search

xgcm / xgcm-examples

Examples and tutorials for xgcm
MIT License
12 stars 12 forks source link

environment: importing from xgcm bad on sciserver #20

Open gjayb opened 2 years ago

gjayb commented 2 years ago

I'm trying to follow along from some of these sample notebooks but can't figure out the environment. I'm on sciserver. I have installed xgcm (it does appear in !conda list). Can y'all help interpret this?

Traceback:

TypingErrorTraceback (most recent call last)

in ----> 1 from xgcm import Grid 2 from xgcm.autogenerate import generate_grid_ds ~/miniconda3/envs/py37/lib/python3.7/site-packages/xgcm/__init__.py in 4 __version__ = "unknown" 5 ----> 6 from .autogenerate import generate_grid_ds 7 from .grid import Axis, Grid ~/miniconda3/envs/py37/lib/python3.7/site-packages/xgcm/autogenerate.py in 1 import xarray as xr 2 ----> 3 from xgcm.grid import Axis, raw_interp_function 4 5 ~/miniconda3/envs/py37/lib/python3.7/site-packages/xgcm/grid.py in 15 import numba 16 ---> 17 from .transform import conservative_interpolation, linear_interpolation 18 except ImportError: 19 numba = None ~/miniconda3/envs/py37/lib/python3.7/site-packages/xgcm/transform.py in 17 ], 18 "(n),(n),(m),(),()->(m)", ---> 19 nopython=True, 20 ) 21 def _interp_1d_linear( ~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/npyufunc/decorators.py in wrap(func) 177 guvec = GUVectorize(func, signature, **kws) 178 for fty in ftylist: --> 179 guvec.add(fty) 180 return guvec.build_ufunc() 181 ~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/npyufunc/ufuncbuilder.py in add(self, sig) 194 targetoptions = self.nb_func.targetoptions 195 cres, args, return_type = _compile_element_wise_function( --> 196 self.nb_func, targetoptions, sig) 197 sig = self._finalize_signature(cres, args, return_type) 198 self._sigs.append(sig) ~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/npyufunc/ufuncbuilder.py in _compile_element_wise_function(nb_func, targetoptions, sig) 128 # Do compilation 129 # Return CompileResult to test --> 130 cres = nb_func.compile(sig, **targetoptions) 131 args, return_type = sigutils.normalize_signature(sig) 132 return cres, args, return_type ~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/npyufunc/ufuncbuilder.py in compile(self, sig, locals, **targetoptions) 77 flags.unset("enable_looplift") 78 ---> 79 return self._compile_core(sig, flags, locals) 80 81 def _compile_core(self, sig, flags, locals): ~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/npyufunc/ufuncbuilder.py in _compile_core(self, sig, flags, locals) 112 self.py_func, args=args, 113 return_type=return_type, --> 114 flags=flags, locals=locals) 115 116 # cache lookup failed before so safe to save ~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler.py in compile_extra(typingctx, targetctx, func, args, return_type, flags, locals, library, pipeline_class) 970 pipeline = pipeline_class(typingctx, targetctx, library, 971 args, return_type, flags, locals) --> 972 return pipeline.compile_extra(func) 973 974 ~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler.py in compile_extra(self, func) 388 self.lifted = () 389 self.lifted_from = None --> 390 return self._compile_bytecode() 391 392 def compile_ir(self, func_ir, lifted=(), lifted_from=None): ~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler.py in _compile_bytecode(self) 901 """ 902 assert self.func_ir is None --> 903 return self._compile_core() 904 905 def _compile_ir(self): ~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler.py in _compile_core(self) 888 self.define_pipelines(pm) 889 pm.finalize() --> 890 res = pm.run(self.status) 891 if res is not None: 892 # Early pipeline completion ~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler_lock.py in _acquire_compile_lock(*args, **kwargs) 30 def _acquire_compile_lock(*args, **kwargs): 31 with self: ---> 32 return func(*args, **kwargs) 33 return _acquire_compile_lock 34 ~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler.py in run(self, status) 264 # No more fallback pipelines? 265 if is_final_pipeline: --> 266 raise patched_exception 267 # Go to next fallback pipeline 268 else: ~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler.py in run(self, status) 255 try: 256 event("-- %s" % stage_name) --> 257 stage() 258 except _EarlyPipelineCompletion as e: 259 return e.result ~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler.py in stage_nopython_frontend(self) 513 self.args, 514 self.return_type, --> 515 self.locals) 516 self.typemap = typemap 517 self.return_type = return_type ~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler.py in type_inference_stage(typingctx, interp, args, return_type, locals) 1122 1123 infer.build_constraint() -> 1124 infer.propagate() 1125 typemap, restype, calltypes = infer.unify() 1126 ~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/typeinfer.py in propagate(self, raise_errors) 925 if errors: 926 if raise_errors: --> 927 raise errors[0] 928 else: 929 return errors TypingError: Failed in nopython mode pipeline (step: nopython frontend) Invalid use of Function() with argument(s) of type(s): (array(float32, 1d, A), array(float32, 1d, A), array(float32, 