GSD-VMD Plugin

[Christopher Ramirez]

Hello,

I'm a sysadmin for an HPC Cluster and one of my users requested that we add the gsd-vmd plugin. With documentation being a bit sparse, I'm not sure how to proceed with troubleshooting.

While testing, the user came across the following errors:

```

Info) File loading in progress, please wait.

ERROR) Unable to determine file type for file

'3SPN_PMFC_HREX_T_274.0_Salt_0.0_Mg_0.003_RSEED_1166284757_gsd_at_beginning.gsd'.

Assuming pdb.

PDB file

'3SPN_PMFC_HREX_T_274.0_Salt_0.0_Mg_0.003_RSEED_1166284757_gsd_at_beginning.gsd'

contains no atoms.

ERROR) Could not read file

3SPN_PMFC_HREX_T_274.0_Salt_0.0_Mg_0.003_RSEED_1166284757_gsd_at_beginning.gsd

ERROR) Loading of startup molecule files aborted.

Instinct tells me these is merely a user error and they need to review some documentation, but I just want to make sure this wasn't caused by a missing dependency. 

Thanks,

Chris

[Joshua Anderson]

"ERROR) Unable to determine file type for file '3SPN_PMFC_HREX_T_274.0_Salt_0.0_Mg_0.003_RSEED_1166284757_gsd_at_beginning.gsd'. Assuming pdb."

This indicates that VMD did not find a registered plugin to read the gsd file. All later error messages result from it interpreting the file as a different format.

Do you have the gsd plugin installed in the correct location? When I start vmd without any arguments, I get this message:

"Info) Dynamically loaded 3 plugins in directory:
Info) /usr/lib/vmd/plugins/LINUXAMD64/molfile"

which indicates that it found the plugins in that directory:

"▶ ls /usr/lib/vmd/plugins/LINUXAMD64/molfile/gsdplugin.so
/usr/lib/vmd/plugins/LINUXAMD64/molfile/gsdplugin.so"

------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
http://www-personal.umich.edu/~joaander/

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[Christopher Ramirez]

Joshua, 

Thank you for the response. I'm actually not seeing that when it loads up. 

We're using module files to load all these applications. Does VMD require that we pass an environment variable for the plugin directory or does it detect it on it's own? 

Thanks,

Chris

[Michael Howard]

Hi Chris,

It depends on where you installed the GSD plugin. If you followed the defaults, then gsd-vmd should install itself into the VMD molfile plugin directory (it’s only one shared library). VMD will then automatically detect it. Is that what you did?

If not, it is pretty difficult to force another directory onto VMD’s plugin search path, hence the warning in the README:

“By default, gsd-vmd will be installed into VMD_PLUGIN_MOLFILE_PATH. You can specify an alternative installation location; however, you must ensure that this is added to your VMD search path, which is a tricky endeavour and not recommended.”

—Mike

[Christopher Ramirez]

Mike,

It wouldn't detect it automatically, so I passed some env vars to point it at the default directories. 

I think this may not have worked as I had hoped, even though the build and installed reported successful. 

I'm wondering if that has to do with the way vmd is installed, or if we're missing some env vars that need to be passed in the environment module to get it working correctly. 

In the mean time, do you have any suggestions for reinstalling the plug-in?

Thanks,

Chris

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[Joshua Anderson]

You could always circumvent the plugin's 'make install' process and just manually copy the `gsdplugin.so` file into vmd's plugin directory.

Understand that we are not VMD developers and have little to no knowledge of the internals of VMD's startup process. I am not aware of any env vars that you can set to control the process.The `vmd` launcher script specifies `set defaultvmddir=/usr/lib/vmd` in the 2nd line (on my system). As far as I know, it uses this base directory to find everything else, including the molfile plugins. On your system, this base directory should be the path where you installed vmd.

------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
http://www-personal.umich.edu/~joaander/

On Wed, Aug 1, 2018 at 8:39 AM, Christopher Ramirez <c.ram...@gmail.com> wrote:

Mike,

It wouldn't detect it automatically, so I passed some env vars to point it at the default directories. 

I think this may not have worked as I had hoped, even though the build and installed reported successful. 

I'm wondering if that has to do with the way vmd is installed, or if we're missing some env vars that need to be passed in the environment module to get it working correctly. 

In the mean time, do you have any suggestions for reinstalling the plug-in?

Thanks,

Chris

On Tue, Jul 31, 2018 at 5:35 PM Michael Howard <howard....@gmail.com> wrote:

Hi Chris,

