Executing Experiments

[Dslab2025]

I am using Local workstation. Its a Linuxmint system with 32core CPU and 2 RTX 40 series GPUs
I dont have SLRUM, but Gromacs and Amber pmemd.cuda installed and called through ~/.bashrc.

As per quick start instruction I copy all the files, but it returns following error

╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ in :3 │
│ │
│ 1 import a3fe as a3 │
│ 2 calc = a3.Calculation(ensemble_size=5) │
│ ❱ 3 calc.setup() │
│ 4 calc.get_optimal_lam_vals() │
│ 5 calc.run(adaptive=False, runtime = 5) # Run non-adaptively for 5 ns per replicate │
│ 6 calc.wait() │
│ │
│ /home/nayan/Desktop/a3fe/a3fe/run/calculation.py:211 in setup │
│ │
│ 208 │ │ │ │ stream_log_level=self.stream_log_level, │
│ 209 │ │ │ ) │
│ 210 │ │ │ self.legs.append(leg) │
│ ❱ 211 │ │ │ leg.setup(configs[leg_type]) │
│ 212 │ │ │
│ 213 │ │ # Save the state │
│ 214 │ │ self.setup_complete = True │
│ │
│ /home/nayan/Desktop/a3fe/a3fe/run/leg.py:230 in setup │
│ │
│ 227 │ │ if self.prep_stage == _PreparationStage.STRUCTURES_ONLY: │
│ 228 │ │ │ self.parameterise_input(slurm=cfg.slurm) │
│ 229 │ │ if self.prep_stage == _PreparationStage.PARAMETERISED: │
│ ❱ 230 │ │ │ self.solvate_input(slurm=cfg.slurm) # This also adds ions │
│ 231 │ │ if self.prep_stage == _PreparationStage.SOLVATED: │
│ 232 │ │ │ system = self.minimise_input(slurm=cfg.slurm) │
│ 233 │ │ if self.prep_stage == _PreparationStage.MINIMISED: │
│ │
│ /home/nayan/Desktop/a3fe/a3fe/run/leg.py:466 in solvate_input │
│ │
│ 463 │ │ │ │ fn = _system_prep.slurm_solvate_free │
│ 464 │ │ │ else: │
│ 465 │ │ │ │ raise ValueError("Invalid leg type.") │
│ ❱ 466 │ │ │ self._run_slurm(fn, wait=True, run_dir=self.input_dir, job_name=job_name) │
│ 467 │ │ │ │
│ 468 │ │ │ # Check that the required input files have been produced, since slurm can fa │
│ 469 │ │ │ for file in _PreparationStage.SOLVATED.get_simulation_input_files( │
│ │
│ /home/nayan/Desktop/a3fe/a3fe/run/leg.py:899 in _run_slurm │
│ │
│ 896 │ │ │ f"{run_dir}/{job_name}.sh", │
│ 897 │ │ ] # The virtual queue adds sbatch │
│ 898 │ │ slurm_file_base = _get_slurm_file_base(slurm_file) │
│ ❱ 899 │ │ job = self.virtual_queue.submit(cmd_list, slurm_file_base=slurm_file_base) │
│ 900 │ │ self._logger.info(f"Submitted job {job}") │
│ 901 │ │ self.jobs.append(job) │
│ 902 │ │ # Update the virtual queue to submit the job │
│ │
│ /home/nayan/Desktop/a3fe/a3fe/run/_virtual_queue.py:170 in submit │
│ │
│ 167 │ │ self._pre_queue.append(job) │
│ 168 │ │ self._logger.info(f"{job} submitted") │
│ 169 │ │ # Now update - the job will be moved to the real queue if there is space │
│ ❱ 170 │ │ self.update() │
│ 171 │ │ return job │
│ 172 │ │
│ 173 │ def kill(self, job: Job) -> None: │
│ │
│ /home/nayan/Desktop/a3fe/a3fe/run/_virtual_queue.py:280 in update │
│ │
│ 277 │ │ """Remove jobs from the queue if they have finished, then move jobs from │
│ 278 │ │ the pre-queue to the real queue if there is space.""" │
│ 279 │ │ # First, remove jobs from the queue if they have finished │
