def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
proclog=None,
resource_appker_vars=None):
"""
Process test appkernel output.
"""
# set App Kernel Description
parser = AppKerOutputParser(name='test',
version=1,
description="Test the resource deployment",
url='http://xdmod.buffalo.edu',
measurement_name='test')
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_statistic('Wall Clock Time')
parser.add_must_have_statistic('Shell is BASH')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
# set statistics
if parser.wallClockTime is not None:
parser.set_statistic("Wall Clock Time",
total_seconds(parser.wallClockTime), "Second")
# read output
lines = []
if os.path.isfile(stdout):
fin = open(stdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
parser.set_statistic('Shell is BASH', 0)
j = 0
while j < len(lines):
if lines[j].count("Checking that the shell is BASH") > 0 and lines[
j + 1].count("bash") > 0:
parser.set_statistic('Shell is BASH', 1)
j += 1
if __name__ == "__main__":
# output for testing purpose
print(("parsing complete:", parser.parsing_complete()))
parser.print_params_stats_as_must_have()
print((parser.get_xml()))
# return complete XML otherwise return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(name='hpcc',
version=1,
description="HPC Challenge Benchmarks",
url='http://icl.cs.utk.edu/hpcc/',
measurement_name='xdmod.benchmark.hpcc')
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:Version')
parser.add_must_have_parameter('Input:DGEMM Problem Size')
parser.add_must_have_parameter('Input:High Performance LINPACK Grid Cols')
parser.add_must_have_parameter('Input:High Performance LINPACK Grid Rows')
parser.add_must_have_parameter(
'Input:High Performance LINPACK Problem Size')
parser.add_must_have_parameter('Input:MPI Ranks')
parser.add_must_have_parameter('Input:MPIRandom Problem Size')
parser.add_must_have_parameter('Input:OpenMP Threads')
parser.add_must_have_parameter('Input:PTRANS Problem Size')
parser.add_must_have_parameter('Input:STREAM Array Size')
parser.add_must_have_parameter('RunEnv:CPU Speed')
parser.add_must_have_parameter('RunEnv:Nodes')
parser.add_must_have_statistic(
'Average Double-Precision General Matrix Multiplication (DGEMM) Floating-Point Performance'
)
parser.add_must_have_statistic("Average STREAM 'Add' Memory Bandwidth")
parser.add_must_have_statistic("Average STREAM 'Copy' Memory Bandwidth")
parser.add_must_have_statistic("Average STREAM 'Scale' Memory Bandwidth")
parser.add_must_have_statistic("Average STREAM 'Triad' Memory Bandwidth")
parser.add_must_have_statistic(
'Fast Fourier Transform (FFTW) Floating-Point Performance')
parser.add_must_have_statistic('High Performance LINPACK Efficiency')
parser.add_must_have_statistic(
'High Performance LINPACK Floating-Point Performance')
parser.add_must_have_statistic('High Performance LINPACK Run Time')
parser.add_must_have_statistic('MPI Random Access')
parser.add_must_have_statistic('Parallel Matrix Transpose (PTRANS)')
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
if parser.appKerWallClockTime is not None:
parser.set_statistic("Wall Clock Time",
total_seconds(parser.appKerWallClockTime),
"Second")
# Intel MPI benchmark suite contains three classes of benchmarks:
#
# Single-transfer, which needs only 2 processes
# Parallel-transfer, which can use as many processes that are available
# Collective, which can use as many processes that are available
# The parameters mapping table
params = {
"CommWorldProcs": ["MPI Ranks", "", ""],
"HPL_N": ["High Performance LINPACK Problem Size", "", ""],
"HPL_nprow": ["High Performance LINPACK Grid Rows", "", ""],
"HPL_npcol": ["High Performance LINPACK Grid Cols", "", ""],
"PTRANS_n": ["PTRANS Problem Size", "", ""],
"MPIRandomAccess_N":
["MPIRandom Problem Size", "MWord", "val/1024/1024"],
"STREAM_VectorSize": ["STREAM Array Size", "MWord", ""],
"DGEMM_N": ["DGEMM Problem Size", "", ""],
"omp_get_num_threads": ["OpenMP Threads", "", ""],
}
# The result mapping table
metrics = {
"HPL_Tflops": [
"High Performance LINPACK Floating-Point Performance",
"MFLOP per Second", "val*1e6"
],
"HPL_time": ["High Performance LINPACK Run Time", "Second", ""],
"PTRANS_GBs":
["Parallel Matrix Transpose (PTRANS)", "MByte per Second", "val*1024"],
"MPIRandomAccess_GUPs":
["MPI Random Access", "MUpdate per Second", "val*1000"],
"MPIFFT_Gflops": [
"Fast Fourier Transform (FFTW) Floating-Point Performance",
"MFLOP per Second", "val*1000"
],
"StarDGEMM_Gflops": [
"Average Double-Precision General Matrix Multiplication (DGEMM) Floating-Point Performance",
"MFLOP per Second", "val*1000"
],
"StarSTREAM_Copy": [
"Average STREAM 'Copy' Memory Bandwidth", "MByte per Second",
"val*1024"
],
"StarSTREAM_Scale": [
"Average STREAM 'Scale' Memory Bandwidth", "MByte per Second",
"val*1024"
],
"StarSTREAM_Add": [
"Average STREAM 'Add' Memory Bandwidth", "MByte per Second",
"val*1024"
],
"StarSTREAM_Triad": [
"Average STREAM 'Triad' Memory Bandwidth", "MByte per Second",
"val*1024"
]
}
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
parser.successfulRun = False
result_begin = None
hpl_tflops = None
num_cores = None
values = {}
j = -1
while j < len(lines) - 1:
j += 1
m = re.search(r'End of HPC Challenge tests', lines[j])
if m:
parser.successfulRun = True
m = re.match(r'^Begin of Summary section', lines[j])
if m:
result_begin = 1
continue
m = re.match(r'^(\w+)=([\w.]+)', lines[j])
if m and result_begin:
metric_name = m.group(1).strip()
values[metric_name] = m.group(2).strip()
if metric_name == "HPL_Tflops":
hpl_tflops = float(values[metric_name])
if metric_name == "CommWorldProcs":
num_cores = int(values[metric_name])
m = re.match(r'^Running on ([0-9.]+) processors', lines[j])
if m:
num_cores = int(m.group(1).strip())
if hpl_tflops is None or num_cores is None:
parser.successfulRun = False
hpcc_version = None
mhz = None
theoretical_gflops = None
if "VersionMajor" in values and "VersionMinor" in values and "VersionMicro" in values:
hpcc_version = values["VersionMajor"] + "." + values[
"VersionMinor"] + "." + values["VersionMicro"]
if "VersionRelease" in values:
hpcc_version += values["VersionRelease"]
if hpcc_version:
parser.set_parameter("App:Version", hpcc_version)
for k, v in params.items():
if k not in values:
continue
val = values[k]
if v[2].find('val') >= 0:
# if convertion formula is used, then first set val variable and then eval the formula
val = get_float_or_int(values[k])
val = eval(v[2])
units = v[1] if [1] != "" else None
parser.set_parameter("Input:" + v[0], val, units)
for k, v in metrics.items():
if k not in values:
continue
val = values[k]
if v[2].find('val') >= 0:
# if convertion formula is used, then first set val variable and then eval the formula
val = get_float_or_int(values[k])
val = eval(v[2])
units = v[1] if [1] != "" else None
parser.set_statistic(v[0], val, units)
if "cpu_speed" in parser.geninfo:
ll = parser.geninfo["cpu_speed"].splitlines()
cpu_speed_max = 0.0
for l in ll:
m = re.search(r'([\d.]+)$', l)
if m:
v = float(m.group(1).strip())
if v > cpu_speed_max:
cpu_speed_max = v
if cpu_speed_max > 0.0:
parser.set_parameter("RunEnv:CPU Speed", cpu_speed_max, "MHz")
mhz = cpu_speed_max
if resource_appker_vars is not None:
if 'resource' in resource_appker_vars and 'app' in resource_appker_vars:
if 'theoreticalGFlopsPerCore' in resource_appker_vars['app']:
resname = resource_appker_vars['resource']['name']
if resname in resource_appker_vars['app'][
'theoreticalGFlopsPerCore']:
theoretical_gflops = resource_appker_vars['app'][
'theoreticalGFlopsPerCore'][resname] * num_cores
print("theoreticalGFlops", resname, theoretical_gflops)
if theoretical_gflops is None and mhz is not None:
# Most modern x86 & POWER processors are superscale and can issue 4 instructions per cycle
theoretical_gflops = mhz * num_cores * 4 / 1000.0
if theoretical_gflops and hpl_tflops:
# Convert both to GFlops and derive the Efficiency
percent = (1000.0 * hpl_tflops / theoretical_gflops) * 100.0
parser.set_statistic("High Performance LINPACK Efficiency",
"%.3f" % percent, "Percent")
if __name__ == "__main__":
# output for testing purpose
print("parsing complete:", parser.parsing_complete(verbose=True))
parser.print_params_stats_as_must_have()
print(parser.get_xml())
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(
name='mpi-tile-io',
version=1,
description="MPI-Tile-IO Benchmark",
url='http://www.mcs.anl.gov/research/projects/pio-benchmark',
measurement_name='MPI-Tile-IO')
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('2D Collective Read Test File System')
parser.add_must_have_parameter('2D Collective Write Test File System')
parser.add_must_have_parameter('2D HDF5 Collective Read Test File System')
parser.add_must_have_parameter('2D HDF5 Collective Write Test File System')
parser.add_must_have_parameter('2D Independent Read Test File System')
parser.add_must_have_parameter('2D Independent Write Test File System')
parser.add_must_have_parameter('2D Per-Process Data Topology')
parser.add_must_have_parameter('2D Per-Process Ghost Zone')
parser.add_must_have_parameter('2D Per-Process Memory')
parser.add_must_have_parameter('2D Process Topology')
parser.add_must_have_parameter('3D Collective Read Test File System')
parser.add_must_have_parameter('3D Collective Write Test File System')
parser.add_must_have_parameter('3D HDF5 Collective Read Test File System')
parser.add_must_have_parameter('3D HDF5 Collective Write Test File System')
parser.add_must_have_parameter('3D Independent Read Test File System')
parser.add_must_have_parameter('3D Independent Write Test File System')
parser.add_must_have_parameter('3D Per-Process Data Topology')
parser.add_must_have_parameter('3D Per-Process Ghost Zone')
parser.add_must_have_parameter('3D Per-Process Memory')
parser.add_must_have_parameter('3D Process Topology')
parser.add_must_have_parameter('App:ExeBinSignature')
parser.add_must_have_parameter('HDF Version')
# parser.add_must_have_parameter('MPI-IO Hints')
parser.add_must_have_parameter('RunEnv:Nodes')
parser.add_must_have_statistic(
'2D Array Collective Read Aggregate Throughput')
parser.add_must_have_statistic(
'2D Array Collective Write Aggregate Throughput')
parser.add_must_have_statistic(
'2D Array HDF5 Collective Read Aggregate Throughput')
parser.add_must_have_statistic(
'2D Array HDF5 Collective Write Aggregate Throughput')
parser.add_must_have_statistic(
'2D Array Independent Read Aggregate Throughput')
parser.add_must_have_statistic(
'2D Array Independent Write Aggregate Throughput')
parser.add_must_have_statistic(
'3D Array Collective Read Aggregate Throughput')
parser.add_must_have_statistic(
'3D Array Collective Write Aggregate Throughput')
parser.add_must_have_statistic(
'3D Array HDF5 Collective Read Aggregate Throughput')
parser.add_must_have_statistic(
'3D Array HDF5 Collective Write Aggregate Throughput')
parser.add_must_have_statistic(
'3D Array Independent Read Aggregate Throughput')
parser.add_must_have_statistic(
'3D Array Independent Write Aggregate Throughput')
parser.add_must_have_statistic('File Close Time (2D Data Collective Read)')
parser.add_must_have_statistic(
'File Close Time (2D Data Collective Write)')
parser.add_must_have_statistic(
'File Close Time (2D Data HDF5 Collective Read)')
parser.add_must_have_statistic(
'File Close Time (2D Data HDF5 Collective Write)')
parser.add_must_have_statistic(
'File Close Time (2D Data Independent Read)')
parser.add_must_have_statistic(
'File Close Time (2D Data Independent Write)')
parser.add_must_have_statistic('File Close Time (3D Data Collective Read)')
parser.add_must_have_statistic(
'File Close Time (3D Data Collective Write)')
parser.add_must_have_statistic(
'File Close Time (3D Data HDF5 Collective Read)')
parser.add_must_have_statistic(
'File Close Time (3D Data HDF5 Collective Write)')
parser.add_must_have_statistic(
'File Close Time (3D Data Independent Read)')
parser.add_must_have_statistic(
'File Close Time (3D Data Independent Write)')
parser.add_must_have_statistic('File Open Time (2D Data Collective Read)')
parser.add_must_have_statistic('File Open Time (2D Data Collective Write)')
parser.add_must_have_statistic(
'File Open Time (2D Data HDF5 Collective Read)')
parser.add_must_have_statistic(
'File Open Time (2D Data HDF5 Collective Write)')
parser.add_must_have_statistic('File Open Time (2D Data Independent Read)')
parser.add_must_have_statistic(
'File Open Time (2D Data Independent Write)')
parser.add_must_have_statistic('File Open Time (3D Data Collective Read)')
parser.add_must_have_statistic('File Open Time (3D Data Collective Write)')
parser.add_must_have_statistic(
'File Open Time (3D Data HDF5 Collective Read)')
parser.add_must_have_statistic(
'File Open Time (3D Data HDF5 Collective Write)')
parser.add_must_have_statistic('File Open Time (3D Data Independent Read)')
parser.add_must_have_statistic(
'File Open Time (3D Data Independent Write)')
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
if hasattr(parser, 'appKerWallClockTime'):
parser.set_statistic("Wall Clock Time",
parser.appKerWallClockTime.total_seconds(),
"Second")
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
# The parameters mapping table
# The result mapping table
pm = {
"processesTopology": {
're': r"^# processes topology:(.+)",
'refun': re.match,
'val': None
},
"localDatasetTopology": {
're': r"^# local dataset topology:(.+)element",
'refun': re.match,
'val': None
},
"localMemoryUsage": {
're': r"^# local dataset memory usage:(.+)byte",
'refun': re.match,
'val': None
},
"datasetGhostZone": {
're': r"^# local dataset ghost zone:(.+)",
'refun': re.match,
'val': None
},
"mpiIOhints": {
're': r"^# mpiio hints:(.+)",
'refun': re.match,
'val': None
},
"maxFileOpenTime": {
're': r"^# Open:.+?max=(\S+)",
'refun': re.match,
'val': None
},
"maxFileCloseTime": {
're': r"^# Close:.+?max=(\S+)",
'refun': re.match,
'val': None
},
"collectiveIO": {
're': r"^# collective IO:(.+)",
'refun': re.match,
'val': None
},
"testFileName": {
're': r"^# filename:(.+)",
'refun': re.match,
'val': None
},
"fileSystem": {
're': r"^# filesystem:(.+)",
'refun': re.match,
'val': None
},
"hdf5Version": {
're': r"^# HDF5 Version:(.+)",
'refun': re.match,
'val': None
},
}
parser.successfulRun = False
j = -1
while j < len(lines) - 1:
for k, v in pm.items():
m = v['refun'](v['re'], lines[j])
if m:
v['val'] = m.group(1).strip()
m = re.match(r'^# (.+?)bandwidth:(.+)bytes', lines[j])
if m:
read_or_write = m.group(1).strip()
io_bandwidth = m.group(2).strip()
