Error with compiler on Windows

[xiazhu111]

Question

Question

Hi, I keep running into an error when I try to execute the ParticleSet, from the Parcels tutorial webpage. I use Windows 10 Pro on a 64-bit operating system. I am using Visual Studio Code to run Python 3.12.3. Can you help me figure out the problem? My code and the error messages can be found below.

# Code
#import relevant packages
import math
from datetime import timedelta
from operator import attrgetter

import matplotlib.pyplot as plt
import numpy as np
import trajan as ta
import xarray as xr
from IPython.display import HTML
from matplotlib.animation import FuncAnimation

import parcels

#run particles by first defining a FieldSet or a collection of hydrodynamic fields
example_dataset_folder = parcels.download_example_dataset("MovingEddies_data")
fieldset = parcels.FieldSet.from_parcels(f"{example_dataset_folder}/moving_eddies") #zonal velocities
print(fieldset)

#load the first time frame of the field set
fieldset.computeTimeChunk()

plt.pcolormesh(fieldset.U.grid.lon, fieldset.U.grid.lat, fieldset.U.data[0,:,:])
plt.xlabel("Zonal distance [m]")
plt.ylabel("Meridional distance [m]")
plt.colorbar()
plt.show()

#define a ParticleSet, start with 2 particles at locations (330km, 100km) and (330km, 280km)
#particles will be advected on the fieldset we defined above
pset = parcels.ParticleSet.from_list(
    fieldset=fieldset, #the fields on which the particles are advected
    pclass=parcels.JITParticle, #the type of particles (JITParticle or ScipyParticle)
    lon=[3.3e5, 3.3e5], #a vector of release longitudes
    lat=[1e5, 2.8e5], #a vector of release latitudes 
)

#print the ParticleSet to see where they the 2 particles start
#output shows (longitude, latitude, depth, time). time is "not_yet_set" because we did not specify a time when we defined pset
print(pset)

#plot positions of particles on the zonal velocity
plt.pcolormesh(fieldset.U.grid.lon, fieldset.U.grid.lat, fieldset.U.data[0,:,:])
plt.xlabel("Zonal distance [m]")
plt.ylabel("Meridional distance [m]")
plt.colorbar()

plt.plot(pset.lon, pset.lat, "ko")
plt.show()

#create ParticleFile object to store the output of the particles at every one-hour interval 
output_file = pset.ParticleFile(
    name="EddyParticles.zarr", #the file name
    outputdt=timedelta(hours=1) #the time step of the outputs
)

print(output_file)

#final step is to run or execute the ParticleSet, i.e. move the particles forward in time
#because time was "not_yet_set", the particles will be advected from the first data available in the fieldset, which is the default behaviour
pset.execute(
    parcels.AdvectionRK4, #the kernel (which defines how particles move)
    runtime=timedelta(days=6), #the total length of the run
    dt=timedelta(minutes=5), #the timestep of the kernel
    output_file=output_file, #every time particles are executed, output file is updated, I believe
)

