NormAE
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luyiyun
ConnectionRefusedError
Hi there, I've been trying out the NormAE program for some data that I would like corrected for batch effects. Unfortunately I'm getting a "ConnectionRefusedError" among other messages by the console when I try to run the program. If I understand correctly, this may involve running a program on a remote server that my computer cannot connect to. I suspect this may potentially be a Mac-related issue (I use a 2020 Macbook pro), but I'm wondering if you have any ideas for a workaround.
Here's the command I tried and the output from the console:
**python main.py --task train --meta_data EX616_metabolomics_input.csv --sample_data EX616_batchdata_input.csv --save __pycache__**
the settings of training：
task: train
meta_data: EX616_metabolomics_input.csv
sample_data: EX616_batchdata_input.csv
train_data: all
save: __pycache__
ae_encoder_units: [1000, 1000]
ae_decoder_units: [1000, 1000]
disc_b_units: [250, 250]
disc_o_units: [250, 250]
bottle_num: 500
dropouts: (0.3, 0.1, 0.3, 0.3)
lambda_b: 1.0
lambda_o: 1.0
lr_rec: 0.0002
lr_disc_b: 0.005
lr_disc_o: 0.0005
epoch: (1000, 10, 700)
use_batch_for_order: True
batch_size: 64
load: None
visdom_env: main
visdom_port: 8097
num_workers: 12
use_log: False
use_batch: None
sample_size: None
random_seed: 1234
device: None
Setting up a new session...
Exception in user code:
------------------------------------------------------------
Traceback (most recent call last):
File "/Users/hani/anaconda3/lib/python3.8/site-packages/urllib3/connection.py", line 159, in _new_conn
conn = connection.create_connection(
File "/Users/hani/anaconda3/lib/python3.8/site-packages/urllib3/util/connection.py", line 84, in create_connection
raise err
File "/Users/hani/anaconda3/lib/python3.8/site-packages/urllib3/util/connection.py", line 74, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 61] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/hani/anaconda3/lib/python3.8/site-packages/urllib3/connectionpool.py", line 670, in urlopen
httplib_response = self._make_request(
File "/Users/hani/anaconda3/lib/python3.8/site-packages/urllib3/connectionpool.py", line 392, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/Users/hani/anaconda3/lib/python3.8/http/client.py", line 1240, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/Users/hani/anaconda3/lib/python3.8/http/client.py", line 1286, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/Users/hani/anaconda3/lib/python3.8/http/client.py", line 1235, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/Users/hani/anaconda3/lib/python3.8/http/client.py", line 1006, in _send_output
self.send(msg)
File "/Users/hani/anaconda3/lib/python3.8/http/client.py", line 946, in send
self.connect()
File "/Users/hani/anaconda3/lib/python3.8/site-packages/urllib3/connection.py", line 187, in connect
conn = self._new_conn()
File "/Users/hani/anaconda3/lib/python3.8/site-packages/urllib3/connection.py", line 171, in _new_conn
raise NewConnectionError(
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7fa9235b1e80>: Failed to establish a new connection: [Errno 61] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/hani/anaconda3/lib/python3.8/site-packages/requests/adapters.py", line 439, in send
resp = conn.urlopen(
File "/Users/hani/anaconda3/lib/python3.8/site-packages/urllib3/connectionpool.py", line 724, in urlopen
retries = retries.increment(
File "/Users/hani/anaconda3/lib/python3.8/site-packages/urllib3/util/retry.py", line 439, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPConnectionPool(host='localhost', port=8097): Max retries exceeded with url: /env/main (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fa9235b1e80>: Failed to establish a new connection: [Errno 61] Connection refused'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/hani/anaconda3/lib/python3.8/site-packages/visdom/__init__.py", line 708, in _send
return self._handle_post(
File "/Users/hani/anaconda3/lib/python3.8/site-packages/visdom/__init__.py", line 677, in _handle_post
r = self.session.post(url, data=data)
File "/Users/hani/anaconda3/lib/python3.8/site-packages/requests/sessions.py", line 578, in post
return self.request('POST', url, data=data, json=json, **kwargs)
File "/Users/hani/anaconda3/lib/python3.8/site-packages/requests/sessions.py", line 530, in request
resp = self.send(prep, **send_kwargs)
File "/Users/hani/anaconda3/lib/python3.8/site-packages/requests/sessions.py", line 643, in send
r = adapter.send(request, **kwargs)
File "/Users/hani/anaconda3/lib/python3.8/site-packages/requests/adapters.py", line 516, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPConnectionPool(host='localhost', port=8097): Max retries exceeded with url: /env/main (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fa9235b1e80>: Failed to establish a new connection: [Errno 61] Connection refused'))
[Errno 61] Connection refused
Batch: 0%| | 0/4 [00:14<?, ?it/s]
Traceback (most recent call last): | 0/4 [00:00<?, ?it/s]
File "main.py", line 83, in <module>
main()
File "main.py", line 49, in main
best_models, hist, early_stop_objs = trainer.fit(datas)
File "/Users/hani/Documents/NormAE-release/train.py", line 103, in fit
for batch_x, batch_y in tqdm(dataloaders['train'], 'Batch: '):
File "/Users/hani/anaconda3/lib/python3.8/site-packages/tqdm/std.py", line 1129, in __iter__
for obj in iterable:
File "/Users/hani/anaconda3/lib/python3.8/site-packages/torch/utils/data/dataloader.py", line 435, in __next__
data = self._next_data()
File "/Users/hani/anaconda3/lib/python3.8/site-packages/torch/utils/data/dataloader.py", line 1085, in _next_data
return self._process_data(data)
File "/Users/hani/anaconda3/lib/python3.8/site-packages/torch/utils/data/dataloader.py", line 1111, in _process_data
data.reraise()
File "/Users/hani/anaconda3/lib/python3.8/site-packages/torch/_utils.py", line 428, in reraise
raise self.exc_type(msg)
TypeError: Caught TypeError in DataLoader worker process 0.