# can output data ?
if pm['processesTopology']['val'] and pm['collectiveIO']['val']:
# construct the label
label = ''
dim = '2D'
m = re.search(r'\d+x\d+x\d', pm['processesTopology']['val'])
if m:
dim = '3D'
if pm['hdf5Version']['val']:
label += 'HDF5 '
parser.set_parameter("HDF Version",
pm['hdf5Version']['val'])
m = re.search(r'yes', pm['collectiveIO']['val'], re.I)
if m:
label += 'Collective '
else:
label += 'Independent '
m0 = re.search(r'read', read_or_write, re.I)
m1 = re.search(r'write', read_or_write, re.I)
if m0:
label += 'Read'
elif m1:
label += 'Write'
else:
label += read_or_write[0].upper() + read_or_write[1:]
parser.set_statistic(
"%s Array %s Aggregate Throughput" % (dim, label),
"%.2f" % (float(io_bandwidth) / 1024.0 / 1024.0),
"MByte per Second")
if pm["maxFileOpenTime"]['val']:
parser.set_statistic(
"File Open Time (%s Data %s)" % (dim, label),
pm["maxFileOpenTime"]['val'], "Second")
if pm["maxFileCloseTime"]['val']:
parser.set_statistic(
"File Close Time (%s Data %s)" % (dim, label),
pm["maxFileCloseTime"]['val'], "Second")
parser.set_parameter("%s Process Topology" % (dim, ),
pm["processesTopology"]['val'])
if pm["localMemoryUsage"]['val']:
parser.set_parameter(
"%s Per-Process Memory" % (dim, ),
float(pm["localMemoryUsage"]['val']) / 1024.0 / 1024.0,
"MByte")
if pm["localDatasetTopology"]['val']:
parser.set_parameter(
"%s Per-Process Data Topology" % (dim, ),
pm["localDatasetTopology"]['val'], "Element")
if pm["datasetGhostZone"]['val']:
parser.set_parameter("%s Per-Process Ghost Zone" % (dim, ),
pm["datasetGhostZone"]['val'])
if pm["mpiIOhints"]['val']:
parser.set_parameter("MPI-IO Hints",
pm["mpiIOhints"]['val'])
# $benchmark->set_parameter( "${dim} ${label} Test File", $testFileName ) if( defined($testFileName) )
if pm["fileSystem"]['val']:
parser.set_parameter(
"%s %s Test File System" % (dim, label),
pm["fileSystem"]['val'])
parser.successfulRun = True
pm["processesTopology"]['val'] = None
pm["localDatasetTopology"]['val'] = None
pm["localMemoryUsage"]['val'] = None
pm["datasetGhostZone"]['val'] = None
pm["mpiIOhints"]['val'] = None
# pm["readOrWrite"]['val']=None
pm["collectiveIO"]['val'] = None
# pm["IObandwidth"]['val']=None
pm["maxFileOpenTime"]['val'] = None
pm["maxFileCloseTime"]['val'] = None
pm["testFileName"]['val'] = None
pm["fileSystem"]['val'] = None
pm["hdf5Version"]['val'] = None
j += 1
if __name__ == "__main__":
# output for testing purpose
print("parsing complete:", parser.parsing_complete(verbose=True))
parser.print_params_stats_as_must_have()
print(parser.get_xml())
# Print out missing parameters for debug purpose
parser.parsing_complete(verbose=True)
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None, stdout=None, stderr=None, geninfo=None, resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(
name='enzo',
version=1,
description="Enzo: an Adaptive Mesh Refinement Code for Astrophysics",
url='http://enzo-project.org',
measurement_name='Enzo'
)
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:Version')
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo, resource_appker_vars)
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
parser.set_parameter("App:Version", "unknown")
# process the output
successful_run = False
j = 0
while j < len(lines):
m = re.match(r'^Mercurial Branch\s+(\S+)', lines[j])
if m:
branch = m.group(1)
revision = ""
if j + 1 < len(lines):
m = re.match(r'^Mercurial Revision\s+(\S+)', lines[j + 1])
if m:
revision = m.group(1)
parser.set_parameter("App:Version", "Branch:" + branch + " Revision:" + revision)
m = re.match(r'^Time\s*=\s*([0-9.]+)\s+CycleNumber\s*=\s*([0-9]+)\s+Wallclock\s*=\s*([0-9.]+)', lines[j])
if m:
parser.set_statistic("Final Simulation Time", m.group(1), "Enzo Time Unit")
parser.set_statistic("Total Cycles", m.group(2))
parser.set_statistic("Wall Clock Time", m.group(3), "Second")
successful_run = True
m = re.match(r'^Successful run, exiting.', lines[j])
if m:
successful_run = True
# performance
m = re.match(r'^Cycle_Number\s+([0-9]+)', lines[j])
if m:
j += 1
performance_metrics = {}
while j < len(lines):
if lines[j].strip() != "":
v = lines[j].strip().split()
if v[0] not in performance_metrics:
performance_metrics[v[0]] = float(v[1])
else:
performance_metrics[v[0]] += float(v[1])
else:
if j + 1 < len(lines):
m = re.match(r'^Cycle_Number\s+([0-9]+)', lines[j + 1])
if m:
pass
else:
break
else:
break
j += 1
metric = "CommunicationTranspose"
if metric in performance_metrics:
parser.set_statistic("Communication Transpose Time", performance_metrics[metric], "Second")
metric = "ComputePotentialFieldLevelZero"
if metric in performance_metrics:
parser.set_statistic("Gravitational Potential Field Computing Time", performance_metrics[metric],
"Second")
metric = "EvolvePhotons"
if metric in performance_metrics:
parser.set_statistic("Radiative Transfer Calculation Time", performance_metrics[metric], "Second")
metric = "Group_WriteAllData"
if metric in performance_metrics:
parser.set_statistic("All Data Group Write Time", performance_metrics[metric], "Second")
metric = "Level_00"
if metric in performance_metrics:
parser.set_statistic("All Grid Level 00 Calculation Time", performance_metrics[metric], "Second")
metric = "Level_01"
if metric in performance_metrics:
parser.set_statistic("All Grid Level 01 Calculation Time", performance_metrics[metric], "Second")
metric = "Level_02"
if metric in performance_metrics:
parser.set_statistic("All Grid Level 02 Calculation Time", performance_metrics[metric], "Second")
metric = "RebuildHierarchy"
if metric in performance_metrics:
parser.set_statistic("Grid Hierarchy Rebuilding Time", performance_metrics[metric], "Second")
metric = "SetBoundaryConditions"
if metric in performance_metrics:
parser.set_statistic("Boundary Conditions Setting Time", performance_metrics[metric], "Second")
metric = "SolveForPotential"
if metric in performance_metrics:
parser.set_statistic("Poisson Equation Solving Time", performance_metrics[metric], "Second")
metric = "SolveHydroEquations"
if metric in performance_metrics:
parser.set_statistic("Hydro Equations Solving Time", performance_metrics[metric], "Second")
metric = "Total"
if metric in performance_metrics:
parser.set_statistic("Total Time Spent in Cycles", performance_metrics[metric], "Second")
j += 1
parser.successfulRun = successful_run
if __name__ == "__main__":
# output for testing purpose
print(("parsing complete:", parser.parsing_complete()))
parser.print_params_stats_as_must_have()
print((parser.get_xml()))
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
resource_appker_vars=None):
# set App Kernel Description
if resource_appker_vars is not None and 'app' in resource_appker_vars and 'name' in resource_appker_vars[
'app']:
akname = resource_appker_vars['app']['name']
else:
akname = 'unknown'
# initiate parser
parser = AppKerOutputParser(name=akname)
# set obligatory parameters and statistics
# set common parameters and statistics (App:ExeBinSignature and RunEnv:Nodes)
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:ExeBinSignature')
parser.add_must_have_parameter('App:Version')
parser.add_must_have_parameter('Number of Darts Throws')
parser.add_must_have_parameter('Number of Rounds')
parser.add_must_have_parameter('RunEnv:Nodes')
parser.add_must_have_statistic('Darts Throws per Second')
parser.add_must_have_statistic('Time for PI Calculation')
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo)
if hasattr(parser, 'appKerWallClockTime'):
parser.set_statistic("Wall Clock Time",
parser.appKerWallClockTime.total_seconds(),
"Second")
# Here can be custom output parsing
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
parser.successfulRun = False
j = 0
while j < len(lines):
m = re.search(r'version:\s+(.+)', lines[j])
if m:
parser.set_parameter('App:Version', m.group(1))
m = re.search(r'number of throws at dartboard:\s+(\d+)', lines[j])
if m:
parser.set_parameter('Number of Darts Throws', m.group(1))
m = re.search(r'number of rounds for dartz throwing\s+(\d+)', lines[j])
if m:
parser.set_parameter('Number of Rounds', m.group(1))
m = re.search(r'Time for PI calculation:\s+([0-9.]+)', lines[j])
if m:
parser.set_statistic("Time for PI Calculation", m.group(1),
"Seconds")
m = re.search(r'Giga Darts Throws per Second \(GDaPS\):\s+([0-9.]+)',
lines[j])
if m:
parser.set_statistic("Darts Throws per Second", m.group(1),
"GDaPS")
m = re.search(r'Giga Darts Throws per Second', lines[j])
if m:
parser.successfulRun = True
j += 1
if __name__ == "__main__":
# output for testing purpose
print(("Parsing complete:", parser.parsing_complete(verbose=True)))
print("Following statistics and parameter can be set as obligatory:")
parser.print_params_stats_as_must_have()
print("\nResulting XML:")
print((parser.get_xml()))
# return complete XML otherwise return None
return parser.get_xml()
def process_appker_output(appstdout=None, stdout=None, stderr=None, geninfo=None, proclog=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(
name='ior',
version=1,
description="IOR (Interleaved-Or-Random) Benchmark",
url='http://freshmeat.net/projects/ior',
measurement_name='IOR'
)
app_vars = None
if resource_appker_vars is not None and 'app' in resource_appker_vars:
app_vars = resource_appker_vars['app']
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:Version')
if app_vars is None or (
app_vars is not None and 'testHDF5' in app_vars and
app_vars['testHDF5'] is True):
parser.add_must_have_parameter('HDF Version')
parser.add_must_have_parameter('HDF5 Collective N-to-1 Test File System')
parser.add_must_have_parameter('HDF5 Independent N-to-1 Test File System')
parser.add_must_have_parameter('HDF5 N-to-N Test File System')
if app_vars is None or (
app_vars is not None and 'testMPIIO' in app_vars and
app_vars['testMPIIO'] is True):
parser.add_must_have_parameter('MPIIO Collective N-to-1 Test File System')
parser.add_must_have_parameter('MPIIO Independent N-to-1 Test File System')
parser.add_must_have_parameter('MPIIO N-to-N Test File System')
if app_vars is None or (
app_vars is not None and 'testPOSIX' in app_vars and
app_vars['testPOSIX'] is True):
parser.add_must_have_parameter('POSIX N-to-1 Test File System')
parser.add_must_have_parameter('POSIX N-to-N Test File System')
if app_vars is None or (
app_vars is not None and 'testNetCDF' in app_vars and
app_vars['testNetCDF'] is True):
parser.add_must_have_parameter('Parallel NetCDF Collective N-to-1 Test File System')
parser.add_must_have_parameter('Parallel NetCDF Independent N-to-1 Test File System')
parser.add_must_have_parameter('Parallel NetCDF Version')
parser.add_must_have_parameter('Per-Process Data Size')
parser.add_must_have_parameter('Per-Process I/O Block Size')
parser.add_must_have_parameter('RunEnv:Nodes')
parser.add_must_have_parameter('Transfer Size Per I/O')
if app_vars is None or (
app_vars is not None and 'testHDF5' in app_vars and
app_vars['testHDF5'] is True):
parser.add_must_have_statistic('HDF5 Collective N-to-1 Read Aggregate Throughput')
parser.add_must_have_statistic('HDF5 Collective N-to-1 Write Aggregate Throughput')
parser.add_must_have_statistic('HDF5 Independent N-to-1 Read Aggregate Throughput')
parser.add_must_have_statistic('HDF5 Independent N-to-1 Write Aggregate Throughput')
parser.add_must_have_statistic('HDF5 N-to-N Read Aggregate Throughput')
parser.add_must_have_statistic('HDF5 N-to-N Write Aggregate Throughput')
if app_vars is None or (
app_vars is not None and 'testMPIIO' in app_vars and
app_vars['testMPIIO'] is True):
parser.add_must_have_statistic('MPIIO Collective N-to-1 Read Aggregate Throughput')
parser.add_must_have_statistic('MPIIO Collective N-to-1 Write Aggregate Throughput')
parser.add_must_have_statistic('MPIIO Independent N-to-1 Read Aggregate Throughput')
parser.add_must_have_statistic('MPIIO Independent N-to-1 Write Aggregate Throughput')
parser.add_must_have_statistic('MPIIO N-to-N Read Aggregate Throughput')
parser.add_must_have_statistic('MPIIO N-to-N Write Aggregate Throughput')
if app_vars is None or (
app_vars is not None and 'testPOSIX' in app_vars and
app_vars['testPOSIX'] is True):
parser.add_must_have_statistic('POSIX N-to-1 Read Aggregate Throughput')
parser.add_must_have_statistic('POSIX N-to-1 Write Aggregate Throughput')
parser.add_must_have_statistic('POSIX N-to-N Read Aggregate Throughput')
parser.add_must_have_statistic('POSIX N-to-N Write Aggregate Throughput')
if app_vars is None or (
app_vars is not None and 'testNetCDF' in app_vars and
app_vars['testNetCDF'] is True):
parser.add_must_have_statistic('Parallel NetCDF Collective N-to-1 Read Aggregate Throughput')
parser.add_must_have_statistic('Parallel NetCDF Collective N-to-1 Write Aggregate Throughput')
parser.add_must_have_statistic('Parallel NetCDF Independent N-to-1 Read Aggregate Throughput')
parser.add_must_have_statistic('Parallel NetCDF Independent N-to-1 Write Aggregate Throughput')
parser.add_must_have_statistic('Number of Tests Passed')
parser.add_must_have_statistic('Number of Tests Started')
parser.add_must_have_statistic('Wall Clock Time')
parser.completeOnPartialMustHaveStatistics = True
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo, resource_appker_vars)
if hasattr(parser, 'appKerWallClockTime'):
parser.set_statistic("Wall Clock Time", total_seconds(parser.appKerWallClockTime), "Second")
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
# find which version of IOR was used
ior_output_version = None
j = 0
while j < len(lines) - 1:
# IOR RELEASE: IOR-2.10.3
m = re.match(r'^#\s+IOR RELEASE:\s(.+)', lines[j])
if m:
ior_output_version = 20
# IOR-3.2.0: MPI Coordinated Test of Parallel I/O
# IOR-3.3.0+dev: MPI Coordinated Test of Parallel I/O
m = re.match(r'^IOR-([3-9])\.([0-9])+\.[0-9]\S*: MPI Coordinated Test of Parallel I/O', lines[j])
if m:
ior_major = int(m.group(1))
ior_minor = int(m.group(2))
if ior_major >=3:
if ior_minor >= 3:
ior_output_version = 33
elif ior_minor >= 2:
ior_output_version = 32
else:
ior_output_version = 30
j += 1
if ior_output_version is None:
print("ERROR: unknown version of IOR output!!!")
