs/cssb/software/devel/gcc/8.4.0/lib64 -L/beegfs/cssb/software/devel/mpc/1.0.3/lib -L/beegfs/cssb/software/devel/mpfr/3.1.4/lib -L/beegfs/cssb/software/devel/hwloc/2.1.0/lib -L/beegfs/cssb/software/devel/ucx/1.8.0/lib -L/beegfs/cssb/software/devel/openmpi/4.0.3/lib -L/usr/local/cuda-10.1/lib64 -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore -lXmippParallel
lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
collect2: error: ld returned 1 exit status
scons: *** [bin/xmipp_mpi_reconstruct_fourier_accel] Error 1
scons: building terminated because of errors.
Some error occurred during the compilation of 'xmipp' ('bin/xmipp_mpi_reconstruct_fourier_accel').
Traceback (most recent call last):
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 443, in <module>
main()
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 287, in main
installPluginMethods()
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods
plugin.installBin({'args': ['-j', numberProcessor]})
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
environment.execute()
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 220, in execute
command.execute()
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 160, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmip
--
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Pablo C. <pc...@cn...> - 2020-07-28 11:58:58
|
Hi wolfgang,
it seems the installer went for a conda installation
("/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib")
xmipp installation, at the beginning should detect the the conda
environment and trigger the installation of the hdf5 lib and others.
I'm right now realizing the output log of the installation is not
kept..probably something to do.
Do you, by any change kept the output log of the installation. Or maybe
triggering the installation again will work to check if xmipp was
detecting the "conda mode" and trigger
One thing you can do is:
1.- conda activate .scipion3env
2.- conda install hdf5
3.- scipion3 installb xmippSrc
If other libraries are missing repeat adapting step 2.
It would be great to learn why is not doing this xmipp itself.
On 28/7/20 11:21, Lugmayr, Wolfgang wrote:
> hi,
>
> i tried to install the (unreleased) scipion3 and came to a hdf5 linking error (full log at end of mail):
>
> /beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
> Some error occurred during the compilation of 'xmipp' ('bin/xmipp_mpi_reconstruct_fourier_accel').
>
> my conda environment contains hdf5
> $ conda list | grep hdf5
> hdf5 1.10.4 hb1b8bf9_0
> but the hidden .scipion3env does not contain one.
>
> do i need the latest hdf5 1.12.0 or is this a buildscript problem?
>
> cheers,
> wolfgang
>
>
>
>
> mpicxx -o lib/libXmippParallelCuda.so -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs -L -shared libraries/parallel_adapt_cuda/mpi_reconstruct_fourier_gpu.os -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp -lXmippInterfaceCuda -lXmippCuda -lcudart -lcufft -lnvidia-ml -lcuFFTAdvisor
> mpicxx -o lib/libXmippParallel.so -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -shared libraries/parallel/mpi_angular_accuracy_pca.os libraries/parallel/mpi_angular_class_average.os libraries/parallel/mpi_angular_continuous_assign.os libraries/parallel/mpi_angular_project_library.os libraries/parallel/mpi_angular_projection_matching.os libraries/parallel/mpi_angular_sph_alignment.os libraries/parallel/mpi_classify_CL2D.os libraries/parallel/mpi_classify_CL2D_core_analysis.os libraries/parallel/mpi_classify_CLTomo_prog.os libraries/parallel/mpi_classify_FTTRI.os libraries/parallel/mpi_image_rotational_pca.os libraries/parallel/mpi_image_sort.os libraries/parallel/mpi_ml_align2d.os libraries/parallel/mpi_multireference_aligneability.os libraries/parallel/mpi_nma_alignment.os libraries/parallel/mpi_nma_alignment_vol.os libraries/parallel/mpi_performance_test.os libraries/parallel/mpi_project_XR.os libraries/parallel/mpi_reconstruct_admm.os libraries/parallel/mpi_reconstruct_art.os libraries/parallel/mpi_reconstruct_fourier.os libraries/parallel/mpi_reconstruct_fourier_accel.os libraries/parallel/mpi_reconstruct_significant.os libraries/parallel/mpi_reconstruct_wbp.os libraries/parallel/mpi_run.os libraries/parallel/mpi_transform_adjust_image_grey_levels.os libraries/parallel/mpi_validation_nontilt.os libraries/parallel/mpi_volumeset_align.os libraries/parallel/xmipp_mpi.os -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp -lpython3.8
> mpicxx -o bin/xmipp_mpi_reconstruct_fourier_accel applications/programs/mpi_reconstruct_fourier_accel/mpi_reconstruct_fourier_accel_main.o -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -L/beegfs/cssb/software/devel/gcc/8.4.0/lib64 -L/beegfs/cssb/software/devel/mpc/1.0.3/lib -L/beegfs/cssb/software/devel/mpfr/3.1.4/lib -L/beegfs/cssb/software/devel/hwloc/2.1.0/lib -L/beegfs/cssb/software/devel/ucx/1.8.0/lib -L/beegfs/cssb/software/devel/openmpi/4.0.3/lib -L/usr/local/cuda-10.1/lib64 -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore -lXmippParallel
> lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
> lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
> /beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
> collect2: error: ld returned 1 exit status
> scons: *** [bin/xmipp_mpi_reconstruct_fourier_accel] Error 1
> scons: building terminated because of errors.
>
> Some error occurred during the compilation of 'xmipp' ('bin/xmipp_mpi_reconstruct_fourier_accel').
