PoreBatch

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PoreBatch

PoreBatch is a smart Batch system that allows multiple operations to be running simultaneously depending on the specifications of the computer, and gives timestamps to shown calculation speed. The Batch system will distribute the operations onto separate threads or cores where the operations can be run in parallel. Some operations can not be run in parallel or are dependent on a preceding operation before the operation can start. The maximum number of parallel operations is one less than the total number of threads your computer has. So if your computer has four threads, three threads can be used for operation calculations and the fourth thread updates the user interface.

 

PoreBatch looks at the list of operations in the operation list and determines the order in which operations need to run to minimise the time taken to run the complete operation list.

 

The fitting and building operations from the initialisation operations can be run using PoreBatch. The fitting operation for one structure type or unit cell can be run simultaneously with other fitting operations. So a commonly used batch file is one that determines the best structure type to use with your experimental data. The building operation has a choice to use the best fit, or the most recent fit when building the cell. If you use the best fit you can have one building operation at the end of the fitting operations which builds the best structure for the experimental data.

 

The calculation and analysis operations can be run at the same time as each other and work with the building operation above the calculation operations.

 

To inform you that an operation is running there is a symbol beneath the operations list which flashes while a batch operation is being performed.

 

Adding operations to a Batch

There are two ways that you can add operations to a Batch.

1.

The first option to add operations to a batch is to use the PoreXpert menu bar and add individual operations to the operations list manually in the order you want the operations performed. Note that to do this, you will need an appropriate operation highlighted in the main operations list, by single clicking on that Operation.  In the example shown below, Operation 2 Unit Cell building has been highlighted, so is showing dark blue, then a permeability operation is about to be added to the batch list. The batch symbol is three cubes stacked on top of each other, or in minimised form, three squares one above the other.  The batch request icon is as shown below - i.e. a grey circle with down arrow with the three cubes next to it.  It means that a batch is waiting to be done. Note that the successive operations step to the right, showing their dependency on each other.  Once the batch list has been set up, then click Run batch list , as shown on the dropdown screen below, or click SHIFT+R.

Batch request perm opn screen

2.

The second option is to use the command Open batch description in the PoreBatch menu on the menu bar. This command will allow you to select a previously saved PoreXpert file, and it adds all of the operations to the operation list.

 

Once the batch is in operation, the icon shows red with a running figure, as illustrated here both in small and large size:

 

operations screen with batch requests

 

PoreXpert version 2 features the sample filename in the top border of the Home screen, as shown in the first screenshot above, to assist when running multiple instances of the program, which is an alternative to running batches.  It also gives a filename prompt when saving files.

 

Editing operations in the operations list

The operations list can be edited by removing unwanted operations or inserting operations between operations if forgotten. If you right click on an operation a menu appears and this allows you to insert an operation directly below the operation you selected.

If you press the delete button while an operation is selected in the operations list you can remove unwanted operations. Alternatively you can right click on the operation and select the delete option in the menu.  However, note that deletion of one operation also deletes all dependent operations, so that the remaining list of operations is consistent.

 

Running a Batch

To run a batch add all of your operations to the operations list and then press "Shift + R" or press the PoreBatch | Run batch list button. An example is shown below - a test of all structure types for the validation sample 5 using a 15x15x15 unit cell, which because of its medium unit cell size will compute in a manageable time. The screen shows the improved progress indicator for PoreXpert version 2 - it now shows the average completion of all operations, with all those completed counted as 100%. The results of the batch shown below are shown in the property validation.

batch progress screen sample 5 all structure types

 

Saving a batch

Save the batch list as a .pXt file, as shown below.  Then you can load it back on to your computer at a later date, or send it to us or a colleague to run.

batch save screen

 

Caveat

Beware of Build operations relating to Fitting operations that are likely to end at similar times.  The Build operation may build the wrong realisation, because it is using, for example, the most recent fit, and several fits happen almost simultaneously.  An example is shown below.  The fits are for stochastic generations 4 and 5, but the Builds are both for stochastic generation 5.  In PoreXpert version 2 we have added stochastic generation number into the Build operations summary in the home screen to avoid any ensuing errors.

 

batch screen build error

Building error within a batch

 

Running a Batch in the Cloud

If your operation list has operations that can be generated on your local system but would take a long time to complete, you have the option of getting the data using the PoreXpert Cloud system. Instead of using the Run batch list option click on the option Run in the cloud or press Shift + C . Then contact us via the PoreXpert website using support@porexpert.com to send us the batch for processing.

If you have operations that are not included in your version of PoreXpert or exceed the capabilities of the version you are using, the Run batch list option is disabled and you have the option to run the batch in the cloud.