Running "Neural Network DMD on Slow Manifold" error

[lk1983823]

I have lightning version 2.0.5 installed. The pykoopman version is 1.0.4.
When I run "dlk_regressor.fit(traj_list)" in the example "tutorial_koopman_nndmd_examples.ipynb".

It shows errors

INFO: GPU available: True (cuda), used: True
[rank_zero.py:48 -                _info() ] GPU available: True (cuda), used: True
INFO: TPU available: False, using: 0 TPU cores
[rank_zero.py:48 -                _info() ] TPU available: False, using: 0 TPU cores
INFO: IPU available: False, using: 0 IPUs
[rank_zero.py:48 -                _info() ] IPU available: False, using: 0 IPUs
INFO: HPU available: False, using: 0 HPUs
[rank_zero.py:48 -                _info() ] HPU available: False, using: 0 HPUs
INFO: Initializing distributed: GLOBAL_RANK: 1, MEMBER: 2[/2](https://file+.vscode-resource.vscode-cdn.net/2)
[distributed.py:245 - _init_dist_connection() ] Initializing distributed: GLOBAL_RANK: 1, MEMBER: 2[/2](https://file+.vscode-resource.vscode-cdn.net/2)
INFO: Initializing distributed: GLOBAL_RANK: 0, MEMBER: 1[/2](https://file+.vscode-resource.vscode-cdn.net/2)
[distributed.py:245 - _init_dist_connection() ] Initializing distributed: GLOBAL_RANK: 0, MEMBER: 1[/2](https://file+.vscode-resource.vscode-cdn.net/2)
INFO: ----------------------------------------------------------------------------------------------------
distributed_backend=nccl
All distributed processes registered. Starting with 2 processes
----------------------------------------------------------------------------------------------------

[rank_zero.py:48 -                _info() ] ----------------------------------------------------------------------------------------------------
distributed_backend=nccl
All distributed processes registered. Starting with 2 processes
----------------------------------------------------------------------------------------------------

2023-09-14 16:20:30.863437: I tensorflow[/core/platform/cpu_feature_guard.cc:193](https://file+.vscode-resource.vscode-cdn.net/core/platform/cpu_feature_guard.cc:193)] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 AVX512F AVX512_VNNI FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-09-14 16:20:31.016351: I tensorflow[/core/util/port.cc:104](https://file+.vscode-resource.vscode-cdn.net/core/util/port.cc:104)] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
2023-09-14 16:20:32.029631: W tensorflow[/compiler/xla/stream_executor/platform/default/dso_loader.cc:64](https://file+.vscode-resource.vscode-cdn.net/compiler/xla/stream_executor/platform/default/dso_loader.cc:64)] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: [/usr/local/cuda-11.7/lib64](https://file+.vscode-resource.vscode-cdn.net/usr/local/cuda-11.7/lib64)
2023-09-14 16:20:32.029742: W tensorflow[/compiler/xla/stream_executor/platform/default/dso_loader.cc:64](https://file+.vscode-resource.vscode-cdn.net/compiler/xla/stream_executor/platform/default/dso_loader.cc:64)] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: [/usr/local/cuda-11.7/lib64](https://file+.vscode-resource.vscode-cdn.net/usr/local/cuda-11.7/lib64)
2023-09-14 16:20:32.029751: W tensorflow[/compiler/tf2tensorrt/utils/py_utils.cc:38](https://file+.vscode-resource.vscode-cdn.net/compiler/tf2tensorrt/utils/py_utils.cc:38)] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.
---------------------------------------------------------------------------
ProcessRaisedException                    Traceback (most recent call last)
Cell In[6], line 1
----> 1 dlk_regressor.fit(traj_list)

File [~/anaconda3/envs/dpc/lib/python3.10/site-packages/pykoopman/regression/_nndmd.py:1187](https://file+.vscode-resource.vscode-cdn.net/media/lk/lksgcc/lk_git/3_Reinforcement_Learning/3_4_MPC/pykoopman/docs/~/anaconda3/envs/dpc/lib/python3.10/site-packages/pykoopman/regression/_nndmd.py:1187), in NNDMD.fit(self, x, y, dt)
   1184     raise ValueError("check `x` and `y` for `self.fit`")
   1186 # trainer starts to train
-> 1187 self.trainer.fit(self._regressor, self.dm)
   1189 # compute Koopman operator information
   1190 self._state_matrix_ = (
   1191     self._regressor._koopman_propagator.get_discrete_time_Koopman_Operator()
   1192     .detach()
   1193     .numpy()
   1194 )

File [~/anaconda3/envs/dpc/lib/python3.10/site-packages/lightning/pytorch/trainer/trainer.py:529](https://file+.vscode-resource.vscode-cdn.net/media/lk/lksgcc/lk_git/3_Reinforcement_Learning/3_4_MPC/pykoopman/docs/~/anaconda3/envs/dpc/lib/python3.10/site-packages/lightning/pytorch/trainer/trainer.py:529), in Trainer.fit(self, model, train_dataloaders, val_dataloaders, datamodule, ckpt_path)
    527 model = _maybe_unwrap_optimized(model)
    528 self.strategy._lightning_module = model
--> 529 call._call_and_handle_interrupt(
    530     self, self._fit_impl, model, train_dataloaders, val_dataloaders, datamodule, ckpt_path
    531 )