│ ❱ 280 │ │ running_slurm_job_ids = self._read_slurm_queue() │
│ 281 │ │ n_running_slurm_jobs = len(running_slurm_job_ids) │
│ 282 │ │ # Remove completed jobs from the queues and update their status │
│ 283 │ │ for job in self._slurm_queue: │
│ │
│ /home/nayan/Desktop/a3fe/a3fe/run/_virtual_queue.py:231 in _read_slurm_queue │
│ │
│ 228 │ │ │ ] │
│ 229 │ │ │ return running_slurm_job_ids │
│ 230 │ │ │
│ ❱ 231 │ │ return _read_slurm_queue_inner() │
│ 232 │ │
│ 233 │ def _submit_job(self, job_command_list: _List[str]) -> int: │
│ 234 │ │ """ │
│ │
│ /home/nayan/Desktop/a3fe/a3fe/run/_utils.py:89 in newfn │
│ │
│ 86 │ │ │ attempt = 0 │
│ 87 │ │ │ while attempt < times: │
│ 88 │ │ │ │ try: │
│ ❱ 89 │ │ │ │ │ return func(*args, **kwargs) │
│ 90 │ │ │ │ except exceptions as e: │
│ 91 │ │ │ │ │ logger.error( │
│ 92 │ │ │ │ │ │ f"Exception thrown when attempting to run {func}, attempt " │
│ │
│ /home/nayan/Desktop/a3fe/a3fe/run/_virtual_queue.py:213 in _read_slurm_queue_inner │
│ │
│ 210 │ │ │ ] │
│ 211 │ │ │ │
│ 212 │ │ │ # Create a pipe for the first command │
│ ❱ 213 │ │ │ process = _subprocess.Popen(commands[0], stdout=_subprocess.PIPE) │
│ 214 │ │ │ │
│ 215 │ │ │ # Chain the commands │
│ 216 │ │ │ for cmd in commands[1:]: │
│ │
│ /home/nayan/miniconda3/envs/a3fe/lib/python3.12/subprocess.py:1026 in init │
│ │
│ 1023 │ │ │ │ │ self.stderr = io.TextIOWrapper(self.stderr, │
│ 1024 │ │ │ │ │ │ │ encoding=encoding, errors=errors) │
│ 1025 │ │ │ │
│ ❱ 1026 │ │ │ self._execute_child(args, executable, preexec_fn, close_fds, │
│ 1027 │ │ │ │ │ │ │ │ pass_fds, cwd, env, │
│ 1028 │ │ │ │ │ │ │ │ startupinfo, creationflags, shell, │
│ 1029 │ │ │ │ │ │ │ │ p2cread, p2cwrite, │
│ │
│ /home/nayan/miniconda3/envs/a3fe/lib/python3.12/subprocess.py:1955 in _execute_child │
│ │
│ 1952 │ │ │ │ │ if errno_num != 0: │
│ 1953 │ │ │ │ │ │ err_msg = os.strerror(errno_num) │
│ 1954 │ │ │ │ │ if err_filename is not None: │
│ ❱ 1955 │ │ │ │ │ │ raise child_exception_type(errno_num, err_msg, err_filename) │
│ 1956 │ │ │ │ │ else: │
│ 1957 │ │ │ │ │ │ raise child_exception_type(errno_num, err_msg) │
│ 1958 │ │ │ │ raise child_exception_type(err_msg) │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
FileNotFoundError: [Errno 2] No such file or directory: 'squeue'

Plese help me to execute this tool inorder to estimate ABFB

[jmichel80]

hi @Dslab2025 - that's your problem, as the docs say you need to install SLURM before you can use a3fe.

[Dslab2025]

thus slurm works on workstation? I dont have any idea, as some one told its only for Server or Cluster? Is that true?

[fjclark]

Hi @Dslab2025, you can set up SLURM on your workstation - you might find this guide helpful: https://signac.io/development/2020/06/26/local-SLURM-environment.html.

[fjclark]

Closing as this is due to lack of SLURM, but please feel free to get in contact if you have any issues with the software.

[fjclark]

Closing as this is due to lack of SLURM, but please feel free to get in contact if you have any issues with the software.