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Changes for page 05. Data processing

Last modified by tabermah on 2024-12-11 11:17
From version 28.1
edited by tabermah
on 2024-03-21 15:14
Change comment: There is no comment for this version
To version 35.1
edited by tabermah
on 2024-09-23 16:45
Change comment: There is no comment for this version

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24 24  1. the form has to be signed and sent back to the Administrator (hard-copy as scan/photo by email/fax in pdf format)
25 25  1. the user receives the initial credentials from the beamline scientist/manager who forwarded the account request. If on site at DESY, the user can authenticate him-/herself by valid ID card or passport at FS-EC's Administrators to retrieve the initial password for the account.
26 26  
27 -(% style="" %)
28 28  **Multi Factor Authentication (MFA) at DESY:**
29 29  
30 -(% style="" %)
31 31  For accessing the DESY computers a two-factor authentication is needed. After you have received your Science Account, you will need to setup an Authenticator App to your smartphone. You can find the instructions [[here>>url:https://it.desy.de/services/mfa/external_people/index_eng.html||style="text-decoration: none;" shape="rect"]].
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33 33  (% style="text-decoration: none;" %)
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82 82  (% style="text-align: justify;" %)
83 83  The processing folders contain two folders, 'xdsapp' and 'manual'. 'Manual' contains a template for manual processing having all the correct parameters. However, to shorten the processing time and make use of the computational structure, reprocessing your data on the maxwell nodes should be done by using a script to queue the jobs in slurm:
84 84  
85 -* a template script (xds.sh) can be found at /asap3/petra3/gpfs/common/p11/
86 -* (% style="color: rgb(0,0,0);" %)the partition in the script is defined psx for external users (ps should be used for internal users of Photon Science)
83 +* a template scripts can be found at /asap3/petra3/gpfs/common/p11/processing_scripts/
84 +** (% style="color: rgb(0,0,0);text-decoration: none;" %)xds_users.sh For (% style="color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0)" %)external users
85 +** xds_inhouse.sh For (% style="color: rgb(255,0,0);" %)in-house users
86 +* (% style="color: rgb(0,0,0);" %)differences on the scripts are on the partition used for the processing (i.e. //pscpu// should be used for internal users of Photon Science and //psxcpu// for external users)
87 87  * (% style="color: rgb(0,0,0);" %)copy the script to the folder where you run the processing
88 -* (% style="color: rgb(0,0,0);" %)launch the script by typing sbatch xds.sh
88 +* (% style="color: rgb(0,0,0);" %)launch the script by typing sbatch xds(% style="color: rgb(0, 0, 0); color: rgb(255, 0, 0)" %)_(% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0)" %)name_of_the_script(% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); text-decoration: none" %).sh (e.g., //sbatch xds_users.sh //for external users )
89 89  * (% style="color: rgb(0,0,0);" %)the script will find a free node for your job to run fast
90 90  * (% style="color: rgb(0,0,0);" %)the xds-log you get in a file xds-job-~#~##.out.
91 91  
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92 92  (% style="text-align: justify;" %)
93 93  **Processing Serial Crystallography data** by nxds should be done via a script to queue the jobs in slurm:
94 94  
95 -* a template script (nxds.sh) as well as an example of input file (nXDS.INP) can be found at /asap3/gpfs/common/p11/
96 -* the partition in the script is defined psx for external users (ps should be used for internal users of Photon Science)
95 +* a template script (nxds.sh) as well as an example of input file (nXDS.INP) can be found at /asap3/gpfs/common/p11/processing_scripts/
96 +* the partition in the script is defined psxpcu for external academic users (pscpu should be used for internal users of Photon Science)
97 97  * (% style="color: rgb(0,0,0);" %)copy the script and the nXDS.INP to the folder where you run the processing
98 98  * (% style="color: rgb(0,0,0);" %)the nXDS.INP file needs some editing to fit your data path and data collection parameters (wavelength, detector distance, oscillation...)
99 99  * (% style="color: rgb(0,0,0);" %)the processing is launch by typing sbatch nxds.sh
100 100  
101 -(% style="" %)
102 102  **If manual processing through a terminal or GUI is absolutely necessary:**
103 103  
104 -* allocate a node to yourself by typing in terminal: salloc ~-~-node=1 ~-~-partition=psx ~-~-time=xx:xx:xx
103 +* allocate a node to yourself by typing in terminal: salloc ~-~-node=1 ~-~-partition=psxcpu ~-~-time=xx:xx:xx
105 105  * ssh to the node allocated to you
106 106  * load the modules of the needed crystallographic softwares on the node (instructions below)
107 107  * HOX! terminate the allocation after usage by typing exit twice on your terminal window
Confluence.Code.ConfluencePageClass[0]
Id
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1 -379127221
1 +379128887
URL
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1 -https://confluence.desy.de/spaces/11/pages/379127221/11. Data processing
1 +https://confluence.desy.de/spaces/11/pages/379128887/11. Data processing