File Server Setup Considerations Shared » History » Version 14
Anchi Cheng, 08/15/2018 11:42 AM
1 | 3 | Anchi Cheng | h1. File Server Setup Considerations |
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2 | 1 | Anchi Cheng | |
3 | 7 | Anchi Cheng | A specific file tree structure has been assumed in Appion/Leginon. Here is a description of it: |
4 | 1 | Anchi Cheng | |
5 | 9 | Anchi Cheng | h2. Head path |
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7 | Leginon and Appion are saved under the same head directory, and it is assumed to have one. |
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8 | For example */your_file_server_mount_point/whatever* is the head directory. |
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9 | 11 | Anchi Cheng | You can have is shorter such as */whatever*, but not just / |
10 | 9 | Anchi Cheng | |
11 | 8 | Anchi Cheng | h2. User not identified in the path |
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13 | 5 | Anchi Cheng | # Leginon default image path is defined in [[Configure leginoncfg|leginon.cfg]]. The acceptable form is */your_file_server_mount_point/whatever/leginon*. The images are saved by sessionname under subdirectory of this directory in a form such as |
14 | 1 | Anchi Cheng | */your_file_server_mount_point/whatever/leginon/sessionname/rawdata/*. |
15 | 7 | Anchi Cheng | # Leginon DD movie frames path is defined relative to the Leginon image path once it is set for the session. In the case of the above example, the resulting path is |
16 | */your_file_server_mount_point/whatever/frames/sessionname/rawdata/*. |
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17 | # Appion processing is default under appion directory parrallel to leginon directory, i.e., /your_file_server_mount_point/whatever/appion. This relationship is hard-coded until v2.2 release. In later releases, the parent directory can be set differently in the webserver myamiweb config.php. The processing are divided by sessionname and then processingtype and then runname of the process. Therefore, your processing results are saved in the following default appion path: */your_file_server_mount_point/whatever/appion/sessionname/processing_type/runname/* |
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18 | 8 | Anchi Cheng | |
19 | 13 | Anchi Cheng | h2. User identified in the path in a subdirectory of leginon |
20 | 8 | Anchi Cheng | |
21 | It is possible to add one more layer below leginon directory to identify users by their username or groupname. In this case; |
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22 | # Leginon default image path can be made to be */your_file_server_mount_point/whatever/leginon/username/sessionname/rawdata*. |
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23 | # frame directory is then */your_file_server_mount_point/whatever/frames/username/sessionname/rawdata*. |
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24 | 12 | Anchi Cheng | # In webserver myamiweb/config.php. *APPION_PARENT_ADDITION* should be set to 1. This will preserve username subdivision and give default appion path of */your_file_server_mount_point/whatever/appion/username/sessionname/processing_type/runname/* |
25 | 1 | Anchi Cheng | |
26 | 13 | Anchi Cheng | h2. User identified in the path in a parent directory of leginon |
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28 | It is possible to add one more layer above leginon directory to identify users by their username or groupname. In this case; |
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29 | # Leginon default image path can be made to be */your_file_server_mount_point/whatever/username/leginon/sessionname/rawdata*. |
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30 | # frame directory is then */your_file_server_mount_point/whatever/username/frames/username/sessionname/rawdata*. |
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31 | # In webserver myamiweb/config.php. *APPION_PARENT_REPLACEMENT* should be set to -1. This will preserve username parent division and give default appion path of */your_file_server_mount_point/whatever/username/appion/sessionname/processing_type/runname/* |
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33 | h2. Permission |
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35 | 1 | Anchi Cheng | The following permission rule is required for multi-unix-user usage of Leginon/Appion: |
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37 | For Leginon: |
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39 | 13 | Anchi Cheng | # The web server redux running user need to have read permission to all images in the rawdata directories in order to display them in the viewer. |
40 | # all users need to have permission to create directory at the level of sessionname. For standard structure, this means */your_file_server_mount_point/whatever/leginon*. |
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41 | 1 | Anchi Cheng | # If DD frames are saved and managed by Leginon, the user running the frame rawtransfer.py (typically root) need to have permission to create directory in */your_file_server_mount_point/whatever/frames* |
42 | 14 | Anchi Cheng | # All users need to have read permission in a leginon rawdata directory that contains reference images. You can specify this through leginon.cfg as |
43 | 13 | Anchi Cheng | <pre> |
44 | [References] |
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45 | path: /common_path/leginon_references |
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46 | </pre> |
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47 | 1 | Anchi Cheng | # Users need to have write permission to the session they created, of course. |
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49 | For Appion: |
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50 | 6 | Anchi Cheng | |
51 | # Images uploaded to Appion is considered as a Leginon session. See above for its file tree structure. |
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52 | 1 | Anchi Cheng | # The web server apache user need to have read permission to processing directories to display the results. |
53 | # All users need to have permission to create directory in */your_file_server_mount_point/whatever/appion* |
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54 | # If more than one user will be processing data in the same session, they all need write permission to the session directory */your_file_server_mount_point/whatever/appion/sessionname/* |