fancaoErik
commented
5 months ago Hi there! Your server seems not to support using sbatch to submit computing jobs. Please go for this script instead https://github.com/KULL-Centre/_2024_Cao_CALVADOSCOM/blob/main/src/simple_singlechain.py, which does not require any HPC configuration.
Hope this could help you. Fan
Hello! I followed the Run single-chain simulations with CALVADOS 3 in README for intrinsically disordered protein then get this error after running submit_ray.py
Traceback (most recent call last): File "/home/petlada/miniconda3/envs/CALVADOS3/lib/python3.8/site-packages/MDAnalysis/coordinates/base.py", line 1512, in del self.close() File "/home/petlada/miniconda3/envs/CALVADOS3/lib/python3.8/site-packages/MDAnalysis/coordinates/DCD.py", line 181, in close self._file.close() AttributeError: 'DCDReader' object has no attribute '_file' Traceback (most recent call last): File "submit_ray.py", line 216, in
proc = subprocess.run(['sbatch', f"{cwd}/{dataset}/{record}/{cycle}/{record}_sim{replicas_list4MD_idx}.sh"],capture_output=True)
File "/home/petlada/miniconda3/envs/CALVADOS3/lib/python3.8/subprocess.py", line 493, in run
with Popen(*popenargs, **kwargs) as process:
File "/home/petlada/miniconda3/envs/CALVADOS3/lib/python3.8/subprocess.py", line 858, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/home/petlada/miniconda3/envs/CALVADOS3/lib/python3.8/subprocess.py", line 1704, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'sbatch'
What should I do?