Firs time installation: Errors while running "lpad reset"

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

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

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

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

Can you tell me the output of :

lpad version

i.e. which version of FWS you have installed

···

On Wednesday, August 7, 2019 at 6:32:51 PM UTC-7, Eng Hock Lee wrote:

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

Also I’d say:

  • first look at “lpad version” (I want to make sure you have the latest FWS installed - we fixed some connection issues back in ~v1.9.0 or so)

  • second try connecting using a my_launchpad.yaml file in your localhost, i.e. connecting from your localhost to the database via Fireworks (rather than from your computing center)

  • third, see if you can use the uri_mode instead of the other parameters

e.g.

my_launchpad.yaml

···

=======

host: <<MongoDB URI from https://docs.mongodb.com/manual/reference/connection-string/>>

uri_mode: true

=======

On Friday, August 9, 2019 at 3:56:59 PM UTC-7, Anubhav Jain wrote:

Can you tell me the output of :

lpad version

i.e. which version of FWS you have installed

On Wednesday, August 7, 2019 at 6:32:51 PM UTC-7, Eng Hock Lee wrote:

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

Hi Anubhav,

Thank you for your assistance. I was able to connect to the database using the uri_mode you mentioned. If it is still relevant, my lpad version is 1.9.4.

Thank you!

Best,

Eng Hock

···

On Friday, August 9, 2019 at 6:01:45 PM UTC-5, Anubhav Jain wrote:

Also I’d say:

  • first look at “lpad version” (I want to make sure you have the latest FWS installed - we fixed some connection issues back in ~v1.9.0 or so)
  • second try connecting using a my_launchpad.yaml file in your localhost, i.e. connecting from your localhost to the database via Fireworks (rather than from your computing center)
  • third, see if you can use the uri_mode instead of the other parameters

e.g.

my_launchpad.yaml

=======

host: <<MongoDB URI from https://docs.mongodb.com/manual/reference/connection-string/>>

uri_mode: true

=======

On Friday, August 9, 2019 at 3:56:59 PM UTC-7, Anubhav Jain wrote:

Can you tell me the output of :

lpad version

i.e. which version of FWS you have installed

On Wednesday, August 7, 2019 at 6:32:51 PM UTC-7, Eng Hock Lee wrote:

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

Ok

If you want to try without URI mode, I would also try setting:

ssl: True

authsource: admin

in your my_launchpad.yaml. It’s possible one of those could also fix it.

···

On Saturday, August 10, 2019 at 6:27:24 PM UTC-7, Eng Hock Lee wrote:

Hi Anubhav,

Thank you for your assistance. I was able to connect to the database using the uri_mode you mentioned. If it is still relevant, my lpad version is 1.9.4.

Thank you!

Best,

Eng Hock

On Friday, August 9, 2019 at 6:01:45 PM UTC-5, Anubhav Jain wrote:

Also I’d say:

  • first look at “lpad version” (I want to make sure you have the latest FWS installed - we fixed some connection issues back in ~v1.9.0 or so)
  • second try connecting using a my_launchpad.yaml file in your localhost, i.e. connecting from your localhost to the database via Fireworks (rather than from your computing center)
  • third, see if you can use the uri_mode instead of the other parameters

e.g.

my_launchpad.yaml

=======

host: <<MongoDB URI from https://docs.mongodb.com/manual/reference/connection-string/>>

uri_mode: true

=======

On Friday, August 9, 2019 at 3:56:59 PM UTC-7, Anubhav Jain wrote:

Can you tell me the output of :

lpad version

i.e. which version of FWS you have installed

On Wednesday, August 7, 2019 at 6:32:51 PM UTC-7, Eng Hock Lee wrote:

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