Batch Scripts
Scripts exist to execute large batches of simulations in serial. They are located in the batch/ directory under the main ESTReMo directory. There are two scripts, create-batch (which is responsible for creating sets of configuration files) and run-batch (which will execute simulations serially using those configuration files).
create-batch
create-batch is used to generate large sets of configuration files. Use this script in the following way:
./create-batch "name" "m" "k" "alpha" "ncrcounts" "ncrsizes" "population" "nodes" "bgsize"
| Parameter | Purpose | Range |
|---|---|---|
| name | A name for the batch | Anything, but don't use spaces, slashes, or anything else that can't be used in a directory name. The script will create a directory with this name under the batch directory. |
| m | The number of mutations per organism, per generation. | Any positive integer (between 1 and 10 is reasonably). |
| k | Selection pressure (larger values mean more pressure). | A positive integer greater than 2. |
| alpha | Probability that a mutation will occur on a non-coding region. | Between 0.0 and 1.0 |
| ncrcounts | The number of non-coding regions per organism. | Any positive integer (16-32 is realistic). |
| ncrsizes | The width of each non-coding region. | Any positive integer (8-20 is realistic) |
| population | The number of organisms in the population. | Any positive integer (must be greater than k). 500 is a good standard. |
| nodes | The number of hidden nodes in each neural network. | Any positive integer. Usually 1,2,4 or 8. |
| bgsize | The size of the genome of each organism. | Any positive integer. This will heavily influence the speed of the simulation (usually 1k (fast), 10k (medium), 100k (slow), or 1 million (days) are good). |
Example 1
Create a batch called Test for m=1, k=2, alpha=0.5, ncrcounts=16, ncrsizes=8, population=500, nodes=1, bgsize=10000 and m=2, k=2, alpha=0.5, ncrcounts=16, ncrsizes=8, population=500, nodes=1, bgsize=10000.
./create-batch "Test" "1 2" "2" "0.5" "16" "8" "500" "1" "10000"
Example 2
Create a batch called Test2 for alpha=0.5, ncrcounts=16, ncrsizes=8, population=500, nodes=1, bgsize=10000 and all combations of m=1,2,3,4 k=2,3,4,5.
./create-batch "Test2" "1 2 3 4" "2 3 4 5" "0.5" "16" "8" "500" "1" "10000"
The only parameter which you cannot specify a range on is the bgsize (this must be a single value).
run-batch
Once a set of configurations is generated you can execute simulations serially for each configuration using run-batch. Alternately, create-batch will create a slurm script which can be executed (do sbatch run.slurm in the directory which has the name of the batch).
./run-batch "name" "duplicates"
| Parameter | Purpose |
|---|---|
| name | The name which you gave to the batch when you ran create-batch |
| duplicates | Number of times to run the simulation per configuration. (5 is usually good). |
Example 1
Run the "Test" batch created above in triplicate:
./run-batch "Test" "3"