def test_processjobs_include(m_validator, m_proccommandline):
"""Test that if user has provided upload-includes that they don't get
overriden.
"""
jobs = {
"jobone": {
"executableargs": ["-i", "input", "-c", "coords", "-p", "topol"],
"localworkdir": os.path.join(os.getcwd(),
"tests/standards/jobs/single"),
"executable": "pmemd.MPI",
"upload-include": "test.file",
"upload-exclude": ""
}
}
m_proccommandline.side_effect = _proccommandline
m_validator.return_value = None
processjobs(jobs)
assert jobs["jobone"]["upload-include"] == \
"test.file, input, coords, topol"
def test_processjobs_singlejob2(m_validator, m_proccommandline):
"""Test for single job, make sure parameters are all set correctly."""
jobs = {
"jobone": {
"executableargs": ["-i", "input", "-c", "coords", "-p", "topol"],
"localworkdir": os.path.join(os.getcwd(),
"tests/standards/jobs/single"),
"executable": "pmemd.MPI",
"upload-include": "",
"upload-exclude": ""
}
}
m_proccommandline.side_effect = _proccommandline
m_validator.return_value = None
processjobs(jobs)
assert jobs["jobone"]["upload-exclude"] == "*"
assert jobs["jobone"]["localworkdir"] == os.path.join(
os.getcwd(), "tests/standards/jobs/single")
assert jobs["jobone"]["executableargs"] == \
"pmemd.MPI -i input -c coords -p topol"
assert jobs["jobone"]["upload-include"] == "input, coords, topol"
def test_processjobs_abspath():
"""Test exception is thrown when using absolute paths on command-line."""
jobs = {
"jobone": {
"executableargs": ["-flag", "/path/to/file"],
"executable": "pmemd.MPI"
}
}
with pytest.raises(exceptions.RequiredinputError):
processjobs(jobs)
def test_processjobs_pardir():
"""
Test exception is thrown when using paths above workdir on command-line.
"""
jobs = {
"jobone": {
"executableargs": ["-flag", "../../file"],
"executable": "pmemd.MPI"
}
}
with pytest.raises(exceptions.RequiredinputError):
processjobs(jobs)
def test_processjobs_direxcept():
"""Test exception is thrown when job directory is missing."""
jobs = {
"jobone": {
"executableargs": ["-i", "input", "-c", "coords", "-p", "topol"],
"localworkdir": os.path.join(os.getcwd(),
"tests/standards/jobs/error"),
"executable": "pmemd.MPI",
"upload-include": "",
"upload-exclude": ""
}
}
with pytest.raises(exceptions.DirectorynotfoundError):
processjobs(jobs)
def test_processjobs_genericexec1():
"""
Test that the generic executable case works with hard path
"""
jobs = {
"jobone": {
"executableargs": ["-f", "input", "-c", "file", "-p", "test"],
"localworkdir": os.getcwd(),
"executable": "/opt/somesoftware/exec",
"upload-include": "",
"upload-exclude": ""
}
}
processjobs(jobs)
assert jobs["jobone"]["executableargs"] == \
"/opt/somesoftware/exec -f input -c file -p test"
assert jobs["jobone"]["upload-include"] == ""
assert jobs["jobone"]["upload-exclude"] == "*.log"
def test_processjobs_genericexec2():
"""
Test that the generic executable case works with module and exec only.
"""
jobs = {
"jobone": {
"executableargs": ["-f", "input", "-c", "file", "-p", "test"],
"localworkdir": os.getcwd(),
"executable": "testexec",
"upload-include": "",
"upload-exclude": "",
"modules": "testsoftware"
}
}
processjobs(jobs)
assert jobs["jobone"]["executableargs"] == \
"testexec -f input -c file -p test"
assert jobs["jobone"]["upload-include"] == ""
assert jobs["jobone"]["upload-exclude"] == "*.log"
def longbow(jobs, parameters):
"""Entry point at the top level of the Longbow library.
Being the top level method that makes calls on the Longbow library.
This is a good place to link against Longbow if a developer does not want
to link against the executable, or if low level linking is not needed or is
over-kill.
Required inputs are:
parameters (dictionary): A dictionary containing the parameters and
overrides from the command-line.
"""
# A failure at this level will result in jobs being killed off before
# escalating the exception to trigger graceful exit.
# Load configurations and initialise Longbow data structures.
jobparams = configuration.processconfigs(parameters)
# Copy to jobs so when exceptions are raised the structure is available.
for param in jobparams:
jobs[param] = jobparams[param]
# Test all connection/s specified in the job configurations
shellwrappers.checkconnections(jobs)
# Test the hosts listed in the jobs configuration file have their
# scheduler environments listed, if not then test and save them.
scheduling.checkenv(jobs, parameters["hosts"])
# Test that for the applications listed in the job configuration
# file are available and that the executable is present.
if parameters["nochecks"] is False:
applications.checkapp(jobs)
# Process the jobs command line arguments and find files for
# staging.
applications.processjobs(jobs)
# Create jobfile and add it to the list of files that needs
# uploading.
scheduling.prepare(jobs)
# Stage all of the job files along with the scheduling script.
staging.stage_upstream(jobs)
# Submit all jobs.
scheduling.submit(jobs)
# Process the disconnect function.
if parameters["disconnect"] is True:
raise exceptions.DisconnectException
# Monitor all jobs.
scheduling.monitor(jobs)
# Clean up all jobs
staging.cleanup(jobs)