For remote execution, NetLogo needs to be installed on remote machines as well. For windows machines, the downloaded file needs to be executed in order to install NetLogo on the local system. If you are running MacOS, please use the Linux tar. The dmg version from the NetLogo homepage is not compatible with nlrx.
You can install the released version of nlrx from CRAN with:. General information that is needed to run NetLogo simulations remotely, such as path to the NetLogo installation folder is stored within a nl class object.
Nested within this nl class are the classes experiment and simdesign. The experiment class stores all experiment specifications. After attaching a valid experiment, a simdesign class object can be attached to the nl class object, by using one of the simdesign helper functions. The nested design allows to store everything related to the experiment within one R object.
Additionally, different simdesign helper functions can be applied to the same nl object in order to repeat the same experiment with different parameter exploration methods simdesigns. The nl object holds all information on the NetLogo version, a path to the NetLogo directory with the defined version, a path to the model file, and the desired memory for the java virtual machine.
Depending on the operation system, paths to NetLogo and the model need to be adjusted. The experiment object is organized in a similar fashion as NetLogo Behavior Space experiments. It contains all information that is needed to generate a simulation parameter matrix and to execute the NetLogo simulations.
Details on the specific slots of the experiment class can be found in the package documentation? While the experiment defines the variables and specifications of the model, the simulation design creates a parameter input table based on these model specifications and the chosen simulation design method.
In this module you will investigate the evolution of cattle body size affected by different selection mechanisms. In this module you will investigate the effects of different factors on the evolution of coloration in a simulated fish population as well as explore the divergence in allopatry and sympatry.
In this module you will investigate the changes in allele and genotype frequencies affected only by genetic drift and by both genetic drift and natural selection. NetLogo Simulation Modules.
Bark Beetle In this module you will explore forest dynamics resulting from the interaction among bark beetle, spruce forest, temperature, and drought severity. Go to the Lesson Download simulatio. Great Salt Lake In this module you will explore the bird and brine shrimp population dynamics in south arm of the Great Salt Lake resulting from the lake salinity, which is affected by stream inflow, north arm water inflow, and evaporation Download simulation.
Sunflower Inheritance In this module you will investigate monohybrid, dihybrid and trihybrid cross in hypothetical sunflowers. Download simulation Run in NetLogo Web. Ladybug Beetle Inheritance In this module you will investigate the polymorphism resulted from multiple allelism and various dominance mechanisms. Genetic Linkage In this module you will investigate the genetic linkage, including both X-linkage and autosomal linkage.
Loberg Stickleback This module simulates the contemporary evolution of threespine stickleback in Loberg Lake, Alaska Simulation Info Download simulation 5. Rocky Pocket Mice In this module you are able to explore the roles of mutation, heritability, and selection in the process of rocky pocket mouse evolution. Download simulation. Pumpkin Contest A simulation on artificial selection. Coevolution This is a simulation modeling the process of coevolution.
Fish Tank A simulation on artificial selection. Galapagos finches Investigate the effect of different food recources on finch beak depth in this module. To run it, log into Iceberg and start a qrsh session. Then do the following to get access to a more recent version of git. The current script is configured to use 4 cores. You'll be able to go up to 16 but no more. I'm playing with this example a little and will write it up in more detail in due course.
I'm not loving the solution suggested in the above link. Makes it difficult to make decent use of centrally installed software. I'll give it a try but apparently not. Seems I have to cd into the directory containing NetLogo for its extension manager to work. Testing this now. I'm only requesting 2 cores and i actually have to spend time in the queues :. We totally need a development queue Of course if you cd to the centrally installed NetLogo, it attempts to dump the output to that directory and you get permission denied.
So I can't find that extension anywhere in the NetLogo install. However, this time I think that the problem is that I don't have all of the input files. Error message is. I found the extension quite restrictive though and it didn't really execute the functions as I wanted it to. It might be worth another look though. If not I can send again. You sent the data! I think I have everything working. The submission script is currently set to 4 cores which should start relatively quickly.
You can go up to 16 cores but doing so will cause you to be stuck in the queue for a few hours. Might be worth it though! Depends how your job parallelises. There seems to be a problem with your model though. The output file contains millions of these error messages. This causes the output file to be several gigabytes in size -- all of which is error messages! You need to fix this because otherwise you'll run out of memory in your home directory.
Once I've fixed that rather frustrating error that is. I don't remember coming across this before, out of interest I don't suppose the output files gave any indication as to how far through the simulation the error s occurred? No problem if not, either way I'll get onto trying to find a fix for that. No worries tombro I'd be very interested in the outcome and really hope that you get some decent speed ups. Will let you know how it goes. Skip to content.
Star New issue. Jump to bottom. Install Netlogo 5. Copy link.
0コメント