>
> Traceback (most recent call last):
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 443, in <module>
> main()
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 287, in main
> installPluginMethods()
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods
> plugin.installBin({'args': ['-j', numberProcessor]})
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
> environment.execute()
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
> self._executeTargets(targetList)
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
> tgt.execute()
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 220, in execute
> command.execute()
> File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 160, in execute
> assert glob(t), ("target '%s' not built (after "
> AssertionError: target '/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmip
>
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Grigory S. <sha...@gm...> - 2020-07-28 10:33:15
|
Yes, there should be .so files etc. I think by default all envs are
supposed to see the packages from the base env but I would try to install
hdf5 inside scipion3env and try to recompile xmipp
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 Tue, Jul 28, 2020 at 11:28 AM Lugmayr, Wolfgang <w.l...@uk...> wrote:
> hi,
>
> no. my hdf5 is in the global conda environment.
>
> here is a grep in the .scipion3env:
> $ find . | grep -i hdf5
>
> ./lib/python3.8/site-packages/PIL/__pycache__/Hdf5StubImagePlugin.cpython-38.pyc
> ./lib/python3.8/site-packages/PIL/Hdf5StubImagePlugin.py
>
> ./lib/python3.8/site-packages/scipy/io/matlab/tests/data/testhdf5_7.4_GLNX86.mat
>
> it should contain a libhdf5.a or .so if the package would be there, right?
>
> cheers,
> wolfgang
>
>
> ------------------------------
> *From: *"Grigory Sharov" <sha...@gm...>
> *To: *"Mailing list for Scipion users" <
> sci...@li...>
> *Sent: *Tuesday, 28 July, 2020 12:04:08
> *Subject: *Re: [scipion-users] scipion 3.0.0 / xmippSrc-v3.20.07b1 / HDF5
> linking error
>
> Hi Wolfgang,
>
> Do you have hdf5 inside .scipion3env?
>
> On Tue, Jul 28, 2020, 10:46 Lugmayr, Wolfgang <w.l...@uk...> wrote:
>
>> hi,
>>
>> i tried to install the (unreleased) scipion3 and came to a hdf5 linking
>> error (full log at end of mail):
>>
>> /beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so:
>> undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
>> Some error occurred during the compilation of 'xmipp'
>> ('bin/xmipp_mpi_reconstruct_fourier_accel').
>>
>> my conda environment contains hdf5
>> $ conda list | grep hdf5
>> hdf5 1.10.4 hb1b8bf9_0
>> but the hidden .scipion3env does not contain one.
>>
>> do i need the latest hdf5 1.12.0 or is this a buildscript problem?
>>
>> cheers,
>> wolfgang
>>
>>
>>
>>
>> mpicxx -o lib/libXmippParallelCuda.so
>> -L/usr/local/cuda-10.1/targets/x86_64-linux/lib
>> -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs
>> -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -shared
>> libraries/parallel_adapt_cuda/mpi_reconstruct_fourier_gpu.os
>> -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib
>> -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp
>> -lXmippInterfaceCuda -lXmippCuda -lcudart -lcufft -lnvidia-ml -lcuFFTAdvisor
>> mpicxx -o lib/libXmippParallel.so
>> -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -shared
>> libraries/parallel/mpi_angular_accuracy_pca.os
>> libraries/parallel/mpi_angular_class_average.os
>> libraries/parallel/mpi_angular_continuous_assign.os
>> libraries/parallel/mpi_angular_project_library.os
>> libraries/parallel/mpi_angular_projection_matching.os
>> libraries/parallel/mpi_angular_sph_alignment.os
>> libraries/parallel/mpi_classify_CL2D.os
>> libraries/parallel/mpi_classify_CL2D_core_analysis.os
>> libraries/parallel/mpi_classify_CLTomo_prog.os
>> libraries/parallel/mpi_classify_FTTRI.os
>> libraries/parallel/mpi_image_rotational_pca.os
>> libraries/parallel/mpi_image_sort.os libraries/parallel/mpi_ml_align2d.os
>> libraries/parallel/mpi_multireference_aligneability.os
>> libraries/parallel/mpi_nma_alignment.os
>> libraries/parallel/mpi_nma_alignment_vol.os
>> libraries/parallel/mpi_performance_test.os
>> libraries/parallel/mpi_project_XR.os
>> libraries/parallel/mpi_reconstruct_admm.os
>> libraries/parallel/mpi_reconstruct_art.os
>> libraries/parallel/mpi_reconstruct_fourier.os
>> libraries/parallel/mpi_reconstruct_fourier_accel.os
>> libraries/parallel/mpi_reconstruct_significant.os
>> libraries/parallel/mpi_reconstruct_wbp.os libraries/parallel/mpi_run.os
>> libraries/parallel/mpi_transform_adjust_image_grey_levels.os
>> libraries/parallel/mpi_validation_nontilt.os
>> libraries/parallel/mpi_volumeset_align.os libraries/parallel/xmipp_mpi.os
>> -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib
>> -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp
>> -lpython3.8
>> mpicxx -o bin/xmipp_mpi_reconstruct_fourier_accel
>> applications/programs/mpi_reconstruct_fourier_accel/mpi_reconstruct_fourier_accel_main.o
>> -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib
>> -Llib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib
>> -L/beegfs/cssb/software/devel/gcc/8.4.0/lib64
>> -L/beegfs/cssb/software/devel/mpc/1.0.3/lib
>> -L/beegfs/cssb/software/devel/mpfr/3.1.4/lib
>> -L/beegfs/cssb/software/devel/hwloc/2.1.0/lib
>> -L/beegfs/cssb/software/devel/ucx/1.8.0/lib
>> -L/beegfs/cssb/software/devel/openmpi/4.0.3/lib
>> -L/usr/local/cuda-10.1/lib64 -lXmipp -lhdf5 -lhdf5_cpp -lfftw3
>> -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread
>> -lpython3.8 -lXmippCore -lXmippParallel
>> lib/libXmipp.so: undefined reference to `non-virtual thunk to
>> H5::H5File::throwException(std::__cxx11::basic_string<char,
>> std::char_traits<char>, std::allocator<char> > const&,
>> std::__cxx11::basic_string<char, std::char_traits<char>,
>> std::allocator<char> > const&) const'
>> lib/libXmipp.so: undefined reference to
>> `H5::H5File::throwException(std::__cxx11::basic_string<char,
>> std::char_traits<char>, std::allocator<char> > const&,
>> std::__cxx11::basic_string<char, std::char_traits<char>,
>> std::allocator<char> > const&) const'
>> /beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so:
>> undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
>> collect2: error: ld returned 1 exit status
>> scons: *** [bin/xmipp_mpi_reconstruct_fourier_accel] Error 1
>> scons: building terminated because of errors.
