Importing pyqg before torch, or importing xarray before torch crashes the ood kernel. When running on command line I get:
[cp3759@cm005 torch_qg]$ sing
coSingularity> cond
Singularity> python3
Python 3.9.12 (main, Apr 5 2022, 06:56:58)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyqg
>>> import torch_qg.model as torch_model
>>> import torch
>>> m32=torch_model.PseudoSpectralModel(nx=256,dtype=torch.float32)
CUDA Not Available, using CPU
/ext3/miniconda3/lib/python3.9/site-packages/torch/functional.py:504: UserWarning: torch.meshgrid: in an upcoming release, it will be required to pass the indexing argument. (Triggered internally at ../aten/src/ATen/native/TensorShape.cpp:3483.)
return _VF.meshgrid(tensors, **kwargs) # type: ignore[attr-defined]
python3: symbol lookup error: /ext3/miniconda3/lib/python3.9/site-packages/mkl/../../../libmkl_intel_thread.so.1: undefined symbol: __kmpc_global_thread_num
Singularity> python3
Python 3.9.12 (main, Apr 5 2022, 06:56:58)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import xarray as xr
>>> import torch
>>> quit()
Singularity> python3
Python 3.9.12 (main, Apr 5 2022, 06:56:58)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import torch
>>> import xarray as xr
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/ext3/miniconda3/lib/python3.9/site-packages/xarray/__init__.py", line 3, in <module>
from xarray import testing, tutorial
File "/ext3/miniconda3/lib/python3.9/site-packages/xarray/testing.py", line 8, in <module>
import pandas as pd
File "/ext3/miniconda3/lib/python3.9/site-packages/pandas/__init__.py", line 48, in <module>
from pandas.core.api import (
File "/ext3/miniconda3/lib/python3.9/site-packages/pandas/core/api.py", line 48, in <module>
from pandas.core.groupby import (
File "/ext3/miniconda3/lib/python3.9/site-packages/pandas/core/groupby/__init__.py", line 1, in <module>
from pandas.core.groupby.generic import (
File "/ext3/miniconda3/lib/python3.9/site-packages/pandas/core/groupby/generic.py", line 70, in <module>
from pandas.core.frame import DataFrame
File "/ext3/miniconda3/lib/python3.9/site-packages/pandas/core/frame.py", line 157, in <module>
from pandas.core.generic import NDFrame
File "/ext3/miniconda3/lib/python3.9/site-packages/pandas/core/generic.py", line 152, in <module>
from pandas.core.window import (
File "/ext3/miniconda3/lib/python3.9/site-packages/pandas/core/window/__init__.py", line 1, in <module>
from pandas.core.window.ewm import ( # noqa:F401
File "/ext3/miniconda3/lib/python3.9/site-packages/pandas/core/window/ewm.py", line 12, in <module>
import pandas._libs.window.aggregations as window_aggregations
ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /ext3/miniconda3/lib/python3.9/site-packages/pandas/_libs/window/aggregations.cpython-39-x86_64-linux-gnu.so)