schrodinger.test.stu.run module

Contains TestJCJob, TestSPJob, TestQueue, and Runner classes.

TestJCJob is a test utility-specific subclass of queue.JobControlJob. TestSPJob is a test utility-specific subclass of queue.SubprocessJob. These classes allow the test utility to track some information that we care about as a job executes (for instance job duration and test_id). TestQueue is a subclass of queue.JobDJ, and allows further control on reporting.

Runner controls all job running parameters. It is also responsible for actually running the jobs and requesting their workups. The meat is in Runner.__call__.

exception schrodinger.test.stu.run.JobDJError

Bases: RuntimeError

__init__(*args, **kwargs)

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.test.stu.run.TestJob

Bases: object

Interface for the TestJCJob and TestSPJob classes

property duration: Optional[int]

property exit_status: str

Returns an exit status from the list of available Jobcontrol exit statuses.

• For TestJCJobs this comes from job.ExitStatus, which will return a Jobcontrol exit status (from Job.pm in MMSHARE_EXEC) if a job object (i.e. schrodinger.job.jobcontrol.job) is found. If a job object is not found, it could be because the job is not started or it failed to launch. These special cases are handled by setting the initial exit status to “Job not started” and resetting it to “Falied to launch” if the job fails to launch (see TestJCJob.docommand).

• For TestSPJobs a we limit the available exit statuses to “finished”, “died”, and “killed” because there is no job object (i.e. schrodinger.job.jobcontrol.job) associated with TestSPJobs. Like TestJCJobs the initial exit status is set to “Job not started” and is reset it to “Failed to launch” if the job fails to launch (see TestSPJob.docommand).

property test_id: int

property canceled_by_timeout: bool

Return True only if the job was cancelled by JobDJ, this mostly due to timeout.

setupTestEnvironment(host: str = 'localhost')

Set environment variables used during testing.

SCHRODINGER_LICENSE_CHECKOUTS to a file in the directory: SHARED-2727 SCHRODINGER_STU_TEST_ID to current test. (SHARED-3352) Remove TOPLEVEL_HOST_ARGS for Jaguar. (SHARED-4089)

infoStatus(status: str)

debugStatus(status: str)

warnStatus(status: str)

class schrodinger.test.stu.run.TestJCJob(command: List[str], command_dir: Optional[str], test_id: Optional[Union[int, str]] = None, test: Optional[schrodinger.test.stu.testscripts.TestScript] = None, timeout: Optional[int] = None, runs_locally: bool = False, **kwargs)

Bases: schrodinger.job.queue.JobControlJob, schrodinger.test.stu.run.TestJob

Like a normal JobControlJob, but::

• Ignore failures to launch.

• Be aware of scriptID.

• Easily access job duration and exit status.

__init__(command: List[str], command_dir: Optional[str], test_id: Optional[Union[int, str]] = None, test: Optional[schrodinger.test.stu.testscripts.TestScript] = None, timeout: Optional[int] = None, runs_locally: bool = False, **kwargs)

Overridden to add the test_id.

Parameters

• command – Command to be run.

• command_dir – Directory to run in.

• test_id – Unique identifier of script.

• test – The representation of all test data for the job that is being run.

• timeout – Duration in seconds after which to kill the job. None is never.

• runs_locally – Should this job be launched on localhost (never remote hosts)?

doCommand(host: str = 'localhost', *args, **kwargs)

Overridden to ignore errors. Executes the command described by self._command. The parent class has two required arguments, but has the call signature doCommand(*args, **kwargs), hence its usage here.

runsLocally() → bool

Force the test to be run on the host on which the JobDJ is running.

property duration: Optional[int]

Duration of the job, according to the job record. Implemented as a property to provide consistent interface with TestSPJob. Also gives duration for RUNNING jobs, so as to be consistent with TestSPJob.

property exit_status: str

Exit status of the job, according to the job record. Implemented as a property to provide consistent interface with TestSPJob.

addFinalizer(function: Callable[[schrodinger.job.queue.BaseJob], None], run_dir: Optional[str] = None)

Add a function to be invoked when the job completes successfully.