>>
>> Some error occurred during the compilation of 'xmipp'
>> ('bin/xmipp_mpi_reconstruct_fourier_accel').
>>
>> Traceback (most recent call last):
>> File
>> "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py",
>> line 443, in <module>
>> main()
>> File
>> "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py",
>> line 287, in main
>> installPluginMethods()
>> File
>> "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py",
>> line 231, in installPluginMethods
>> plugin.installBin({'args': ['-j', numberProcessor]})
>> File
>> "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py",
>> line 166, in installBin
>> environment.execute()
>> File
>> "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py",
>> line 748, in execute
>> self._executeTargets(targetList)
>> File
>> "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py",
>> line 690, in _executeTargets
>> tgt.execute()
>> File
>> "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py",
>> line 220, in execute
>> command.execute()
>> File
>> "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py",
>> line 160, in execute
>> assert glob(t), ("target '%s' not built (after "
>> AssertionError: target
>> '/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmipp/bin/xmipp_reconstruct_significant'
>> not built (after running 'cd . && ./xmip
>>
>> --
>> 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/
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
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From: Lugmayr, W. <w.l...@uk...> - 2020-07-28 10:28:05
|
hi,
no. my hdf5 is in the global conda environment.
here is a grep in the .scipion3env:
$ find . | grep -i hdf5
./lib/python3.8/site-packages/PIL/__pycache__/Hdf5StubImagePlugin.cpython-38.pyc
./lib/python3.8/site-packages/PIL/Hdf5StubImagePlugin.py
./lib/python3.8/site-packages/scipy/io/matlab/tests/data/testhdf5_7.4_GLNX86.mat
it should contain a libhdf5.a or .so if the package would be there, right?
cheers,
wolfgang
From: "Grigory Sharov" <sha...@gm...>
To: "Mailing list for Scipion users" <sci...@li...>
Sent: Tuesday, 28 July, 2020 12:04:08
Subject: Re: [scipion-users] scipion 3.0.0 / xmippSrc-v3.20.07b1 / HDF5 linking error
Hi Wolfgang,
Do you have hdf5 inside .scipion3env?
On Tue, Jul 28, 2020, 10:46 Lugmayr, Wolfgang < [ mailto:w.l...@uk... | w.l...@uk... ] > wrote:
hi,
i tried to install the (unreleased) scipion3 and came to a hdf5 linking error (full log at end of mail):
/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
Some error occurred during the compilation of 'xmipp' ('bin/xmipp_mpi_reconstruct_fourier_accel').
my conda environment contains hdf5
$ conda list | grep hdf5
hdf5 1.10.4 hb1b8bf9_0
but the hidden .scipion3env does not contain one.
do i need the latest hdf5 1.12.0 or is this a buildscript problem?
