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google-deepmind / ferminet

An implementation of the Fermionic Neural Network for ab-initio electronic structure calculations
Apache License 2.0
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ValueError: Using default_file_mode other than 'r' is no longer supported. Pass the mode to h5py.File() instead. JAX branch. #32

Closed ghost closed 3 years ago

ghost commented 3 years ago

Hi, I am trying to run (with the JAX branch):

ferminet --config ferminet/configs/atom.py --config.system.atom Li --config.batch_size 256 --config.pretrain.iterations 100

I am getting this error:

ValueError: Using default_file_mode other than 'r' is no longer supported. Pass the mode to h5py.File() instead.

Here is the full error:

Traceback (most recent call last): File "/home/ben/miniconda3/envs/sch_eqn/bin/ferminet", line 7, in exec(compile(f.read(), file, 'exec')) File "/home/ben/Documents/sch_eqn/ferminet_jax/bin/ferminet", line 21, in from ferminet import train File "/home/ben/Documents/sch_eqn/ferminet_jax/ferminet/train.py", line 25, in from ferminet import hamiltonian File "/home/ben/Documents/sch_eqn/ferminet_jax/ferminet/hamiltonian.py", line 17, in from ferminet import networks File "/home/ben/Documents/sch_eqn/ferminet_jax/ferminet/networks.py", line 21, in from ferminet.utils import scf File "/home/ben/Documents/sch_eqn/ferminet_jax/ferminet/utils/scf.py", line 38, in import pyscf File "/home/ben/miniconda3/envs/sch_eqn/lib/python3.7/site-packages/pyscf/init.py", line 71, in from pyscf import lib File "/home/ben/miniconda3/envs/sch_eqn/lib/python3.7/site-packages/pyscf/lib/init.py", line 24, in from pyscf.lib import numpy_helper File "/home/ben/miniconda3/envs/sch_eqn/lib/python3.7/site-packages/pyscf/lib/numpy_helper.py", line 27, in from pyscf.lib import misc File "/home/ben/miniconda3/envs/sch_eqn/lib/python3.7/site-packages/pyscf/lib/misc.py", line 46, in h5py.get_config().default_file_mode = 'a' File "h5py/h5.pyx", line 179, in h5py.h5.H5PYConfig.default_file_mode.set ValueError: Using default_file_mode other than 'r' is no longer supported. Pass the mode to h5py.File() instead.

jsspencer commented 3 years ago

This is fixed upstream in pyscf but is not released on PyPI. For now, please pin the version of h5py (see #31, which we'll merge soon).