See also the add_multi_job_finalizer function.

addGroupPrereq(job: schrodinger.job.queue.BaseJob)

Make all jobs connected to job prerequisites of all jobs connected to this Job.

addPrereq(job: schrodinger.job.queue.BaseJob)

Add a job that is an immediate prerequisite for this one.

cancel()

Send kill request to jobcontrol managed job. This method will eventually deprecate JobControlJob.kill

cancelSubmitted() → bool

If the job is still in the ‘submitted’ state, cancel it, purge the jobrecord and set the job handle to None.

Return True if this was successful, False otherwise.

property canceled_by_timeout: bool

Return True only if the job was cancelled by JobDJ, this mostly due to timeout.

debugStatus(status: str)

finalize()

Clean up after a job successfully runs.

genAllJobs(seen: Optional[Set[schrodinger.job.queue.BaseJob]] = None) → Generator[schrodinger.job.queue.BaseJob, None, None]

A generator that yields all jobs connected to this one.

genAllPrereqs(seen=None) → Generator[schrodinger.job.queue.BaseJob, None, None]

A generator that yields all jobs that are prerequisites on this one.

getCommand() → List[str]

Return the command used to run this job.

getCommandDir() → str

Return the launch/command directory name. If None is returned, the job will be launched in the current directory.

getDuration() → Optional[int]

Return the duration of the Job as recorded by job server. The duration does not include queue wait time.

If the job is running or has not launched, returns None.

Note that this method makes a blocking call to the job server.

getJob() → Optional[schrodinger.job.jobcontrol.Job]

Return the job record as a schrodinger.job.jobcontrol.Job instance.

Returns None if the job hasn’t been launched.

getJobDJ() → schrodinger.job.queue.JobDJ

Return the JobDJ instance that this job has been added to.

getPrereqs()

Return a set of all immediate prerequisites for this job.

getStatusStrings() → Tuple[str, str, str]

Return a tuple of status strings for printing by JobDJ.

The strings returned are (status, jobid, host).

hasExited() → bool

Returns True if this job finished, successfully or not.

hasStarted() → bool

Returns True if this job has started (not waiting)

infoStatus(status: str)

init_count = 0

isComplete() → bool

Returns True if this job finished successfully

kill()

Send kill request to jobcontrol managed job

maxFailuresReached(msg: str)

Print an error summary, including the last 20 lines from each log file in the LogFiles list of the job record.

postCommand()

A method to restore things to the pre-command state.

preCommand()

A method to make pre-command changes, like cd’ing to the correct directory to run the command in.

retryFailure(max_retries: int = 0) → bool

This method will be called when the job has failed, and JobDJ needs to know whether the job should be retried or not.

JobDJ’s value for the max_retries parameter is passed in, to be used when the job doesn’t have its own max_retries value.

Return True if this job should be retried, otherwise False.

run(*args, **kwargs)

Run the job.

The steps taken are as follows:

1. Execute the preCommand method for things like changing the working directory.

2. Call the doCommand to do the actual work of computation or job launching.

3. Call the postCommand method to undo the changes from the preCommand that need to be undone.

setup()

A method to do initial setup; executed after preCommand, just before doCommand.

setupTestEnvironment(host: str = 'localhost')

Set environment variables used during testing.

SCHRODINGER_LICENSE_CHECKOUTS to a file in the directory: SHARED-2727 SCHRODINGER_STU_TEST_ID to current test. (SHARED-3352) Remove TOPLEVEL_HOST_ARGS for Jaguar. (SHARED-4089)

property state: schrodinger.job.queue.JobState

Return the current state of the job.

Note that this method can be overridden by subclasses that wish to provide for restartability at a higher level than unpickling BaseJob instances. For example, by examining some external condition (e.g. presence of output files) the state JobState.DONE could be returned immediately and the job would not run.

property test_id: int

update()

Checks for changes in job status, and updates the object appropriately (marks for restart, etc).

Raises

RuntimeError – if an unknown Job Status or ExitStatus is encountered.

usesJobServer() → bool

Detect, by looking at the jobId, whether this job uses a job server.

warnStatus(status: str)

class schrodinger.test.stu.run.TestSPJob(command: List[str], command_dir: Optional[str] = None, test_id: Optional[Union[int, str]] = None, test: Optional[schrodinger.test.stu.testscripts.TestScript] = None, timeout: Optional[int] = None, **kwargs)

Bases: schrodinger.job.queue.SubprocessJob, schrodinger.test.stu.run.TestJob

Like a normal SubprocessJob job, but:

• Ignore failures to launch.