cheers,
wolfgang
mpicxx -o lib/libXmippParallelCuda.so -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -shared libraries/parallel_adapt_cuda/mpi_reconstruct_fourier_gpu.os -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp -lXmippInterfaceCuda -lXmippCuda -lcudart -lcufft -lnvidia-ml -lcuFFTAdvisor
mpicxx -o lib/libXmippParallel.so -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -shared libraries/parallel/mpi_angular_accuracy_pca.os libraries/parallel/mpi_angular_class_average.os libraries/parallel/mpi_angular_continuous_assign.os libraries/parallel/mpi_angular_project_library.os libraries/parallel/mpi_angular_projection_matching.os libraries/parallel/mpi_angular_sph_alignment.os libraries/parallel/mpi_classify_CL2D.os libraries/parallel/mpi_classify_CL2D_core_analysis.os libraries/parallel/mpi_classify_CLTomo_prog.os libraries/parallel/mpi_classify_FTTRI.os libraries/parallel/mpi_image_rotational_pca.os libraries/parallel/mpi_image_sort.os libraries/parallel/mpi_ml_align2d.os libraries/parallel/mpi_multireference_aligneability.os libraries/parallel/mpi_nma_alignment.os libraries/parallel/mpi_nma_alignment_vol.os libraries/parallel/mpi_performance_test.os libraries/parallel/mpi_project_XR.os libraries/parallel/mpi_reconstruct_admm.os libraries/parallel/mpi_reconstruct_art.os libraries/parallel/mpi_reconstruct_fourier.os libraries/parallel/mpi_reconstruct_fourier_accel.os libraries/parallel/mpi_reconstruct_significant.os libraries/parallel/mpi_reconstruct_wbp.os libraries/parallel/mpi_run.os libraries/parallel/mpi_transform_adjust_image_grey_levels.os libraries/parallel/mpi_validation_nontilt.os libraries/parallel/mpi_volumeset_align.os libraries/parallel/xmipp_mpi.os -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp -lpython3.8
mpicxx -o bin/xmipp_mpi_reconstruct_fourier_accel applications/programs/mpi_reconstruct_fourier_accel/mpi_reconstruct_fourier_accel_main.o -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -L/beegfs/cssb/software/devel/gcc/8.4.0/lib64 -L/beegfs/cssb/software/devel/mpc/1.0.3/lib -L/beegfs/cssb/software/devel/mpfr/3.1.4/lib -L/beegfs/cssb/software/devel/hwloc/2.1.0/lib -L/beegfs/cssb/software/devel/ucx/1.8.0/lib -L/beegfs/cssb/software/devel/openmpi/4.0.3/lib -L/usr/local/cuda-10.1/lib64 -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore -lXmippParallel
lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
collect2: error: ld returned 1 exit status
scons: *** [bin/xmipp_mpi_reconstruct_fourier_accel] Error 1
scons: building terminated because of errors.
Some error occurred during the compilation of 'xmipp' ('bin/xmipp_mpi_reconstruct_fourier_accel').
Traceback (most recent call last):
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 443, in <module>
main()
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 287, in main
installPluginMethods()
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods
plugin.installBin({'args': ['-j', numberProcessor]})
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
environment.execute()
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 220, in execute
command.execute()
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 160, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmip
--
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: [ mailto:wol...@cs... | wol...@cs... ]
[ http://www.cssb-hamburg.de/ | http://www.cssb-hamburg.de/ ]
_______________________________________________
scipion-users mailing list
[ mailto:sci...@li... | sci...@li... ]
[ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ]
_______________________________________________
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sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
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|
From: Grigory S. <sha...@gm...> - 2020-07-28 10:04:26
|
Hi Wolfgang,
Do you have hdf5 inside .scipion3env?
On Tue, Jul 28, 2020, 10:46 Lugmayr, Wolfgang <w.l...@uk...> wrote:
> hi,
>
> i tried to install the (unreleased) scipion3 and came to a hdf5 linking
> error (full log at end of mail):
>
> /beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so:
> undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
> Some error occurred during the compilation of 'xmipp'
> ('bin/xmipp_mpi_reconstruct_fourier_accel').
>
> my conda environment contains hdf5
> $ conda list | grep hdf5
> hdf5 1.10.4 hb1b8bf9_0
> but the hidden .scipion3env does not contain one.
>
> do i need the latest hdf5 1.12.0 or is this a buildscript problem?
>
> cheers,
> wolfgang
>
>
>
>
> mpicxx -o lib/libXmippParallelCuda.so
> -L/usr/local/cuda-10.1/targets/x86_64-linux/lib
> -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs
> -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -shared
> libraries/parallel_adapt_cuda/mpi_reconstruct_fourier_gpu.os
> -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib
> -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp
> -lXmippInterfaceCuda -lXmippCuda -lcudart -lcufft -lnvidia-ml -lcuFFTAdvisor
> mpicxx -o lib/libXmippParallel.so
> -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -shared
> libraries/parallel/mpi_angular_accuracy_pca.os
> libraries/parallel/mpi_angular_class_average.os
> libraries/parallel/mpi_angular_continuous_assign.os
> libraries/parallel/mpi_angular_project_library.os
> libraries/parallel/mpi_angular_projection_matching.os
> libraries/parallel/mpi_angular_sph_alignment.os
> libraries/parallel/mpi_classify_CL2D.os
> libraries/parallel/mpi_classify_CL2D_core_analysis.os
> libraries/parallel/mpi_classify_CLTomo_prog.os
> libraries/parallel/mpi_classify_FTTRI.os
> libraries/parallel/mpi_image_rotational_pca.os
> libraries/parallel/mpi_image_sort.os libraries/parallel/mpi_ml_align2d.os
> libraries/parallel/mpi_multireference_aligneability.os
> libraries/parallel/mpi_nma_alignment.os
> libraries/parallel/mpi_nma_alignment_vol.os
> libraries/parallel/mpi_performance_test.os
> libraries/parallel/mpi_project_XR.os
> libraries/parallel/mpi_reconstruct_admm.os
> libraries/parallel/mpi_reconstruct_art.os
> libraries/parallel/mpi_reconstruct_fourier.os
> libraries/parallel/mpi_reconstruct_fourier_accel.os
> libraries/parallel/mpi_reconstruct_significant.os
> libraries/parallel/mpi_reconstruct_wbp.os libraries/parallel/mpi_run.os
> libraries/parallel/mpi_transform_adjust_image_grey_levels.os
> libraries/parallel/mpi_validation_nontilt.os
> libraries/parallel/mpi_volumeset_align.os libraries/parallel/xmipp_mpi.os
> -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib
> -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp
> -lpython3.8
> mpicxx -o bin/xmipp_mpi_reconstruct_fourier_accel
> applications/programs/mpi_reconstruct_fourier_accel/mpi_reconstruct_fourier_accel_main.o
> -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib
> -Llib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib
> -L/beegfs/cssb/software/devel/gcc/8.4.0/lib64
> -L/beegfs/cssb/software/devel/mpc/1.0.3/lib
> -L/beegfs/cssb/software/devel/mpfr/3.1.4/lib
> -L/beegfs/cssb/software/devel/hwloc/2.1.0/lib
> -L/beegfs/cssb/software/devel/ucx/1.8.0/lib
> -L/beegfs/cssb/software/devel/openmpi/4.0.3/lib
> -L/usr/local/cuda-10.1/lib64 -lXmipp -lhdf5 -lhdf5_cpp -lfftw3
> -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread
> -lpython3.8 -lXmippCore -lXmippParallel
> lib/libXmipp.so: undefined reference to `non-virtual thunk to
> H5::H5File::throwException(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > const&) const'
> lib/libXmipp.so: undefined reference to
> `H5::H5File::throwException(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > const&) const'
> /beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so:
> undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
> collect2: error: ld returned 1 exit status
> scons: *** [bin/xmipp_mpi_reconstruct_fourier_accel] Error 1
> scons: building terminated because of errors.
