Module 'numpy' has no attribute 'asscalar'

[ABignaud]

Instagraal is not workinng with numpy 1.23.0 as numpy asscalar function has been removed. Use numpy 1.22.4 or below.

̍""" INFO :: Selected_device: Quadro P2200 INFO :: filtering already done... WARNING :: /home/usr/repo/instaGRAAL/instagraal/pyramid_sparse.py:122: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details. pyramid_handle = h5py.File(hdf5_pyramid_file)

INFO :: level already built... INFO :: level already built INFO :: level already built INFO :: level already built INFO :: level already built INFO :: level already built INFO :: level already built INFO :: level already built INFO :: level already built INFO :: pyramid built. INFO :: init pyramid WARNING :: /home/usr/repo/instaGRAAL/instagraal/pyramid_sparse.py:1532: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details. self.data = h5py.File(self.pyramid_file)

INFO :: pyramid loaded INFO :: loading data from level = 4 INFO :: import reference genome INFO :: loading data from level = 3 INFO :: mean frag area = 488.21014404296875 INFO :: N frag duplicated = 0 INFO :: MAX ID CONTIG = 375 INFO :: total mem used by sparse data = 0.97566 Traceback (most recent call last): File "/usr/local/bin/instagraal", line 11, in load_entry_point('instagraal', 'console_scripts', 'instagraal')() File "/home/usr/repo/instaGRAAL/instagraal/instagraal.py", line 2150, in main p2 = window( File "/home/usr/repo/instaGRAAL/instagraal/instagraal.py", line 213, in init self.simulation = simulation( File "/home/usr/repo/instaGRAAL/instagraal/simu_single.py", line 139, in init self.sampler = sampler_lib( File "/home/usr/repo/instaGRAAL/instagraal/cuda_lib_gl_single.py", line 254, in init self.setup_all_gpu_struct() File "/home/usr/repo/instaGRAAL/instagraal/cuda_lib_gl_single.py", line 378, in setup_all_gpu_struct self.gpu_list_len_cont = ga.zeros(self.n_frags, dtype=np.int32) File "/usr/local/lib/python3.8/dist-packages/pycuda-2020.1-py3.8-linux-x86_64.egg/pycuda/gpuarray.py", line 1209, in zeros result = GPUArray(shape, dtype, allocator, order=order) File "/usr/local/lib/python3.8/dist-packages/pycuda-2020.1-py3.8-linux-x86_64.egg/pycuda/gpuarray.py", line 219, in init s = np.asscalar(s) File "/home/usr/.local/lib/python3.8/site-packages/numpy/init.py", line 311, in getattr raise AttributeError("module {!r} has no attribute " AttributeError: module 'numpy' has no attribute 'asscalar' #------------------------------------------------------------------- PyCUDA ERROR: The context stack was not empty upon module cleanup. #------------------------------------------------------------------- A context was still active when the context stack was being cleaned up. At this point in our execution, CUDA may already have been deinitialized, so there is no way we can finish cleanly. The program will be aborted now. Use Context.pop() to avoid this problem. #------------------------------------------------------------------- Aborted (core dumped) """