Difference between revisions of "CSD"

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(Added 'How to update CSD with data upgrade')
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If you want help using ConQuest, try the documentation:
 
If you want help using ConQuest, try the documentation:
 
  http://www.ccdc.cam.ac.uk/support/documentation/conquest/ConQuest/toc.html
 
  http://www.ccdc.cam.ac.uk/support/documentation/conquest/ConQuest/toc.html
 +
 +
===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.
 +
  
 
Return to [[:Category:Software]]
 
Return to [[:Category:Software]]

Revision as of 10:18, 24 May 2019

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.

login to sgehead and run the following command to correctly initialize your environment:

source /nfs/software/csd/current/env.csh

You can then run Conquest by executing the command:

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

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.


Return to Category:Software