>
> Some error occurred during the compilation of 'xmipp'
> ('bin/xmipp_mpi_reconstruct_fourier_accel').
>
> Traceback (most recent call last):
> File
> "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py",
> line 443, in <module>
> main()
> File
> "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py",
> line 287, in main
> installPluginMethods()
> File
> "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py",
> line 231, in installPluginMethods
> plugin.installBin({'args': ['-j', numberProcessor]})
> File
> "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py",
> line 166, in installBin
> environment.execute()
> File
> "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py",
> line 748, in execute
> self._executeTargets(targetList)
> File
> "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py",
> line 690, in _executeTargets
> tgt.execute()
> File
> "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py",
> line 220, in execute
> command.execute()
> File
> "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py",
> line 160, in execute
> assert glob(t), ("target '%s' not built (after "
> AssertionError: target
> '/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmipp/bin/xmipp_reconstruct_significant'
> not built (after running 'cd . && ./xmip
>
> --
> 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/
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: Lugmayr, W. <w.l...@uk...> - 2020-07-28 09:46:27
|
hi,
i tried to install the (unreleased) scipion3 and came to a hdf5 linking error (full log at end of mail):
/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
Some error occurred during the compilation of 'xmipp' ('bin/xmipp_mpi_reconstruct_fourier_accel').
my conda environment contains hdf5
$ conda list | grep hdf5
hdf5 1.10.4 hb1b8bf9_0
but the hidden .scipion3env does not contain one.
do i need the latest hdf5 1.12.0 or is this a buildscript problem?
cheers,
wolfgang
mpicxx -o lib/libXmippParallelCuda.so -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -shared libraries/parallel_adapt_cuda/mpi_reconstruct_fourier_gpu.os -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp -lXmippInterfaceCuda -lXmippCuda -lcudart -lcufft -lnvidia-ml -lcuFFTAdvisor
mpicxx -o lib/libXmippParallel.so -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -shared libraries/parallel/mpi_angular_accuracy_pca.os libraries/parallel/mpi_angular_class_average.os libraries/parallel/mpi_angular_continuous_assign.os libraries/parallel/mpi_angular_project_library.os libraries/parallel/mpi_angular_projection_matching.os libraries/parallel/mpi_angular_sph_alignment.os libraries/parallel/mpi_classify_CL2D.os libraries/parallel/mpi_classify_CL2D_core_analysis.os libraries/parallel/mpi_classify_CLTomo_prog.os libraries/parallel/mpi_classify_FTTRI.os libraries/parallel/mpi_image_rotational_pca.os libraries/parallel/mpi_image_sort.os libraries/parallel/mpi_ml_align2d.os libraries/parallel/mpi_multireference_aligneability.os libraries/parallel/mpi_nma_alignment.os libraries/parallel/mpi_nma_alignment_vol.os libraries/parallel/mpi_performance_test.os libraries/parallel/mpi_project_XR.os libraries/parallel/mpi_reconstruct_admm.os libraries/parallel/mpi_reconstruct_art.os libraries/parallel/mpi_reconstruct_fourier.os libraries/parallel/mpi_reconstruct_fourier_accel.os libraries/parallel/mpi_reconstruct_significant.os libraries/parallel/mpi_reconstruct_wbp.os libraries/parallel/mpi_run.os libraries/parallel/mpi_transform_adjust_image_grey_levels.os libraries/parallel/mpi_validation_nontilt.os libraries/parallel/mpi_volumeset_align.os libraries/parallel/xmipp_mpi.os -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp -lpython3.8
mpicxx -o bin/xmipp_mpi_reconstruct_fourier_accel applications/programs/mpi_reconstruct_fourier_accel/mpi_reconstruct_fourier_accel_main.o -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -L/beegfs/cssb/software/devel/gcc/8.4.0/lib64 -L/beegfs/cssb/software/devel/mpc/1.0.3/lib -L/beegfs/cssb/software/devel/mpfr/3.1.4/lib -L/beegfs/cssb/software/devel/hwloc/2.1.0/lib -L/beegfs/cssb/software/devel/ucx/1.8.0/lib -L/beegfs/cssb/software/devel/openmpi/4.0.3/lib -L/usr/local/cuda-10.1/lib64 -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore -lXmippParallel
lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
collect2: error: ld returned 1 exit status
scons: *** [bin/xmipp_mpi_reconstruct_fourier_accel] Error 1
scons: building terminated because of errors.
