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Merge pull request #254 from NeuroML/experimental
To v1.1.0; Update to jnml v0.12.3 jar
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| #!/usr/bin/env python3 | ||
| """ | ||
| Module for working with NSG. See https://github.com/OpenSourceBrain/pynsgr | ||
| File: pyneuroml/nsgr/__init__.py | ||
| Copyright 2023 NeuroML contributors | ||
| """ | ||
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| import logging | ||
| import os | ||
| import pathlib | ||
| import shutil | ||
| import time | ||
| import typing | ||
| from zipfile import ZipFile | ||
|
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| from pyneuroml.archive import get_model_file_list | ||
| from pyneuroml.pynml import run_lems_with | ||
| from pyneuroml.utils import get_files_generated_after, get_pyneuroml_tempdir | ||
| from pynsgr.commands.nsgr_submit import nsgr_submit | ||
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| logger = logging.getLogger(__name__) | ||
| logger.setLevel(logging.DEBUG) | ||
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| def run_on_nsg( | ||
| engine: str, | ||
| lems_file_name: str, | ||
| nsg_sim_config: typing.Dict[typing.Any, typing.Any] = {}, | ||
| run_dir: typing.Optional[str] = None, | ||
| dry_run: bool = False, | ||
| *engine_args: typing.Any, | ||
| **engine_kwargs: typing.Any, | ||
| ): | ||
| """Run NeuroML/LEMS simulation on NSG. | ||
| Since the versions of tools on NSG may differ from what you have installed | ||
| locally, this method first generates the simulation engine specific files | ||
| (runner script for NEURON and mod files, for example) for the provided | ||
| engine in a new folder, zips them up, writes the config files, and then | ||
| submits the job to NSG using pynsgr. | ||
| The data generated by the job (if the command is not interrupted) is also | ||
| downloaded to the newly created directory. | ||
| Please ensure that you have set up an account and have your NSG | ||
| configuration file populated as noted in pynsgr. | ||
| - https://nsgr.sdsc.edu:8443/restusers/documentation | ||
| - https://nsgr.sdsc.edu:8443/restusers/docs/tools | ||
| Default for the nsg_sim_config is below, keys provided by the user in | ||
| nsg_sim_config overwrite these: | ||
| .. code:: python | ||
| nsg_sim_config_dict = { | ||
| "number_cores_": "1", | ||
| "number_nodes_": "1", | ||
| "tasks_per_node_": "1", | ||
| "runtime_": "0.5", | ||
| 'toolId': "PY_EXPANSE", | ||
| 'nrnivmodl_o_': "1" | ||
| } | ||
| .. versionadded:: 1.0.10 | ||
| :param engine: name of engine: suffixes of the run_lems_with.. functions | ||
| :type engine: str | ||
| :param lems_file_name: name of LEMS simulation file | ||
| :type lems_file_name: str | ||
| :param nsg_sim_config: dict containing params and values that will be | ||
| printed to testParam.properties | ||
| :type nsg_sim_config: dict | ||
| :param run_dir: directory in which model files are copied, backend specific | ||
| files are generated, and from which the archive is sent to NSG. Results | ||
| from the NSG run will also be downloaded to this directory. | ||
| By default, this is the directory that the command is run from (".") | ||
| It is good practice to separate directories where simulations are run | ||
| from the source of the model/simulations. | ||
| :type run_dir: str | ||
| :param *engine_args: positional args to be passed to the engine runner | ||
| function | ||
| :param **engine_kwargs: keyword args to be be passed to the engine runner | ||
| function | ||
| :param dry_run: do everything but do not submit | ||
| :type dry_run: bool | ||
| """ | ||
| supported_engines = ["jneuroml_neuron", "jneuroml_netpyne"] | ||
| if engine not in supported_engines: | ||
| print(f"Engine {engine} is not currently supported on NSG") | ||
| print(f"Supported engines are: {supported_engines}") | ||
| return | ||
|
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| logger.debug(f"NSGR: engine is {engine}") | ||
|
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| zipfile_name = lems_file_name.replace(".xml", "") + "_NSG.zip" | ||
| # default dictionary | ||
| nsg_sim_config_dict = { | ||
| "number_cores_": "1", | ||
| "number_nodes_": "1", | ||
| "tasks_per_node_": "1", | ||
| "runtime_": "0.5", | ||
| "toolId": "PY_EXPANSE", | ||
| "nrnivmodl_o_": "1", | ||
| } | ||
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| # update dict based on user values | ||
| for key, val in nsg_sim_config.items(): | ||
| nsg_sim_config_dict[key] = val | ||
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| if run_dir is None: | ||
| run_dir = "." | ||
