Giving a group identifier to particles released with each repeatdt timestep

[TomMBIO]

Question

Question

Hi, I am releasing all my particles every 7 days and want to give each group an ID. Initially I tried doing this with a kernel but it did not work, and I don't think it's very useful because the ID shouldn't have to be recalculated with each timestep. How can I achieve something similar, do you have any ideas? Perhaps use a different particle set for each release event?

Supporting code/error messages

extra_vars = [
    Variable('age', dtype=np.float32, initial=0, to_write=False),
    Variable('on_land', dtype=np.int32, to_write=False),
    Variable('temperature', dtype=np.float32),
    Variable('cohort', dtype=np.float32)
]

Particle = JITParticle.add_variables(extra_vars)
 def Cohort(particle, fieldset, time):
  """Assign each release event a cohort ID"""
    cohort = time / repeatdt
    particle.cohort = cohort

# Paste your error message within this block
CalledProcessError                        Traceback (most recent call last)
File ~\anaconda3\envs\parcels\Lib\site-packages\parcels\compilation\codecompiler.py:234, in CCompiler._create_compile_process_(self, cmd, src, log)
    233 try:
--> 234     subprocess.check_call(cmd, stdout=logfile, stderr=logfile)
    235 except OSError:

File ~\anaconda3\envs\parcels\Lib\subprocess.py:413, in check_call(*popenargs, **kwargs)
    412         cmd = popenargs[0]
--> 413     raise CalledProcessError(retcode, cmd)
    414 return 0

CalledProcessError: Command '['gcc', '-Wall', '-fPIC', '-std=gnu11', '-IC:\\Users\\benth\\anaconda3\\envs\\parcels\\Lib\\site-packages\\parcels\\include', '-I.', '-g', '-O3', '-DDOUBLE_COORD_VARIABLES', '-m64', '-o', 'C:\\Users\\benth\\AppData\\Local\\Temp\\parcels-tmp\\lib6be3d00af1d541d45c11aae69e9a90e1_0.dll', 'C:\\Users\\benth\\AppData\\Local\\Temp\\parcels-tmp\\6be3d00af1d541d45c11aae69e9a90e1_0.c', '-shared', '-lm', '-m64']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

RuntimeError                              Traceback (most recent call last)
Cell In[50], line 86
     83 # Define kernels and execute pset
     84 kernels = pset.Kernel(Cohort) + pset.Kernel(Sample_land) + pset.Kernel(Unbeaching) + pset.Kernel(AdvectionRK4) + pset.Kernel(DiffusionUniformKh) + pset.Kernel(SampleT) + pset.Kernel(SampleAge) + pset.Kernel(Particle_death)
---> 86 pset.execute(
     87     kernels,
     88     runtime=runtime,
     89     dt=timedelta(minutes=60),
     90     output_file=output_file)

File ~\anaconda3\envs\parcels\Lib\site-packages\parcels\particleset.py:851, in ParticleSet.execute(self, pyfunc, pyfunc_inter, endtime, runtime, dt, output_file, verbose_progress, postIterationCallbacks, callbackdt)
    849         self.kernel.remove_lib()
    850         cppargs = ['-DDOUBLE_COORD_VARIABLES'] if self.particledata.lonlatdepth_dtype else None
--> 851         self.kernel.compile(compiler=GNUCompiler(cppargs=cppargs, incdirs=[path.join(get_package_dir(), 'include'), "."]))
    852         self.kernel.load_lib()
    853 if output_file:

File ~\anaconda3\envs\parcels\Lib\site-packages\parcels\kernel.py:404, in Kernel.compile(self, compiler)
    402         if self.src_file is not None:
    403             all_files_array.append(self.src_file)
--> 404         compiler.compile(self.src_file, self.lib_file, self.log_file)
    405 if len(all_files_array) > 0:
    406     if self.delete_cfiles is False:

File ~\anaconda3\envs\parcels\Lib\site-packages\parcels\compilation\codecompiler.py:298, in GNUCompiler_SS.compile(self, src, obj, log)
    295 lib_pathdir = os.path.dirname(obj)
    296 obj = os.path.join(lib_pathdir, lib_pathfile)
--> 298 super().compile(src, obj, log)

File ~\anaconda3\envs\parcels\Lib\site-packages\parcels\compilation\codecompiler.py:270, in CCompiler_SS.compile(self, src, obj, log)
    268 with open(log, 'w') as logfile:
    269     logfile.write(f"Compiling: {cc}\n")
--> 270 self._create_compile_process_(cc, src, log)

File ~\anaconda3\envs\parcels\Lib\site-packages\parcels\compilation\codecompiler.py:239, in CCompiler._create_compile_process_(self, cmd, src, log)
    237     except subprocess.CalledProcessError:
    238         with open(log) as logfile2:
--> 239             raise RuntimeError(f"Error during compilation:\n"
    240                                f"Compilation command: {cmd}\n"
    241                                f"Source/Destination file: {src}\n"
    242                                f"Log file: {logfile.name}\n"
    243                                f"Log output: {logfile2.read()}\n"
    244                                f"\n"
    245                                f"If you are on macOS, it might help to type 'export CC=gcc'")
    246 return True

