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Changes for page 05. Data processing

Last modified by tabermah on 2024-12-11 11:17
From version 26.1
edited by tabermah
on 2022-10-20 15:24
Change comment: There is no comment for this version
To version 17.1
edited by hakanj
on 2021-04-12 20:51
Change comment: There is no comment for this version

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1 -XWiki.tabermah
1 +XWiki.hakanj
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8 8  
9 9  **11.2. Manual data processing onsite**
10 10  
11 -Please do not use the control computers of the beamline (haspp11user01-04) nor the haspp11eval01 for data processing (latter is now fully dedicated to autoprocessing).
11 +Please do not use the control computers of the beamline (haspp11user01-04) nor the haspp11eval01 for data processing (latter is now fully dedicated to autoprocessing.
12 12  
13 -Use Maxwell-cluster for data processing as described in the next chapter; on-site, you can directly ssh to username@desy-ps-cpu. Access to Maxwell requires a Scientific Account.
13 +Use Maxwell-cluster for data processing as described in the next chapter; on-site, you can directly ssh to username@desy-ps-cpu or use Max-display by connecting to [[https:~~/~~/max-display.desy.de:3443>>url:https://max-display.desy.de:3443||shape="rect"]] via web browser. Access to Maxwell requires a Scientific Account.
14 14  
15 -Manual data processing after the beamtime or during a remote session is only available for registered [[DESY Scientific Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]].
16 -
17 17  \\
18 18  
19 -//Accessing data from outside the DESY network~://
17 +**11.3. Manual data processing after your beamtime or during remote session**
20 20  
21 -Accessing the Maxwell cluster is easiest with Max-display:  connect to [[https:~~/~~/max-fs-display.desy.de:3389/auth/ssh/>>url:https://max-fs-display.desy.de:3389/auth/ssh/||shape="rect"]] via web browser with the credentials of your scientific account.
19 +Manual data processing after the beamtime or during a remote session is only available for registered [[DESY Scientific Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]].
22 22  
23 -Accesss via terminal window:
21 +//Accessing data from outside the DESY network~://
22 +In a terminal window:
24 24  ssh (% class="Object" %)[[username@desy-ps-ext.desy.de>>mailto:username@desy-ps-ext.desy.de||shape="rect"]](%%)
25 25  ssh username@desy-ps-cpu
26 -
27 27  Give your password when prompted
28 28  Navigate to data by:
29 29  cd /asap3/petra3/gpfs/p11/2020/data/beamtimeID
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30 30  
31 31  Data is accessible to users who were registered participants to the experiment in Door prior to the beamtime ID being opened at the beamline. If you cannot access the data, please contact your LC or the beamline manager.
32 32  
33 -(% style="color: rgb(51,51,51);text-decoration: none;" %)Our processing folders now contain two folders, 'full' and 'manual'. 'Manual' contains a template that has all the correct parameters and processing will run just by typing xds_par there. However, to shorten the processing time and make use of the computational structure, you should use a script to queue the jobs in slurm. A template script (xds.sh) can be found at /asap3/petra3/gpfs/common/p11/xds.sh
34 -
35 -The partition in the script is defined psx for external users (ps should be used for internal users of Photon Science).
31 +(% style="color: rgb(51,51,51);text-decoration: none;" %)Our processing folders now contain two folders, 'full' and 'manual'. 'Manual' contains a template that has all the correct parameters and processing will run just by typing xds_par there. However, to shorten the processing time and make use of the computational structure, you should use a script to queue the jobs in slurm. A template script (xds.sh) can be found at /asap3/petra3/gpfs/common/p11/xds.sh(%%)
36 36  (% style="color: rgb(51,51,51);text-decoration: none;" %)Copy the script to the folder where you run the processing and launch by (%%)
37 37  (% style="color: rgb(51,51,51);text-decoration: none;" %)sbatch xds.sh(%%)
38 38  (% style="color: rgb(51,51,51);text-decoration: none;" %)It will find a free node for your job and run faster than just typing xds_par(%%)
39 -(% style="color: rgb(51,51,51);text-decoration: none;" %)The xds-log you get in a file xds-job-~#~##.out
40 -
41 -(% style="color: rgb(51,51,51);text-decoration: none;" %)nxds can be used for processing Serial Crystallography data in a similar way than xds. As the computing time is long, nxds should should be used via a script to queue the jobs in slurm. The template script (nxds.sh) as well as an example of input file (nXDS.INP) can be found in /asap3/gpfs/common/p11/.
42 -
43 -(% style="color: rgb(51,51,51);text-decoration: none;" %)Copy the script and the nXDS.INP to the folder where you run the processing. The nXDS.INP file needs some editing to fit your data path and data collection parameters (wavelength, detector distance, oscillation...). The processing is launch by
44 -sbatch nxds.sh
45 -
46 -//List of software you can use is at~://
47 -(% class="Object" %)[[https:~~/~~/confluence.desy.de/display/MXW/Photon+Science>>doc:MXW.Photon Science.WebHome||shape="rect"]](%%)
35 +(% style="color: rgb(51,51,51);text-decoration: none;" %)The xds-log you get in a file xds-job-~#~##.out(%%)
36 +\\//List of software you can use is at~://
37 +(% class="Object" %)[[https:~~/~~/confluence.desy.de/display/IS/Photon+Science>>doc:IS.Photon Science.WebHome||shape="rect"]](%%)
48 48  \\//You can store analysis results in scratch_cc (temporary/testing results) or processed (final results).//
49 49  \\//To use crystallographic programs~://
50 50  module avail
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51 51  module load xray     # sets the environment for xds and helper GUIs such as XDSAPP
52 52  module load ccp4/6.4
53 53  module load phenix 
54 -
55 -\\
56 -
57 -\\
58 -
59 -(((
60 -\\
61 -)))
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1 -297521360
1 +202398829
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1 -https://confluence.desy.de/spaces/11/pages/297521360/11. Data processing
1 +https://confluence.desy.de/spaces/11/pages/202398829/11. Data processing