Some error occurred during the compilation of 'xmipp' ('bin/xmipp_mpi_reconstruct_fourier_accel').
Traceback (most recent call last):
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 443, in <module>
main()
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 287, in main
installPluginMethods()
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods
plugin.installBin({'args': ['-j', numberProcessor]})
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
environment.execute()
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 220, in execute
command.execute()
File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 160, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmip
--
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/
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From: Karim R. <kar...@um...> - 2020-07-17 08:22:51
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Hi Jose Miguel and Grigory, I managed to fix my issue. It turns out the xmipp binaries weren’t properly installed the first time. Just FYI I have multiple relion installations on our local station (both 3.0 and 3.1 with each GPU or CPU acceleration) and I switch them out using the module command. When loading a certain relion module in the terminal that I then launch Scipion in allows me to utilize either acceleration. Cheers, Karim ############################################## Karim Rafie; PhD, AMRSC Olle Engkvist Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå, Sweden [associate-member-amrsc-of-the-royal-society-of-chemistry] From: Jose Miguel de la Rosa Trevin <del...@gm...> Sent: 15 July 2020 22:23 To: Mailing list for Scipion users <sci...@li...> Subject: Re: [scipion-users] Import particles "error" Dear Karim, Are you using Scipion in local workstations on the HP2C cluster? I have contacted their stuff to start testing Scipion 3 as soon as possible. Best Regards, Jose Miguel On Wed, Jul 15, 2020 at 9:54 PM Karim Rafie <kar...@um...<mailto:kar...@um...>> wrote: Hi Grigory, Great, thanks for the update. Cheers, Karim ############################################## Karim Rafie; PhD, AMRSC Olle Engkvist Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå, Sweden [associate-member-amrsc-of-the-royal-society-of-chemistry] From: Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> Sent: 15 July 2020 21:51 To: Mailing list for Scipion users <sci...@li...<mailto:sci...@li...>> Subject: Re: [scipion-users] Import particles "error" Hi Karim, I'm afraid Scipion 2.0 and relion plugin for it do not support relion 3.1. Scipion 3.0 which will be beta-released soon will have relion 3.1 support. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Jul 15, 2020 at 8:07 PM Karim Rafie <kar...@um...<mailto:kar...@um...>> wrote: Hi all, I'm encountering a curious "error" in scipion v2.0. I am trying to import particles from a relion 3.1 star file and whenever I hit execute a window pops up telling me an integer is required. However, it doesn't say where and all fields have a correct integer/float. I reinstalled scipion and now get an error message saying: 'NoneType' object has no attribute 'read' I am guessing it has something to do with the new file format of relion 3.1 star files. Does anyone have a "fix" or an idea what the issue is? Any help is greatly appreciated. Cheers, Karim ############################################## Karim Rafie; PhD, AMRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå / Sweden _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Karim R. <kar...@um...> - 2020-07-15 20:27:55
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Dear Jose Miguel, I’m working on our local station. So I’ll need to wait for the release ☺. Cheers, Karim ############################################## Karim Rafie; PhD, AMRSC Olle Engkvist Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå, Sweden [associate-member-amrsc-of-the-royal-society-of-chemistry] From: Jose Miguel de la Rosa Trevin <del...@gm...> Sent: 15 July 2020 22:23 To: Mailing list for Scipion users <sci...@li...> Subject: Re: [scipion-users] Import particles "error" Dear Karim, Are you using Scipion in local workstations on the HP2C cluster? I have contacted their stuff to start testing Scipion 3 as soon as possible. Best Regards, Jose Miguel On Wed, Jul 15, 2020 at 9:54 PM Karim Rafie <kar...@um...<mailto:kar...@um...>> wrote: Hi Grigory, Great, thanks for the update. Cheers, Karim ############################################## Karim Rafie; PhD, AMRSC Olle Engkvist Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå, Sweden [associate-member-amrsc-of-the-royal-society-of-chemistry] From: Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> Sent: 15 July 2020 21:51 To: Mailing list for Scipion users <sci...@li...<mailto:sci...@li...>> Subject: Re: [scipion-users] Import particles "error" Hi Karim, I'm afraid Scipion 2.0 and relion plugin for it do not support relion 3.1. Scipion 3.0 which will be beta-released soon will have relion 3.1 support. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Jul 15, 2020 at 8:07 PM Karim Rafie <kar...@um...<mailto:kar...@um...>> wrote: Hi all, I'm encountering a curious "error" in scipion v2.0. I am trying to import particles from a relion 3.1 star file and whenever I hit execute a window pops up telling me an integer is required. However, it doesn't say where and all fields have a correct integer/float. I reinstalled scipion and now get an error message saying: 'NoneType' object has no attribute 'read' I am guessing it has something to do with the new file format of relion 3.1 star files. Does anyone have a "fix" or an idea what the issue is? Any help is greatly appreciated. Cheers, Karim ############################################## Karim Rafie; PhD, AMRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå / Sweden _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Jose M. de la R. T. <del...@gm...> - 2020-07-15 20:22:59
