Install Request: CCDC Gold (and Hermes?)

[heatherkellyucl]

IN:06702706

I am going to run CCDC Gold on Myriad, to do the docking with 1 MOF and many ligands. I asked ccdc supports, and they told me:

"Note that we recommend using a license server for running GOLD on a cluster. I can see that your institution already has a license server set up, however, we do not have access information. Kindly reach out to your department for more information on the license server"

Could you give me some information about this license server? and some instructions about how could I run Gold on Myriad?

CCDC installers and license keys are at https://swdb.ucl.ac.uk/package/view/id/756?filter=ccdc Am checking if we are actually running a central license server.

I am testing using CSD 2024.1 Linux Online Installer.

To run the online installer on Myriad, need to ssh in with X-forwarding on, and:

module load xorg-utils
module load xcb-util
module load libxkbcommon

./CSDInstallerOnline-linux

Should launch a GUI, asks you for which software to install. Seems to look at the size of / rather than /tmp for how much temporary space is available, so will fail if you try to do a full install, but can pick Gold and Hermes and the software activator and none of the data.

You can put in the license details straight away or use the software activator later to add them. That can also be run on the command line.

Activator lives in CCDC/ccdc-utilities/software-activation/c_linux-64/bin/ Gold gets installed in CCDC/ccdc-software/gold/GOLD/

It has some wrapper scripts that don't seem to work very well (and all unset LD_LIBRARY_PATH while running, which might cause some problems).

After using the license key rather than the license server, for testing, and running the executable directly got:

[cceahke@login12 GOLD]$ gold/d_linux_64/bin/gold_linux_64 
FATAL: Your licence does not include use of the 'docking' feature.

(The top level wrapper fails because it looks for c_linux_64 not d_linux_64).

Ticket in to ask about license server, IN:06705651

Not certain whether/which parts of this might work in the end.

[heatherkellyucl]

IN:06636040 is the one asking for Hermes.

"Hermes and docking through the CCDC API"

UCL has a license for CSD-Enterprise, which includes access to Hermes and the CSD Python API.

Hermes exists in CCDC/ccdc-software/hermes/c_linux-64/bin/hermes.x

Running their wrappers higher up in the hierarchy tends to break X-forwarding for me until I log in again.

[heatherkellyucl]

Hermes GUI tells me that CDS isostar data is not found (because I didn't install it) and you can point to it or install, seeing if I can install it. It did.

[heatherkellyucl]

I can view the Hermes GUI. There are quite a few OpenGL errors and complaints in the terminal, but it has buttons.

[heatherkellyucl]

Not particularly happy gui:

libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast
Fontconfig error: Cannot load default config file: No such file: (null)
Warning: detected OpenGL error 'stack underflow' at after RenderBin::draw(..)
WARNING: QOpenGLShaderProgram: could not create shader program
WARNING: Vertex shader for simpleShaderProg (MainVertexShader & PositionOnlyVertexShader) failed to compile
WARNING: QOpenGLShader: could not create shader
WARNING: Fragment shader for simpleShaderProg (MainFragmentShader & ShockingPinkSrcFragmentShader) failed to compile
ERROR: Errors linking simple shader: 
WARNING: QOpenGLShaderProgram: could not create shader program
WARNING: Vertex shader for blitShaderProg (MainWithTexCoordsVertexShader & UntransformedPositionVertexShader) failed to compile
WARNING: QOpenGLShader: could not create shader
WARNING: Fragment shader for blitShaderProg (MainFragmentShader & ImageSrcFragmentShader) failed to compile
ERROR: Errors linking blit shader: 
Warning: detected OpenGL error 'stack underflow' at after RenderBin::draw(..)
Warning: detected OpenGL error 'stack underflow' at after RenderBin::draw(..)
WARNING: QXcbConnection: XCB error: 166 (Unknown), sequence: 1937, resource id: 4, major code: 150 (Unknown), minor code: 1
WARNING: QXcbConnection: XCB error: 166 (Unknown), sequence: 1963, resource id: 4, major code: 150 (Unknown), minor code: 1
WARNING: QXcbConnection: XCB error: 166 (Unknown), sequence: 1985, resource id: 4, major code: 150 (Unknown), minor code: 1
[129709:176089:0704/153153.310139:ERROR:context_group.cc(274)] ContextResult::kFatalFailure: too few texture units supported (0, should be 8).
Warning: detected OpenGL error 'stack underflow' at after RenderBin::draw(..)
Warning: detected OpenGL error 'stack underflow' at after RenderBin::draw(..)
WARNING: QXcbConnection: XCB error: 166 (Unknown), sequence: 5338, resource id: 4, major code: 150 (Unknown), minor code: 1
Warning: detected OpenGL error 'stack underflow' at after RenderBin::draw(..)
Warning: detected OpenGL error 'stack underflow' at after RenderBin::draw(..)
WARNING: QXcbConnection: XCB error: 166 (Unknown), sequence: 5360, resource id: 4, major code: 150 (Unknown), minor code: 1
WARNING: QXcbConnection: XCB error: 166 (Unknown), sequence: 5407, resource id: 4, major code: 150 (Unknown), minor code: 1
WARNING: QXcbConnection: XCB error: 166 (Unknown), sequence: 5421, resource id: 4, major code: 150 (Unknown), minor code: 1