RuntimeError: Error during compilation:
Compilation command: ['gcc', '-Wall', '-fPIC', '-std=gnu11', '-IC:\\Users\\benth\\anaconda3\\envs\\parcels\\Lib\\site-packages\\parcels\\include', '-I.', '-g', '-O3', '-DDOUBLE_COORD_VARIABLES', '-m64', '-o', 'C:\\Users\\benth\\AppData\\Local\\Temp\\parcels-tmp\\lib6be3d00af1d541d45c11aae69e9a90e1_0.dll', 'C:\\Users\\benth\\AppData\\Local\\Temp\\parcels-tmp\\6be3d00af1d541d45c11aae69e9a90e1_0.c', '-shared', '-lm', '-m64']
Source/Destination file: C:\Users\benth\AppData\Local\Temp\parcels-tmp\6be3d00af1d541d45c11aae69e9a90e1_0.c
Log file: C:\Users\benth\AppData\Local\Temp\parcels-tmp\6be3d00af1d541d45c11aae69e9a90e1_0.log
Log output: C:\Users\benth\AppData\Local\Temp\parcels-tmp\6be3d00af1d541d45c11aae69e9a90e1_0.c:1:0: warning: -fPIC ignored for target (all code is position independent)
 #include "parcels.h"
 ^
C:\Users\benth\AppData\Local\Temp\parcels-tmp\6be3d00af1d541d45c11aae69e9a90e1_0.c: In function 'CohortSample_landUnbeachingAdvectionRK4DiffusionUniformKhSampleTSampleAgeParticle_death':
C:\Users\benth\AppData\Local\Temp\parcels-tmp\6be3d00af1d541d45c11aae69e9a90e1_0.c:78:20: error: 'repeatdt' undeclared (first use in this function)
   cohort = (time / repeatdt);
                    ^
C:\Users\benth\AppData\Local\Temp\parcels-tmp\6be3d00af1d541d45c11aae69e9a90e1_0.c:78:20: note: each undeclared identifier is reported only once for each function it appears in


If you are on macOS, it might help to type 'export CC=gcc'

[erikvansebille]

Hi @TomMBIO, thanks for this question

I think the easiest approach is to not use repeatdt but instead create the whole particles with different starting times at the beginning; then you can also set a identifier for each particle when you create the ParticleSet.

cohort = ... # Here code to create an array that calculates the cohort number for each particle
pset = ParticleSet(fieldset=fieldset, pclass=parcels.JITParticle, lon=lon, lat=lat, time=time, cohort=cohort)

See also the assigning each particle its own time section of the delayed start tutorial.

Note, by the way, that for Variables that don't change, you can use to_write='once' when you create them:

Variable('cohort', dtype=np.float32, to_write='once')

Does that help?

[TomMBIO]

Hi Erik,

Thanks for your response,

For this purpose would it be worth creating a loop, something like this? A loop that updates the cohort number and release time after the particle set is done running, and then runs another pset with these values. I'm not sure of the specifics of how to do this, but I imagine it would look something like this:

iterations = range(9)  # Say to simulate for 9 weeks
psets = [] 

cohort = 0  
release_time = 0

for i in iterations:
    # Create a new ParticleSet for each iteration with updated release time and cohort ID
    pset = ParticleSet(
        fieldset=fieldset,
        pclass=JITParticle,
        lon=lon,
        lat=lat,
        time=release_time, 
        cohort=cohort 
    )
    
    psets.append(pset)
    
    # Execute the simulation for this ParticleSet
    pset.execute(
        kernels,
        runtime=timedelta(hours=4380), 
        dt=timedelta(minutes=60),
        output_file=<my_filepath>  
    )
    
    # Increment the cohort ID and release time for the next batch of particles
    cohort += 1
    release_time += timedelta(days=7)

Does this seem like a reasonable solution? Sorry if this is extremely obvious, still new to all this.

Cheers,
Tom

[VeckoTheGecko]

Hi @TomMBIO , yes, that looks like it should work. minor note is that release_time would need to be a datetime object.

So something like

+ from datetime import datetime, timedelta
iterations = range(9)  # Say to simulate for 9 weeks
psets = [] 

cohort = 0  
- release_time = 0
+ # Create a datetime object for October 3, 2024, at 14:30:00
+ release_time = datetime(2024, 10, 3, 14, 30, 0)
for i in iterations:
    # Create a new ParticleSet for each iteration with updated release time and cohort ID
    pset = ParticleSet(
        fieldset=fieldset,
        pclass=JITParticle,
        lon=lon,
        lat=lat,
        time=release_time, 
        cohort=cohort 
    )
    
    psets.append(pset)
    
    # Execute the simulation for this ParticleSet
    pset.execute(
        kernels,
        runtime=timedelta(hours=4380), 
        dt=timedelta(minutes=60),
        output_file=<my_filepath>  
    )
    
    # Increment the cohort ID and release time for the next batch of particles
    cohort += 1
    release_time += timedelta(days=7)

[TomMBIO]

Great I'll give this a shot, thanks both!

Tom