Known problems solutions - NOC-MSM/Belize_workshop GitHub Wiki
Known problems and solution
- wget or mpirun commands not working
If you are not using Linux, probably you do not have those commands natively in your OS. However, as we are working inside a Docker container with Linux on it, you must be able to run wget and mpirun with no problem.
Make sure you are using the commands INSIDE the docker container. Remember that you must have Docker already installed in your PC and use the following command in the Docker prompt:
docker run -v $HOME/Belize_workshop:/Belize_workshop -t -i jelt/nemocompile:firsttry /bin/bash
- wget is working but does not download anything
If your wget command stays in a loop while trying to download the files, it is very likely that the files have been deleted from the FTP server. Please contact us so we can re-upload the files.
- mpirun is aborting a process/not running properly
You may experience this problem when running the code line:
mpirun -n 3 ./nemo.exe : -n 1 ./xios_server.exe
The cause of this problem is the lack of essential files in the EXP_DEMO folder. You must double check that you have ALL the essential files listed in the third part of this tutorial inside your EXP_DEMO folder. Beware that you may have a second EXP_DEMO folder inside your parent EXP_DEMO folder, if this is the case you need to transfer all the files to the parent folder and run the code again.
Remember that this code takes some time to run and its output in the console should look like a performance report.
- tinyBelize_Parcels.py not running
If you are not able to run the script succesfully, you may end with a folder as output, with a name like "out-XXXXX".
This problem can be solved by changing a code line from the script:
Open the python script with any IDE or your notepad, go to the bottom of the script and find the code line:
pset.execute(kernels, runtime=delta(days=0.5), dt=delta(hours=0.1), output_file=pfile)
Comment out or delete that code line and replace it for this one:
pset.execute(kernels, runtime=delta(hours=0.5), dt=delta(hours=0.1), output_file=ParticleFile("TestResult", pset, outputdt=delta(hours=0.1)))
You can replace the name "TestResult" for whichever you want, or just leave it like that. We will also need to change the file to plot in the VisualizeParticles script as explained in the following point.
- visualizeParticles.py not running
If you followed the previous point, you will have to open this script as well and go to this line:
plotTrajectoriesFile('YourFileName.nc');
You have to change YourFileName for whichever name you gave it in the previous point (by default it would be TestResult.nc.
- visualizeParticles.py not saving figure/error with plt.savefig
If you have this problem, open this script (with any IDE or your notepad) and go to the code line:
plt.savefig('./pFIGURES/postTrajPlotT1.png', dpi=100)
Change the directory ./pFIGURES/postTrajPlotT1.png and write instead any name you want for your file. Take as example the following code:
plt.savefig('postTrajPlotT1.png', dpi=100)
This is a workaround for the problem, as now the code will not save figures inside the FIGURES folder but it will save them inside the PARCELS_DEMO folder (where we are running the script).
- Not enough space in disk when installing Miniconda or downloading/installing a library inside a Docker container
To solve this problem, you will have to exit whichever container you are in and type inside the Docker prompt:
docker system prune
Select yes and wait for the process to finish.
Once done you should be able to install Miniconda or install any library inside your container.
- I already installed Miniconda/Parcels but I cannot activate it
If you closed your Docker container after installing any of those, you will have to install them again following the same process.
You may experience a "Not enough space in disk" error, so I suggest you to follow the steps of the previous point before repeating the process.
- Found a error/fix? Send us a message and we will help you or add it to this section!