These forums are for discussion and help with the CSD Python API specifically, rather than the other components of the CSD System such as ConQuest. For help with these we'd recommend contacting our user support team (email@example.com).
However, for this issue I'd recommend the following:
1. Open a Terminal window
rm -rf csds_data
That should then allow ConQuest to start. If problems persist, as mentioned above please do contact CCDC support for further help.
For issues such as this with ConQuest, the following steps will usually allow the program to open up successfully again:
1. Open a terminal window
2. In the terminal window, type the following three commands:
rm -rf csds_data
As this forum is for CSD Python API discussion, rather than ConQuest, I will now close this thread, but if you do continue to experience problems please do contact us at firstname.lastname@example.org
Yes this should be entirely possible and the method is indeed similar to a standard PC install. The main difference is that you'll want to install to a location that is accessible by each node in the cluster (clusters usually have disk space that is accessible by all nodes). The easiest way to install the CSD Python API is to install the CSD System sofware on to the cluster - this installs the CSDS software, CSDS data and also the CSD Python API with its own miniconda distribution and the CSD Python API pre-installed and ready for use.
You can also perform a more 'advanced' install into your own Python distribution using the pip or conda packages we supply. This will need at least a data CSDS install via the above mentioned installer in order to use the API. See https://www.ccdc.cam.ac.uk/forum/csd_python_api/General/6a879cb7-a497-e611-bb54-005056975d8a for more details.
For your cluster the main issue you will likely encounter is licensing - each computer node of the cluster will need to be registered, as CSD licensing is based on node-locked registration. We do have a batch registration tool that should help you to automate this registration - see https://www.ccdc.cam.ac.uk/support-and-resources/support/case/?caseid=c9c53a6b-e7e6-e611-8591-005056868fc8
On Windows the CSD Python API should use the registry key entries set up by the CSDS installer to work out where your data directory is, and if that contains a csd_licence.dat licence file then it should pick it up from there. You can use CSDHOME to override this, but usually it should not be necessary.
Mercury is one of the programs in the CSD package that can be started without a licence present (it will have reduced functionality until the package is licensed) so it is worth checking it by going to Help->About Mercury. Does it state it is registered, and if so where is the licence file it is stating it is using? Note that for the API to pick up the licence file automatically it will need to either be in the CSD data directory (in your case C:\Program Files (x86)\CCDC\CSD_2016\CSD V5.37) or in the home area of the user that is running it. With use of admin/user accounts in your post, I'd recommend the licence file being located in the database directory so all users can access it.
Note that rather than trying to run the tests, the correct reading of a licence can be tested with the following at your python command line prompt:
This should output the CSD databases in use if the licence check passes and give the error you have described if not.
Lastly, if your organisation has access to the 2017 release, I would recommend taking a look at that - it comes with its own python pre-installed for ease of use.
The main CSDS and SQLite installers can be run in an unattended mode at the command line - see this FAQ for more details:
All of our installers should detail the various command line options if you run them with the --help argument. This should allow you to install these packages in a simpler way than in the script you provided.
You are also correct that with the current release, licensing expects the ability to use a GUI for standard licensing - we do have some tools to help here, though, and a command line registration utility will be included with the forthcoming CSDS release to make this process a little easier.
Other than these two difficulties, as you've noted there are some package dependencies (such as libGL) that once installed should allow you to use the Python API on your headless system without too much difficulty.
For future reference this forum is for discussion of the CSD Python API - for support of our other products please contact at us at email@example.com.
Exporting to PDF should be resolved in the first update we released for the 2016 CSD System in February - please ensure that this has been installed (if it has, ConQuest's Help->About ConQuest menu should report itself as 'Build RC2').
The software update can be obtained via the details given here: http://www.ccdc.cam.ac.uk/support-and-resources/ccdcresources/downloadcsd2016-updatecsd2016/
Firstly we'd highly recommend using Anaconda python rather than standard python on Mac OS X. Anaconda comes with many packages pre-installed, like lxml which appears to be the package you're having trouble with here.
That said, as the error message suggests, installing xcode from the apple store then running "xcode-select --install" from a terminal window should help ensure the required libraries are installed.
We have noticed there can sometimes be problems with creating a digram via the crystal structure report option in the Mercury scripts menu. If you experience this problem, the issue can be resolved by adding the following before line 59 in crystal_structure_report.py in Mercury's scripts folder:
so that this section reads:
# Read crystal relating to entry_id from any supported file format
entry = helper.current_entry
crystal = entry.crystal
molecule = crystal.molecule
tableno = 1
The script will be updated with the fix in a future release.
With the 1.0 release of the CSD Python API we have made an installer specifically for Anaconda Python, and this is now the recommend way to use the CSD Python API on Mac OS X. If using standard Python, we would recommend using the pre-compiled installer as provided on the Python download website.
When running a script via the Mercury interface, Mercury will wait for a maximum of 3 minutes for that script to complete before releasing the interface to allow it to be used again.
If the script is still running after 3 minutes then you will receive the "The python process did not finish before the time-out" error, but the script will also continue running in the background. The error message also details where the output for the script is being produced, so you can review the files there at a later time. You should be able to open the geometry report in that output folder directly once it is complete.