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Dear Karim, Are you using Scipion in local workstations on the HP2C cluster? I have contacted their stuff to start testing Scipion 3 as soon as possible. Best Regards, Jose Miguel On Wed, Jul 15, 2020 at 9:54 PM Karim Rafie <kar...@um...> wrote: > Hi Grigory, > > > > Great, thanks for the update. > > > > Cheers, > > Karim > > ############################################## > > Karim Rafie; PhD, AMRSC > > Olle Engkvist Postdoctoral Research Fellow > > Carlson Lab > > Department of Medical Biochemistry and Biophysics > > Umeå University > > Umeå, Sweden > > [image: associate-member-amrsc-of-the-royal-society-of-chemistry] > > > > *From:* Grigory Sharov <sha...@gm...> > *Sent:* 15 July 2020 21:51 > *To:* Mailing list for Scipion users <sci...@li...> > *Subject:* Re: [scipion-users] Import particles "error" > > > > Hi Karim, > > > > I'm afraid Scipion 2.0 and relion plugin for it do not support relion 3.1. > Scipion 3.0 which will be beta-released soon will have relion 3.1 support. > > > 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, Jul 15, 2020 at 8:07 PM Karim Rafie <kar...@um...> wrote: > > Hi all, > > > > I'm encountering a curious "error" in scipion v2.0. I am trying to import > particles from a relion 3.1 star file and whenever I hit execute a window > pops up telling me an integer is required. However, it doesn't say where > and all fields have a correct integer/float. > > I reinstalled scipion and now get an error message saying: > > *'NoneType' object has no attribute 'read'* > > > > I am guessing it has something to do with the new file format of relion > 3.1 star files. > > > > Does anyone have a "fix" or an idea what the issue is? > > > > Any help is greatly appreciated. > > > > Cheers, > > Karim > > ############################################## > > Karim Rafie; PhD, AMRSC > > Postdoctoral Research Fellow > > Carlson Lab > > Department of Medical Biochemistry and Biophysics > > Umeå University > > Umeå / Sweden > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Karim R. <kar...@um...> - 2020-07-15 19:54:29
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Hi Grigory, Great, thanks for the update. Cheers, Karim ############################################## Karim Rafie; PhD, AMRSC Olle Engkvist Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå, Sweden [associate-member-amrsc-of-the-royal-society-of-chemistry] From: Grigory Sharov <sha...@gm...> Sent: 15 July 2020 21:51 To: Mailing list for Scipion users <sci...@li...> Subject: Re: [scipion-users] Import particles "error" Hi Karim, I'm afraid Scipion 2.0 and relion plugin for it do not support relion 3.1. Scipion 3.0 which will be beta-released soon will have relion 3.1 support. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Jul 15, 2020 at 8:07 PM Karim Rafie <kar...@um...<mailto:kar...@um...>> wrote: Hi all, I'm encountering a curious "error" in scipion v2.0. I am trying to import particles from a relion 3.1 star file and whenever I hit execute a window pops up telling me an integer is required. However, it doesn't say where and all fields have a correct integer/float. I reinstalled scipion and now get an error message saying: 'NoneType' object has no attribute 'read' I am guessing it has something to do with the new file format of relion 3.1 star files. Does anyone have a "fix" or an idea what the issue is? Any help is greatly appreciated. Cheers, Karim ############################################## Karim Rafie; PhD, AMRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå / Sweden _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2020-07-15 19:51:16
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Hi Karim, I'm afraid Scipion 2.0 and relion plugin for it do not support relion 3.1. Scipion 3.0 which will be beta-released soon will have relion 3.1 support. 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, Jul 15, 2020 at 8:07 PM Karim Rafie <kar...@um...> wrote: > Hi all, > > > I'm encountering a curious "error" in scipion v2.0. I am trying to import > particles from a relion 3.1 star file and whenever I hit execute a window > pops up telling me an integer is required. However, it doesn't say where > and all fields have a correct integer/float. > > I reinstalled scipion and now get an error message saying: > > *'NoneType' object has no attribute 'read'* > > > I am guessing it has something to do with the new file format of relion > 3.1 star files. > > > Does anyone have a "fix" or an idea what the issue is? > > > Any help is greatly appreciated. > > > Cheers, > > Karim > > ############################################## > > Karim Rafie; PhD, AMRSC > > Postdoctoral Research Fellow > > Carlson Lab > > Department of Medical Biochemistry and Biophysics > > Umeå University > > Umeå / Sweden > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Karim R. <kar...@um...> - 2020-07-15 19:07:14
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Hi all, I'm encountering a curious "error" in scipion v2.0. I am trying to import particles from a relion 3.1 star file and whenever I hit execute a window pops up telling me an integer is required. However, it doesn't say where and all fields have a correct integer/float. I reinstalled scipion and now get an error message saying: 'NoneType' object has no attribute 'read' I am guessing it has something to do with the new file format of relion 3.1 star files. Does anyone have a "fix" or an idea what the issue is? Any help is greatly appreciated. Cheers, Karim ############################################## Karim Rafie; PhD, AMRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå / Sweden |