File [~/anaconda3/envs/dpc/lib/python3.10/site-packages/lightning/pytorch/trainer/call.py:41](https://file+.vscode-resource.vscode-cdn.net/media/lk/lksgcc/lk_git/3_Reinforcement_Learning/3_4_MPC/pykoopman/docs/~/anaconda3/envs/dpc/lib/python3.10/site-packages/lightning/pytorch/trainer/call.py:41), in _call_and_handle_interrupt(trainer, trainer_fn, *args, **kwargs)
     39 try:
     40     if trainer.strategy.launcher is not None:
---> 41         return trainer.strategy.launcher.launch(trainer_fn, *args, trainer=trainer, **kwargs)
     42     return trainer_fn(*args, **kwargs)
     44 except _TunerExitException:

File [~/anaconda3/envs/dpc/lib/python3.10/site-packages/lightning/pytorch/strategies/launchers/multiprocessing.py:124](https://file+.vscode-resource.vscode-cdn.net/media/lk/lksgcc/lk_git/3_Reinforcement_Learning/3_4_MPC/pykoopman/docs/~/anaconda3/envs/dpc/lib/python3.10/site-packages/lightning/pytorch/strategies/launchers/multiprocessing.py:124), in _MultiProcessingLauncher.launch(self, function, trainer, *args, **kwargs)
    116 process_context = mp.start_processes(
    117     self._wrapping_function,
    118     args=process_args,
   (...)
    121     join=False,  # we will join ourselves to get the process references
    122 )
    123 self.procs = process_context.processes
--> 124 while not process_context.join():
    125     pass
    127 worker_output = return_queue.get()

File [~/anaconda3/envs/dpc/lib/python3.10/site-packages/torch/multiprocessing/spawn.py:160](https://file+.vscode-resource.vscode-cdn.net/media/lk/lksgcc/lk_git/3_Reinforcement_Learning/3_4_MPC/pykoopman/docs/~/anaconda3/envs/dpc/lib/python3.10/site-packages/torch/multiprocessing/spawn.py:160), in ProcessContext.join(self, timeout)
    158 msg = "\n\n-- Process %d terminated with the following error:\n" % error_index
    159 msg += original_trace
--> 160 raise ProcessRaisedException(msg, error_index, failed_process.pid)

ProcessRaisedException: 

-- Process 1 terminated with the following error:
Traceback (most recent call last):
  File "[/home/lk/anaconda3/envs/dpc/lib/python3.10/site-packages/torch/multiprocessing/spawn.py](https://file+.vscode-resource.vscode-cdn.net/home/lk/anaconda3/envs/dpc/lib/python3.10/site-packages/torch/multiprocessing/spawn.py)", line 69, in _wrap
    fn(i, *args)
  File "[/home/lk/anaconda3/envs/dpc/lib/python3.10/site-packages/lightning/pytorch/strategies/launchers/multiprocessing.py](https://file+.vscode-resource.vscode-cdn.net/home/lk/anaconda3/envs/dpc/lib/python3.10/site-packages/lightning/pytorch/strategies/launchers/multiprocessing.py)", line 147, in _wrapping_function
    results = function(*args, **kwargs)
  File "[/home/lk/anaconda3/envs/dpc/lib/python3.10/site-packages/lightning/pytorch/trainer/trainer.py](https://file+.vscode-resource.vscode-cdn.net/home/lk/anaconda3/envs/dpc/lib/python3.10/site-packages/lightning/pytorch/trainer/trainer.py)", line 568, in _fit_impl
    self._run(model, ckpt_path=ckpt_path)
  File "[/home/lk/anaconda3/envs/dpc/lib/python3.10/site-packages/lightning/pytorch/trainer/trainer.py](https://file+.vscode-resource.vscode-cdn.net/home/lk/anaconda3/envs/dpc/lib/python3.10/site-packages/lightning/pytorch/trainer/trainer.py)", line 934, in _run
    call._call_setup_hook(self)  # allow user to setup lightning_module in accelerator environment
  File "[/home/lk/anaconda3/envs/dpc/lib/python3.10/site-packages/lightning/pytorch/trainer/call.py](https://file+.vscode-resource.vscode-cdn.net/home/lk/anaconda3/envs/dpc/lib/python3.10/site-packages/lightning/pytorch/trainer/call.py)", line 83, in _call_setup_hook
    _call_lightning_datamodule_hook(trainer, "setup", stage=fn)
  File "[/home/lk/anaconda3/envs/dpc/lib/python3.10/site-packages/lightning/pytorch/trainer/call.py](https://file+.vscode-resource.vscode-cdn.net/home/lk/anaconda3/envs/dpc/lib/python3.10/site-packages/lightning/pytorch/trainer/call.py)", line 164, in _call_lightning_datamodule_hook
    return fn(*args, **kwargs)
  File "[/home/lk/anaconda3/envs/dpc/lib/python3.10/site-packages/pykoopman/regression/_nndmd.py](https://file+.vscode-resource.vscode-cdn.net/home/lk/anaconda3/envs/dpc/lib/python3.10/site-packages/pykoopman/regression/_nndmd.py)", line 902, in setup
    self._tr_x, self._tr_yseq, self._tr_ys, self.normalization
AttributeError: 'SeqDataModule' object has no attribute '_tr_x' 

Anyone can help ?

[pswpswpsw]

I actually just created a blank conda env and there is no error coming out for running that jupyter notebook.

So you need to setup conda env carefully:

1. conda env create --name pyk python=3.10
2. conda activate pyk
3. python -m pip install -r requirements-dev.txt

Then if there is no error coming out, this environment should be good to go. Maybe you won't have GPU-version of pytorch depending on which OS and which pytorch you are using but the code will run anyway.