Difference between revisions of "CSD"

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(Added 'How to update CSD with data upgrade')
 
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The Cambridge Structural Database contains crystallographic data on small organic molecules (much like the PDB).
 
The Cambridge Structural Database contains crystallographic data on small organic molecules (much like the PDB).
Our license for 2014 is installed on sgehead in [[cluster 1]].
+
Our license is installed on gimel in [[Cluster 2]] (2020-03-26)
 +
$ source /nfs/soft/csd/csd-2020/env.csh
  
login to sgehead and run the following command to correctly initialize your environment:
+
To activate the license, become root on gimel
source /nfs/software/csd/current/env.csh
+
 
You can then run Conquest by executing the command:
+
  $ ccdc_activator -A -a -k <activation-key> -f /nfs/soft/csd/csd-2020/csd/csd_license.dat
  cq
+
In case you are prompted for a licence for any reason, it is located in
+
/nfs/software/csd/current/csd/csd_licence.dat
+
If this fails with the error Tcl Error about no display, you may have to login using:
+
ssh -Y sgehead
+
Which forwards your X session.
+
If you want help using ConQuest, try the documentation:
+
http://www.ccdc.cam.ac.uk/support/documentation/conquest/ConQuest/toc.html
+
  
 
===Applying Data Updates===
 
===Applying Data Updates===

Latest revision as of 17:29, 26 March 2020

The Cambridge Structural Database contains crystallographic data on small organic molecules (much like the PDB). Our license is installed on gimel in Cluster 2 (2020-03-26)

$ source /nfs/soft/csd/csd-2020/env.csh

To activate the license, become root on gimel

$ ccdc_activator -A -a -k <activation-key> -f /nfs/soft/csd/csd-2020/csd/csd_license.dat

Applying Data Updates

We get emails from CCDC that announce updates. For whatever reason, the automatic update via the GUI doesn't work for us, probaby due to the way we route software from nfs-soft to the rest of the cluster so we manually download the update packages from CCDC. scp or rsync the runfile from CCDC to nfs-soft's /tmp directory.

Run these updates on bet/nfs-soft directly:

[root@bet tmp]# ./CSDDataUpdate-May19-linux-x64-installer.run 
----------------------------------------------------------------------------
Welcome to the CSD 2019 Data Update Setup Wizard.

----------------------------------------------------------------------------
Please read the following License Agreement. You must accept the terms of this 
agreement before continuing with the installation.

Press [Enter] to continue:
Use of this software is governed by an Agreement between the CCDC
and your organisation. A copy of the standard Licence Agreement can
be viewed by copying this URL and pasting it into your browser's 
address bar:  https://downloads.ccdc.cam.ac.uk/licence_agreement.txt
If you have any questions, please contact admin@ccdc.cam.ac.uk


Press [Enter] to continue: 

Do you accept this license? [y/n]: y

----------------------------------------------------------------------------
The location of your CSD System data.

Defaults: 

    Windows   : C:\Program Files (x86)\CCDC\CSD_2019\CSD_540\
    Linux     : INSTALL_DIR/CCDC/CSD_2019/csd/
    Mac       : /Applications/CCDC/CSD_2019/DATA/CSD_540
  
            

Installation Directory [/csd]: /export/soft/csd/current/CSD_2019/csd

----------------------------------------------------------------------------
Setup is now ready to begin installing CSD 2019 Data Update on your computer.

Do you want to continue? [Y/n]: y 

----------------------------------------------------------------------------
Please wait while Setup installs CSD 2019 Data Update on your computer.

Installing
0% ______________ 50% ______________ 100%
######################################### 

----------------------------------------------------------------------------
Setup has finished installing CSD 2019 Data Update on your computer.


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