parser.successfulRun = False
total_number_of_tests, tests_passed = process_ior_output_v33(parser, lines)
if app_vars is not None and 'doAllWritesFirst' in app_vars:
if app_vars['doAllWritesFirst']:
# i.e. separate read and write
total_number_of_tests = total_number_of_tests // 2
else:
# by default separate read and write
total_number_of_tests = total_number_of_tests // 2
parser.set_statistic('Number of Tests Passed', tests_passed)
parser.set_statistic('Number of Tests Started', total_number_of_tests)
if __name__ == "__main__":
# output for testing purpose
print("parsing complete:", parser.parsing_complete(verbose=True))
parser.print_params_stats_as_must_have()
parser.print_template_for_pytest()
print(parser.get_xml())
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(
name='gromacs_micro',
version=1,
description="GROMACS: micro-benchmark for testing purposes",
url='http://www.gromacs.org/',
measurement_name='GROMACS-Micro')
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:Version')
parser.add_must_have_statistic('Simulation Speed')
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
successful_run = False
j = 0
while j < len(lines):
m = re.search(r'^GROMACS:\s+ gmx mdrun, version\s+(\S+)$', lines[j])
if m:
parser.set_parameter("App:Version", m.group(1))
m = re.search(r'^Performance: \s+([0-9.]+)', lines[j])
if m:
parser.set_statistic("Simulation Speed", float(m.group(1)),
"ns/day")
m = re.search(r'^ \s+Time: \s+([0-9.]+) \s+([0-9.]+)', lines[j])
if m:
parser.set_statistic("Wall Clock Time", m.group(2), "Second")
parser.set_statistic("Core Clock Time", m.group(1), "Second")
m = re.match(r'^GROMACS reminds you', lines[j])
if m:
successful_run = True
j += 1
parser.successfulRun = successful_run
if __name__ == "__main__":
# output for testing purpose
print("parsing complete:", parser.parsing_complete())
parser.print_params_stats_as_must_have()
print(parser.get_xml())
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(
name='nwchem',
version=1,
description="NWChem: Northwest Computational Chemistry Package",
url='http://www.emsl.pnl.gov/docs/nwchem',
measurement_name='NWChem')
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:Version')
parser.add_must_have_parameter('App:Branch')
parser.add_must_have_parameter('Input:File')
parser.add_must_have_statistic('Wall Clock Time')
parser.add_must_have_statistic('User Time')
parser.add_must_have_statistic("Global Arrays 'Create' Calls")
parser.add_must_have_statistic("Global Arrays 'Destroy' Calls")
parser.add_must_have_statistic("Global Arrays 'Get' Calls")
parser.add_must_have_statistic("Global Arrays 'Put' Calls")
parser.add_must_have_statistic("Global Arrays 'Accumulate' Calls")
parser.add_must_have_statistic("Global Arrays 'Get' Amount")
parser.add_must_have_statistic("Global Arrays 'Put' Amount")
parser.add_must_have_statistic("Global Arrays 'Accumulate' Amount")
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
j = 0
while j < len(lines):
m = re.search(
r'Northwest Computational Chemistry Package \(NWChem\) (.+)',
lines[j])
if m:
parser.set_parameter("App:Version", m.group(1).strip())
m = re.search(r'nwchem branch *=(.+)', lines[j])
if m:
parser.set_parameter("App:Branch", m.group(1).strip())
m = re.search(r'input\s+= (.+)', lines[j])
if m:
parser.set_parameter("Input:File", m.group(1).strip())
m = re.search(r'Total times\s+cpu:\s+([0-9.]+)s\s+wall:\s+([0-9.]+)s',
lines[j])
if m:
parser.set_statistic("Wall Clock Time",
m.group(2).strip(), "Second")
parser.set_statistic("User Time", m.group(1).strip(), "Second")
# GA Statistics for process 0
# ------------------------------
#
# create destroy get put acc scatter gather read&inc
# calls: 521 521 6.28e+05 6.45e+04 6.78e+05 0 0 0
# number of processes/call 1.05e+00 1.36e+00 1.03e+00 0.00e+00 0.00e+00
# bytes total: 7.33e+09 4.35e+08 1.53e+09 0.00e+00 0.00e+00 0.00e+00
# bytes remote: 5.74e+09 1.31e+08 1.09e+09 0.00e+00 0.00e+00 0.00e+00
# Max memory consumed for GA by this process: 47428032 bytes
if re.search(r'GA Statistics for process', lines[j]):
if re.match(r'^calls', lines[j + 4]):
v = lines[j + 4].strip().split()
parser.set_statistic("Global Arrays 'Create' Calls",
"%.0f" % float(v[1]), "Number of Calls")
parser.set_statistic("Global Arrays 'Destroy' Calls",
"%.0f" % float(v[2]), "Number of Calls")
parser.set_statistic("Global Arrays 'Get' Calls",
"%.0f" % float(v[3]), "Number of Calls")
parser.set_statistic("Global Arrays 'Put' Calls",
"%.0f" % float(v[4]), "Number of Calls")
parser.set_statistic("Global Arrays 'Accumulate' Calls",
"%.0f" % float(v[5]), "Number of Calls")
v = lines[j + 6].strip().split()
parser.set_statistic("Global Arrays 'Get' Amount",
(float(v[2])) / 1048576.0, "MByte")
parser.set_statistic("Global Arrays 'Put' Amount",
(float(v[3])) / 1048576.0, "MByte")
parser.set_statistic("Global Arrays 'Accumulate' Amount",
(float(v[4])) / 1048576.0, "MByte")
# NWChem can be optionally compiled with PAPI, and it will
# report some GLOPS at the end
# thus here it is optional
m = re.search(r'Aggregate GFLOPS \(Real_time\):\s+([0-9.]+)', lines[j])
if m:
parser.set_statistic(
"Floating-Point Performance (Wall Clock Time)",
1000.0 * float(m.group(1).strip()), "MFLOP per Second")
m = re.search(r'Aggregate GFLOPS \(Proc_time\):\s+([0-9.]+)', lines[j])
if m:
parser.set_statistic("Floating-Point Performance (User Time)",
1000.0 * float(m.group(1).strip()),
"MFLOP per Second")
j += 1
if __name__ == "__main__":
# output for testing purpose
print("parsing complete:", parser.parsing_complete())
parser.print_params_stats_as_must_have()
print(parser.get_xml())
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(
name='lammps',
version=1,
description=
"LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator",
url='http://lammps.sandia.gov',
measurement_name='LAMMPS')
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:Version')
parser.add_must_have_parameter('Input:Number of Atoms')
parser.add_must_have_parameter('Input:Number of Steps')
parser.add_must_have_parameter('Input:Timestep')
parser.add_must_have_statistic('Molecular Dynamics Simulation Performance')
parser.add_must_have_statistic('Per-Process Memory')
parser.add_must_have_statistic('Time Spent in Bond Potential Calculation')
parser.add_must_have_statistic('Time Spent in Communication')
parser.add_must_have_statistic(
'Time Spent in Long-Range Coulomb Potential (K-Space) Calculation')
parser.add_must_have_statistic('Time Spent in Neighbor List Regeneration')
parser.add_must_have_statistic(
'Time Spent in Pairwise Potential Calculation')
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
parser.successfulRun = False
wall_clock_time = None
simulation_units = None
num_steps = None
step_size = None
j = 0
while j < len(lines):
m = re.match(r'^LAMMPS\s+\(([\w ]+)\)', lines[j])
if m:
parser.set_parameter("App:Version", m.group(1).strip())
m = re.match(r'^Memory usage per processor = ([\d.]+) Mbyte', lines[j])
if m:
parser.set_statistic("Per-Process Memory",
m.group(1).strip(), "MByte")
m = re.match(r'^Loop time of ([\d.]+) on', lines[j])
if m:
parser.successfulRun = True
wall_clock_time = float(m.group(1).strip())
parser.set_statistic("Wall Clock Time", wall_clock_time, "Second")
m1 = re.search(r'(\d+) atoms', lines[j])
if m1:
parser.set_parameter("Input:Number of Atoms",
m1.group(1).strip())
m = re.match(r'^units\s+(\w+)', lines[j])
if m:
simulation_units = m.group(1).strip().lower()
m = re.match(r'^run\s+(\d+)', lines[j])
if m:
num_steps = int(m.group(1).strip())
parser.set_parameter("Input:Number of Steps", num_steps)
m = re.match(r'^timestep\s+([\d.]+)', lines[j])
if m:
step_size = float(m.group(1).strip())
m = re.match(r'^Pair\s+time.+= ([\d.]+)', lines[j])
if parser.successfulRun and m:
parser.set_statistic(
"Time Spent in Pairwise Potential Calculation",
m.group(1).strip(), "Second")
m = re.match(r'^Bond\s+time.+= ([\d.]+)', lines[j])
if parser.successfulRun and m:
parser.set_statistic("Time Spent in Bond Potential Calculation",
m.group(1).strip(), "Second")
m = re.match(r'^Kspce\s+time.+= ([\d.]+)', lines[j])
if parser.successfulRun and m:
parser.set_statistic(
"Time Spent in Long-Range Coulomb Potential (K-Space) Calculation",
m.group(1).strip(), "Second")
m = re.match(r'^Neigh\s+time.+= ([\d.]+)', lines[j])
if parser.successfulRun and m:
parser.set_statistic("Time Spent in Neighbor List Regeneration",
m.group(1).strip(), "Second")
m = re.match(r'^Comm\s+time.+= ([\d.]+)', lines[j])
if parser.successfulRun and m:
parser.set_statistic("Time Spent in Communication",
m.group(1).strip(), "Second")
j += 1
if parser.successfulRun and num_steps and simulation_units != "lj":
