A probelm in atomate test workflow

Atomate
1

Hi

I tried to run the simple test workflow in the introduction page, but I encountered an error printed in the output file :

Traceback (most recent call last):

File “/opt/ohpc/pub/marom/anaconda3/bin/rlaunch”, line 11, in

sys.exit(rlaunch())

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/fireworks/scripts/rlaunch_run.py”, line 125, in rlaunch

launchpad = LaunchPad.from_file(args.launchpad_file) if args.launchpad_file else LaunchPad(

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/fireworks/utilities/fw_serializers.py”, line 286, in from_file

return cls.from_format(f.read(), f_format=f_format)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/fireworks/utilities/fw_serializers.py”, line 254, in from_format

yaml.safe_load(f_str)))

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/fireworks/core/launchpad.py”, line 224, in from_dict

ssl_ca_certs, ssl_certfile, ssl_keyfile, ssl_pem_passphrase)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/fireworks/core/launchpad.py”, line 155, in init

self.db.authenticate(username, password)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/pymongo/database.py”, line 1274, in authenticate

connect=True)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/pymongo/mongo_client.py”, line 609, in _cache_credentials

writable_preferred_server_selector)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/pymongo/topology.py”, line 224, in select_server

address))

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/pymongo/topology.py”, line 183, in select_servers

selector, server_timeout, address)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/pymongo/topology.py”, line 199, in _select_servers_loop

self._error_message(selector))

pymongo.errors.ServerSelectionTimeoutError: ds231242.mlab.com:31242: [Errno -2] Name or service not known

Do you know how to fix it ?

Thanks !

Best,

Sunny

2

I confirm that I can successfully run the rlaunch command. However, this error always occur when I run qlaunch or write the rlaunch in script and run it.

在 2018年8月24日星期五 UTC-7上午9:41:37，wol…@gmail.com写道：

···

Hi

I tried to run the simple test workflow in the introduction page, but I encountered an error printed in the output file :

Traceback (most recent call last):

File “/opt/ohpc/pub/marom/anaconda3/bin/rlaunch”, line 11, in

sys.exit(rlaunch())

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/fireworks/scripts/rlaunch_run.py”, line 125, in rlaunch

launchpad = LaunchPad.from_file(args.launchpad_file) if args.launchpad_file else LaunchPad(

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/fireworks/utilities/fw_serializers.py”, line 286, in from_file

return cls.from_format(f.read(), f_format=f_format)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/fireworks/utilities/fw_serializers.py”, line 254, in from_format

yaml.safe_load(f_str)))

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/fireworks/core/launchpad.py”, line 224, in from_dict

ssl_ca_certs, ssl_certfile, ssl_keyfile, ssl_pem_passphrase)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/fireworks/core/launchpad.py”, line 155, in init

self.db.authenticate(username, password)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/pymongo/database.py”, line 1274, in authenticate

connect=True)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/pymongo/mongo_client.py”, line 609, in _cache_credentials

writable_preferred_server_selector)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/pymongo/topology.py”, line 224, in select_server

address))

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/pymongo/topology.py”, line 183, in select_servers

selector, server_timeout, address)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/pymongo/topology.py”, line 199, in _select_servers_loop

self._error_message(selector))

pymongo.errors.ServerSelectionTimeoutError: ds231242.mlab.com:31242: [Errno -2] Name or service not known

Do you know how to fix it ?

Thanks !

Best,

Sunny

3

Hi Sunny,

It seems like you are using a HPC with compute nodes that you access through a queue.

Is it possible that compute nodes you are trying to run on have a firewall that prevents you from communicating with your Mongo instance on mlab?

Maybe you could try to log in to a node that you are trying to run your jobs on and try to

  1. Ping the outside world (make sure there’s any connection out at all)

  2. Ping your mongo instance (make sure the node can see your Mongo instance)

  3. Instantiate a connection to the mongo instance via pymongo

Seeing where you get stuck might help to debug this further.

···

On Monday, August 27, 2018 at 2:48:00 PM UTC-4, [email protected] wrote:

I confirm that I can successfully run the rlaunch command. However, this error always occur when I run qlaunch or write the rlaunch in script and run it.

在 2018年8月24日星期五 UTC-7上午9:41:37，wolfsu…@gmail.com写道：

Hi

I tried to run the simple test workflow in the introduction page, but I encountered an error printed in the output file :

Traceback (most recent call last):

File “/opt/ohpc/pub/marom/anaconda3/bin/rlaunch”, line 11, in

sys.exit(rlaunch())

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/fireworks/scripts/rlaunch_run.py”, line 125, in rlaunch

launchpad = LaunchPad.from_file(args.launchpad_file) if args.launchpad_file else LaunchPad(

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/fireworks/utilities/fw_serializers.py”, line 286, in from_file

return cls.from_format(f.read(), f_format=f_format)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/fireworks/utilities/fw_serializers.py”, line 254, in from_format

yaml.safe_load(f_str)))

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/fireworks/core/launchpad.py”, line 224, in from_dict

ssl_ca_certs, ssl_certfile, ssl_keyfile, ssl_pem_passphrase)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/fireworks/core/launchpad.py”, line 155, in init

self.db.authenticate(username, password)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/pymongo/database.py”, line 1274, in authenticate

connect=True)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/pymongo/mongo_client.py”, line 609, in _cache_credentials

writable_preferred_server_selector)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/pymongo/topology.py”, line 224, in select_server

address))

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/pymongo/topology.py”, line 183, in select_servers

selector, server_timeout, address)

File “/opt/ohpc/pub/marom/anaconda3/lib/python3.6/site-packages/pymongo/topology.py”, line 199, in _select_servers_loop

self._error_message(selector))

pymongo.errors.ServerSelectionTimeoutError: ds231242.mlab.com:31242: [Errno -2] Name or service not known

Do you know how to fix it ?

Thanks !

Best,

Sunny