• Kill subjobs when killing this job.

• Be aware of scriptID.

• Access job duration and status.

__init__(command: List[str], command_dir: Optional[str] = None, test_id: Optional[Union[int, str]] = None, test: Optional[schrodinger.test.stu.testscripts.TestScript] = None, timeout: Optional[int] = None, **kwargs)

Overridden to add the test_id.

Parameters

• command – Command to be run.

• command_dir – Directory to run in.

• test_id – Unique identifier of script.

• test – The representation of all test data for the job that is being run.

• timeout – Duration in seconds after which to kill the job. None is never.

preCommand(*args, **kwargs)

Overridden to open standard files for recording standard error and standard out. Also marks the start time of the job.

doCommand(*args, **kwargs)

Overridden to ignore errors. Executes the command described by self._command.

update()

Overridden to make errors non fatal.

cleanUp()

Close standard files for recording standard error and standard out.

getStatusStrings() → Tuple[str, str, str]

Return a tuple of status strings for printing by JobDJ.

Returns

(status, jobid, host)

property exit_status: str

Exit status of the job, according to subprocess. Implemented as a property to provide consistent interface with TestJCJob.

kill()

First, kill children, then myself

addFinalizer(function: Callable[[schrodinger.job.queue.BaseJob], None], run_dir: Optional[str] = None)

Add a function to be invoked when the job completes successfully.

See also the add_multi_job_finalizer function.

addGroupPrereq(job: schrodinger.job.queue.BaseJob)

Make all jobs connected to job prerequisites of all jobs connected to this Job.

addPrereq(job: schrodinger.job.queue.BaseJob)

Add a job that is an immediate prerequisite for this one.

cancel()

Send termination request to subprocess managed job. This method will eventually deprecate SubprocessJob.kill

property canceled_by_timeout: bool

Return True only if the job was cancelled by JobDJ, this mostly due to timeout.

debugStatus(status: str)

property duration: Optional[int]

finalize()

Clean up after a job successfully runs.

genAllJobs(seen: Optional[Set[schrodinger.job.queue.BaseJob]] = None) → Generator[schrodinger.job.queue.BaseJob, None, None]

A generator that yields all jobs connected to this one.

genAllPrereqs(seen=None) → Generator[schrodinger.job.queue.BaseJob, None, None]

A generator that yields all jobs that are prerequisites on this one.

getCommand() → List[str]

Return the command used to run this job.

getCommandDir() → str

Return the launch/command directory name. If None is returned, the job will be launched in the current directory.

getDuration() → Optional[int]

Return the CPU time of the job in seconds.

If the job is still running, returns None.

getJobDJ() → schrodinger.job.queue.JobDJ

Return the JobDJ instance that this job has been added to.

getPrereqs()

Return a set of all immediate prerequisites for this job.

hasExited() → bool

Returns True if this job finished, successfully or not.

hasStarted() → bool

Returns True if this job has started (not waiting)

infoStatus(status: str)

init_count = 0

isComplete() → bool

Returns True if this job finished successfully

maxFailuresReached(msg: str)

This is a method that will be called after the job has failed and the maximum number of failures per JobDJ run has been reached. After invoking this method, JobDJ will raise a RuntimeError and the process will exit.

postCommand()

A method to restore things to the pre-command state.

run(*args, **kwargs)

Run the job.

The steps taken are as follows:

1. Execute the preCommand method for things like changing the working directory.

2. Call the doCommand to do the actual work of computation or job launching.

3. Call the postCommand method to undo the changes from the preCommand that need to be undone.

runsLocally() → bool

Return True if the job runs on the JobDJ control host, False if not. Jobs that run locally don’t need hosts.

There is no limit on the number of locally run jobs.

setup()

A method to do initial setup; executed after preCommand, just before doCommand.

setupTestEnvironment(host: str = 'localhost')

Set environment variables used during testing.

SCHRODINGER_LICENSE_CHECKOUTS to a file in the directory: SHARED-2727 SCHRODINGER_STU_TEST_ID to current test. (SHARED-3352) Remove TOPLEVEL_HOST_ARGS for Jaguar. (SHARED-4089)

property state: schrodinger.job.queue.JobState

Return the current state of the job.