1d, A)) * parameterized In definition 0: TypingError: Failed in nopython mode pipeline (step: nopython frontend) Invalid use of Function(.impl at 0x7f44f60215f0>) with argument(s) of type(s): (array(float32, 1d, A), array(float32, 1d, A), array(float32, 1d, A), dtype(float64)) * parameterized In definition 0: TypingError: Failed in nopython mode pipeline (step: nopython frontend) Cannot unify array(float32, 1d, C) and array(float64, 1d, C) for 'slopes', defined at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2120) File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2120: def impl(x, xp, fp, dtype): if lenxp <= lenx: slopes = (dy[1:] - dy[:-1]) / (dx[1:] - dx[:-1]) ^ [1] During: typing of assignment at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2122) File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2122: def impl(x, xp, fp, dtype): else: slopes = np.empty(0, dtype=dtype) ^ raised from /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/typeinfer.py:927 In definition 1: TypingError: Failed in nopython mode pipeline (step: nopython frontend) Cannot unify array(float32, 1d, C) and array(float64, 1d, C) for 'slopes', defined at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2120) File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2120: def impl(x, xp, fp, dtype): if lenxp <= lenx: slopes = (dy[1:] - dy[:-1]) / (dx[1:] - dx[:-1]) ^ [1] During: typing of assignment at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2122) File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2122: def impl(x, xp, fp, dtype): else: slopes = np.empty(0, dtype=dtype) ^ raised from /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/typeinfer.py:927 This error is usually caused by passing an argument of a type that is unsupported by the named function. [1] During: resolving callee type: Function(.impl at 0x7f44f60215f0>) [2] During: typing of call at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2237) File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2237: def np_interp_impl(x, xp, fp): return inner(x, xp, fp, dtype) ^ raised from /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/typeinfer.py:927 In definition 1: TypingError: Failed in nopython mode pipeline (step: nopython frontend) Invalid use of Function(.impl at 0x7f44f60215f0>) with argument(s) of type(s): (array(float32, 1d, A), array(float32, 1d, A), array(float32, 1d, A), dtype(float64)) * parameterized In definition 0: TypingError: Failed in nopython mode pipeline (step: nopython frontend) Cannot unify array(float32, 1d, C) and array(float64, 1d, C) for 'slopes', defined at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2120) File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2120: def impl(x, xp, fp, dtype): if lenxp <= lenx: slopes = (dy[1:] - dy[:-1]) / (dx[1:] - dx[:-1]) ^ [1] During: typing of assignment at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2122) File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2122: def impl(x, xp, fp, dtype): else: slopes = np.empty(0, dtype=dtype) ^ raised from /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/typeinfer.py:927 In definition 1: TypingError: Failed in nopython mode pipeline (step: nopython frontend) Cannot unify array(float32, 1d, C) and array(float64, 1d, C) for 'slopes', defined at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2120) File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2120: def impl(x, xp, fp, dtype): if lenxp <= lenx: slopes = (dy[1:] - dy[:-1]) / (dx[1:] - dx[:-1]) ^ [1] During: typing of assignment at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2122) File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2122: def impl(x, xp, fp, dtype): else: slopes = np.empty(0, dtype=dtype) ^ raised from /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/typeinfer.py:927 This error is usually caused by passing an argument of a type that is unsupported by the named function. [1] During: resolving callee type: Function(.impl at 0x7f44f60215f0>) [2] During: typing of call at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2237) File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2237: def np_interp_impl(x, xp, fp): return inner(x, xp, fp, dtype) ^ raised from /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/typeinfer.py:927 This error is usually caused by passing an argument of a type that is unsupported by the named function. [1] During: resolving callee type: Function() [2] During: typing of call at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/xgcm/transform.py (31) File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/xgcm/transform.py", line 31: def _interp_1d_linear( output[:] = np.interp(target_theta_levels, theta, phi) ^
jbusecke commented 2 years ago

This is xgcm transform, right? Can you post the line where you are actually calling this? It seems like there is an issue with the types of data being put in. If you could post a type(variable) for all inputs to grid.transform(...), that might help. In general this could also be an issue with numba (which is an optional dependency for this fuctionality only), could you also print and post the numba version in your environment?