Molcas Forum

Leo

Member

Registered: 2018-11-20

Posts: 15

Calculation terminates suddenly

Dear Developers,

Lately, while running NAMD trajectories with OpenMolcas v24.02 (or v24.06), I am coming across this problem:

Traceback (most recent call last):
  File "/home/user/openmolcas_24_06//pymolcas", line 598, in <module>
    sys.exit(main(os.path.realpath(f)))
  File "<string>", line 221, in main
  File "<string>", line 782, in auto
  File "<string>", line 198, in run
  File "<string>", line 198, in run
  File "<string>", line 346, in run
  File "<string>", line 846, in run_module
  File "<string>", line 1354, in run
  File "<string>", line 1209, in _copy_files
  File "<string>", line 1268, in _copy_or_move
  File "/opt/share/sw_inst/python-3.9.6/lib/python3.9/shutil.py", line 435, in copy2
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/opt/share/sw_inst/python-3.9.6/lib/python3.9/shutil.py", line 276, in copyfile
    return dst
OSError: [Errno 116] Stale file handle

Concurrently, the calculation terminates with a "happy landing" flag, before finishing the number of iterations requested with MOLCAS_MAXITER.

--- Start Module: seward at Wed Jul  3 23:07:30 2024 ---
--- Stop Module: seward at Wed Jul  3 23:07:54 2024 /rc=_RC_ALL_IS_WELL_ ---
*** files: xmldump
    saved to directory /home/user/test
--- Module seward spent 23 seconds ---

*** symbolic link created: INPORB -> mol.RasOrb
--- Start Module: espf at Wed Jul  3 23:07:54 2024 ---

--- Stop Module: espf at Wed Jul  3 23:08:42 2024 /rc=_RC_ALL_IS_WELL_ ---
*** files: xmldump
    saved to directory /home/user/test
--- Module espf spent 48 seconds ---

*** symbolic link created: INPORB -> mol.RasOrb
--- Start Module: rasscf at Wed Jul  3 23:08:42 2024 ---
--- Stop Module: rasscf at Wed Jul  3 23:14:01 2024 /rc=_RC_ALL_IS_WELL_ ---

.##################.
.# Happy landing! #.
.##################.

    Timing: Wall=83540.42 User=75706.41 System=5799.97

Should I assume a network problem or something similar? I tried on a couple different HPC machines (over 2 different networks), and got the same problem. Wanted to ask if anyone has seen something similar. I will try to replicate this with older OpenMolcas versions.

Kindest regards,
Leonardo

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,085

Re: Calculation terminates suddenly

That looks like a network or filesystem issue. Do you get it at the exact same point/timestep? Could it be you're hitting some disk usage quota or time limit?