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Changes for page 05. Data processing

Last modified by tabermah on 2024-12-11 11:17
From version 30.1
edited by tabermah
on 2024-09-19 16:41
Change comment: There is no comment for this version
To version 28.1
edited by tabermah
on 2024-03-21 15:14
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="" %)
27 27  **Multi Factor Authentication (MFA) at DESY:**
28 28  
30 +(% style="" %)
29 29  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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31 31  (% style="text-decoration: none;" %)
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80 80  (% style="text-align: justify;" %)
81 81  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:
82 82  
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_Acad_ext_users.sh For (% style="color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0)" %)external (% style="color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0); color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0)" %)a(% style="color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0); color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0); color: rgb(255, 0, 0)" %)cademic (% style="color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0)" %)users
85 -** xds_Ind_users.sh (% style="color: rgb(0,0,0);" %)For (% style="color: rgb(0, 0, 0); color: rgb(255, 0, 0)" %)industry users
86 -** xds_inhouse_users.sh For (% style="color: rgb(255,0,0);" %)in-house users
87 -* (% 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, //psxcpu// for external academic users and //com// for industrial users) and the used xds version
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)
88 88  * (% style="color: rgb(0,0,0);" %)copy the script to the folder where you run the processing
89 -* (% 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., for academic external users //sbatch xds_Acad_ext_users.sh// and for industrial users //sbatch xds_Ind_users.sh//)
88 +* (% style="color: rgb(0,0,0);" %)launch the script by typing sbatch xds.sh
90 90  * (% style="color: rgb(0,0,0);" %)the script will find a free node for your job to run fast
91 91  * (% style="color: rgb(0,0,0);" %)the xds-log you get in a file xds-job-~#~##.out.
92 92  
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94 94  **Processing Serial Crystallography data** by nxds should be done via a script to queue the jobs in slurm:
95 95  
96 96  * a template script (nxds.sh) as well as an example of input file (nXDS.INP) can be found at /asap3/gpfs/common/p11/
97 -* the partition in the script is defined psxpcu for external academic users (pscpu should be used for internal users of Photon Science)
96 +* the partition in the script is defined psx for external users (ps should be used for internal users of Photon Science)
98 98  * (% style="color: rgb(0,0,0);" %)copy the script and the nXDS.INP to the folder where you run the processing
99 99  * (% 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...)
100 100  * (% style="color: rgb(0,0,0);" %)the processing is launch by typing sbatch nxds.sh
101 101  
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=psxcpu ~-~-time=xx:xx:xx
104 +* allocate a node to yourself by typing in terminal: salloc ~-~-node=1 ~-~-partition=psx ~-~-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 -379128829
1 +379127221
URL
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1 -https://confluence.desy.de/spaces/11/pages/379128829/11. Data processing
1 +https://confluence.desy.de/spaces/11/pages/379127221/11. Data processing