error while running the run.sh file for the nacl association in gromacs

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Ibrahim Mohamed

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Aug 27, 2023, 1:41:55 PM8/27/23
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i ran the init.sh and env.sh and no error was produced. but the run.sh file produced this error:

-- ERROR    [westpa.core.propagators.executable] -- could not read pcoord from '/tmp/tmpzfhf2tzj': ValueError('cannot reshape array of size 0 into shape (51,1)')
-- ERROR    [westpa.core.propagators.executable] -- could not read pcoord from '/tmp/tmpbj4cg2el': ValueError('cannot reshape array of size 0 into shape (51,1)')
-- ERROR    [westpa.core.sim_manager] -- propagation failed for 2 segment(s):
0
1
exception caught; shutting down
-- ERROR    [w_run] -- error message: propagation failed for 2 segments
-- ERROR    [w_run] -- Traceback (most recent call last):
  File "/home/cairo029u1/.local/lib/python3.9/site-packages/westpa/cli/core/w_run.py", line 62, in run_simulation
    sim_manager.run()
  File "/home/cairo029u1/.local/lib/python3.9/site-packages/westpa/core/sim_manager.py", line 753, in run
    self.check_propagation()
  File "/home/cairo029u1/.local/lib/python3.9/site-packages/westpa/core/sim_manager.py", line 650, in check_propagation
    raise PropagationError('propagation failed for {:d} segments'.format(len(failed_segments)))
westpa.core.sim_manager.PropagationError: propagation failed for 2 segments

Exception in thread receiver:
Traceback (most recent call last):
  File "/share/apps/conda_envs/gmxMMPBSA/lib/python3.9/threading.py", line 980, in _bootstrap_inner

How to solve this error?

Leung, Jeremy

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Aug 27, 2023, 3:12:37 PM8/27/23
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Hi Ibrahim,

This is a classic error when you did not successfully pass your pcoord to WESTPA. This might be due to the fact that it didn't propagate the segment properly, or you didn't calculate the value properly. Make sure you carefully debug your runseg.sh. Did you correctly point to your GROMACS installation in env.sh? Check your per-segment error log in seg_logs for more detailed information.

See here:

-- JL
---
Jeremy M. G. Leung
PhD Candidate, Chemistry
Graduate Student Researcher, Chemistry (Chong Lab)
University of Pittsburgh | 219 Parkman Avenue, Pittsburgh, PA 15260
jml...@pitt.edu | [He, Him, His]

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Ibrahim Mohamed

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Aug 28, 2023, 6:11:27 AM8/28/23
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thank you it worked now. but after finishing and inspecting the west.log file, i found this:

Updating system with the options from the configuration file
Maximum wallclock time: 3 days, 0:00:00

Mon Aug 28 05:58:22 2023
Iteration 1 (2 requested)
Beginning iteration 1
2 segments remain in iteration 1 (2 total)
1 of 26 (3.846154%) active bins are populated
per-bin minimum non-zero probability:       1
per-bin maximum probability:                1
per-bin probability dynamic range (kT):     0
per-segment minimum non-zero probability:   0.5
per-segment maximum non-zero probability:   0.5
per-segment probability dynamic range (kT): 0
norm = 1, error in norm = 0 (0*epsilon)
Waiting for segments to complete...
Iteration completed successfully
Iteration wallclock: 0:03:03.953103, cputime: 0:06:01.215546


Mon Aug 28 06:01:26 2023
Iteration 2 (2 requested)
Beginning iteration 2
2 segments remain in iteration 2 (2 total)
1 of 26 (3.846154%) active bins are populated
per-bin minimum non-zero probability:       1
per-bin maximum probability:                1
per-bin probability dynamic range (kT):     0
per-segment minimum non-zero probability:   0.5
per-segment maximum non-zero probability:   0.5
per-segment probability dynamic range (kT): 0
norm = 1, error in norm = 0 (0*epsilon)
Waiting for segments to complete...
Iteration completed successfully
Iteration wallclock: 0:03:03.148139, cputime: 0:06:00.442233


Mon Aug 28 06:04:29 2023
WEST run complete.

Exception in thread receiver:
Traceback (most recent call last):
  File "/share/apps/conda_envs/gmxMMPBSA/lib/python3.9/threading.py", line 980, in _bootstrap_inner

 what is the error in the last three line? is it important or is it related to the conda environment?

thanks

Leung, Jeremy

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Aug 28, 2023, 10:42:05 AM8/28/23
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Hi Ibrahim,

That's safe to ignore. On some systems, python didn't shut down cleanly, leading to this specific error. The `WEST run complete.` line indicate WESTPA has terminated successfully.

-- JL
---
Jeremy M. G. Leung
PhD Candidate, Chemistry
Graduate Student Researcher, Chemistry (Chong Lab)
University of Pittsburgh | 219 Parkman Avenue, Pittsburgh, PA 15260
jml...@pitt.edu | [He, Him, His]
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