examples: TI

[SalomeRonja]

In the TI example notebook examples/example_TI_gromos_simulation.ipynb, the file /examples/example_files/TI_Calculation/TI_input/M030_6KET.disres is specified, but this file isn't in the repository. This leads to the following error:

---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<ipython-input-13-14f2d2d90c97> in <module>
      6 grom_system = Gromos_System(in_cnf_path=cnf_path, in_top_path=top_path,
      7                             in_disres_path=disres_path,
----> 8                             system_name=sys_name, work_folder=input_dir)
      9 
     10 

/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/files/gromos_system/gromos_system.py in __init__(self, work_folder, system_name, in_smiles, in_top_path, in_cnf_path, in_imd_path, in_disres_path, in_ptp_path, in_posres_path, in_refpos_path, in_gromosXX_bin_dir, in_gromosPP_bin_dir, rdkitMol, readIn, Forcefield, auto_convert, adapt_imd_automatically, verbose)
    136                         "refpos": in_refpos_path,
    137                         }
--> 138         self.parse_attribute_files(file_mapping, readIn=readIn, verbose=verbose)
    139 
    140         ##System Information:

/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/files/gromos_system/gromos_system.py in parse_attribute_files(self, file_mapping, readIn, verbose)
    523         [check_file_paths.append(x) for k, x in file_mapping.items() if (not x is None)]
    524         if (len(check_file_paths) > 0):
--> 525             bash.check_path_dependencies(check_file_paths, verbose=verbose)
    526 
    527         # SET Attribute-FILES

/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/utils/bash.py in check_path_dependencies(check_required_paths, check_warn_paths, verbose)
    123         print("\n==================\nAUTSCH\n==================\n")
    124         missing_str = "\n\t".join(map(str, missing))
--> 125         raise IOError("COULD NOT FIND all DEPENDENCY!\n\t Could not find path to: \n\t" + str(missing_str), "\n\n")
    126     elif verbose:
    127         print("All dependencies are correct!", "\n\n")

OSError: [Errno COULD NOT FIND all DEPENDENCY!
	 Could not find path to: 
	./example_files/TI_Calculation/TI_input/M030_6KET.disres] 

@schroederb I think you originally wrote this tutorial. Do you still have the file on one of your local branches?

[RiesBen]

WHUPS! I added it on the #67 branch :)

[SalomeRonja]

thanks!

[SalomeRonja]

Now that I added the file, I get a bit further, but the execution of the energy minimization fails with the following output:

/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/files/gromos_system/gromos_system.py:128: UserWarning: No data provided to gromos_system
manual work needed
  if verbose: warnings.warn("No data provided to gromos_system\nmanual work needed")



==================
	CHECK dependencies

Check ./example_files/TI_Calculation/M030_to_6KET/input/test
./example_files/TI_Calculation/M030_to_6KET/input/test
All dependencies are correct! 


Generate Empty:  imd
Generate Empty:  top
Generate Empty:  cnf
################################################################################

a_emin
################################################################################

Script:  /cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/hpc_queuing/job_scheduling/schedulers/simulation_scheduler.py
################################################################################
Simulation PREPERATION
################################################################################



################################################################################
Simulation Setup:
################################################################################

steps_per_run:  3000
equis:  0
simulation runs:  1

/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/hpc_queuing/submission_systems/local.py:159: UserWarning: Queue search was called, but no queue present!
  warnings.warn("Queue search was called, but no queue present!")

#####################################################################################
		ERROR in Submission
#####################################################################################

Traceback (most recent call last):
  File "/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/hpc_queuing/submission_systems/local.py", line 71, in submit_to_queue
    process = bash.execute(command=command, catch_STD=True, env=self._enviroment)
  File "/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/utils/bash.py", line 829, in execute
    return execute_subprocess(command=command, verbose=verbose, catch_STD=catch_STD, env=env)
  File "/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/utils/bash.py", line 752, in execute_subprocess
    raise ChildProcessError(msg)
ChildProcessError: SubProcess Failed due to returncode: 1
 COMMAND: 
	./job_a_emin_1.sh
STDOUT:
	
STDERR:
	b'Traceback (most recent call last):\n'
	b'  File "/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/hpc_queuing/job_scheduling/workers/simulation_workers/simulation_run_worker.py", line 5, in <module>\n'
	b'    from pygromos.gromos import gromosXX as mdGromosXX\n'
	b"ModuleNotFoundError: No module named 'pygromos'\n"