Note that this method can be overridden by subclasses that wish to provide for restartability at a higher level than unpickling BaseJob instances. For example, by examining some external condition (e.g. presence of output files) the state JobState.DONE could be returned immediately and the job would not run.

property test_id: int

warnStatus(status: str)

class schrodinger.test.stu.run.TestQueue(hosts: Optional[List[Tuple[str, int]]] = None, verbosity: str = 'quiet', timeout: Optional[int] = None)

Bases: schrodinger.job.queue.JobDJ

Like a normal JobDJ, but:

• Print the script ID at status points

• Run workups

__init__(hosts: Optional[List[Tuple[str, int]]] = None, verbosity: str = 'quiet', timeout: Optional[int] = None)

Constructor.

Parameters

• hosts – A list of (<hostname>, <maximum_concurrent_subjobs>) tuples, where <hostname> is a string and <maximum_concurrent_subjobs> is an integer. The default value of None is determined automatically and is usually desired.

• local – No longer functional in JOB_SERVER.

• max_retries – Number of allowed retries per subjob. If this is set, it is never overridden by the SCHRODINGER_MAX_RETRIES environment variable. If it is not set, the value in default_max_retries is used, and SCHRODINGER_MAX_RETRIES is allowed to override. If you wish to disable restarting altogether, set this value to zero.

• default_max_retries – Number of allowed retries per subjob. This value can always be overridden by the SCHRODINGER_MAX_RETRIES environment variable. Default is zero.

• max_failures – Total number of allowed subjob failures before JobDJ exits. If it is not defined, a default of zero will be used (exit on any failure after attempting to restart), but this can be overridden with the SCHRODINGER_MAX_FAILURES environment variable. To allow an unlimited number of subjob failures, set max_failures to the module level NOLIMIT constant.

• verbosity – There are three allowed verbosity levels: “quiet” - only warnings and errors are printed; “normal” - JobDJ progress is printed; and “verbose” - additional debugging info is printed. Default is “quiet”.

• job_class – The class to use as the default job constructor when the addJob argument is not a BaseJob instance.

• update_delay – The number of seconds to wait between job control database reads for JobControlJob jobs. (This delay is for an individual job, not for any job database read.) Default is None, which causes the module level constant UPDATE_DELAY to be used.

printStatus(job: Optional[schrodinger.test.stu.run.TestJob] = None, action: Optional[str] = None)

Prints the status of JobDJ and the action/status for the job.

If no job is specified, prints the status header.

If no action is specified, the status_string attribute of the job is used.

printHeader()

Print the header

formatStatus(job: Optional[schrodinger.test.stu.run.TestJob] = None, action: Optional[str] = None)

Override to print script ID. :param job: queue.BaseJob object of interest. :param action: Status to be printed.

addJob(job: schrodinger.test.stu.run.TestJob, add_connected: bool = True, timeout: Optional[int] = None, **kwargs)

Add a job to run. If job is not a BaseJob instance, a BaseJob instance is constructed with job as the first argument. The default BaseJob class for the JobDJ instance can be specified in the constructor for JobDJ.

Additional keyword arguments are passed on to the job constructor.

All job prerequisites and dependencies need to be specified before adding a job to JobDJ.

Parameters

add_connected – If True, for jobs with dependencies only one job per connected group should be added and all connected jobs will be discovered and added automatically. If False, it is the user’s responsibility to make sure that any prerequisites of a job are also added.

property active_jobs: List[schrodinger.job.queue.BaseJob]

property all_jobs: List[schrodinger.job.queue.BaseJob]

disableSmartDistribution()

Disable smart distribution of jobs.

Smart distribution allows subjobs to run on the machine that JobDJ is running on when JobDJ itself is running under a queuing system. This is usually desirable since the JobDJ process doesn’t generally consume significant computational resources and you don’t want to leave a queue slot mostly idle.

property done_jobs: List[schrodinger.job.queue.BaseJob]

Successfully completed jobs, sorted into the order they were marked as completed by JobDJ.

dump(filename: pathlib.Path)

Pickle the JobDJ instance to the specified file name.

property failed_jobs: List[schrodinger.job.queue.BaseJob]

getActiveProcCounts() → Dict[str, int]

Return a dictionary containing the number of active jobs on each host.

getFirstHost()

Get first host from the lists of hosts.