# Error messages
Traceback (most recent call last):
  File "C:\Users\pc\Desktop\Alice\parcels_tutorials (v3.1.0)\.venv\Lib\site-packages\parcels\compilation\codecompiler.py", line 235, in _create_compile_process_
    subprocess.check_call(cmd, stdout=logfile, stderr=logfile)
  File "C:\Users\pc\AppData\Local\Programs\Python\Python312\Lib\subprocess.py", line 413, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['gcc', '-Wall', '-fPIC', '-std=gnu11', '-IC:\\Users\\pc\\Desktop\\Alice\\Software\\parcels_tutorials (v3.1.0)\\.venv\\Lib\\site-packages\\parcels\\include', '-I.', '-g', '-O3', '-DDOUBLE_COORD_VARIABLES', 
'-m64', '-o', 'C:\\Users\\pc\\AppData\\Local\\Temp\\parcels-tmp\\lib619ccf35f0f8c1332826baadcd0f4ce7_0.dll', 'C:\\Users\\pc\\AppData\\Local\\Temp\\parcels-tmp\\619ccf35f0f8c1332826baadcd0f4ce7_0.c', '-shared', '-lm', '-m64']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "c:\Users\pc\Desktop\Alice\Software\parcels_tutorials (v3.1.0)\.venv\quickstarttoparcels.py", line 67, in <module>
    pset.execute(
  File "C:\Users\pc\Desktop\Alice\Software\parcels_tutorials (v3.1.0)\.venv\Lib\site-packages\parcels\particleset.py", line 1051, in execute
    self._kernel.compile(
  File "C:\Users\pc\Desktop\Alice\Software\parcels_tutorials (v3.1.0)\.venv\Lib\site-packages\parcels\kernel.py", line 483, in compile
    compiler.compile(self.src_file, self.lib_file, self.log_file)
  File "C:\Users\pc\Desktop\Alice\Software\parcels_tutorials (v3.1.0)\.venv\Lib\site-packages\parcels\compilation\codecompiler.py", line 311, in compile
    super().compile(src, obj, log)
  File "C:\Users\pc\Desktop\Alice\Software\parcels_tutorials (v3.1.0)\.venv\Lib\site-packages\parcels\compilation\codecompiler.py", line 275, in compile
    self._create_compile_process_(cc, src, log)
  File "C:\Users\pc\Desktop\Alice\Software\parcels_tutorials (v3.1.0)\.venv\Lib\site-packages\parcels\compilation\codecompiler.py", line 240, in _create_compile_process_
    raise RuntimeError(
RuntimeError: Error during compilation:
Compilation command: ['gcc', '-Wall', '-fPIC', '-std=gnu11', '-IC:\\Users\\pc\\Desktop\\Alice\\Software\\parcels_tutorials (v3.1.0)\\.venv\\Lib\\site-packages\\parcels\\include', '-I.', '-g', '-O3', '-DDOUBLE_COORD_VARIABLES', '-m64', '-o', 'C:\\Users\\pc\\AppData\\Local\\Temp\\parcels-tmp\\lib619ccf35f0f8c1332826baadcd0f4ce7_0.dll', 'C:\\Users\\pc\\AppData\\Local\\Temp\\parcels-tmp\\619ccf35f0f8c1332826baadcd0f4ce7_0.c', '-shared', '-lm', '-m64']
Source/Destination file: C:\Users\pc\AppData\Local\Temp\parcels-tmp\619ccf35f0f8c1332826baadcd0f4ce7_0.c
Log file: C:\Users\pc\AppData\Local\Temp\parcels-tmp\619ccf35f0f8c1332826baadcd0f4ce7_0.log
Log output: cc1.exe: error: unrecognized command line option "-std=gnu11"
C:\Users\pc\AppData\Local\Temp\parcels-tmp\619ccf35f0f8c1332826baadcd0f4ce7_0.c:1: warning: -fPIC ignored for target (all code is position independent)
C:\Users\pc\AppData\Local\Temp\parcels-tmp\619ccf35f0f8c1332826baadcd0f4ce7_0.c:1: sorry, unimplemented: 64-bit mode not compiled in

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

[erikvansebille]

This seems the same issue as #1753 from three days ago. Does the solution at #1753 (comment) also work for you?

@VeckoTheGecko, it seems newer versions of gcc don't support -m64 anymore; should we fix this in Parcels and release an update?

[xiazhu111]

I tried it and it didn't work, but also I just realized I am not using miniconda. I am going to install that first and try everything again!

[xiazhu111]

Okay the original Parcels tutorial code worked without having to modify the codecompiler.py file! Thank you!

[VeckoTheGecko]

Hi @xiazhu111 . Did you originally install Parcels through pip? Miniconda is more reliable (especially when on Windows) since it can also install the C compiler dependencies that we have.

[xiazhu111]

Yes that is correct, I originally installed the Parcels package using pip. I tried again with miniconda and it worked. Thank you!