Merge pull request #11 from qiqi/niangxiu

recover some previous apps

apps/adFVM_mpi.py

@@ -0,0 +1,200 @@
+import os
+import sys
+import subprocess
+import numpy as np
+import shutil
+import glob
+
+def isfloat(s):
+    try:
+        float(s)
+        return True
+    except ValueError:
+        return False
+fileName = os.path.abspath(__file__)
+python = sys.executable
+
+nProcessors = 128
+nProcsPerNode = 8
+nRuns = 32
+subBlockShape = '1x2x2x2x2'
+
+parameter = 1.0
+dims = 128
+segments = 20
+steps = 5000
+
+time = 1.0
+source = '/projects/LESOpt/talnikar/'
+problem = 'periodic_wake_fds.py'
+case = source + 'periodic_wake/'
+
+def getTime(time):
+    stime = str(time)
+    if time.is_integer():
+        stime = str(int(time))
+    return stime
+stime = getTime(time)
+
+fieldNames = ['rho', 'rhoU', 'rhoE']
+program = source + 'local/src/adFVM/apps/problem.py'
+
+reference = [1., 200., 2e5]
+
+def getParallelInfo():
+    import h5py
+    from mpi4py import MPI
+    mpi = MPI.COMM_WORLD
+    rank = mpi.rank 
+
+    with h5py.File(case + 'mesh.hdf5', 'r') as mesh:
+        nCount = mesh['parallel/end'][rank]-mesh['parallel/start'][rank]
+        nInternalCells = nCount[4]
+        nGhostCells = nCount[2]-nCount[3]
+        nCells = nInternalCells + nGhostCells
+        cellStart = mpi.exscan(nCells)
+        if cellStart == None:
+            cellStart = 0
+        cellEnd = cellStart + nInternalCells
+
+    size = nInternalCells*5
+    start = mpi.exscan(size)
+    end = mpi.scan(size)
+    size = mpi.bcast(end, root=nProcessors-1)
+    return cellStart, cellEnd, start, end, size, mpi
+
+def getInternalFields(case, time, fieldFile):
+    import h5py
+    time = float(time)
+    cellStart, cellEnd, start, end, size, mpi = getParallelInfo()
+    fields = []
+    with h5py.File(case + getTime(time) + '.hdf5', 'r', driver='mpio', comm=mpi) as phi:
+        for name in fieldNames:
+            fields.append(phi[name + '/field'][cellStart:cellEnd])
+    fields = [x/y for x, y in zip(fields, reference)]
+    field = np.hstack(fields).ravel()
+    with h5py.File(fieldFile, 'w', driver='mpio', comm=mpi) as handle:
+        fieldData = handle.create_dataset('field', shape=(size,), dtype=field.dtype)
+        fieldData[start:end] = field
+    return
+
+def writeFields(fieldFile, caseDir, ntime):
+    import h5py
+    ntime = float(ntime)
+    cellStart, cellEnd, start, end, size, mpi = getParallelInfo()
+    with h5py.File(fieldFile, 'r', driver='mpio', comm=mpi) as handle:
+        fields = handle['field'][start:end]
+    fields = fields.reshape((fields.shape[0]/5, 5))
+    fields = fields[:,[0]], fields[:,1:4], fields[:,[4]]
+    fields = [x*y for x, y in zip(fields, reference)]
+    timeFile = caseDir + getTime(ntime) + '.hdf5' 
+    with h5py.File(timeFile, 'r+', driver='mpio', comm=mpi) as phi:
+        for index, name in enumerate(fieldNames):
+            field = phi[name + '/field']
+            field[cellStart:cellEnd] = fields[index]
+            phi[name + '/field'][:] = field
+    return
+
+def getHostDir(run_id):
+    return '{}/temp/{}/'.format(case, run_id)
+
+def spawnJob(exe, args, **kwargs):
+    global cobalt
+    if 'interprocess' in kwargs:
+        cobalt.interprocess = kwargs['interprocess']
+        del kwargs['interprocess']
+    block, corner = cobalt.get_alloc()
+    print('spawnJob', exe, args, block, corner)
+    returncode = subprocess.call(['runjob', '-n', str(nProcessors), 
+                       '-p', str(nProcsPerNode),
+                       '--block', block,
+                       '--corner', corner,
+                       '--shape', subBlockShape,
+                       '--exp-env', 'PYTHONPATH',