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From: Carlos O. S. <co...@cn...> - 2020-07-08 13:37:27
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I think the only dependence is eman, and it may not even be so, now. On 7/8/20 2:40 PM, Dmitry A. Semchonok wrote: > Dear Carlos Oscar and all, > > > > So for the localrec I will need the cryosparc to be installed on my > system additionally to the SCIPION, right? > > If so, are there any recommendations from SCIPION point of view how to > install the cryosparc on CentOS 7? > > Thank you! > > Sincerely, > Dmitry > > > ------ Original Message ------ > From: "Carlos Oscar Sorzano" <co...@cn... <mailto:co...@cn...>> > To: "Dmitry A. Semchonok" <sem...@gm... > <mailto:sem...@gm...>>; "sci...@li... > <mailto:sci...@li...>" > <sci...@li... > <mailto:sci...@li...>>; "sc...@cn... > <mailto:sc...@cn...>" <sc...@cn... > <mailto:sc...@cn...>> > Sent: 08-Jul-20 2:33:18 PM > Subject: Re: [scipion] micelles density subtraction > >> Hi Dmitry, >> >> my experience with the standard tools in Scipion to subtract the >> membrane was not good (not for Scipion, but for the tools >> underneath). The one I did not try was localrec, that may be able to >> help and recently they announced an update of the plugin. We are >> working on our own subtraction, but it is still not ready. >> >> Cheers, Carlos Oscar >> >> On 7/7/20 9:54 PM, Dmitry A. Semchonok wrote: >>> Dear colleagues, >>> >>> I would like to ask how to subtract the micelles density around your >>> membrane protein in the proper way? >>> >>> What are the steps? >>> >>> Thank you! >>> >>> Sincerely, >>> Dmitry >>> >>> |
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From: Juha H. <juh...@he...> - 2020-07-08 13:06:16
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Hi Dmitry, Either Xmipp or RELION protocols can be used for this. You can search for them (CTRL+F) using keyword "subtract". Both require a mask that defines the part you want to subtract plus a map used for subtraction (for me it works better if this map is not sharpened, e.g. comes from Relion auto-refine, not PostProcess). Also, just to avoid confusion: our LocalRec is a plugin for localized reconstruction of subunits. It does not have its own protocol for partial signal subtraction (it is also independent of cryosparc). Best wishes, Juha On Wed, Jul 8, 2020 at 3:42 PM Dmitry A. Semchonok <sem...@gm...> wrote: > Dear Carlos Oscar and all, > > > > So for the localrec I will need the cryosparc to be installed on my system > additionally to the SCIPION, right? > > If so, are there any recommendations from SCIPION point of view how to > install the cryosparc on CentOS 7? > > Thank you! > > Sincerely, > Dmitry > > > ------ Original Message ------ > From: "Carlos Oscar Sorzano" <co...@cn...> > To: "Dmitry A. Semchonok" <sem...@gm...>; " > sci...@li..." <sci...@li...>; > "sc...@cn..." <sc...@cn...> > Sent: 08-Jul-20 2:33:18 PM > Subject: Re: [scipion] micelles density subtraction > > Hi Dmitry, > > my experience with the standard tools in Scipion to subtract the membrane > was not good (not for Scipion, but for the tools underneath). The one I did > not try was localrec, that may be able to help and recently they announced > an update of the plugin. We are working on our own subtraction, but it is > still not ready. > > Cheers, Carlos Oscar > On 7/7/20 9:54 PM, Dmitry A. Semchonok wrote: > > Dear colleagues, > > I would like to ask how to subtract the micelles density around your > membrane protein in the proper way? > > What are the steps? > > Thank you! > > Sincerely, > Dmitry > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry A. S. <sem...@gm...> - 2020-07-08 12:40:47
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Dear Carlos Oscar and all, So for the localrec I will need the cryosparc to be installed on my system additionally to the SCIPION, right? If so, are there any recommendations from SCIPION point of view how to install the cryosparc on CentOS 7? Thank you! Sincerely, Dmitry ------ Original Message ------ From: "Carlos Oscar Sorzano" <co...@cn...> To: "Dmitry A. Semchonok" <sem...@gm...>; "sci...@li..." <sci...@li...>; "sc...@cn..." <sc...@cn...> Sent: 08-Jul-20 2:33:18 PM Subject: Re: [scipion] micelles density subtraction >Hi Dmitry, > >my experience with the standard tools in Scipion to subtract the >membrane was not good (not for Scipion, but for the tools underneath). >The one I did not try was localrec, that may be able to help and >recently they announced an update of the plugin. We are working on our >own subtraction, but it is still not ready. > >Cheers, Carlos Oscar > >On 7/7/20 9:54 PM, Dmitry A. Semchonok wrote: >>Dear colleagues, >> >>I would like to ask how to subtract the micelles density around your >>membrane protein in the proper way? >> >>What are the steps? >> >>Thank you! >> >>Sincerely, >>Dmitry >> >> |
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From: Carlos O. S. <co...@cn...> - 2020-07-08 12:33:36
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Hi Dmitry, my experience with the standard tools in Scipion to subtract the membrane was not good (not for Scipion, but for the tools underneath). The one I did not try was localrec, that may be able to help and recently they announced an update of the plugin. We are working on our own subtraction, but it is still not ready. Cheers, Carlos Oscar On 7/7/20 9:54 PM, Dmitry A. Semchonok wrote: > Dear colleagues, > > I would like to ask how to subtract the micelles density around your > membrane protein in the proper way? > > What are the steps? > > Thank you! > > Sincerely, > Dmitry > > |
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