# The default value for $stepSize is (see http://lammps.sandia.gov/doc/units.html):
#
# 0.005 tau for $simulationUnits eq "lj"
# 1e-15 second for $simulationUnits eq "real" or "metal"
# 1e-18 second for $simulationUnits eq "electron"
# 1e-8 second for $simulationUnits eq "si" or "cgs"
# If $simulationUnits is (see http://lammps.sandia.gov/doc/units.html)
#
# "lj", the unit for $stepSize is tau
# "real" or "electron", the unit for $stepSize is 1e-15 second
# "metal", the unit for $stepSize is 1e-12 second
# "si" or "cgs", the unit for $stepSize is second
# The default $simulationUnits is "lj"
#
# We ignore "lj" since "lj" is unitless.
if step_size is None:
if simulation_units == "real":
step_size = 1.0
if simulation_units.find("electron") >= 0 or simulation_units.find(
"metal") >= 0:
step_size = 0.001
if simulation_units.find("si") >= 0 or simulation_units.find(
"cgs") >= 0:
step_size = 1.0e-8
step_size_in_sec = step_size
if step_size:
if simulation_units.find("electron") >= 0 or simulation_units.find(
"real") >= 0:
step_size_in_sec = step_size * 1.0e-15
if simulation_units == "metal":
step_size_in_sec = step_size * 1.0e-12
if step_size_in_sec:
parser.set_parameter("Input:Timestep", step_size_in_sec,
"Second per Step")
parser.set_statistic(
"Molecular Dynamics Simulation Performance",
1.0e-9 * (1.0e9 * step_size_in_sec * num_steps) /
(wall_clock_time / 86400.0), "Second per Day")
if __name__ == "__main__":
# output for testing purpose
print("parsing complete:", parser.parsing_complete())
parser.print_params_stats_as_must_have()
print(parser.get_xml())
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
proclog=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(
name='gamess',
version=1,
description=
"Gamess: General Atomic and Molecular Electronic Structure System",
url='http://www.msg.ameslab.gov',
measurement_name='Gamess')
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:Version')
parser.add_must_have_statistic('Wall Clock Time')
parser.add_must_have_statistic('User Time')
parser.add_must_have_statistic('Time Spent in MP2 Energy Calculation')
parser.add_must_have_statistic(
'Time Spent in Restricted Hartree-Fock Calculation')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
start_time = None
end_time = None
mp2_energy_calculation_time = 0.0
rhf_calculation_time = 0.0
efficiency = None
j = 0
while j < len(lines):
m = re.search(r'GAMESS VERSION = ([^*]+)', lines[j])
if m:
parser.set_parameter("App:Version", m.group(1).strip())
m = re.search(
r'PARALLEL VERSION RUNNING ON\s*([\d.]+) PROCESSORS IN\s*([\d.]+) NODE',
lines[j])
if m:
parser.set_parameter("App:NCores", m.group(1).strip())
parser.set_parameter("App:NNodes", m.group(2).strip())
m = re.search(r'EXECUTION OF GAMESS BEGUN (.+)', lines[j])
if m:
start_time = parser.get_datetime_local(m.group(1).strip())
m = re.search(r'EXECUTION OF GAMESS TERMINATED NORMALLY (.+)',
lines[j])
if m:
end_time = parser.get_datetime_local(m.group(1).strip())
if re.search(r'DONE WITH MP2 ENERGY', lines[j]):
j += 1
m = re.search(r'STEP CPU TIME=\s*([\d.]+)', lines[j])
if m:
mp2_energy_calculation_time += float(m.group(1).strip())
if re.search(r'END OF RHF CALCULATION', lines[j]):
j += 1
m = re.search(r'STEP CPU TIME=\s*([\d.]+)', lines[j])
if m:
rhf_calculation_time += float(m.group(1).strip())
m = re.search(r'TOTAL WALL CLOCK TIME.+CPU UTILIZATION IS\s+([\d.]+)',
lines[j])
if m:
efficiency = float(m.group(1).strip())
j += 1
if start_time and end_time:
walltime = total_seconds(end_time - start_time)
if walltime >= 0.0:
parser.set_statistic('Wall Clock Time', str(walltime), "Second")
if efficiency:
parser.set_statistic("User Time",
str((0.01 * efficiency * walltime)),
"Second")
parser.set_statistic("Time Spent in MP2 Energy Calculation",
str(mp2_energy_calculation_time), "Second")
parser.set_statistic("Time Spent in Restricted Hartree-Fock Calculation",
str(rhf_calculation_time), "Second")
if "attemptsToLaunch" in parser.geninfo:
parser.set_statistic("Attempts to Launch",
parser.geninfo['attemptsToLaunch'])
else:
parser.set_statistic("Attempts to Launch", 1)
if __name__ == "__main__":
# output for testing purpose
print(("parsing complete:", parser.parsing_complete()))
parser.print_params_stats_as_must_have()
print((parser.get_xml()))
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
proclog=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(name='hpcg',
version=1,
description="HPCG Benchmark",
url='http://www.hpcg-benchmark.org/index.html',
measurement_name='HPCG')
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:ExeBinSignature')
parser.add_must_have_parameter('App:Version')
parser.add_must_have_parameter('Input:Distributed Processes')
parser.add_must_have_parameter('Input:Global Problem Dimensions Nx')
parser.add_must_have_parameter('Input:Global Problem Dimensions Ny')
parser.add_must_have_parameter('Input:Global Problem Dimensions Nz')
parser.add_must_have_parameter('Input:Local Domain Dimensions Nx')
parser.add_must_have_parameter('Input:Local Domain Dimensions Ny')
parser.add_must_have_parameter('Input:Local Domain Dimensions Nz')
parser.add_must_have_parameter('Input:Number of Coarse Grid Levels')
parser.add_must_have_parameter('Input:Threads per processes')
parser.add_must_have_parameter('RunEnv:CPU Speed')
parser.add_must_have_parameter('RunEnv:Nodes')
parser.add_must_have_statistic('Floating-Point Performance, Raw DDOT')
parser.add_must_have_statistic('Floating-Point Performance, Raw MG')
parser.add_must_have_statistic('Floating-Point Performance, Raw SpMV')
parser.add_must_have_statistic('Floating-Point Performance, Raw Total')
parser.add_must_have_statistic('Floating-Point Performance, Raw WAXPBY')
parser.add_must_have_statistic('Floating-Point Performance, Total')
parser.add_must_have_statistic('Memory Bandwidth, Read')
parser.add_must_have_statistic('Memory Bandwidth, Total')
parser.add_must_have_statistic('Memory Bandwidth, Write')
parser.add_must_have_statistic('Setup Time')
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
if hasattr(parser, 'appKerWallClockTime'):
parser.set_statistic("Wall Clock Time",
total_seconds(parser.appKerWallClockTime),
"Second")
# get path to YAML file
# read data
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# Parse YAML lines because YAML is often malformed
yaml_lines = []
# get yaml lines from appstdout
bool_in_yaml_section = False
for line in lines:
if re.match(r"^====== .+\.yaml End ======", line):
break
if bool_in_yaml_section:
yaml_lines.append(line)
if re.match(r"^====== .+\.yaml Start ======", line):
bool_in_yaml_section = True
from pprint import pprint
import yaml
# fix some issues with yaml
if re.search(r"After confirmation please upload results from the YAML",
yaml_lines[-1]):
yaml_lines.pop()
if re.search(r"You have selected the QuickPath option", yaml_lines[-1]):
yaml_lines.pop()
yaml_text = "".join(yaml_lines)
yaml_text = re.sub(r"^ {6}HPCG 2\.4 Rating \(for historical value\) is:",
" HPCG 2.4 Rating (for historical value) is:",
yaml_text,
flags=re.M)
results_yaml = yaml.load(yaml_text)
# Set Parameters
# App version
app_version_list = []
for ver in [x for x in results_yaml.keys() if re.search("version", x)]:
app_version_list.append(ver + " " + str(results_yaml[ver]))
app_version = ", ".join(app_version_list)
parser.set_parameter('App:Version', app_version)
# Problem size
parser.set_parameter(
'Input:Number of Coarse Grid Levels',
results_yaml['Multigrid Information']['Number of coarse grid levels'])
parser.set_parameter(
'Input:Global Problem Dimensions Nx',
results_yaml['Global Problem Dimensions']['Global nx'])
parser.set_parameter(
'Input:Global Problem Dimensions Ny',
results_yaml['Global Problem Dimensions']['Global ny'])
parser.set_parameter(
'Input:Global Problem Dimensions Nz',
results_yaml['Global Problem Dimensions']['Global nz'])
parser.set_parameter('Input:Local Domain Dimensions Nx',
results_yaml['Local Domain Dimensions']['nx'])
parser.set_parameter('Input:Local Domain Dimensions Ny',
results_yaml['Local Domain Dimensions']['ny'])
parser.set_parameter('Input:Local Domain Dimensions Nz',
results_yaml['Local Domain Dimensions']['nz'])
parser.set_parameter(
'Input:Distributed Processes',
results_yaml['Machine Summary']['Distributed Processes'])
parser.set_parameter(
'Input:Threads per processes',
results_yaml['Machine Summary']['Threads per processes'])
if "cpu_speed" in parser.geninfo:
ll = parser.geninfo["cpu_speed"].splitlines()
cpu_speed_max = 0.0
for l in ll:
m = re.search(r'([\d.]+)$', l)
if m:
v = float(m.group(1).strip())
if v > cpu_speed_max:
cpu_speed_max = v
if cpu_speed_max > 0.0:
parser.set_parameter("RunEnv:CPU Speed", cpu_speed_max, "MHz")
# Set Statistics
parser.successfulRun = results_yaml['Reproducibility Information'][
'Result'] == 'PASSED'
parser.set_statistic('Setup Time',
results_yaml['Setup Information']['Setup Time'],
'Seconds')
parser.set_statistic('Memory Bandwidth, Read',
results_yaml['GB/s Summary']['Raw Read B/W'], 'GB/s')
parser.set_statistic('Memory Bandwidth, Write',
results_yaml['GB/s Summary']['Raw Write B/W'], 'GB/s')
parser.set_statistic('Memory Bandwidth, Total',
results_yaml['GB/s Summary']['Raw Total B/W'], 'GB/s')
parser.set_statistic(
'Floating-Point Performance, Total',
results_yaml['__________ Final Summary __________']
['HPCG result is VALID with a GFLOP/s rating of'], 'GFLOP/s')
parser.set_statistic('Floating-Point Performance, Raw DDOT',
results_yaml['GFLOP/s Summary']['Raw DDOT'],
'GFLOP/s')
parser.set_statistic('Floating-Point Performance, Raw WAXPBY',
results_yaml['GFLOP/s Summary']['Raw WAXPBY'],
'GFLOP/s')
parser.set_statistic('Floating-Point Performance, Raw SpMV',
results_yaml['GFLOP/s Summary']['Raw SpMV'],
'GFLOP/s')
parser.set_statistic('Floating-Point Performance, Raw MG',
results_yaml['GFLOP/s Summary']['Raw MG'], 'GFLOP/s')
parser.set_statistic('Floating-Point Performance, Raw Total',
results_yaml['GFLOP/s Summary']['Raw Total'],
'GFLOP/s')
if __name__ == "__main__":
# output for testing purpose
print("parsing complete:", parser.parsing_complete(verbose=True))
parser.print_params_stats_as_must_have()
print(parser.get_xml())
# return complete XML otherwise return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
proclog=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(name='bundle',
version=1,
description='bundled tasks',
url='https://xdmod.ccr.buffalo.edu',
measurement_name='BUNDLE')
parser.add_must_have_parameter('RunEnv:Nodes')
parser.add_must_have_statistic('Wall Clock Time')
parser.add_must_have_statistic("Success Rate")
parser.add_must_have_statistic("Successful Subtasks")
parser.add_must_have_statistic("Total Number of Subtasks")
# set obligatory parameters and statistics
# set common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
if hasattr(parser, 'wallClockTime'):
parser.set_statistic("Wall Clock Time",
total_seconds(parser.wallClockTime), "Second")
# check the status of subtasks
# resource_appker_vars['taskId']=self.task_id
# resource_appker_vars['subTasksId']=self.subTasksId
success_rate = 0.0
total_subtasks = 0
successful_subtasks = 0
try:
db, cur = akrr.db.get_akrr_db()
for subTaskId in resource_appker_vars['subTasksId']:
cur.execute(
'''SELECT instance_id,status FROM akrr_xdmod_instanceinfo
WHERE instance_id=%s ;''', (subTaskId, ))
raw = cur.fetchall()
instance_id, status = raw[0]
success_rate += status
successful_subtasks += status
success_rate /= len(resource_appker_vars['subTasksId'])
total_subtasks = len(resource_appker_vars['subTasksId'])
cur.close()
del db
except:
print(traceback.format_exc())
parser.set_statistic("Success Rate", success_rate)
parser.set_statistic("Successful Subtasks", successful_subtasks)
parser.set_statistic("Total Number of Subtasks", total_subtasks)
# if successfulSubtasks==totalSubtasks:
if __name__ == "__main__":
# output for testing purpose
print("parsing complete:", parser.parsing_complete(verbose=True))
parser.print_params_stats_as_must_have()
print(parser.get_xml())
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
proclog=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(name='imb',
version=1,
description="Intel MPI Benchmarks",
url='http://www.intel.com/software/imb',
measurement_name='Intel MPI Benchmarks')
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:MPI Thread Environment')
parser.add_must_have_parameter('App:MPI Version')
parser.add_must_have_parameter('App:Max Message Size')
parser.add_must_have_statistic('Max Exchange Bandwidth')
parser.add_must_have_statistic(
"Max MPI-2 Bidirectional 'Get' Bandwidth (aggregate)")
parser.add_must_have_statistic(
"Max MPI-2 Bidirectional 'Get' Bandwidth (non-aggregate)")
parser.add_must_have_statistic(
"Max MPI-2 Bidirectional 'Put' Bandwidth (aggregate)")
parser.add_must_have_statistic(
