From the error log, it doesn't seem like the most updated version of ARC.
Could you update ARC on the server, unless it was just installed?
(to update, in the ARC folder type git pull)
Please let me know what's the top most commit you see whey you type git log.

Indeed, it was not up to date. So I update the ARC codes. However, a lot of errors then showed up. Firstly, 'openbabel' could not be loaded. Then I also upgrade RMG and ARC environment in case it is then causing that. After all these steps, it is also a problem here.
FYI, the commit of ARC log is:
commit 8220e6c
and commit of RMG log is:
commit 7fbb9e4a62ce6055451efa0262b671b555cad870
And the error info is:
**Starting project minimal

/home/svu/e0444166/conda_envs/arc_env/lib/python3.7/site-packages/openbabel/init.py:14: UserWarning: "import openbabel" is deprecated, instead use "from openbabel import openbabel"
warnings.warn('"import openbabel" is deprecated, instead use "from openbabel import openbabel"')
Traceback (most recent call last):
File "/home/svu/e0444166/ARC/ARC.py", line 69, in
main()
File "/home/svu/e0444166/ARC/ARC.py", line 64, in main
arc_object = ARC(input_dict)
File "/home/svu/e0444166/ARC/arc/main.py", line 340, in init
converted_species.append(ARCSpecies(species_dict=spc))
File "/home/svu/e0444166/ARC/arc/species/species.py", line 508, in init
self.set_mol_list()
File "/home/svu/e0444166/ARC/arc/species/species.py", line 955, in set_mol_list
save_order=True,
File "rmgpy/molecule/molecule.py", line 2101, in rmgpy.molecule.molecule.Molecule.generate_resonance_structures
TypeError: generate_resonance_structures() got an unexpected keyword argument 'save_order'

This is the example case: minimal. For testing.

Please compile RMG. Activate either the arc_env or rmg_env and type make clean and then make under the RMG-Py folder.

Hi @alongd ,
I compiled RMG before. Need I compile it everytime I update the codes?
I recompile RMG-Py again now. However, the same porblem showed up agian like the first coment:
Running job scan_a340 for DME (pivots: [4, 1, 2, 3], dihedrals: ['4.00', '1.00', '2.00', '3.00'])
Traceback (most recent call last):
File "/home/svu/e0444166/ARC/ARC.py", line 69, in
main()
File "/home/svu/e0444166/ARC/ARC.py", line 65, in main
arc_object.execute()
File "/home/svu/e0444166/ARC/arc/main.py", line 569, in execute
fine_only=self.fine_only,
File "/home/svu/e0444166/ARC/arc/scheduler.py", line 467, in init
self.schedule_jobs()
File "/home/svu/e0444166/ARC/arc/scheduler.py", line 565, in schedule_jobs
self.spawn_post_opt_jobs(label=label, job_name=job_name)
File "/home/svu/e0444166/ARC/arc/scheduler.py", line 1250, in spawn_post_opt_jobs
self.run_scan_jobs(label)
File "/home/svu/e0444166/ARC/arc/scheduler.py", line 1152, in run_scan_jobs
self.spawn_directed_scan_jobs(label, rotor_index=i)
File "/home/svu/e0444166/ARC/arc/scheduler.py", line 1319, in spawn_directed_scan_jobs
pivots=pivots)
File "/home/svu/e0444166/ARC/arc/scheduler.py", line 770, in run_job
self.job_dict[label][job_type][job.job_name].run()
File "/home/svu/e0444166/ARC/arc/job/job.py", line 1287, in run
self.write_input_file()
File "/home/svu/e0444166/ARC/arc/job/job.py", line 973, in write_input_file
scans.append(' '.join([str(num) for num in directed_scan]))
TypeError: 'int' object is not iterable
error.txt

You need to compile RMG every time a change was introduced to cythonized files. Users typically aren't aware of this kind of information, so it is recommended to try recompiling every time you update RMG, by simply tiping make which is a relatively fast operation, not make clean -> make which compiles everything.

Please upload your input file, and I'll try to reproduce this error and debug it.

Hi @alongd
Thank you so much. The input file is attached with '.txt
input.txt
'

@NUSCondy, please try running on the fixup branch. That pull request isn't ready yet, but it still might solve your problem.
Let me know if it did.

git fetch origin
git checkout -b directed_scan_fix origin/directed_scan_fix

@alongd
Thank you so much! It works with the original settings. I will try more runs.

Great to hear. Let me know if you experience any other issues.
I'm closing this issue for now, I'll either work on the PR in #467, or merge a more advanced branch that also solves this issue. Stay tuned to update your repository.