climpred on CPU vs GPU
Contents
#!conda create -n ML_gpu tensorflow-gpu pytorch-gpu xarray dask matplotlib nb_conda_kernels jupyterlab cudatoolkit cupy esmtools climpred -y
#!pip install git+https://github.com/jacobtomlinson/cupy-xarray.git
!conda list cupy
# packages in environment at /home/docs/checkouts/readthedocs.org/user_builds/climpred/conda/latest:
#
# Name Version Build Channel
def nvidia_smi():
import subprocess
p = subprocess.check_output('nvidia-smi').strip().decode('utf-8')
return p
climpred on CPU vs GPU#
import xarray as xr
import numpy as np
from climpred.tutorial import load_dataset
from climpred import PerfectModelEnsemble
/home/docs/checkouts/readthedocs.org/user_builds/climpred/conda/latest/lib/python3.9/site-packages/tqdm/auto.py:22: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
from .autonotebook import tqdm as notebook_tqdm
CPU#
v = "tos"
ds3d = load_dataset("MPI-PM-DP-3D")[v]
ds3d.lead.attrs["unit"] = "years"
control3d = load_dataset("MPI-control-3D")[v]
pm_cpu = PerfectModelEnsemble(ds3d)
pm_cpu = pm_cpu.add_control(control3d)
/home/docs/checkouts/readthedocs.org/user_builds/climpred/conda/latest/lib/python3.9/site-packages/xarray/backends/plugins.py:71: RuntimeWarning: Engine 'cfgrib' loading failed:
Cannot find the ecCodes library
warnings.warn(f"Engine {name!r} loading failed:\n{ex}", RuntimeWarning)
/home/docs/checkouts/readthedocs.org/user_builds/climpred/checkouts/latest/climpred/utils.py:195: UserWarning: Assuming annual resolution starting Jan 1st due to numeric inits. Please change ``init`` to a datetime if it is another resolution. We recommend using xr.CFTimeIndex as ``init``, see https://climpred.readthedocs.io/en/stable/setting-up-data.html.
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/climpred/checkouts/latest/climpred/utils.py:195: UserWarning: Assuming annual resolution starting Jan 1st due to numeric inits. Please change ``init`` to a datetime if it is another resolution. We recommend using xr.CFTimeIndex as ``init``, see https://climpred.readthedocs.io/en/stable/setting-up-data.html.
warnings.warn(
type(ds3d.data)
numpy.ndarray
%timeit _ = pm_cpu.mean(['x','y'])
24.9 ms ± 742 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
%timeit skill_cpu = pm_cpu.verify(metric="pearson_r", comparison="m2m", dim=["init", "member"])[v]
533 ms ± 30.9 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
GPU#
import cupy_xarray
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
Cell In[9], line 1
----> 1 import cupy_xarray
ModuleNotFoundError: No module named 'cupy_xarray'
v = "tos"
ds3d = load_dataset("MPI-PM-DP-3D")[v].as_cupy()
ds3d.lead.attrs["unit"] = "years"
control3d = load_dataset("MPI-control-3D")[v].as_cupy()
pm_gpu = PerfectModelEnsemble(ds3d)
pm_gpu = pm_gpu.add_control(control3d)
/mnt/lustre01/pf/zmaw/m300524/climpred/climpred/utils.py:140: UserWarning: Assuming annual resolution due to numeric inits. Change init to a datetime if it is another resolution.