"Max MPI-2 Bidirectional 'Put' Bandwidth (non-aggregate)")
parser.add_must_have_statistic(
"Max MPI-2 Unidirectional 'Get' Bandwidth (aggregate)")
parser.add_must_have_statistic(
"Max MPI-2 Unidirectional 'Get' Bandwidth (non-aggregate)")
parser.add_must_have_statistic(
"Max MPI-2 Unidirectional 'Put' Bandwidth (aggregate)")
parser.add_must_have_statistic(
"Max MPI-2 Unidirectional 'Put' Bandwidth (non-aggregate)")
parser.add_must_have_statistic('Max PingPing Bandwidth')
parser.add_must_have_statistic('Max PingPong Bandwidth')
parser.add_must_have_statistic('Max SendRecv Bandwidth')
parser.add_must_have_statistic('Min AllGather Latency')
parser.add_must_have_statistic('Min AllGatherV Latency')
parser.add_must_have_statistic('Min AllReduce Latency')
parser.add_must_have_statistic('Min AllToAll Latency')
parser.add_must_have_statistic('Min AllToAllV Latency')
parser.add_must_have_statistic('Min Barrier Latency')
parser.add_must_have_statistic('Min Broadcast Latency')
parser.add_must_have_statistic('Min Gather Latency')
parser.add_must_have_statistic('Min GatherV Latency')
# parser.add_must_have_statistic("Min MPI-2 'Accumulate' Latency (aggregate)")
# parser.add_must_have_statistic("Min MPI-2 'Accumulate' Latency (non-aggregate)")
parser.add_must_have_statistic('Min MPI-2 Window Creation Latency')
parser.add_must_have_statistic('Min Reduce Latency')
parser.add_must_have_statistic('Min ReduceScatter Latency')
parser.add_must_have_statistic('Min Scatter Latency')
parser.add_must_have_statistic('Min ScatterV Latency')
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
if hasattr(parser, 'appKerWallClockTime'):
parser.set_statistic("Wall Clock Time",
total_seconds(parser.appKerWallClockTime),
"Second")
# Intel MPI benchmark suite contains three classes of benchmarks:
#
# Single-transfer, which needs only 2 processes
# Parallel-transfer, which can use as many processes that are available
# Collective, which can use as many processes that are available
# The parameters mapping table
params = {
"MPI Thread Environment": ["MPI Thread Environment", "", ""],
"MPI Version": ["MPI Version", "", ""],
"Maximum message length in bytes":
["Max Message Size", "MByte", "<val>/1024/1024"]
}
# The result mapping table
metrics = {
"PingPing": ["PingPing Bandwidth", "MByte per Second", "max"],
"PingPong": ["PingPong Bandwidth", "MByte per Second", "max"],
"Multi-PingPing": ["PingPing Bandwidth", "MByte per Second", "max"],
"Multi-PingPong": ["PingPong Bandwidth", "MByte per Second", "max"],
"Sendrecv": ["SendRecv Bandwidth", "MByte per Second", "max"],
"Exchange": ["Exchange Bandwidth", "MByte per Second", "max"],
"Allreduce": ["AllReduce Latency", "us", "min"],
"Reduce": ["Reduce Latency", "us", "min"],
"Reduce_scatter": ["ReduceScatter Latency", "us", "min"],
"Allgather": ["AllGather Latency", "us", "min"],
"Allgatherv": ["AllGatherV Latency", "us", "min"],
"Gather": ["Gather Latency", "us", "min"],
"Gatherv": ["GatherV Latency", "us", "min"],
"Scatter": ["Scatter Latency", "us", "min"],
"Scatterv": ["ScatterV Latency", "us", "min"],
"Alltoall": ["AllToAll Latency", "us", "min"],
"Alltoallv": ["AllToAllV Latency", "us", "min"],
"Bcast": ["Broadcast Latency", "us", "min"],
"Barrier": ["Barrier Latency", "us", "min"],
"Window": ["MPI-2 Window Creation Latency", "us", "min"],
"Multi-Unidir_Get":
["MPI-2 Unidirectional 'Get' Bandwidth", "MByte per Second", "max"],
"Multi-Unidir_Put":
["MPI-2 Unidirectional 'Put' Bandwidth", "MByte per Second", "max"],
"Multi-Bidir_Get":
["MPI-2 Bidirectional 'Get' Bandwidth", "MByte per Second", "max"],
"Multi-Bidir_Put":
["MPI-2 Bidirectional 'Put' Bandwidth", "MByte per Second", "max"],
"Unidir_Get":
["MPI-2 Unidirectional 'Get' Bandwidth", "MByte per Second", "max"],
"Unidir_Put":
["MPI-2 Unidirectional 'Put' Bandwidth", "MByte per Second", "max"],
"Bidir_Get":
["MPI-2 Bidirectional 'Get' Bandwidth", "MByte per Second", "max"],
"Bidir_Put":
["MPI-2 Bidirectional 'Put' Bandwidth", "MByte per Second", "max"],
"Accumulate": ["MPI-2 'Accumulate' Latency", "us", "min"]
}
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
parser.successfulRun = False
aggregate_mode = None
metric = None
j = -1
while j < len(lines) - 1:
j += 1
m = re.search(r'All processes entering MPI_Finalize', lines[j])
if m:
parser.successfulRun = True
m = re.match(r'^# Benchmarking\s+(\S+)', lines[j])
if m:
if m.group(1) in metrics:
metric = m.group(1)
continue
m = re.match(r'^#\s+MODE:\s+(\S+)', lines[j])
if m and metric and aggregate_mode is None:
aggregate_mode = m.group(1)
continue
m = re.match(r'^# (.+): (.+)', lines[j])
if m: # benchmark parameters
param = m.group(1).strip()
if param in params:
val = m.group(2).strip()
v = params[param][2]
if v.find('<val>') >= 0:
val = get_float_or_int(val)
val = eval(v.replace('<val>', 'val'))
parser.set_parameter("App:" + params[param][0],
str(val) + " ", params[param][1])
continue
m = re.match(r'^\s+([1-9]\d*)\s+\d+', lines[j])
if m and metric: # this effectively skips the first line of result, which has #bytes = 0
results = []
while m:
numbers = lines[j].split()
results.append(
float(numbers[-1]
)) # tokenize the line, and extract the last column
j += 1
if j < len(lines):
m = re.match(r'^\s+([1-9]\d*)\s+\d+', lines[j])
if lines[j].count('IMB_init_buffers_iter') > 0:
break
else:
break
metric_name = metrics[metric][0]
if aggregate_mode:
metric_name += " (" + aggregate_mode.lower() + ")"
if len(results) > 0:
if metrics[metric][1] == 'us':
statname = metrics[metric][2][0].upper(
) + metrics[metric][2][1:] + " " + metric_name
statval = eval(metrics[metric][2] + "(results)")
parser.set_statistic(statname, statval * 1e-6, "Second")
else:
statname = metrics[metric][2][0].upper(
) + metrics[metric][2][1:] + " " + metric_name
statval = eval(metrics[metric][2] + "(results)")
parser.set_statistic(statname, statval, metrics[metric][1])
aggregate_mode = None
metric = None
if parser.get_parameter("App:MPI Thread Environment") is None:
parser.set_parameter("App:MPI Thread Environment", "")
if __name__ == "__main__":
# output for testing purpose
print("parsing complete:", parser.parsing_complete(verbose=True))
parser.print_params_stats_as_must_have()
print(parser.get_xml())
# Print out missing parameters for debug purpose
parser.parsing_complete(verbose=True)
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
proclog=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(name='akrr network check',
version=1,
description="network benchmarking",
url='http://www.xdmod.org',
measurement_name='akrr network check')
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_must_have_parameter('App:ExeBinSignature')
parser.add_must_have_statistic('Ping, Mean')
parser.add_must_have_statistic('Secure Copy Bandwidth (in), Mean')
parser.add_must_have_statistic('Secure Copy Bandwidth (out), Mean')
parser.add_must_have_statistic('WGet Bandwidth, Mean')
parser.add_must_have_statistic('Wall Clock Time')
# set app kernel custom sets
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
if hasattr(parser, 'wallClockTime') and parser.wallClockTime is not None:
parser.set_statistic("Wall Clock Time",
total_seconds(parser.wallClockTime), "Second")
if hasattr(
parser,
'appKerWallClockTime') and parser.appKerWallClockTime is not None:
parser.set_statistic("Wall Clock Time",
total_seconds(parser.appKerWallClockTime),
"Second")
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
successful_run = False
j = 0
start = None
while j < len(lines):
if lines[j].strip() == "AKRR Network Check Results:":
start = j
if lines[j].strip() == "Done":
end = j
j += 1
if start is not None and end is not None:
r = json.loads(" ".join(lines[(start + 1):end]))
successful_run = True
if 'ping' in r:
count = 0
ping = 0.0
for k, v in r['ping'].items():
if v is None:
successful_run = False
else:
ping += float(v['rtt_avg'])
count += 1
parser.set_statistic("Ping, Mean", ping / count, "ms")
if 'wget' in r:
count = 0
val = 0.0
for k, v in r['wget'].items():
if v is None:
successful_run = False
else:
val += float(v['bandwidth'])
count += 1
parser.set_statistic("WGet Bandwidth, Mean", val / count, "MB/s")
if 'scp' in r:
count = 0
val_in = 0.0
val_out = 0.0
for k, v in r['scp'].items():
if v is None:
successful_run = False
else:
val_in += float(v['bandwidth_ingress'])
val_out += float(v['bandwidth_egress'])
count += 1
parser.set_statistic("Secure Copy Bandwidth (in), Mean",
val_in / count, "MB/s")
parser.set_statistic("Secure Copy Bandwidth (out), Mean",
val_out / count, "MB/s")
parser.successfulRun = successful_run
if __name__ == "__main__":
# output for testing purpose
print("parsing complete:", parser.parsing_complete())
parser.print_params_stats_as_must_have()
print(parser.get_xml())
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
proclog=None,
resource_appker_vars=None):
"""
Process test appkernel output.
"""
# set App Kernel Description
parser = AppKerOutputParser(name='test',
version=1,
description="Test the resource deployment",
url='http://xdmod.buffalo.edu',
measurement_name='test')
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
# parser.add_must_have_statistic('Wall Clock Time')
# parser.add_must_have_statistic('Shell is BASH')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
# set statistics
if parser.wallClockTime is not None:
parser.set_statistic("Wall Clock Time",
total_seconds(parser.wallClockTime), "Second")
# read output
lines = []
if os.path.isfile(stdout):
fin = open(stdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
parser.set_statistic('Shell is BASH', 0)
j = 0
while j < len(lines):
if lines[j].count("Checking that the shell is BASH") > 0 and lines[
j + 1].count("bash") > 0:
parser.set_statistic('Shell is BASH', 1)
j += 1
# process proc log
if proclog is not None:
os_start = None
os_first_login = None
os_start_shutdown = None
os_terminated = None
with open(proclog, "rt") as fin:
for line in fin:
m = re.search(
"Starting OpenStack instance \(([0-9]+)-([0-9]+)-([0-9]+) ([0-9]+):([0-9]+):([0-9]+)\)",
line)
if m:
os_start = datetime.datetime(int(m.group(1)),
int(m.group(2)),
int(m.group(3)),
int(m.group(4)),
int(m.group(5)),
int(m.group(6)))
m = re.search(
"OpenStack Instance should be up and running \(([0-9]+)-([0-9]+)-([0-9]+) ([0-9]+):([0-9]+):([0-9]+)\)",
line)
if m:
os_first_login = datetime.datetime(int(m.group(1)),
int(m.group(2)),
int(m.group(3)),
int(m.group(4)),
int(m.group(5)),
int(m.group(6)))
m = re.search(
"Shutting down OpenStack instance \(([0-9]+)-([0-9]+)-([0-9]+) ([0-9]+):([0-9]+):([0-9]+)\)",
line)
if m:
os_start_shutdown = datetime.datetime(
int(m.group(1)), int(m.group(2)), int(m.group(3)),
int(m.group(4)), int(m.group(5)), int(m.group(6)))
m = re.search(
"OpenStack Instance should be down and terminated \(([0-9]+)-([0-9]+)-([0-9]+) ([0-9]+):([0-9]+):([0-9]+)\)",
line)
if m:
os_terminated = datetime.datetime(int(m.group(1)),
int(m.group(2)),
int(m.group(3)),
int(m.group(4)),
int(m.group(5)),
int(m.group(6)))
# googlecloud
m = re.search(
"Starting Google Cloud instance \(([0-9]+)-([0-9]+)-([0-9]+) ([0-9]+):([0-9]+):([0-9]+)\)",
line)
if m:
os_start = datetime.datetime(int(m.group(1)),
int(m.group(2)),
int(m.group(3)),
int(m.group(4)),
int(m.group(5)),
int(m.group(6)))
m = re.search(
"Google Cloud Instance should be up and running \(([0-9]+)-([0-9]+)-([0-9]+) ([0-9]+):([0-9]+):([0-9]+)\)",
line)
if m:
os_first_login = datetime.datetime(int(m.group(1)),
int(m.group(2)),
int(m.group(3)),
int(m.group(4)),
int(m.group(5)),
int(m.group(6)))
m = re.search(
"Shutting down Google Cloud instance \(([0-9]+)-([0-9]+)-([0-9]+) ([0-9]+):([0-9]+):([0-9]+)\)",
line)
if m:
os_start_shutdown = datetime.datetime(
int(m.group(1)), int(m.group(2)), int(m.group(3)),
int(m.group(4)), int(m.group(5)), int(m.group(6)))
m = re.search(
"Google Cloud Instance should be down and terminated \(([0-9]+)-([0-9]+)-([0-9]+) ([0-9]+):([0-9]+):([0-9]+)\)",
line)
if m:
os_terminated = datetime.datetime(int(m.group(1)),
int(m.group(2)),
int(m.group(3)),
int(m.group(4)),
int(m.group(5)),
int(m.group(6)))
if os_start is not None and os_first_login is not None:
parser.set_statistic('Cloud Instance, Start Time to Login',
total_seconds(os_first_login - os_start))
if os_start_shutdown is not None and os_terminated is not None:
parser.set_statistic(
'Cloud Instance, Shut Down Time',
total_seconds(os_terminated - os_start_shutdown))
# log.info("OpenStack Instance should be up and running (%s)"
# log.info("Shutting down OpenStack instance (%s)" % datetime.datetime.today().strftime("%Y-%m-%d %H:%M:%S"))
# log.info("OpenStack Instance should be down and terminated (%s)"
if __name__ == "__main__":
# output for testing purpose
print(("parsing complete:", parser.parsing_complete()))
parser.print_params_stats_as_must_have()
print((parser.get_xml()))
