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Job Settings Dialog Box |
The Job Settings dialog box is used to specify settings that are used when starting jobs from Maestro. Settings are stored for each application (with a few exceptions).
To open the Job Settings dialog box, you can:
Click the Settings button in any of the application panels that run jobs.
The features present in the Job Settings dialog box depend on the calculation to be carried out. Each instance of this dialog box has a Job section and a set of action buttons. If the job produces structural output and properties, the dialog box can also have an Output section. Other, job-specific controls are made available as needed. The controls that are common to many instances of the Job Settings dialog box are described below.
The Output section, if present, contains an Incorporate option menu for choosing the manner in which the structural and property results of the calculation are incorporated into the project. The menu has the following options:
Each structure in the output file is added to the project as a new entry, and the entries are grouped. The group name is set to the name of the file from which the entries were read, minus the extension. This is the default option.
Each new entry is added to the project immediately below its source entry, i.e. the entry that was used as input for the job. If there is no source entry, the new entry is added to the end of the entry list in the project as an individual entry.
Each structure in the output file is added to the project as a new entry, but the entries are not grouped.
Any entries that served as input for the job are replaced with the new structures returned from the calculation.
No change is made to the project when the job is complete.
Some of these controls may be absent for a given instance of the dialog box.
Specify the title to be used in the input structure file. The default is the entry title.
Enter a name for the job. When a job is started, a subdirectory of the working directory is created using the job name (depending on the application), for writing job files in. Job files are named with the job name as the first part (stem or prefix) of the file names.
The initial name shown is a standard name for the application, which might include calculation settings. A standard name that contains settings is updated when the settings change. You can modify a standard name; if you do and it still retains some settings, the name is updated if the settings change. You can also replace the entire job name.
When a standard name or modified standard name is used, the job name is made unique by appending an integer. This is done by checking for job directories or files in the current working directory. However, if you replace the job name to create a custom job name, the name might no longer be unique, and it is not automatically made unique. In that case, a warning is posted before any files are overwritten.
After a job is submitted, a new job name is automatically created for the next job from the current job name, by appending an integer or incrementing the integer. This is done for custom job names as well as standard or modified names.
The Host menu displays all the hosts defined in the $SCHRODINGER/schrodinger.hosts file, with the number of CPUs available on the host in parentheses. To run the selected job on a remote host, choose the host from this menu.
Specify the number of processors to use to run the job. Absent if the job cannot be distributed or run in parallel. The number of processors actually used is limited by the number of licenses available for the type of job.
Choose an option for how to distribute the subjobs for parallel execution. These options apply to Jaguar jobs, which can use both MPI processes and OMP threads for parallelization.
For jobs that can be distributed over multiple CPUs (and multiple hosts), specify the number of subjobs to split the job into. This number can be larger than the number of CPUs used, and it is often a good idea to choose a number that is several times the number of CPUs for optimal load balancing.
Select the scratch directory (used for temporary storage during the running of the job). The available scratch directories are taken from the tmpdir settings in the $SCHRODINGER/schrodinger.hosts file.
The Host list table is available for applications that can distribute jobs over multiple hosts. The table displays all the hosts defined in the $SCHRODINGER/schrodinger.hosts file, with the number of processors available on the host in the Processors column. The Use column specifies the number of processors to use from the given host. The default number is the number available, or * if it is a queue host. You can edit this column to set the number of processors, and you can reset the values to the default by clicking Reset All.
To specify the hosts and number of processors to use for a job, edit the values in the Use column as needed, and select the desired hosts in the table. The total number of processors for the job is reported in the Total to use text box.
When you select hosts for the job, you can only select one queue host, and you cannot select both queue and non-queue hosts. If you select a queue host, all other table rows are deselected.
This option and table is present only for applications that can run on a graphics processor (GPU). The option is made available when you choose a GPU-enabled host from the Host option menu. The Total processors text box changes to Total GPUs. If you select Automatically select GPUs, then you can enter the total number of GPUs to use in the Total GPUs text box. If you deselect this option, you can select GPUs in the table by clicking on the row for each of the GPUs. Clicking again deselects the GPU. The number of GPUs you select is reported in the Total GPUs text box, which is noneditable in this situation.
There are three actions you can take after making settings, by clicking one of these buttons:
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