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/hpc_queuing/job_scheduling/schedulers/simulation_scheduler.py", line 147, in do
    verbose = job_verb)
  File "/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/hpc_queuing/job_scheduling/schedulers/scheduler_functions.py", line 186, in chain_submission
    sumbit_from_file=True, verbose=verbose)
  File "/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/hpc_queuing/submission_systems/local.py", line 86, in submit_to_queue
    str(command))
ChildProcessError: command failed: 
./job_a_emin_1.sh
/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/files/gromos_system/gromos_system.py:550: UserWarning: Did not change file path as its only promised ./example_files/TI_Calculation/M030_to_6KET/a_emin/analysis/data/a_emin.cnf
  if(self.verbose or True): warnings.warn("Did not change file path as its only promised " + str(file_obj.path))

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-10-8b5ee5469c36> in <module>
      3                           step_name=step_name, submission_system=subSystem(), in_imd_path=None)
      4 
----> 5 emin_gromos_system.save(step_dir+"/emin_out.obj")
      6 emin_gromos_system

/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/files/gromos_system/gromos_system.py in save(self, path, safe)
    770                 safe_skip = True
    771             else:
--> 772                 bufferdWriter = open(path, "wb")
    773         elif (isinstance(path, io.BufferedWriter)):
    774             bufferdWriter = path

FileNotFoundError: [Errno 2] No such file or directory: './example_files/TI_Calculation/M030_to_6KET/a_emin/emin_out.obj'

[RiesBen]

Hi thanks, I'm working on the jnb.... I think I found some strange problems as well .. :(
related to what you found.

[SalomeRonja]

yes, it seems like a weird issue. thanks for looking into it!

[RiesBen]

Hi, I checked the jupy again and updated the code. Now this notebook works for me! :)
It should be fixed in #71 ?

[SalomeRonja]

Thanks a lot!

[SalomeRonja]

I'm now re-running the notebook to double-check, and I get the message

File imd is empty , can not be written!

for the command

grom_system.rebase_files()

I'm not sure if this is just a warning, or if this means something went wrong. I assume that this should create an imd file in M030_to_6KET/input, which is not the case

[SalomeRonja]

I also get an error in the submission of the energy minimization:

Traceback (most recent call last):
  File "/cluster/work/igc/wsalome/code/PyGromosTools/pygromos/hpc_queuing/submission_systems/local.py", line 71, in submit_to_queue
    process = bash.execute(command=command, catch_STD=True, env=self._enviroment)
  File "/cluster/work/igc/wsalome/code/PyGromosTools/pygromos/utils/bash.py", line 829, in execute
    return execute_subprocess(command=command, verbose=verbose, catch_STD=catch_STD, env=env)
  File "/cluster/work/igc/wsalome/code/PyGromosTools/pygromos/utils/bash.py", line 752, in execute_subprocess
    raise ChildProcessError(msg)
ChildProcessError: SubProcess Failed due to returncode: 1
 COMMAND: 
	/cluster/work/igc/wsalome/code/PyGromosTools/examples/example_files/TI_Calculation/M030_to_6KET/a_emin/simulation/a_emin_1/job_a_emin_1.sh
STDOUT:
	
STDERR:
	b'Traceback (most recent call last):\n'
	b'  File "/cluster/work/igc/wsalome/code/PyGromosTools/pygromos/hpc_queuing/job_scheduling/workers/simulation_workers/simulation_run_worker.py", line 5, in <module>\n'
	b'    from pygromos.gromos import gromosXX as mdGromosXX\n'
	b"ModuleNotFoundError: No module named 'pygromos'\n"

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/cluster/work/igc/wsalome/code/PyGromosTools/pygromos/hpc_queuing/job_scheduling/schedulers/simulation_scheduler.py", line 147, in do
    verbose = job_verb)
  File "/cluster/work/igc/wsalome/code/PyGromosTools/pygromos/hpc_queuing/job_scheduling/schedulers/scheduler_functions.py", line 193, in chain_submission
    sumbit_from_file=True, verbose=verbose)
  File "/cluster/work/igc/wsalome/code/PyGromosTools/pygromos/hpc_queuing/submission_systems/local.py", line 86, in submit_to_queue
    str(command))
ChildProcessError: command failed: 
/cluster/work/igc/wsalome/code/PyGromosTools/examples/example_files/TI_Calculation/M030_to_6KET/a_emin/simulation/a_emin_1/job_a_emin_1.sh

It's a ModuleNotFoundError indicating that there is no module pygromos - even though pygromom was successfuly imported in the earlier steps

[RiesBen]

Uh that looks like an environment problem in the bash call of the scheduler.