# return complete XML otherwise return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
proclog=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(name='hpcg',
version=1,
description="HPCG Benchmark",
url='http://www.hpcg-benchmark.org/index.html',
measurement_name='HPCG')
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:ExeBinSignature')
parser.add_must_have_parameter('App:Version')
parser.add_must_have_parameter('Input:Distributed Processes')
parser.add_must_have_parameter('Input:Global Problem Dimensions Nx')
parser.add_must_have_parameter('Input:Global Problem Dimensions Ny')
parser.add_must_have_parameter('Input:Global Problem Dimensions Nz')
parser.add_must_have_parameter('Input:Local Domain Dimensions Nx')
parser.add_must_have_parameter('Input:Local Domain Dimensions Ny')
parser.add_must_have_parameter('Input:Local Domain Dimensions Nz')
parser.add_must_have_parameter('Input:Number of Coarse Grid Levels')
parser.add_must_have_parameter('Input:Threads per processes')
parser.add_must_have_parameter('RunEnv:CPU Speed')
parser.add_must_have_parameter('RunEnv:Nodes')
parser.add_must_have_statistic('Floating-Point Performance, Raw DDOT')
parser.add_must_have_statistic('Floating-Point Performance, Raw MG')
parser.add_must_have_statistic('Floating-Point Performance, Raw SpMV')
parser.add_must_have_statistic('Floating-Point Performance, Raw Total')
parser.add_must_have_statistic('Floating-Point Performance, Raw WAXPBY')
parser.add_must_have_statistic('Floating-Point Performance, Total')
parser.add_must_have_statistic('Memory Bandwidth, Read')
parser.add_must_have_statistic('Memory Bandwidth, Total')
parser.add_must_have_statistic('Memory Bandwidth, Write')
parser.add_must_have_statistic('Setup Time')
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
if hasattr(parser, 'appKerWallClockTime') and getattr(
parser, 'appKerWallClockTime') is not None:
parser.set_statistic("Wall Clock Time",
total_seconds(parser.appKerWallClockTime),
"Second")
# get path to YAML file
# read data
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# older version stores results in yaml
# Parse YAML lines because YAML is often malformed
yaml_lines = []
# get yaml lines from appstdout
bool_in_yaml_section = False
for line in lines:
if re.match(r"^====== .+\.yaml End ======", line):
break
if bool_in_yaml_section:
yaml_lines.append(line)
if re.match(r"^====== .+\.yaml Start ======", line):
bool_in_yaml_section = True
# newer in summary txt
# txt "====== HPCG-Benchmark_3.1_2020-09-23_17-54-20.txt Start ======"
txt_lines = []
bool_in_txt_section = False
for line in lines:
if re.match(r"^====== HPCG-Benchmark.*\.txt End ======", line):
break
if bool_in_txt_section:
txt_lines.append(line)
if re.match(r"^====== HPCG-Benchmark.*\.txt Start ======", line):
bool_in_txt_section = True
if len(yaml_lines) > 5:
process_yaml(yaml_lines, parser)
else:
process_txt(txt_lines, parser)
if __name__ == "__main__":
# output for testing purpose
print("parsing complete:", parser.parsing_complete(verbose=True))
parser.print_params_stats_as_must_have()
print(parser.get_xml())
# return complete XML otherwise return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
proclog=None,
resource_appker_vars=None):
# initiate parser
parser = AppKerOutputParser(name='mdtest')
# set obligatory parameters and statistics
# set common parameters and statistics (App:ExeBinSignature and RunEnv:Nodes)
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('RunEnv:Nodes')
parser.add_must_have_parameter('Arguments (single directory per process)')
parser.add_must_have_parameter('Arguments (single directory)')
parser.add_must_have_parameter(
'Arguments (single tree directory per process)')
parser.add_must_have_parameter('Arguments (single tree directory)')
parser.add_must_have_parameter(
'files/directories (single directory per process)')
parser.add_must_have_parameter('files/directories (single directory)')
parser.add_must_have_parameter(
'files/directories (single tree directory per process)')
parser.add_must_have_parameter('files/directories (single tree directory)')
parser.add_must_have_parameter('tasks (single directory per process)')
parser.add_must_have_parameter('tasks (single directory)')
parser.add_must_have_parameter('tasks (single tree directory per process)')
parser.add_must_have_parameter('tasks (single tree directory)')
parser.add_must_have_statistic(
'Directory creation (single directory per process)')
parser.add_must_have_statistic('Directory creation (single directory)')
parser.add_must_have_statistic(
'Directory creation (single tree directory per process)')
parser.add_must_have_statistic(
'Directory creation (single tree directory)')
parser.add_must_have_statistic(
'Directory removal (single directory per process)')
parser.add_must_have_statistic('Directory removal (single directory)')
parser.add_must_have_statistic(
'Directory removal (single tree directory per process)')
parser.add_must_have_statistic('Directory removal (single tree directory)')
parser.add_must_have_statistic(
'Directory stat (single directory per process)')
parser.add_must_have_statistic('Directory stat (single directory)')
parser.add_must_have_statistic(
'Directory stat (single tree directory per process)')
parser.add_must_have_statistic('Directory stat (single tree directory)')
parser.add_must_have_statistic(
'File creation (single directory per process)')
parser.add_must_have_statistic('File creation (single directory)')
parser.add_must_have_statistic(
'File creation (single tree directory per process)')
parser.add_must_have_statistic('File creation (single tree directory)')
parser.add_must_have_statistic('File read (single directory per process)')
parser.add_must_have_statistic('File read (single directory)')
parser.add_must_have_statistic(
'File read (single tree directory per process)')
parser.add_must_have_statistic('File read (single tree directory)')
parser.add_must_have_statistic(
'File removal (single directory per process)')
parser.add_must_have_statistic('File removal (single directory)')
parser.add_must_have_statistic(
'File removal (single tree directory per process)')
parser.add_must_have_statistic('File removal (single tree directory)')
parser.add_must_have_statistic('File stat (single directory per process)')
parser.add_must_have_statistic('File stat (single directory)')
parser.add_must_have_statistic(
'File stat (single tree directory per process)')
parser.add_must_have_statistic('File stat (single tree directory)')
parser.add_must_have_statistic(
'Tree creation (single directory per process)')
parser.add_must_have_statistic('Tree creation (single directory)')
parser.add_must_have_statistic(
'Tree creation (single tree directory per process)')
parser.add_must_have_statistic('Tree creation (single tree directory)')
parser.add_must_have_statistic(
'Tree removal (single directory per process)')
parser.add_must_have_statistic('Tree removal (single directory)')
parser.add_must_have_statistic(
'Tree removal (single tree directory per process)')
parser.add_must_have_statistic('Tree removal (single tree directory)')
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
if hasattr(parser, 'appKerWallClockTime'):
parser.set_statistic("Wall Clock Time",
total_seconds(parser.appKerWallClockTime),
"Second")
# Here can be custom output parsing
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
testname = ""
parser.successfulRun = False
j = 0
while j < len(lines):
m = re.match(r'^#Testing (.+)', lines[j])
if m:
testname = " (" + m.group(1).strip() + ")"
m = re.match(r'^SUMMARY.*:', lines[j])
if m:
j = j + 3
while j < len(lines):
m = re.match(
r'([A-Za-z0-9 ]+):\s+[0-9.]+\s+[0-9.]+\s+([0-9.]+)\s+([0-9.]+)',
lines[j])
if m:
parser.set_statistic(
m.group(1).strip() + testname, m.group(2),
"Operations/Second")
else:
break
j = j + 1
m = re.search(r'finished at', lines[j])
if m:
parser.successfulRun = True
m = re.match(r'^Command line used:.+mdtest\s+(.+)', lines[j])
if m:
parser.set_parameter("Arguments" + testname, m.group(1).strip())
m = re.search(r'([0-9]+) tasks, ([0-9]+) files/directories', lines[j])
if m:
parser.set_parameter("tasks" + testname, m.group(1).strip())
parser.set_parameter("files/directories" + testname,
m.group(2).strip())
j = j + 1
# parser.set_parameter("mega parameter",m.group(1))
#
# m=re.search(r'My mega parameter\s+(\d+)',lines[j])
# if m:parser.set_statistic("mega statistics",m.group(1),"Seconds")
#
# m=re.search(r'Done',lines[j])
# if m:parser.successfulRun=True
#
# j+=1
if __name__ == "__main__":
# output for testing purpose
print("Parsing complete:", parser.parsing_complete(verbose=True))
print("Following statistics and parameter can be set as obligatory:")
parser.print_params_stats_as_must_have()
print("\nResulting XML:")
print(parser.get_xml())
# return complete XML otherwise return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(
name='wrf',
version=1,
description="Weather Research and Forecasting Model",
url='http://www.wrf-model.org',
measurement_name='WRF')
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:Version')
parser.add_must_have_parameter('Input:Grid Resolution')
parser.add_must_have_parameter('Input:Simulation Length')
parser.add_must_have_parameter('Input:Simulation Start Date')
parser.add_must_have_parameter('Input:Timestep')
parser.add_must_have_parameter('RunEnv:Nodes')
parser.add_must_have_parameter('WRF Dynamical Solver')
# parser.add_must_have_statistic('Average Floating-Point Performance')
parser.add_must_have_statistic('Average Simulation Speed')
parser.add_must_have_statistic('Mean Time To Simulate One Timestep')
parser.add_must_have_statistic('Output Data Size')
# parser.add_must_have_statistic('Peak Floating-Point Performance')
parser.add_must_have_statistic('Peak Simulation Speed')
parser.add_must_have_statistic('Time Spent on I/O')
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
io_size = None
wall_clock_time = None
iteration_wall_clock_time = []
sim_time_per_iteration = None
dx = None
dy = None
flops_conversion = None
j = 0
while j < len(lines):
m = re.search(r'XDMOD\*\*\*SIZE OF CURRENT DIR BEFORE WRF RUN\s*(\d+)',
lines[j])
if m:
io_size = int(m.group(1).strip())
m = re.search(r'XDMOD\*\*\*SIZE OF CURRENT DIR AFTER WRF RUN\s*(\d+)',
lines[j])
if m and io_size:
parser.set_statistic("Output Data Size",
(int(m.group(1).strip()) - io_size) / 1024.0 /
1024.0, "MByte")
m = re.search(r'XDMOD\*\*\*WRF RUN BEGINS HERE --(.+)', lines[j])
if m:
wall_clock_time = parser.get_datetime_local(m.group(1).strip())
m = re.search(r'XDMOD\*\*\*WRF RUN HAS FINISHED --(.+)', lines[j])
if m and wall_clock_time:
wall_clock_time = parser.get_datetime_local(
m.group(1).strip()) - wall_clock_time
parser.set_statistic("Wall Clock Time",
wall_clock_time.total_seconds(), "Second")
if lines[j].find('XDMOD***RESULT OF rsl.out.0000 BEGINS') >= 0:
# the output from MPI rank #0
io_time = None
while j < len(lines):
if lines[j].find('XDMOD***RESULT OF rsl.out.0000 ENDS') >= 0:
break
m = re.search(
r'Timing for processing restart file.+?:\s+(\d\S+)',
lines[j], re.I)
if m:
if io_time is None:
io_time = 0.0
io_time += float(m.group(1).strip())
m = re.search(r'Timing for Writing.+?:\s+(\d\S+)', lines[j],
re.I)
if m:
if io_time is None:
io_time = 0.0
io_time += float(m.group(1).strip())
m = re.search(
r'Timing for main: time.+?on domain.+?:\s+(\d\S+)',
lines[j], re.I)
if m:
iteration_wall_clock_time.append(float(m.group(1).strip()))
m = re.search(r'WRF NUMBER OF TILES.+?(\d+)', lines[j])
if m:
omp_threads = int(m.group(1).strip())
if omp_threads > 1:
parser.set_parameter("Number of OpenMP Threads",
omp_threads)
m = re.match(r'^\s+WRF V(\S+) MODEL', lines[j])
if m:
parser.set_parameter("App:Version", m.group(1).strip())
j += 1
parser.set_statistic("Time Spent on I/O", io_time, "Second")
if re.search('XDMOD\*\*\*RESULT OF wrfout.+?BEGINS',
lines[j]) is not None:
# the output file's header (netCDF dump)
io_time = None
while j < len(lines):
if re.search('XDMOD\*\*\*RESULT OF wrfout.+?ENDS',
lines[j]) is not None:
break
m = re.search(r':DX = (\d+)', lines[j], re.I)
if m:
dx = float(m.group(1).strip()) * 0.001 # in meters
m = re.search(r':DY = (\d+)', lines[j], re.I)
if m:
dy = float(m.group(1).strip()) * 0.001 # in meters
m = re.search(r':DT = (\d+)', lines[j], re.I)
if m:
sim_time_per_iteration = float(
m.group(1).strip()) # in seconds
parser.set_parameter("Input:Timestep",
sim_time_per_iteration,
"Second per Step")
m = re.search(r':SIMULATION_START_DATE = "(.+?)"', lines[j],
re.I)
if m:
parser.set_parameter("Input:Simulation Start Date",
(m.group(1).strip()))
m = re.search(r':GRIDTYPE = "(.+?)"', lines[j], re.I)
if m:
solver = m.group(1).strip()
if solver == 'C':
solver = 'Advanced Research WRF (ARW)'
if solver == 'E':
solver = 'Nonhydrostatic Mesoscale Model (NMM)'
parser.set_parameter("WRF Dynamical Solver", solver)