+                       '--verbose', 'INFO',
+                       ':', exe] + args, **kwargs)
+    cobalt.free_alloc((block, corner))
+    #returncode = subprocess.call(['mpirun', '-np', str(nProcessors), exe] + args, **kwargs)
+    return returncode
+
+def runCase(initFields, parameter, nSteps, run_id, interprocess):
+    cobalt.interprocess = interprocess
+
+    # generate case folders
+    caseDir = getHostDir(run_id)
+    if not os.path.exists(caseDir):
+        os.makedirs(caseDir)
+    shutil.copy(case + 'mesh.hdf5', caseDir)
+    for pkl in glob.glob(case + '*.pkl'):
+        shutil.copy(pkl, caseDir)
+    timeFile = caseDir + stime + '.hdf5' 
+    shutil.copy(case + stime + '.hdf5', timeFile)
+
+    # write initial field
+    outputFile = caseDir  + 'writeFields.log'
+    with open(outputFile, 'w') as f:
+        if spawnJob(python, [fileName, 'RUN', 'writeFields', initFields, caseDir, str(time)], stdout=f, stderr=f):
+            raise Exception('initial field conversion failed')
+    print('initial field written', initFields)
+
+    # modify problem file
+    shutil.copy(case + problem, caseDir)
+    problemFile = caseDir + problem
+    with open(problemFile, 'r') as f:
+        lines = f.readlines()
+    with open(problemFile, 'w') as f:
+        for line in lines:
+            writeLine = line.replace('NSTEPS', str(nSteps))
+            writeLine = writeLine.replace('STARTTIME', str(time))
+            writeLine = writeLine.replace('CASEDIR', '\'{}\''.format(caseDir))
+            writeLine = writeLine.replace('PARAMETER', str(parameter))
+            f.write(writeLine)
+
+    outputFile = caseDir  + 'output.log'
+    errorFile = caseDir  + 'error.log'
+    with open(outputFile, 'w') as f, open(errorFile, 'w') as fe:
+        #if spawnJob(python, [problemFile], stdout=f, stderr=f):
+        if spawnJob(python, [program, problemFile, '--mira', '-n', '--coresPerNode', str(nProcsPerNode), '--unloadingStages', '4'], stdout=f, stderr=fe):
+            raise Exception('Execution failed, check error log:', outputFile)
+    print('execution finished', caseDir)
+
+    # read final fields
+    times = [float(x[:-5]) for x in os.listdir(caseDir) if isfloat(x[:-5]) and x.endswith('.hdf5')]
+    lastTime = sorted(times)[-1]
+    finalFields = caseDir + 'output.h5'
+    outputFile = caseDir  + 'getInternalFields.log'
+    with open(outputFile, 'w') as f:
+        if spawnJob(python, [fileName, 'RUN', 'getInternalFields', caseDir, str(lastTime), finalFields], stdout=f, stderr=f):
+            raise Exception('final field conversion failed')
+    print('final field written', finalFields)
+
+    # read objective values
+    objectiveSeries = np.loadtxt(caseDir + 'timeSeries.txt')
+    print caseDir
+
+    cobalt.interprocess = None
+    return finalFields, objectiveSeries[:-1]
+
+if __name__ == '__main__':
+
+    if len(sys.argv) > 1 and sys.argv[1] == 'RUN':
+        func = locals()[sys.argv[2]]
+        args = sys.argv[3:]
+        func(*args)
+    else:
+        from fds.cobalt import CobaltManager
+        cobalt = CobaltManager(subBlockShape, 128)
+        cobalt.boot_blocks()
+
+        init = getHostDir('init')
+        if not os.path.exists(init):
+            os.makedirs(init)
+        u0 = init + 'init.h5'
+        if spawnJob(sys.executable, [fileName, 'RUN', 'getInternalFields', case, str(time), u0]):
+            raise Exception('final field conversion failed')
+
+        #runCase(u0, parameter, steps, 'random', None)
+        from fds import shadowing
+        shadowing(runCase, u0, parameter, dims, segments, steps, 0, simultaneous_runs=nRuns, get_host_dir=getHostDir, spawn_compute_job=spawnJob)
+
+        cobalt.free_blocks()