Return type

str

Returns

First host

hasStarted() → bool

Returns True if JobDJ has started already

isComplete() → bool

Returns True if JobDJ has completed, False otherwise.

killJobs()

Kill all active jobs

markForRestart(job: schrodinger.job.queue.BaseJob, action: str)

Mark a job as dead, but make sure that it gets restarted.

Parameters

action – Describes the reason the job is being restarted.

run(*, status_change_callback: Optional[Callable[[schrodinger.job.queue.BaseJob], None]] = None, periodic_callback: Optional[Callable[[schrodinger.job.queue.BaseJob], None]] = None, callback_interval: int = 300, restart_failed: bool = True)

Call this method to run all jobs that have been added. The method will return control when all jobs have completed.

Parameters

• status_change_callback – A function to call every time a job status changes. For example, JobState.RUNNING->JobState.DONE. This function takes a single argument of a schrodinger.job.queue.BaseJob object.

• periodic_callback – A command to call periodically, regardless of whether job status has changed or not. The function will be called without any arguments.

• callback_interval – The interval at which the periodic interval will be called. This time is only approximately enforced and will depend on the timing delay settings (e.g. MONITOR_DELAY).

• restart_failed – True (default) if previously failed jobs should be restarted, False if not.

setHostList(host_list: List[Tuple[str, int]])

Define compute hosts to run subjobs on.

Active jobs are not affected by a change in the host list.

Parameters

host_list – A list of (<host_entry_name>, <maximum_concurrent_subjobs>) tuples, where <host_entry_name> is a string and <maximum_concurrent_subjobs> is an integer.

setSmartDistribution(state: bool)

Set smart distribution of jobs.

Parameters

state (bool) – Whether to enable smart distribution

property total_active: int

The number of jobs currently running.

property total_added: int

The number of individual jobs that have been added to the JobDJ instance.

property total_failed: int

The number of jobs that have failed.

property total_finished: int

The number of jobs that have finished successfully.

property waiting_jobs: List[schrodinger.job.queue.BaseJob]

Jobs waiting to be started.

class schrodinger.test.stu.run.Runner(ui: base_executable.TestUtility)

Bases: object

Runner controls all job running parameters within the backend test utility code. It is also responsible for actually running the jobs and requesting their workups. The meat is in Runner.addScript and Runner.__call__.

__init__(ui: base_executable.TestUtility)

Initialize Runner Class

Parameters

ui – Contains information about the user interface (i.e. the command line arguments)

addScript(test: schrodinger.test.stu.testscripts.TestScript)

Add test to be executed by self.__call__. Adds the test information to self.job_runner.

Parameters

test – Test to be executed.

jobStatusChange(workups: Dict[str, Callable], job: schrodinger.test.stu.run.TestJob)

schrodinger.test.stu.run.run_workup(test: schrodinger.test.stu.testscripts.TestScript, job: schrodinger.test.stu.run.TestJob, workups: Dict[str, Callable], generate_postmortem: bool, reporter: Optional[schrodinger.test.stu.client.ResultReporter]) → List[str]

Run workup code and report results.

If an upload failed or an unexpected error occurred (a workup failure is considered expected, since it can be reporter upon), then return a list of str error messages.

schrodinger.test.stu.run.get_xvfb_cmd() → List[str]

xvfb-run needs the -a (auto server number) option, except on CentOS 7 (and possibly other OSes) where that option is superceded by the -d (auto display) option. As a bonus, the long option –auto-display is shown in the help on CentOS 7 but does not actually work. Furthermore, xvfb-run does not have a –version flag which could be used to reason about supported options. To determine what flags are supported, try to run a no-op command with xvfb-run -d, and if that fails, use -a.

schrodinger.test.stu.run.use_license_checking(test: schrodinger.test.stu.testscripts.TestScript) → bool

Return True if license checking should be enabled for this test run.

schrodinger.test.stu.run.add_jobcontrol_handler(filename: str)

Within a context, modify jobcontrol logger to log messages to a particular file.

Parameters

filename – name of file to log jobcontrol launch messages to