m = re.search(r'Timing for Writing.+?:\s+(\d\S+)', lines[j],
re.I)
if m:
if io_time is None:
io_time = 0.0
io_time += float(m.group(1).strip())
m = re.search(
r'Timing for main: time.+?on domain.+?:\s+(\d\S+)',
lines[j], re.I)
if m:
iteration_wall_clock_time.append(float(m.group(1).strip()))
m = re.search(r'WRF NUMBER OF TILES.+?(\d+)', lines[j])
if m:
omp_threads = int(m.group(1).strip())
if omp_threads > 1:
parser.set_parameter("Number of OpenMP Threads",
omp_threads)
m = re.match(r'^\s+WRF V(\S+) MODEL', lines[j])
if m:
parser.set_parameter("App:Version", m.group(1).strip())
j += 1
if dx and dy:
if (dx - int(dx)) * 1000 < 0.1 and (
dy - int(dy)
) * 1000 < 0.1: # back compatibility with output format
parser.set_parameter("Input:Grid Resolution",
"%.0f x %.0f" % (dx, dy), "km^2")
else:
parser.set_parameter("Input:Grid Resolution",
str(dx) + " x " + str(dy), "km^2")
m = re.search(r'XDMOD\*\*\*FLOATING-POINT PERFORMANCE CONVERSION',
lines[j])
if m:
flops_conversion = lines[j + 1].strip()
j += 1
if wall_clock_time:
parser.successfulRun = True
else:
parser.successfulRun = False
if len(iteration_wall_clock_time) > 0 and sim_time_per_iteration:
parser.set_parameter("Input:Simulation Length",
(len(iteration_wall_clock_time)) *
sim_time_per_iteration / 3600.0, "Hour")
iteration_wall_clock_time = sorted(iteration_wall_clock_time)
iteration_wall_clock_time.pop()
t = 0.0
min_t = iteration_wall_clock_time[0]
for tt in iteration_wall_clock_time:
t += tt
t = t / len(iteration_wall_clock_time)
parser.set_statistic("Mean Time To Simulate One Timestep", t, "Second")
parser.set_statistic("Average Simulation Speed",
sim_time_per_iteration / t,
"Simulated Second per Second")
parser.set_statistic("Peak Simulation Speed",
sim_time_per_iteration / min_t,
"Simulated Second per Second")
if flops_conversion:
flops_conversion = flops_conversion.replace("$", "").replace(
"gflops=", "")
gflops = eval(flops_conversion, {'T': t})
parser.set_statistic("Average Floating-Point Performance",
1000.0 * gflops, "MFLOP per Second")
gflops = eval(flops_conversion, {'T': min_t})
parser.set_statistic("Peak Floating-Point Performance",
1000.0 * gflops, "MFLOP per Second")
if __name__ == "__main__":
# output for testing purpose
parsing_complete = parser.parsing_complete(True)
print("parsing complete:", parsing_complete)
if hasattr(parser, 'successfulRun'):
print("successfulRun", parser.successfulRun)
parser.print_params_stats_as_must_have()
print(parser.get_xml())
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None, stdout=None, stderr=None, geninfo=None, resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(
name='graph500',
version=1,
description="Graph500 Benchmark",
url='http://www.Graph500.org',
measurement_name='Graph500'
)
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:Version')
parser.add_must_have_parameter('Edge Factor')
parser.add_must_have_parameter('Input File')
parser.add_must_have_parameter('Number of Roots to Check')
parser.add_must_have_parameter('Number of Edges')
parser.add_must_have_parameter('Number of Vertices')
parser.add_must_have_parameter('Scale')
parser.add_must_have_statistic('Harmonic Mean TEPS')
parser.add_must_have_statistic('Harmonic Standard Deviation TEPS')
parser.add_must_have_statistic('Median TEPS')
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo, resource_appker_vars)
if parser.appKerWallClockTime is not None:
parser.set_statistic("Wall Clock Time", total_seconds(parser.appKerWallClockTime), "Second")
elif parser.wallClockTime is not None:
parser.set_statistic("Wall Clock Time", total_seconds(parser.wallClockTime), "Second")
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
parser.successfulRun = True
num_of_errors = 0
j = 0
while j < len(lines):
m = re.match(r'^Graph500 version:\s+(.+)', lines[j])
if m:
parser.set_parameter("App:Version", m.group(1).strip())
m = re.match(r'ERROR:\s+(.+)', lines[j])
if m:
num_of_errors += 1
m = re.match(r'^Reading input from\s+(.+)', lines[j])
if m:
parser.set_parameter("Input File", m.group(1))
m = re.match(r'^SCALE:\s+(\d+)', lines[j])
if m:
parser.set_parameter("Scale", m.group(1))
m = re.match(r'^edgefactor:\s+(\d+)', lines[j])
if m:
parser.set_parameter("Edge Factor", m.group(1))
m = re.match(r'^NBFS:\s+(\d+)', lines[j])
if m:
parser.set_parameter("Number of Roots to Check", m.group(1))
m = re.match(r'^median_TEPS:\s+(\d[0-9.e+]+)', lines[j])
if m:
parser.set_statistic("Median TEPS", m.group(1), "Traversed Edges Per Second")
m = re.match(r'^harmonic_mean_TEPS:\s+(\d[0-9.e+]+)', lines[j])
if m:
parser.successfulRun = True
parser.set_statistic("Harmonic Mean TEPS", m.group(1), "Traversed Edges Per Second")
m = re.match(r'^harmonic_stddev_TEPS:\s+(\d[0-9.e+]+)', lines[j])
if m:
parser.set_statistic("Harmonic Standard Deviation TEPS", m.group(1), "Traversed Edges Per Second")
m = re.match(r'^median_validate:\s+([\d.]+)\s+s', lines[j])
if m:
parser.set_statistic("Median Validation Time", m.group(1), "Second")
m = re.match(r'^mean_validate:\s+([\d.]+)\s+s', lines[j])
if m:
parser.set_statistic("Mean Validation Time", m.group(1), "Second")
m = re.match(r'^stddev_validate:\s+([\d.]+)\s+s', lines[j])
if m:
parser.set_statistic("Standard Deviation Validation Time", m.group(1), "Second")
j += 1
if num_of_errors > 0:
parser.successfulRun = False
if parser.get_parameter('Scale') is not None and parser.get_parameter('Edge Factor') is not None:
scale = int(parser.get_parameter('Scale'))
edgefactor = int(parser.get_parameter('Edge Factor'))
parser.set_parameter("Number of Vertices", 2 ** scale)
parser.set_parameter("Number of Edges", edgefactor * 2 ** scale)
if __name__ == "__main__":
# output for testing purpose
parser.parsing_complete(True)
print("parsing complete:", parser.parsing_complete())
parser.print_params_stats_as_must_have()
print(parser.get_xml())
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
proclog=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(name='quantum_espresso',
version=1,
description="Quantum ESPRESSO (PWSCF)",
url='http://www.quantum-espresso.org',
measurement_name='Quantum_ESPRESSO')
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:Version')
parser.add_must_have_parameter('Input:Number of Atoms per Cell')
parser.add_must_have_parameter('Input:Number of Atomic Types')
parser.add_must_have_parameter('Input:Number of Electrons')
parser.add_must_have_statistic('Wall Clock Time')
parser.add_must_have_statistic('User Time')
parser.add_must_have_statistic("Per-Process Dynamical Memory")
parser.add_must_have_statistic("Time Spent in Program Initialization")
parser.add_must_have_statistic("Time Spent in Electron Energy Calculation")
parser.add_must_have_statistic("Time Spent in Force Calculation")
# This statistic probably was working for a different set of inputs, optional now
# parser.add_must_have_statistic("Time Spent in Stress Calculation")
# This statistic probably was working for a different set of inputs, optional now
# parser.add_must_have_statistic("Time Spent in Potential Updates "\
# "(Charge Density and Wavefunctions Extrapolations)")
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
parser.successfulRun = False
j = 0
while j < len(lines):
m = re.match(r'^\s+Program PWSCF\s+([\w.]+)\s+starts', lines[j])
if m:
parser.set_parameter("App:Version", m.group(1).strip())
m = re.match(r'^\s+number of atoms/cell\s*=\s*([\d.]+)', lines[j])
if m:
parser.set_parameter("Input:Number of Atoms per Cell",
m.group(1).strip())
m = re.match(r'^\s+number of atomic types\s*=\s*([\d.]+)', lines[j])
if m:
parser.set_parameter("Input:Number of Atomic Types",
m.group(1).strip())
m = re.match(r'^\s+number of electrons\s*=\s*([\d.]+)', lines[j])
if m:
parser.set_parameter("Input:Number of Electrons",
m.group(1).strip())
m = re.match(r'^\s+per-process dynamical memory:\s*([\d.]+)\s*Mb',
lines[j])
if m:
parser.set_statistic("Per-Process Dynamical Memory",
(m.group(1).strip()), "MByte")
m = re.match(r'^\s+init_run\s+:\s*([\d.]+)s CPU', lines[j])
if m:
parser.set_statistic("Time Spent in Program Initialization",
(m.group(1).strip()), "Second")
m = re.match(r'^\s+electrons\s+:\s*([\d.]+)s CPU', lines[j])
if m:
parser.set_statistic("Time Spent in Electron Energy Calculation",
(m.group(1).strip()), "Second")
m = re.match(r'^\s+forces\s+:\s*([\d.]+)s CPU', lines[j])
if m:
parser.set_statistic("Time Spent in Force Calculation",
(m.group(1).strip()), "Second")
m = re.match(r'^\s+stress\s+:\s*([\d.]+)s CPU', lines[j])
if m:
parser.set_statistic("Time Spent in Stress Calculation",
(m.group(1).strip()), "Second")
m = re.match(r'^\s+update_pot\s+:\s*([\d.]+)s CPU', lines[j])
if m:
parser.set_statistic(
"Time Spent in Potential Updates (Charge Density and Wavefunctions Extrapolations)",
float(m.group(1).strip()), "Second")
m = re.match(r'^\s+PWSCF\s+:(.+CPU.+)', lines[j])
if m:
run_times = m.group(1).strip().split(',')
for run_time in run_times:
v = run_time.split()
if len(v) > 1:
if v[0].lower().find("m") >= 0:
m = re.match(r'^([0-9]+)m([0-9.]+)s', v[0])
sec = float(m.group(1)) * 60.0 + float(m.group(2))
else:
m = re.match(r'^([0-9.]+)s', v[0])
sec = float(m.group(1))
if v[1].upper().find("CPU") >= 0:
parser.set_statistic("User Time", sec, "Second")
if v[1].upper().find("WALL") >= 0:
parser.set_statistic("Wall Clock Time", sec, "Second")
if re.match(r'^\s+JOB DONE', lines[j]):
parser.successfulRun = True
j += 1
if __name__ == "__main__":
# output for testing purpose
print("parsing complete:", parser.parsing_complete(True))
if hasattr(parser, 'successfulRun'):
print("successfulRun", parser.successfulRun)
parser.print_params_stats_as_must_have()
print(parser.get_xml())
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None, stdout=None, stderr=None, geninfo=None, proclog=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(
name='amber',
version=1,
description="Amber: Assisted Model Building with Energy Refinement",
url='http://ambermd.org',
measurement_name='Amber'
)
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:Version')
parser.add_must_have_parameter('Input:Coordinate File')
parser.add_must_have_parameter('Input:Number of Angles')
parser.add_must_have_parameter('Input:Number of Atoms')
parser.add_must_have_parameter('Input:Number of Bonds')
parser.add_must_have_parameter('Input:Number of Dihedrals')
parser.add_must_have_parameter('Input:Number of Steps')
parser.add_must_have_parameter('Input:Structure File')
parser.add_must_have_parameter('Input:Timestep')
parser.add_must_have_statistic('Molecular Dynamics Simulation Performance')
parser.add_must_have_statistic('Time Spent in Direct Force Calculation')
parser.add_must_have_statistic('Time Spent in Non-Bond List Regeneration')
parser.add_must_have_statistic('Time Spent in Reciprocal Force Calculation')
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo, resource_appker_vars)
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
parser.successfulRun = False
num_steps = 0
step_size = 0
j = 0
while j < len(lines):
m = re.search(r'Amber\s+([0-9a-zA-Z]+)\s+SANDER\s+20[0-9]+', lines[j])
if m:
parser.set_parameter("App:Version", "SANDER " + m.group(1))
m = re.match(r'^\|\s+PMEMD implementation of SANDER, Release\s+([0-9.]+)', lines[j])
if m:
parser.set_parameter("App:Version", "PMEMD " + m.group(1))
m = re.match(r'^\|\s+INPCRD:\s+(\S+)', lines[j])
if m:
parser.set_parameter("Input:Coordinate File", m.group(1))
m = re.match(r'^\|\s+PARM:\s+(\S+)', lines[j])
if m:
parser.set_parameter("Input:Structure File", m.group(1))
if re.search(r'CONTROL\s+DATA\s+FOR\s+THE\s+RUN', lines[j]):
j += 2
for k in range(256):
if re.match(r'^-----------------------------', lines[j]):
break
m = re.search(r'nstlim\s+=\s+([0-9]+)', lines[j])
if m:
num_steps = int(m.group(1).strip())
parser.set_parameter("Input:Number of Steps", num_steps)
m = re.search(r'dt\s+=\s+([0-9.]+)', lines[j])
if m:
step_size = 1000.0 * float(m.group(1).strip())
parser.set_parameter("Input:Timestep", step_size * 1e-15, "Second per Step")
j += 1
if re.search(r'RESOURCE\s+USE', lines[j]):
j += 2
num_bonds = 0
num_angles = 0
num_dihedrals = 0
for k in range(256):
if re.match(r'^-----------------------------', lines[j]):
break
m = re.search(r'NATOM\s+=\s+([0-9]+)', lines[j])
if m:
parser.set_parameter("Input:Number of Atoms", m.group(1).strip())
m = re.search(r'NBONH\s+=\s+([0-9]+)', lines[j])
if m:
num_bonds += int(m.group(1).strip())
m = re.search(r'NBONA\s+=\s+([0-9]+)', lines[j])
if m:
num_bonds += int(m.group(1).strip())
m = re.search(r'NTHETH\s+=\s+([0-9]+)', lines[j])
if m:
num_angles += int(m.group(1).strip())
m = re.search(r'NTHETA\s+=\s+([0-9]+)', lines[j])
if m:
num_angles += int(m.group(1).strip())
m = re.search(r'NPHIH\s+=\s+([0-9]+)', lines[j])
if m:
num_dihedrals += int(m.group(1).strip())
m = re.search(r'NPHIA\s+=\s+([0-9]+)', lines[j])
