FAQs
How do I use PVM via the GOLD graphical interface?
Solution
Please note that the 2019 CSD Release is the last to include the ability to use GOLD with Parallel Virtual Machine (PVM) for UNIX-based platforms. We recommend using a grid-engine based environment rather than PVM.
You must first ensure that the environment variable PVM_ROOT is set to the directory of the PVM installation you are using. By default this should be the GOLD/pvm3 directory of the goldsuite installation, e.g. /usr/local/CCDC/GoldSuite_2016/GOLD/pvm3.
To set process scheduling, click on Parallel GOLD from the list of Global Options given on the left of the GOLD Setup window.
The scheduling window allows you to select a set of machines, across which a parallel GOLD job will be distributed. A GOLD job may be distributed across multiple processors on a single machine, or across several single-processor machines, or across several multiple-processor machines.
The process scheduler allows you to add suitable hosts into the schedule for use in docking a ligand.
By clicking on the Add button you can add new machines to your schedule. In the resulting Edit PVM Host dialog enter a Hostname. For each host chosen, you need to specify a value for Number of processes. This tells GOLD how many separate docking runs to start on that machine. For single processor machines, Number of processes should usually be set to 1; on machines with more than one processor, it should usually be greater than one, depending on how many of the machine's processors you wish to use.
To edit a host, e.g. to change the number of processes, highlight the host in the list and click on the Edit button. Alternatively, to remove a host from the scheduler, highlight it and click on Delete.
The Host file name button allows you to read a file that contains a host configuration previously created when using parallel GOLD. If you click on this button, GOLD then prompts you for a file to read. It will read hosts and numbers of processes from this file, and attempt to add these hosts to your configuration.
The entry box labelled Total number of processes allows specification of the maximum number of GOLD processes that can run simultaneously. This should normally be set equal to the number of processors available for the GOLD job to run on.
If the Total number of processes is set to a number greater than the total no. of processes listed for each individual host in the PVM configuration, GOLD will spawn more jobs than specified on each machine until the total no. set in the Total number of processes are being run, i.e. a discrepancy between the number of processors listed and the maximum number of processes can lead to more or less processes than intended being run on each machine.
GOLD by default is limited to running jobs on up to 50 hosts. If more hosts are required, the setting MAXIMUM_NUMBER_OF_HOSTS in gold.params should be uncommented and set to a number large enough to cover the desired number of hosts.