numpy version causing runtime error #5
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Hi Yk, This it seems like a numpy problem, it is probably worthy to reinstall the newer numpy. please see my conda list for your info: Name Version Build Channel_libgcc_mutex 0.1 main |
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Thanks! May I also ask if the cuDNN is required for the reconstruction and Misalignments Correction in RELION? From Miniconda, using 'conda search' with default and Nvidia channels, the only cuDNN versions available and greater than 8 are 8.2 and 8.9. I am not sure which one I need, or if cuDNN is not required. Thank You |
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Hi, There are cudnn in "anaconda" channel and also the "conda-forge" channel. Also you can do the manually install by downloading from official Nvidia website. I will try to standardize the installation in the near future because many complains are raised related to pytorch and cuda. |
Hi,
I am testing the software on Ubuntu 22.04.4 with an Intel CPU and Nvidia 4090. Using the yml file provided to create a conda env using miniconda, I have encountered a runtime error while generating the 3DSFC map by saying:
~/spIsoNet_tutorial$ spisonet.py fsc3d emd_8731_half_map_1.mrc emd_8731_half_map_2.mrc emd_8731_msk_1.mrc --ncpus 16 --limit_res 3.5 04-16 15:34:42, INFO Limit resolution to 3.5 for spIsoNet 3D FSC calculation. You can also tune this paramerter with --limit_res . 04-16 15:34:42, INFO calculating fast 3DFSC, this will take few minutes 100%|███████████████████████████████████████████| 95/95 [00:03<00:00, 31.27it/s] 99%|██████████████████████████████████████████▌| 94/95 [00:06<00:00, 5.77it/s]Traceback (most recent call last): File "/home/ykgong/miniconda3/envs/spisonet/lib/python3.10/multiprocessing/pool.py", line 138, in worker task = job = result = func = args = kwds = None RuntimeError: Object of type <class 'numpy.ndarray'> appears to be C subclassed NumPy array, void scalar, or allocated in a non-standard way.NumPy reserves the right to change the size of these structures. Projects are required to take this into account by either recompiling against a specific NumPy version or padding the struct and enforcing a maximum NumPy version. Exception ignored in: 'PyDataMem_UserFREE' Traceback (most recent call last): File "/home/ykgong/miniconda3/envs/spisonet/lib/python3.10/multiprocessing/pool.py", line 138, in worker task = job = result = func = args = kwds = None ValueError: PyCapsule_GetPointer called with invalid PyCapsule object Traceback (most recent call last): File "/home/ykgong/miniconda3/envs/spisonet/lib/python3.10/multiprocessing/pool.py", line 138, in worker task = job = result = func = args = kwds = None RuntimeError: Object of type <class 'numpy.ndarray'> appears to be C subclassed NumPy array, void scalar, or allocated in a non-standard way.NumPy reserves the right to change the size of these structures. Projects are required to take this into account by either recompiling against a specific NumPy version or padding the struct and enforcing a maximum NumPy version. Exception ignored in: 'PyDataMem_UserFREE' Traceback (most recent call last): File "/home/ykgong/miniconda3/envs/spisonet/lib/python3.10/multiprocessing/pool.py", line 138, in worker task = job = result = func = args = kwds = None ValueError: PyCapsule_GetPointer called with invalid PyCapsule object Traceback (most recent call last): File "/home/ykgong/miniconda3/envs/spisonet/lib/python3.10/multiprocessing/pool.py", line 138, in worker task = job = result = func = args = kwds = None RuntimeError: Object of type <class 'numpy.ndarray'> appears to be C subclassed NumPy array, void scalar, or allocated in a non-standard way.NumPy reserves the right to change the size of these structures. Projects are required to take this into account by either recompiling against a specific NumPy version or padding the struct and enforcing a maximum NumPy version. Exception ignored in: 'PyDataMem_UserFREE' Traceback (most recent call last): File "/home/ykgong/miniconda3/envs/spisonet/lib/python3.10/multiprocessing/pool.py", line 138, in worker task = job = result = func = args = kwds = None ValueError: PyCapsule_GetPointer called with invalid PyCapsule object 100%|███████████████████████████████████████████| 95/95 [00:07<00:00, 12.31it/s]I am not sure if the 3DFSC is generated correctly. I have attached the exact dependencies txt file from my conda env.
Do you have any suggestions?
req.txt
Thank you!
YK
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