integer out of bounds

[davidhoover]

I installed cryopros like this:

conda create --yes -n CRYOPROS_ENV python==3.12
conda activate CRYOPROS_ENV
pip install torch==2.3.1 torchvision==0.18.1 --extra-index-url https://download.pytorch.org/whl/cu118
wget https://github.com/mxhulab/cryopros/blob/main/cryoPROS-1.0-cp312-cp312-linux_x86_64.whl
git clone https://github.com/mxhulab/cryopros.git
cd cryopros
pip install cryoPROS-1.0-cp312-cp312-linux_x86_64.whl

I downloaded all the example files and ran this command:

cryopros-train \
--opt ${CONDA_ENV_PATH}/lib/python3.12/site-packages/cryoPROS/options/train.json \
--gpu_ids 0 1 2 3 \
--task_name HAtrimer_iteration_1 \
--box_size 256 \
--Apix 1.31 \
--volume_scale 50 \
--init_volume_path 6idd_align_lp10.mrc \
--data_path T00_HA_130K-Equalized-Particle-Stack.mrcs \
--param_path autorefinement.star \
--invert \
--dataloader_batch_size 8

I got this error:

Traceback (most recent call last):
  File "/usr/local/apps/cryopros/1.0.0/mamba/envs/CRYOPROS_ENV/bin/cryopros-train", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "cryoPROS/main_train.py", line 115, in cryoPROS.main_train.main
  File "/usr/local/apps/cryopros/1.0.0/mamba/envs/CRYOPROS_ENV/lib/python3.12/site-packages/cryoPROS/data/dataset.py", line 25, in __init__
    with mrcfile.mmap(self.data_path, mode='r', permissive=True) as mrc:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/apps/cryopros/1.0.0/mamba/envs/CRYOPROS_ENV/lib/python3.12/site-packages/mrcfile/load_functions.py", line 268, in mmap
    return MrcMemmap(name, mode=mode, permissive=permissive)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/apps/cryopros/1.0.0/mamba/envs/CRYOPROS_ENV/lib/python3.12/site-packages/mrcfile/mrcfile.py", line 115, in __init__
    self._read(header_only)
  File "/usr/local/apps/cryopros/1.0.0/mamba/envs/CRYOPROS_ENV/lib/python3.12/site-packages/mrcfile/mrcfile.py", line 131, in _read
    super(MrcFile, self)._read(header_only)
  File "/usr/local/apps/cryopros/1.0.0/mamba/envs/CRYOPROS_ENV/lib/python3.12/site-packages/mrcfile/mrcinterpreter.py", line 173, in _read
    self._read_data()
  File "/usr/local/apps/cryopros/1.0.0/mamba/envs/CRYOPROS_ENV/lib/python3.12/site-packages/mrcfile/mrcmemmap.py", line 112, in _read_data
    self._open_memmap(dtype, shape)
  File "/usr/local/apps/cryopros/1.0.0/mamba/envs/CRYOPROS_ENV/lib/python3.12/site-packages/mrcfile/mrcmemmap.py", line 121, in _open_memmap
    self._data = np.memmap(self._iostream,
                 ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/apps/cryopros/1.0.0/mamba/envs/CRYOPROS_ENV/lib/python3.12/site-packages/numpy/_core/memmap.py", line 277, in __new__
    bytes -= start
OverflowError: Python integer 34078721024 out of bounds for int32

Any clue what to do?

[zhengdihan]

Hi,

It appears this issue is related to numpy>=2.0.0.
Using numpy==1.26.4 should solve this problem.

[davidhoover]

Aha, yes, that worked:

conda create --yes -n CRYOPROS_ENV python==3.12 numpy==1.26.4

Thank you!