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Changes for page 05. Data processing

Last modified by tabermah on 2024-12-11 11:17
From version 31.1
edited by tabermah
on 2024-09-23 16:09
Change comment: There is no comment for this version
To version 33.1
edited by tabermah
on 2024-09-23 16:39
Change comment: There is no comment for this version

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82 82  
83 83  * a template scripts can be found at /asap3/petra3/gpfs/common/p11/processing_scripts/
84 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 (% 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_industry.sh (% style="color: rgb(0,0,0);" %)For (% style="color: rgb(0, 0, 0); color: rgb(255, 0, 0)" %)industry users
86 86  ** xds_inhouse.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
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 academic users)
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_users.sh// and for industrial users //sbatch xds_industry.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 )
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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93 93  (% style="text-align: justify;" %)
94 94  **Processing Serial Crystallography data** by nxds should be done via a script to queue the jobs in slurm:
95 95  
96 -* a template script (nxds.sh) as well as an example of input file (nXDS.INP) can be found at /asap3/gpfs/common/p11/
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/
97 97  * the partition in the script is defined psxpcu for external academic users (pscpu 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...)
Confluence.Code.ConfluencePageClass[0]
Id
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1 -379128830
1 +379128863
URL
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1 -https://confluence.desy.de/spaces/11/pages/379128830/11. Data processing
1 +https://confluence.desy.de/spaces/11/pages/379128863/11. Data processing