It depends on where you installed the GSD plugin. If you followed the defaults, then gsd-vmd should install itself into the VMD molfile plugin directory (it’s only one shared library). VMD will then automatically detect it. Is that what you did?

If not, it is pretty difficult to force another directory onto VMD’s plugin search path, hence the warning in the README:

“By default, gsd-vmd will be installed into VMD_PLUGIN_MOLFILE_PATH. You can specify an alternative installation location; however, you must ensure that this is added to your VMD search path, which is a tricky endeavour and not recommended.”

—Mike

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[Christopher Ramirez]

Josh,

Thanks, I'll give that a shot as well. I know ya'll aren't developers, and so I appreciate the help that much more. 

I'm going to have to tinker with it a bit to see what else needs to be done.

Thanks again,

Chris

On Wed, Aug 1, 2018 at 7:46 AM Joshua Anderson <joaa...@umich.edu> wrote:

You could always circumvent the plugin's 'make install' process and just manually copy the `gsdplugin.so` file into vmd's plugin directory.

Understand that we are not VMD developers and have little to no knowledge of the internals of VMD's startup process. I am not aware of any env vars that you can set to control the process.The `vmd` launcher script specifies `set defaultvmddir=/usr/lib/vmd` in the 2nd line (on my system). As far as I know, it uses this base directory to find everything else, including the molfile plugins. On your system, this base directory should be the path where you installed vmd.

------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
http://www-personal.umich.edu/~joaander/

On Wed, Aug 1, 2018 at 8:39 AM, Christopher Ramirez <c.ram...@gmail.com> wrote:

Mike,

It wouldn't detect it automatically, so I passed some env vars to point it at the default directories. 

I think this may not have worked as I had hoped, even though the build and installed reported successful. 

I'm wondering if that has to do with the way vmd is installed, or if we're missing some env vars that need to be passed in the environment module to get it working correctly. 

In the mean time, do you have any suggestions for reinstalling the plug-in?

Thanks,

Chris

On Tue, Jul 31, 2018 at 5:35 PM Michael Howard <howard....@gmail.com> wrote:

Hi Chris,

It depends on where you installed the GSD plugin. If you followed the defaults, then gsd-vmd should install itself into the VMD molfile plugin directory (it’s only one shared library). VMD will then automatically detect it. Is that what you did?

If not, it is pretty difficult to force another directory onto VMD’s plugin search path, hence the warning in the README:

“By default, gsd-vmd will be installed into VMD_PLUGIN_MOLFILE_PATH. You can specify an alternative installation location; however, you must ensure that this is added to your VMD search path, which is a tricky endeavour and not recommended.”

—Mike

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[Michael Howard]

Hi Chris,

The only environment variable you should need to modify is PATH to include the vmd launcher script. I installed vmd locally into:

VMD=/home/<user>/packages/vmd

This directory contains bin/ and lib/. The sole content of $VMD/bin is the vmd launcher script (could be sh or ksh). If you open $VMD/bin/vmd, you should see the variable defaultvmddir being set, as Josh pointed out, which for a local installation should be equal to $VMD/lib.

The VMD plugins directory should be found in $VMD/lib/plugins. If CMake runs correctly, it should find and set (in the CMake cache) on a Linux installation of VMD:

VMD_PLUGIN_INCLUDE_PATH=$VMD/lib/plugins/include

VMD_PLUGIN_MOLFILE_PATH=$VMD/lib/plugins/LINUXAMD64/molfile

You should check your CMake cache to see if it has determined those correctly for your installation. If you go to VMD_PLUGIN_MOLFILE_PATH, you should see a bunch of shared libraries (e.g., xyzplugin.so). This is where gsdplugin.so will need to be installed.

CMake should be able to figure all of that automatically if you have vmd on your PATH and you've installed as I've described above. Alternatively, you can set VMDDIR, either in the environment or in CMake, equal to the location of the VMD libraries:

VMDDIR=$VMD/lib

to hint at the installation location. Or, you can manually set the two VMD_PLUGIN_*_PATH variables in CMake, but that is a last resort.

Regards,

Mike

[Christopher Ramirez]

Mike, 

Thanks for your help doing the following: " " cmake -DVMDDIR=/software/vmd/1.9.3/lib .."  worked. I was able to get it installed and, at least from my limited knowledge of the app, was able to get it working correctly. I'm having a user test now, but this seems to be resolved. 

I really appreciate all your input. 

Have a great week,

Chris