warnings.warn(
type(ds3d.data)
cupy.core.core.ndarray
%timeit _ = pm_gpu.mean(['x','y'])
423 µs ± 15 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)
%timeit skill_gpu = pm_gpu.verify(metric="pearson_r", comparison="m2m", dim=["init", "member"])[v]
64.1 ms ± 11.6 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)
🚀 GPU has the potential to increase verify by factor 10! 🚀
GPU Limitations#
with PerfectModelEnsemble.bootstrap()
pm_gpu.bootstrap(metric="pearson_r", comparison="m2m", dim=["init", "member"], iterations=10)[v]
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-20-45b2445bf7cd> in <module>
----> 1 pm_gpu.bootstrap(metric="pearson_r", comparison="m2m", dim=["init", "member"], iterations=10)[v]
/mnt/lustre01/pf/zmaw/m300524/climpred/climpred/classes.py in bootstrap(self, metric, comparison, dim, reference, iterations, sig, pers_sig, **metric_kwargs)
860 "init": True,
861 }
--> 862 return self._apply_climpred_function(
863 bootstrap_perfect_model,
864 input_dict=input_dict,
/mnt/lustre01/pf/zmaw/m300524/climpred/climpred/classes.py in _apply_climpred_function(self, func, input_dict, **kwargs)
545 if control:
546 control = control.drop_vars(ctrl_vars)
--> 547 return func(ensemble, control, **kwargs)
548
549 def _vars_to_drop(self, init=True):
/mnt/lustre01/pf/zmaw/m300524/climpred/climpred/bootstrap.py in bootstrap_perfect_model(init_pm, control, metric, comparison, dim, reference, resample_dim, sig, iterations, pers_sig, reference_compute, **metric_kwargs)
1259 )
1260 lead_units_equal_control_time_stride(init_pm, control)
-> 1261 return bootstrap_compute(
1262 init_pm,
1263 control,
/mnt/lustre01/pf/zmaw/m300524/climpred/climpred/bootstrap.py in bootstrap_compute(hind, verif, hist, alignment, metric, comparison, dim, reference, resample_dim, sig, iterations, pers_sig, compute, resample_uninit, reference_compute, **metric_kwargs)
899
900 # get confidence intervals CI
--> 901 init_ci = _distribution_to_ci(bootstrapped_init_skill, ci_low, ci_high)
902 if "uninitialized" in reference:
903 uninit_ci = _distribution_to_ci(bootstrapped_uninit_skill, ci_low, ci_high)
/mnt/lustre01/pf/zmaw/m300524/climpred/climpred/bootstrap.py in _distribution_to_ci(ds, ci_low, ci_high, dim)
211 if np.issubdtype(ds.dtype, np.bool_):
212 ds = ds.astype(np.float_) # fails on py>36 if boolean dtype
--> 213 return ds.quantile(q=[ci_low, ci_high], dim=dim, skipna=False)
214
215
/work/mh0727/m300524/conda-envs/ML_gpu/lib/python3.9/site-packages/xarray/core/dataset.py in quantile(self, q, dim, interpolation, numeric_only, keep_attrs, skipna)
5819 # the former is often more efficient
5820 reduce_dims = None
-> 5821 variables[name] = var.quantile(
5822 q,
5823 dim=reduce_dims,
/work/mh0727/m300524/conda-envs/ML_gpu/lib/python3.9/site-packages/xarray/core/variable.py in quantile(self, q, dim, interpolation, keep_attrs, skipna)
1951
1952 axis = np.arange(-1, -1 * len(dim) - 1, -1)
-> 1953 result = apply_ufunc(
1954 _wrapper,
1955 self,
/work/mh0727/m300524/conda-envs/ML_gpu/lib/python3.9/site-packages/xarray/core/computation.py in apply_ufunc(func, input_core_dims, output_core_dims, exclude_dims, vectorize, join, dataset_join, dataset_fill_value, keep_attrs, kwargs, dask, output_dtypes, output_sizes, meta, dask_gufunc_kwargs, *args)
1136 # feed Variables directly through apply_variable_ufunc
1137 elif any(isinstance(a, Variable) for a in args):
-> 1138 return variables_vfunc(*args)
1139 else:
1140 # feed anything else through apply_array_ufunc
/work/mh0727/m300524/conda-envs/ML_gpu/lib/python3.9/site-packages/xarray/core/computation.py in apply_variable_ufunc(func, signature, exclude_dims, dask, output_dtypes, vectorize, keep_attrs, dask_gufunc_kwargs, *args)
722 )
723
--> 724 result_data = func(*input_data)
725
726 if signature.num_outputs == 1:
/work/mh0727/m300524/conda-envs/ML_gpu/lib/python3.9/site-packages/xarray/core/variable.py in _wrapper(npa, **kwargs)
1948 def _wrapper(npa, **kwargs):
1949 # move quantile axis to end. required for apply_ufunc
-> 1950 return np.moveaxis(_quantile_func(npa, **kwargs), 0, -1)
1951
1952 axis = np.arange(-1, -1 * len(dim) - 1, -1)
<__array_function__ internals> in quantile(*args, **kwargs)
TypeError: no implementation found for 'numpy.quantile' on types that implement __array_function__: [<class 'cupy.core.core.ndarray'>, <class 'numpy.ndarray'>]