apps/adFVM_serial.py

@@ -0,0 +1,121 @@
+import os
+import subprocess
+import numpy as np
+import shutil
+import glob
+import h5py
+
+def isfloat(s):
+    try:
+        float(s)
+        return True
+    except ValueError:
+        return False
+
+nProcessors = 16
+nRuns = 2
+parameter = 1.0
+dims = 50
+segments = 20
+steps = 50
+
+time = 1.0
+source = '/home/talnikar/adFVM/'
+problem = 'periodic_wake.py'
+case = source + 'cases/periodic_wake2/'
+#problem = 'cylinder.py'
+#case = source + 'cases/cylinder/orig/'
+
+def getTime(time):
+    stime = str(time)
+    if time.is_integer():
+        stime = str(int(time))
+    return stime
+stime = getTime(time)
+
+internalCells = []
+with h5py.File(case + 'mesh.hdf5', 'r') as mesh:
+    nCount = mesh['parallel/end'][:]-mesh['parallel/start'][:]
+    nInternalCells = nCount[:,4]
+    nGhostCells = nCount[:,2]-nCount[:,3]
+    start = 0
+    for i in range(0, nProcessors):
+        n = nInternalCells[i] 
+        internalCells.append(np.arange(start, start + n))
+        start += n + nGhostCells[i]
+internalCells = np.concatenate(internalCells)
+
+fieldNames = ['rho', 'rhoU', 'rhoE']
+program = source + 'apps/problem.py'
+
+reference = [1., 200., 2e5]
+def getInternalFields(case, time):
+    fields = []
+    with h5py.File(case + getTime(time) + '.hdf5', 'r') as phi:
+        for name in fieldNames:
+            fields.append(phi[name + '/field'][:][internalCells])
+    fields = [x/y for x, y in zip(fields, reference)]
+    return np.hstack(fields).ravel()
+
+def writeFields(fields, caseDir, ntime):
+    fields = fields.reshape((fields.shape[0]/5, 5))
+    fields = fields[:,[0]], fields[:,1:4], fields[:,[4]]
+    fields = [x*y for x, y in zip(fields, reference)]
+    timeFile = caseDir + getTime(ntime) + '.hdf5' 
+    shutil.copy(case + stime + '.hdf5', timeFile)
+    with h5py.File(timeFile, 'r+') as phi:
+        for index, name in enumerate(fieldNames):
+            field = phi[name + '/field'][:]
+            field[internalCells] = fields[index]
+            phi[name + '/field'][:] = field
+
+def runCase(initFields, parameters, nSteps, run_id):
+
+    # generate case folders
+    caseDir = '{}/temp/{}/'.format(case, run_id)
+    mesh.case = caseDir
+    if not os.path.exists(caseDir):
+        os.makedirs(caseDir)
+    shutil.copy(case + problem, caseDir)
+    shutil.copy(case + 'mesh.hdf5', caseDir)
+    for pkl in glob.glob(case + '*.pkl'):
+        shutil.copy(pkl, caseDir)
+
+    # write initial field
+    writeFields(initFields, caseDir, time)
+
+    # modify problem file
+    problemFile = caseDir + problem
+    with open(problemFile, 'r') as f:
+        lines = f.readlines()
+    with open(problemFile, 'w') as f:
+        for line in lines:
+            writeLine = line.replace('NSTEPS', str(nSteps))
+            writeLine = writeLine.replace('STARTTIME', str(time))
+            writeLine = writeLine.replace('CASEDIR', '\'{}\''.format(caseDir))
+            writeLine = writeLine.replace('PARAMETER', str(parameter))
+            f.write(writeLine)
+
+    outputFile = caseDir  + 'output.log'
+    with open(outputFile, 'w') as f:
+        returncode = subprocess.call(['mpirun', '-np', str(nProcessors),
+                          program, problemFile, 'orig'],
+                          stdout=f, stderr=f)
+    if returncode:
+        raise Exception('Execution failed, check error log:', outputFile)
+
+    # read final fields
+    times = [float(x[:-5]) for x in os.listdir(caseDir) if isfloat(x[:-5]) and x.endswith('.hdf5')]
+    lastTime = sorted(times)[-1]
+    finalFields = getInternalFields(caseDir, lastTime)
+    # read objective values
+    objectiveSeries = np.loadtxt(caseDir + 'timeSeries.txt')
+    print caseDir
+
+    return finalFields, objectiveSeries[:-1]
+
+if __name__ == '__main__':
+    u0 = getInternalFields(case, time)
+    #runCase(u0, parameters, steps, 'random')
+    from fds import shadowing
+    shadowing(runCase, u0, parameter, dims, segments, steps, 0, simultaneous_runs=nRuns)