if m:
num_dihedrals += int(m.group(1).strip())
j += 1
if num_bonds > 0:
parser.set_parameter("Input:Number of Bonds", num_bonds)
if num_angles > 0:
parser.set_parameter("Input:Number of Angles", num_angles)
if num_dihedrals > 0:
parser.set_parameter("Input:Number of Dihedrals", num_dihedrals)
if re.search(r'PME Nonbond Pairlist CPU Time', lines[j]):
j += 2
for k in range(20):
m = re.search(r'Total\s+([\d.]+)', lines[j])
if m:
parser.set_statistic("Time Spent in Non-Bond List Regeneration", m.group(1), "Second")
break
j += 1
if re.search(r'PME Direct Force CPU Time', lines[j]):
j += 2
for k in range(20):
m = re.search(r'Total\s+([\d.]+)', lines[j])
if m:
parser.set_statistic("Time Spent in Direct Force Calculation", m.group(1), "Second")
break
j += 1
if re.search(r'PME Reciprocal Force CPU Time', lines[j]):
j += 2
for k in range(20):
m = re.search(r'Total\s+([\d.]+)', lines[j])
if m:
parser.set_statistic("Time Spent in Reciprocal Force Calculation", m.group(1), "Second")
break
j += 1
m = re.match(r'^\|\s+Master Total wall time:\s+([0-9.]+)\s+seconds', lines[j])
if m:
parser.set_statistic("Wall Clock Time", m.group(1), "Second")
parser.successfulRun = True
# calculate the performance
simulation_time = step_size * num_steps * 0.000001 # measured in nanoseconds
if simulation_time > 0.0:
parser.set_statistic("Molecular Dynamics Simulation Performance",
1.e-9 * simulation_time / (float(m.group(1)) / 86400.0), "Second per Day")
j += 1
if __name__ == "__main__":
# output for testing purpose
print("parsing complete:", parser.parsing_complete())
parser.print_params_stats_as_must_have()
print(parser.get_xml())
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
proclog=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(
name='namd',
version=1,
description="NAMD: Scalable Molecular Dynamics Package",
url='http://www.ks.uiuc.edu/Research/namd/',
measurement_name='NAMD')
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:Version')
parser.add_must_have_parameter('Input:Coordinate File')
parser.add_must_have_parameter('Input:Number of Angles')
parser.add_must_have_parameter('Input:Number of Atoms')
parser.add_must_have_parameter('Input:Number of Bonds')
parser.add_must_have_parameter('Input:Number of Dihedrals')
parser.add_must_have_parameter('Input:Number of Steps')
parser.add_must_have_parameter('Input:Structure File')
parser.add_must_have_parameter('Input:Timestep')
parser.add_must_have_statistic('Memory')
parser.add_must_have_statistic('Molecular Dynamics Simulation Performance')
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
successful_run = False
j = 0
while j < len(lines):
m = re.match(r'^Info: NAMD ([0-9a-zA-Z.]+)', lines[j])
if m:
parser.set_parameter("App:Version", m.group(1))
m = re.match(r'^Info: TIMESTEP\s+([0-9.]+)', lines[j])
if m:
parser.set_parameter("Input:Timestep",
m.group(1) + "e-15", "Second per Step")
m = re.match(r'^Info: NUMBER OF STEPS\s+([0-9.]+)', lines[j])
if m:
parser.set_parameter("Input:Number of Steps", m.group(1))
m = re.match(r'^Info: COORDINATE PDB\s+(.+)', lines[j])
if m:
parser.set_parameter("Input:Coordinate File", m.group(1))
m = re.match(r'^Info: STRUCTURE FILE\s+(.+)', lines[j])
if m:
parser.set_parameter("Input:Structure File", m.group(1))
m = re.match(
r'^Info: Running on ([0-9.]+) processors, ([0-9.]+) nodes, ([0-9.]+) physical nodes.',
lines[j])
if m:
parser.set_parameter("App:NCores", m.group(1).strip())
parser.set_parameter("App:NNodes", m.group(3).strip())
if re.match(r'^Info: STRUCTURE SUMMARY', lines[j]):
j += 1
for k in range(25):
if re.match(r'^Info: \*\*\*\*\*', lines[j]):
break
m = re.match(r'^Info:\s+([0-9]+)\s+ATOMS\n', lines[j])
if m:
parser.set_parameter("Input:Number of Atoms", m.group(1))
m = re.match(r'^Info:\s+([0-9]+)\s+BONDS\n', lines[j])
if m:
parser.set_parameter("Input:Number of Bonds", m.group(1))
m = re.match(r'^Info:\s+([0-9]+)\s+ANGLES\n', lines[j])
if m:
parser.set_parameter("Input:Number of Angles", m.group(1))
m = re.match(r'^Info:\s+([0-9]+)\s+DIHEDRALS\n', lines[j])
if m:
parser.set_parameter("Input:Number of Dihedrals",
m.group(1))
j += 1
if re.search(r'Info: Benchmark time:', lines[j]):
m = re.search(r' ([0-9.]+) days/ns', lines[j])
if m:
parser.set_statistic(
"Molecular Dynamics Simulation Performance",
str(1.0e-9 / float(m.group(1))), "Second per Day")
m = re.match(
r'^WallClock:\s+([0-9.]+)\s+CPUTime:\s+([0-9.]+)\s+Memory:\s+([0-9.]+)',
lines[j])
if m:
parser.set_statistic("Wall Clock Time", m.group(1), "Second")
parser.set_statistic("Memory", m.group(3), "MByte")
successful_run = True
m = re.match(r'^End of program', lines[j])
if m:
successful_run = True
j += 1
parser.successfulRun = successful_run
if __name__ == "__main__":
# output for testing purpose
print("parsing complete:", parser.parsing_complete())
parser.print_params_stats_as_must_have()
print(parser.get_xml())
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
resource_appker_vars=None):
# set App Kernel Description
parser = AppKerOutputParser(
name='charmm',
version=1,
description="CHARMM: Chemistry at Harvard Macromolecular Mechanics",
url='http://www.charmm.org',
measurement_name='CHARMM')
# set obligatory parameters and statistics
# set common parameters and statistics
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
parser.add_must_have_parameter('App:Version')
parser.add_must_have_parameter('Input:Number of Angles')
parser.add_must_have_parameter('Input:Number of Atoms')
parser.add_must_have_parameter('Input:Number of Bonds')
parser.add_must_have_parameter('Input:Number of Dihedrals')
parser.add_must_have_parameter('Input:Number of Steps')
parser.add_must_have_parameter('Input:Timestep')
parser.add_must_have_statistic('Molecular Dynamics Simulation Performance')
parser.add_must_have_statistic('Time Spent in External Energy Calculation')
parser.add_must_have_statistic('Time Spent in Integration')
parser.add_must_have_statistic('Time Spent in Internal Energy Calculation')
parser.add_must_have_statistic('Time Spent in Non-Bond List Generation')
parser.add_must_have_statistic(
'Time Spent in Waiting (Load Unbalance-ness)')
parser.add_must_have_statistic('User Time')
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
# read output
lines = []
if os.path.isfile(appstdout):
fin = open(appstdout, "rt")
lines = fin.readlines()
fin.close()
# process the output
parser.successfulRun = False
wall_clock_time = 0.0
num_steps = 0
step_size = 0.0
time_breakdown_columns = None
num_atoms = 0
num_bonds = 0
num_angles = 0
num_dihedrals = 0
j = 0
while j < len(lines):
m0 = re.search(r'\s+Chemistry at HARvard Macromolecular Mechanics',
lines[j])
m1 = re.search(r'\sVersion\s+([\da-zA-Z]+)', lines[j + 1])
if m0 and m1:
parser.set_parameter("App:Version", m1.group(1).strip())
if re.search(r'Summary of the structure file counters', lines[j]):
j += 1
for k in range(256):
if re.search(r'CHARMM>', lines[j]):
break
m = re.search(r'Number of atoms\s+=\s+(\d+)', lines[j])
if m:
num_atoms += int(m.group(1).strip())
m = re.search(r'Number of bonds\s+=\s+(\d+)', lines[j])
if m:
num_bonds += int(m.group(1).strip())
m = re.search(r'Number of angles\s+=\s+(\d+)', lines[j])
if m:
num_angles += int(m.group(1).strip())
m = re.search(r'Number of dihedrals\s+=\s+(\d+)', lines[j])
if m:
num_dihedrals += int(m.group(1).strip())
j += 1
if re.search(r'<MAKGRP> found', lines[j]):
j += 1
for k in range(256):
if re.search(r'NUMBER OF DEGREES OF FREEDOM', lines[j]):
break
m = re.search(r'NSTEP\s+=\s+(\d+)', lines[j])
if m:
num_steps = int(m.group(1).strip())
parser.set_parameter("Input:Number of Steps", num_steps)
if re.search(r'TIME STEP\s+=', lines[j]):
m = re.search(r'([\d\-Ee.]+)\s+PS', lines[j])
if m:
step_size = 1000.0 * float(m.group(1).strip())
parser.set_parameter("Input:Timestep",
step_size * 1e-15,
"Second per Step")
j += 1
if re.search(r'NORMAL TERMINATION BY NORMAL STOP', lines[j]):
parser.successfulRun = True
if re.search(r'JOB ACCOUNTING INFORMATION', lines[j]):
parser.successfulRun = True
j += 1
for k in range(256):
if j > len(lines) - 1:
break
m = re.search(r'ELAPSED TIME:\s*([\d.]+)\s*MINUTES', lines[j])
if m:
wall_clock_time = 60.0 * float(m.group(1).strip())
parser.set_statistic("Wall Clock Time", wall_clock_time,
"Second")
m = re.search(r'CPU TIME:\s*([\d.]+)\s*MINUTES', lines[j])
if m:
parser.set_statistic("User Time",
60.0 * float(m.group(1).strip()),
"Second")
m = re.search(r'ELAPSED TIME:\s*([\d.]+)\s*SECONDS', lines[j])
if m:
wall_clock_time = float(m.group(1).strip())
parser.set_statistic("Wall Clock Time", wall_clock_time,
"Second")
m = re.search(r'CPU TIME:\s*([\d.]+)\s*SECONDS', lines[j])
if m:
parser.set_statistic("User Time",
m.group(1).strip(), "Second")
j += 1
if j > len(lines) - 1:
break
if re.search(r'Parallel load balance \(sec', lines[j]):
j += 1
# grab the column headers from the output, e.g.
#
# Parallel load balance (sec.):
# Node Eext Eint Wait Comm List Integ Total
# 0 205.5 6.4 1.2 31.2 23.2 2.8 270.4
# 1 205.2 7.3 1.1 31.2 23.3 3.2 271.2
# 2 205.2 7.7 0.6 32.3 23.3 3.2 272.3
# 3 205.2 7.8 0.6 32.1 23.3 3.3 272.3
# PARALLEL> Average timing for all nodes:
# 4 205.3 7.3 0.9 31.7 23.3 3.1 271.6
time_breakdown_columns = lines[j].strip().split()
if re.search(r'PARALLEL>\s*Average timing for all nodes',
lines[j]) and time_breakdown_columns:
j += 1
time_breakdown = lines[j].strip().split()
if len(time_breakdown_columns) == len(time_breakdown):
for k in range(len(time_breakdown)):
if time_breakdown_columns[k] == "Eext":
parser.set_statistic(
"Time Spent in External Energy Calculation",
time_breakdown[k], "Second")
if time_breakdown_columns[k] == "Eint":
parser.set_statistic(
"Time Spent in Internal Energy Calculation",
time_breakdown[k], "Second")
if time_breakdown_columns[k] == "Wait":
parser.set_statistic(
"Time Spent in Waiting (Load Unbalance-ness)",
time_breakdown[k], "Second")
if time_breakdown_columns[k] == "List":
parser.set_statistic(
"Time Spent in Non-Bond List Generation",
time_breakdown[k], "Second")
if time_breakdown_columns[k] == "Integ":
parser.set_statistic("Time Spent in Integration",
time_breakdown[k], "Second")
j += 1
if num_atoms > 0:
parser.set_parameter("Input:Number of Atoms", num_atoms)
if num_bonds > 0:
parser.set_parameter("Input:Number of Bonds", num_bonds)
if num_angles > 0:
parser.set_parameter("Input:Number of Angles", num_angles)
if num_dihedrals > 0:
parser.set_parameter("Input:Number of Dihedrals", num_dihedrals)
if wall_clock_time > 0.0 and num_steps > 0 and step_size > 0.0:
# $stepSize is in femtoseconds
# $wallClockTime is in seconds
parser.set_statistic("Molecular Dynamics Simulation Performance",
(1e-6 * step_size * num_steps) /
(wall_clock_time / 86400.0) * 1e-9,
"Second per Day")
if __name__ == "__main__":
# output for testing purpose
print("parsing complete:", parser.parsing_complete())
parser.print_params_stats_as_must_have()
print(parser.get_xml())
# return complete XML overwize return None
return parser.get_xml()
def process_appker_output(appstdout=None,
stdout=None,
stderr=None,
geninfo=None,
resource_appker_vars=None):
# set App Kernel Description
if resource_appker_vars is not None and 'app' in resource_appker_vars and 'name' in resource_appker_vars[
'app']:
ak_name = resource_appker_vars['app']['name']
else:
ak_name = 'unknown'
# initiate parser
parser = AppKerOutputParser(name=ak_name)
# set obligatory parameters and statistics
# set common parameters and statistics (App:ExeBinSignature and RunEnv:Nodes)
parser.add_common_must_have_params_and_stats()
# set app kernel custom sets
# parser.add_must_have_parameter('App:Version')
parser.add_must_have_statistic('Wall Clock Time')
# parse common parameters and statistics
parser.parse_common_params_and_stats(appstdout, stdout, stderr, geninfo,
resource_appker_vars)
if hasattr(parser, 'appKerWallClockTime'):
parser.set_statistic("Wall Clock Time",
total_seconds(parser.appKerWallClockTime),
"Second")
# Here can be custom output parsing
# #read output
# lines=[]
# if os.path.isfile(appstdout):
# fin=open(appstdout,"rt")
# lines=fin.readlines()
# fin.close()
#
# #process the output
# parser.successfulRun=False
# j=0
# while j<len(lines):
# m=re.search(r'My mega parameter\s+(\d+)',lines[j])
# if m:parser.set_parameter("mega parameter",m.group(1))
#
# m=re.search(r'My mega parameter\s+(\d+)',lines[j])
# if m:parser.set_statistic("mega statistics",m.group(1),"Seconds")
#
# m=re.search(r'Done',lines[j])
# if m:parser.successfulRun=True
#
# j+=1
if __name__ == "__main__":
# output for testing purpose
print("Parsing complete:", parser.parsing_complete(verbose=True))
print("Following statistics and parameter can be set as obligatory:")
parser.print_params_stats_as_must_have()
print("\nResulting XML:")
print(parser.get_xml())
# return complete XML otherwise return None
return parser.get_xml()