Closed Thapeachydude closed 5 months ago
Can you share the contents of /pathto/scripts/cellot_run/config.yaml
?
Sure.
data:
condition: drug
features: /pathto/cellot/datasets/4i/features.txt
path: /pathto/cellot/datasets/4i/8h.h5ad
source: control
target: cisplatin
type: cell
dataloader:
batch_size: 256
shuffle: true
datasplit:
groupby: drug
name: train_test
test_size: 0.2
model:
g:
fnorm_penalty: 1
hidden_units:
- 64
- 64
- 64
- 64
kernel_init_fxn:
b: 0.1
name: uniform
latent_dim: 50
name: cellot
softplus_W_kernels: false
optim:
beta1: 0.5
beta2: 0.9
lr: 0.0001
optimizer: Adam
weight_decay: 0
training:
cache_freq: 1000
eval_freq: 250
logs_freq: 50
n_inner_iters: 10
n_iters: 100000
hmm ok Im not able to reproduce on my end. I think the script is not finding the config.yaml
so some paths might be unspecified. Could you double check that? I added some better asserts and warnings, so if you dont find something, can you pull the new changes, re-run and send output if you still have an error?
Hi, so I pulled the repo again. Now there is a warning, that indeed it can't find the config file. Is there a way to specify it?
WARNING: config path not found
Traceback (most recent call last):
Hi M,
aha ok I figured out what happened -- we had assumed that outdirs are named like <experiment_name>/model-<model>
. So I was now able to reproduce your error and fixed it. Let me know if this works for you?
best, Stefan
So it finished with:
... storing 'transport' as categorical
I0301 17:15:05.610995 48003472152704 utils.py:145] Note: detected 192 virtual cores but NumExpr set to maximum of 64, check "NUMEXPR_MAX_THREADS" environment variable.
I0301 17:15:05.611438 48003472152704 utils.py:148] Note: NumExpr detected 192 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
Output looks like this:
ls cellot_run/evals_iid_data_space/
evals.csv imputed.h5ad
Best
Is your question resolved?
Hi,
I'm trying to run the simple 4i tutorial, but
evaluate.py
crashes halfway. Unfortuantely, without more info on what each script is doing its difficult to troubleshoot this by oneself.I'm running
python /pathto/cellot/scripts/evaluate.py --outdir /pathto/scripts/cellot_run/ --setting iid --where data_space
Training finished without errors and the output directory
/pathto/scripts/cellot_run/
looks like this:Any insights would be appreciated, Best, M