Original Traceback (most recent call last):
File "/Users/hani/anaconda3/lib/python3.8/site-packages/torch/utils/data/_utils/worker.py", line 198, in _worker_loop
data = fetcher.fetch(index)
File "/Users/hani/anaconda3/lib/python3.8/site-packages/torch/utils/data/_utils/fetch.py", line 47, in fetch
return self.collate_fn(data)
File "/Users/hani/anaconda3/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 83, in default_collate
return [default_collate(samples) for samples in transposed]
File "/Users/hani/anaconda3/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 83, in <listcomp>
return [default_collate(samples) for samples in transposed]
File "/Users/hani/anaconda3/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 61, in default_collate
raise TypeError(default_collate_err_msg_format.format(elem.dtype))
TypeError: default_collate: batch must contain tensors, numpy arrays, numbers, dicts or lists; found object
rec_pretrain: 0%|
hi, I have a same problem,too.
Here's the command I tried and the output from the console:
task: train
meta_data: C:\Users\edwardkuo\Downloads\NormAE-release/path/to/meta.csv
sample_data: C:\Users\edwardkuo\Downloads\NormAE-release/path/to/sample.information.csv
train_data: all
save: C:\Users\edwardkuo\Downloads\NormAE-release\path\to\save_dir
ae_encoder_units: [1000, 1000]
ae_decoder_units: [1000, 1000]
disc_b_units: [250, 250]
disc_o_units: [250, 250]
bottle_num: 500
dropouts: (0.3, 0.1, 0.3, 0.3)
lambda_b: 1.0
lambda_o: 1.0
lr_rec: 0.0002
lr_disc_b: 0.005
lr_disc_o: 0.0005
epoch: (1000, 10, 700)
use_batch_for_order: True
batch_size: 64
load: None
visdom_env: main
visdom_port: 8097
num_workers: 12
use_log: False
use_batch: None
sample_size: None
random_seed: 1234
device: None
Setting up a new session...
Exception in user code:
------------------------------------------------------------
Traceback (most recent call last):
File "C:\Users\edwardkuo\Downloads\NormAE-release\venv\lib\site-packages\urllib3\connection.py", line 170, in _new_conn
(self._dns_host, self.port), self.timeout, **extra_kw
File "C:\Users\edwardkuo\Downloads\NormAE-release\venv\lib\site-packages\urllib3\util\connection.py", line 96, in create_connection
raise err
File "C:\Users\edwardkuo\Downloads\NormAE-release\venv\lib\site-packages\urllib3\util\connection.py", line 86, in create_connection
sock.connect(sa)
ConnectionRefusedError: [WinError 10061] 無法連線，因為目標電腦拒絕連線。
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\edwardkuo\Downloads\NormAE-release\venv\lib\site-packages\urllib3\connectionpool.py", line 706, in urlopen
chunked=chunked,
File "C:\Users\edwardkuo\Downloads\NormAE-release\venv\lib\site-packages\urllib3\connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "C:\Users\edwardkuo\Downloads\NormAE-release\venv\lib\site-packages\urllib3\connection.py", line 234, in request
super(HTTPConnection, self).request(method, url, body=body, headers=headers)
File "C:\Users\edwardkuo\Downloads\NormAE-release\PycharmProjects\pythonProject\.idea\inspectionProfiles\lib\http\client.py", line 1239, in request
self._send_request(method, url, body, headers, encode_chunked)
File "C:\Users\edwardkuo\Downloads\NormAE-release\PycharmProjects\pythonProject\.idea\inspectionProfiles\lib\http\client.py", line 1285, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "C:\Users\edwardkuo\Downloads\NormAE-release\PycharmProjects\pythonProject\.idea\inspectionProfiles\lib\http\client.py", line 1234, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "C:\Users\edwardkuo\Downloads\NormAE-release\PycharmProjects\pythonProject\.idea\inspectionProfiles\lib\http\client.py", line 1026, in _send_output
self.send(msg)
File "C:\Users\edwardkuo\Downloads\NormAE-release\PycharmProjects\pythonProject\.idea\inspectionProfiles\lib\http\client.py", line 964, in send
self.connect()
File "C:\Users\edwardkuo\Downloads\NormAE-release\venv\lib\site-packages\urllib3\connection.py", line 200, in connect
conn = self._new_conn()
File "C:\Users\edwardkuo\Downloads\NormAE-release\venv\lib\site-packages\urllib3\connection.py", line 182, in _new_conn
self, "Failed to establish a new connection: %s" % e
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x000001F478586E48>: Failed to establish a new connection: [WinError 10061] 無法連線，因為目標電腦拒絕
連線。
I don't know the reason about this error, because I don't use urllib library or connection networks. I guess it is caused by visdom, so you can check the documentation of visdom.
Hi, I have the same problem(s) as @hhabra.
The first part of the problem I solved by installing visdom correctly - just follow this link. One must run python -m visdom.server in the activated conda environment to open the server.
The second part I still haven't solved, but it seems that dataloaders["train"] returns objects instead of batch x and batch y in the training loop.
