Error in parallel simulation with scoop

[zerayhg]

I am having a problem with scoopzmq or brokerzmq while I run it to the cluster. The error message is shown below. Do you have any fix for that? Thanks.

[2024-07-24 14:34:16,673] launcher INFO SCOOP 0.7 2.0 on linux2 using Python 2.7.18 |Anaconda, Inc.| (default, Apr 23 2020, 22:17:58) [GCC 7.3.0], API: 1013
[2024-07-24 14:34:16,673] launcher INFO Detected SLURM environment.
[2024-07-24 14:34:16,673] launcher INFO Deploying 8 worker(s) over 1 host(s).
[2024-07-24 14:34:16,673] launcher INFO Worker distribution:
[2024-07-24 14:34:16,673] launcher INFO cn01: 7 + origin
Launching 8 worker(s) using /bin/bash.
[2024-07-24 14:38:32,944] brokerzmq (127.0.0.1:42541) ERROR Could not unpickle status update message.
[2024-07-24 14:41:55,646] brokerzmq (127.0.0.1:42541) ERROR Could not unpickle status update message.
[2024-07-24 14:45:42,042] brokerzmq (127.0.0.1:42541) ERROR Could not unpickle status update message.
[2024-07-24 14:46:31,798] brokerzmq (127.0.0.1:42541) ERROR Could not unpickle status update message.
[2024-07-24 14:51:08,895] brokerzmq (127.0.0.1:42541) ERROR Could not unpickle status update message.
[2024-07-24 14:53:15,431] scoopzmq (192.168.0.111:64689) ERROR A worker exited unexpectedly. Read the worker logs for more information. SCOOP pool will now shutdown.
Traceback (most recent call last):
File "/opt/ohpc/pub/apps/miniconda3/py311_23.5.2/envs/py27/lib/python2.7/runpy.py", line 174, in _run_module_as_main
"main", fname, loader, pkg_name)
File "/opt/ohpc/pub/apps/miniconda3/py311_23.5.2/envs/py27/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/opt/ohpc/pub/apps/miniconda3/py311_23.5.2/envs/py27/lib/python2.7/site-packages/scoop/bootstrap/main.py", line 298, in
b.main()
File "/opt/ohpc/pub/apps/miniconda3/py311_23.5.2/envs/py27/lib/python2.7/site-packages/scoop/bootstrap/main.py", line 92, in main
self.run()
File "/opt/ohpc/pub/apps/miniconda3/py311_23.5.2/envs/py27/lib/python2.7/site-packages/scoop/bootstrap/main.py", line 285, in run
futures_startup()
File "/opt/ohpc/pub/apps/miniconda3/py311_23.5.2/envs/py27/lib/python2.7/site-packages/scoop/bootstrap/main.py", line 266, in futures_startup
run_name="main"
File "/opt/ohpc/pub/apps/miniconda3/py311_23.5.2/envs/py27/lib/python2.7/site-packages/scoop/futures.py", line 71, in _startup
result = _controller.switch(rootFuture, *args, **kargs)
File "/opt/ohpc/pub/apps/miniconda3/py311_23.5.2/envs/py27/lib/python2.7/site-packages/scoop/_control.py", line 258, in runController
future = execQueue.pop()
File "/opt/ohpc/pub/apps/miniconda3/py311_23.5.2/envs/py27/lib/python2.7/site-packages/scoop/_types.py", line 359, in pop
self.updateQueue()
File "/opt/ohpc/pub/apps/miniconda3/py311_23.5.2/envs/py27/lib/python2.7/site-packages/scoop/_types.py", line 382, in updateQueue
for future in self.socket.recvFuture():
File "/opt/ohpc/pub/apps/miniconda3/py311_23.5.2/envs/py27/lib/python2.7/site-packages/scoop/_comm/scoopzmq.py", line 352, in recvFuture
received = self._recv()
File "/opt/ohpc/pub/apps/miniconda3/py311_23.5.2/envs/py27/lib/python2.7/site-packages/scoop/_comm/scoopzmq.py", line 239, in _recv
thisFuture = pickle.loads(msg[1])
cPickle.UnpicklingError: pickle data was truncated

[JacksonBurns]

Hi @zerayhg it looks like you are running on Python 2 - we can no longer provide support on this version of RMG. Please update to RMG 3 or newer, which runs on Python 3. You can find installation instructions here: https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html. You will likely want to install from source to run on a cluster.

[zerayhg]

Thank you so much @JacksonBurns . I will upgrade it Python 3.

[zerayhg]

Hi @JacksonBurns. How do Scoop and RMG relate? I need to be able to familiarize myself with RMG. Thanks.

[JacksonBurns]

scoop was a library used in a previous version of RMG to parallelize reaction generation (see their repository). It is not used in the current version of RMG.