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Changes for page 05. Data processing

Last modified by tabermah on 2024-12-11 11:17
From version 36.1
edited by tabermah
on 2024-09-23 17:12
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"]].
30 30  
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_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)
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)
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(% 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 )
88 +* (% style="color: rgb(0,0,0);" %)launch the script by typing sbatch xds.sh
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/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)
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)
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="" %)
101 101  **If manual processing through a terminal or GUI is absolutely necessary:**
102 102  
103 -* 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
104 104  * ssh to the node allocated to you
105 105  * load the modules of the needed crystallographic softwares on the node (instructions below)
106 106  * HOX! terminate the allocation after usage by typing exit twice on your terminal window
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121 121  To use crystallographic programs type in terminal (for example):
122 122  
123 123  * **module avail** #to check what programs and versions are available
124 -* **module load xray** # sets the environment for old xds and helper GUIs such as (% style="color: rgb(0,0,0);" %)XDSAPP
125 -* (% style="color: rgb(0,0,0);" %)**module load maxwell xds** # sets the environment for new xds
125 +* **module load xray** # sets the environment for xds and helper GUIs such as (% style="color: rgb(0,0,0);" %)XDSAPP
126 126  * **module load ccp4/7** # sets the environment for ccp4 version 7
127 127  * **module load phenix** # sets the environment for phenix
128 128  
Confluence.Code.ConfluencePageClass[0]
Id
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1 -379129280
1 +379127221
URL
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1 -https://confluence.desy.de/spaces/11/pages/379129280/11. Data processing
1 +https://confluence.desy.de/spaces/11/pages/379127221/11. Data processing