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| tdir = get_pyneuroml_tempdir(rootdir=run_dir, prefix="pyneuroml") | ||
| os.mkdir(tdir) | ||
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| logger.debug("Getting list of model files") | ||
| model_file_list = [] # type: list | ||
| lems_def_dir = None | ||
| lems_def_dir = get_model_file_list( | ||
| lems_file_name, model_file_list, ".", lems_def_dir | ||
| ) | ||
|
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| for model_file in model_file_list: | ||
| logger.debug(f"Copying: {model_file} -> {tdir + '/' + model_file}") | ||
| # if model file has directory structures in it, recreate the dirs in | ||
| # the temporary directory | ||
| if len(model_file.split("/")) > 1: | ||
| # throw error if files in parent directories are referred to | ||
| if "../" in model_file: | ||
| raise ValueError( | ||
| """ | ||
| Cannot handle parent directories because we | ||
| cannot create these directories correctly in | ||
| the temporary location. Please re-organize | ||
| your code such that all included files are in | ||
| sub-directories of this main directory. | ||
| """ | ||
| ) | ||
|
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| model_file_path = pathlib.Path(tdir + "/" + model_file) | ||
| parent = model_file_path.parent | ||
| parent.mkdir(parents=True, exist_ok=True) | ||
| shutil.copy(model_file, tdir + "/" + model_file) | ||
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| if lems_def_dir is not None: | ||
| logger.info(f"Removing LEMS definitions directory {lems_def_dir}") | ||
| shutil.rmtree(lems_def_dir) | ||
|
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| os.chdir(tdir) | ||
| logger.info(f"Generating simulator specific files in {tdir}") | ||
| start_time = time.time() - 1.0 | ||
|
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| if engine == "jneuroml_neuron": | ||
| run_lems_with( | ||
| engine, | ||
| lems_file_name=lems_file_name, | ||
| compile_mods=False, | ||
| only_generate_scripts=True, | ||
| *engine_args, | ||
| **engine_kwargs, | ||
| ) | ||
| elif engine == "jneuroml_netpyne": | ||
| run_lems_with( | ||
| engine, | ||
| lems_file_name=lems_file_name, | ||
| only_generate_scripts=True, | ||
| *engine_args, | ||
| **engine_kwargs, | ||
| ) | ||
|
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| generated_files = get_files_generated_after( | ||
| start_time, ignore_suffixes=["xml", "nml"] | ||
| ) | ||
| logger.debug(f"Generated files are: {generated_files}") | ||
|
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||
| logger.info("Generating zip file") | ||
| runner_file = "" | ||
| # NSG requires that the top level directory exist | ||
| nsg_dir = pathlib.Path(zipfile_name.replace(".zip", "")) | ||
| logger.debug(f"Creating directory and moving generated files to it: {nsg_dir}") | ||
|
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||
| # remove it if it exists | ||
| if nsg_dir.is_dir(): | ||
| shutil.rmtree(str(nsg_dir)) | ||
| nsg_dir.mkdir() | ||
|
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||
| with ZipFile(zipfile_name, "w") as archive: | ||
| for f in generated_files: | ||
| if engine == "jneuroml_neuron": | ||
| if f.endswith("_nrn.py"): | ||
| runner_file = f | ||
| elif engine == "jneuroml_netpyne": | ||
| if f.endswith("_netpyne.py"): | ||
| runner_file = f | ||
| fpath = pathlib.Path(f) | ||
| moved_path = fpath.rename(nsg_dir / fpath) | ||
| archive.write(str(moved_path)) | ||
|
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| logger.debug("Printing testParam.properties") | ||
| nsg_sim_config_dict["filename_"] = runner_file | ||
| logger.debug(f"NSG sim config is: {nsg_sim_config_dict}") | ||
|
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| with open("testParam.properties", "w") as file: | ||
| for key, val in nsg_sim_config_dict.items(): | ||
| print(f"{key}={val}", file=file) | ||
|
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| logger.debug("Printing testInput.properties") | ||
| with open("testInput.properties", "w") as file: | ||
| print(f"infile_=@./{zipfile_name}", file=file) | ||
|
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| print(f"{zipfile_name} generated") | ||
| # uses argv, where the first argument is the script itself, so we must pass | ||
| # something as the 0th index of the list | ||
| if not dry_run: | ||
| if nsgr_submit(["", ".", "validate"]) == 0: | ||
| print("Attempting to submit to NSGR") | ||
| return nsgr_submit(["", ".", "run"]) | ||
| else: | ||
| print("Dry run mode enabled. Not submitting to NSG.") | ||
|
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| return True |
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