Hi all,
I am facing a very similar situation as described in this post while trying to install atomate onto my institution’s HPC resources. Specifically, I received an error when running ‘lpad reset’:
Traceback (most recent call last):
File “/home/lowt/leex7132/.local/bin/lpad”, line 11, in
sys.exit(lpad())
File “/home/lowt/leex7132/.local/lib/python3.7/site-packages/fireworks/scripts/lpad_run.py”, line 1176, in lpad
args.func(args)
File “/home/lowt/leex7132/.local/lib/python3.7/site-packages/fireworks/scripts/lpad_run.py”, line 163, in reset
lp.workflows.count()))[0].upper() == ‘Y’:
File “/home/lowt/leex7132/.local/lib/python3.7/site-packages/pymongo/collection.py”, line 1779, in count
return self._count(cmd, collation, session)
File “/home/lowt/leex7132/.local/lib/python3.7/site-packages/pymongo/collection.py”, line 1574, in _count
with self._socket_for_reads(session) as (sock_info, slave_ok):
File “/panfs/roc/msisoft/anaconda/anaconda3-2018.12/lib/python3.7/contextlib.py”, line 112, in enter
return next(self.gen)
File “/home/lowt/leex7132/.local/lib/python3.7/site-packages/pymongo/mongo_client.py”, line 1135, in _socket_for_reads
server = topology.select_server(read_preference)
File “/home/lowt/leex7132/.local/lib/python3.7/site-packages/pymongo/topology.py”, line 226, in select_server
address))
File “/home/lowt/leex7132/.local/lib/python3.7/site-packages/pymongo/topology.py”, line 184, in select_servers
selector, server_timeout, address)
File “/home/lowt/leex7132/.local/lib/python3.7/site-packages/pymongo/topology.py”, line 200, in _select_servers_loop
self._error_message(selector))
pymongo.errors.ServerSelectionTimeoutError: connection closed,connection closed,connection closed
I’ve tried Brandon’s advise but could not spot any mistake in my_launchpad.yaml file. The file content is shown below:
host: mongodb+srv://heterostructuredatabase-sdtzx.mongodb.net
port: 27017
name: fireworks
username: admin_username
password: admin_password
ssl_ca_certs: null
logdir: null
strm_lvl: INFO
user_indices: []
wf_user_indices: []
To provide more context on my setup, I created a free version of MongoDB Atlas database and was able to connect to the database through my local machine via mongo shell (using my admin username and password). I have also found out that there is no firewall blocking the connection between MongoDB server and my institution’s HPC resource.
Any help would be very appreciated.
Thank you.
Best,
Eng Hock
···
On Wednesday, June 5, 2019 at 3:57:01 AM UTC-5, Kapil Gupta wrote:
Hi Brandon,
Thank you for your prompt reply to my query.
I will try to follow your suggestions.
Thanks
Kapil
On Wednesday, 5 June 2019 14:25:14 UTC+5:30, Brandon B wrote:
Hi Kapil,
This error message usually means that your my_launchpad.yaml file is not configured correctly. Please check that the URL/port and authentication information (particularly for the admin user, in this case) are set up correctly.
If you want to run VASP locally, you should use “rlaunch” commands instead of “qlaunch”, e.g. “rlaunch singleshot” or “rlaunch rapidfire”. If you are not using “qlaunch” to launch through a queue, it doesn’t matter how “my_qadapter.yaml” is configured as it won’t be used.
Cheers,
Brandon
On Wednesday, June 5, 2019 at 4:50:30 PM UTC+8, Kapil Gupta wrote:
Hi,
After the first time installation of the atomate package, i tried running “lpad reset”.
And i am getting following error message.
Any suggestions on how can i overcome this and start using atomate.
Also, if i prefer to run VASP on a local machine(without any Queueing system), how do i set up my_qadapter.yaml file in that case?
I will appreciate any help on this.
Error Message:
======================
raceback (most recent call last):
File “/home/kapil/atomate/atomate_env/bin/lpad”, line 10, in
sys.exit(lpad())
File “/home/kapil/atomate/atomate_env/lib/python3.6/site-packages/fireworks/scripts/lpad_run.py”, line 1173, in lpad
args.func(args)
File “/home/kapil/atomate/atomate_env/lib/python3.6/site-packages/fireworks/scripts/lpad_run.py”, line 163, in reset
lp.workflows.count()))[0].upper() == ‘Y’:
File “/home/kapil/atomate/atomate_env/lib/python3.6/site-packages/pymongo/collection.py”, line 1779, in count
return self._count(cmd, collation, session)
File “/home/kapil/atomate/atomate_env/lib/python3.6/site-packages/pymongo/collection.py”, line 1574, in _count
with self._socket_for_reads(session) as (sock_info, slave_ok):
File “/usr/lib/python3.6/contextlib.py”, line 81, in enter
return next(self.gen)
File “/home/kapil/atomate/atomate_env/lib/python3.6/site-packages/pymongo/mongo_client.py”, line 1135, in _socket_for_reads
server = topology.select_server(read_preference)
File “/home/kapil/atomate/atomate_env/lib/python3.6/site-packages/pymongo/topology.py”, line 226, in select_server
address))
File “/home/kapil/atomate/atomate_env/lib/python3.6/site-packages/pymongo/topology.py”, line 184, in select_servers
selector, server_timeout, address)
File “/home/kapil/atomate/atomate_env/lib/python3.6/site-packages/pymongo/topology.py”, line 200, in _select_servers_loop
self._error_message(selector))
pymongo.errors.ServerSelectionTimeoutError: connection closed
====================
Thanks
Kapil