Changeset 213

Timestamp:

03/18/10 16:28:02 (6 years ago)

Author:

mmckerns

Message:

allow settable tmpfile directory, to better deal with queue launches;
allow type and ppn config within setting for 'nnodes' (e.g. '3:core4:ppn=2');
updated QSUB example to use compound nodestring

Files:

• branches/UQ/math/examples/QSUB_surrogate_diam_batchgrid.py (modified) (1 diff)
• pyina/applications/ezrun.py (modified) (1 diff)
• pyina/applications/ezrun2.py (modified) (1 diff)
• pyina/examples_other/test_ezmap.py (modified) (1 diff)
• pyina/pyina/differential_evolution_ezmap.py (modified) (1 diff)
• pyina/pyina/ez_map.py (modified) (7 diffs)
• pyina/pyina/launchers.py (modified) (2 diffs)

branches/UQ/math/examples/QSUB_surrogate_diam_batchgrid.py

@@ -62 +62 @@
 
 # MPI config
-nnodes = 4   # = npop
+nnodes = '4:core4:ppn=1'   # = npop
 
 # QUEUE config
-queue = 'normal'
+queue = 'weekdayQ'
 timelimit = '00:10'
 

pyina/applications/ezrun.py

@@ -23 +23 @@
         func = pickle.load(open(funcname,'r'))
     else:  # used ez_map
+        sys.path = [sys.argv[4]] + sys.path
         module = __import__(funcname)
+        sys.path.pop(0)
         func = module.FUNC
     arglist = pickle.load(open(sys.argv[2],'r'))

pyina/applications/ezrun2.py

@@ -23 +23 @@
         func = pickle.load(open(funcname,'r'))
     else:  # used ez_map
+        sys.path = [sys.argv[4]] + sys.path
         module = __import__(funcname)
+        sys.path.pop(0)
         func = module.FUNC
     arglist = pickle.load(open(sys.argv[2],'r'))

pyina/examples_other/test_ezmap.py

@@ -8 +8 @@
     return "Rank: %d -- %s" % (id, socket.gethostname())
 
-res = ez_map(host, range(5), nnodes=10, mapper=carddealer_mapper) 
+res = ez_map(host, range(10), nnodes=3, mapper=carddealer_mapper) 
+#res = ez_map(host, range(10), nnodes=3, mapper=equalportion_mapper) 
 #res = ez_map(host, range(5), nnodes=2, mapper=carddealer_mapper)
+#res = ez_map(host, range(5), nnodes=2, mapper=equalportion_mapper)
+#res = ez_map(host, range(5), nnodes=10, mapper=carddealer_mapper) 
+#res = ez_map(host, range(5), nnodes=10, mapper=equalportion_mapper) 
+#NOTE: bug?  map algorithm performs correctly when nnodes > range ???
 
 print '\n'.join(res)

pyina/pyina/differential_evolution_ezmap.py

@@ -431 +431 @@
         self._launcher     = None
         self._nnodes       = None
+        self._queue        = None
+        self._timelimit    = None
 
     def SetMapper(self, mapper):

pyina/pyina/ez_map.py

@@ -79 +79 @@
     import dill as pickle #XXX: to address costfactories
     import tempfile
-    #pickle.dump(src(func), file)
-    file = tempfile.NamedTemporaryFile(suffix='.py', dir='.')
+    #XXX: assumes '.' is writable and on $PYTHONPATH
+    file = tempfile.NamedTemporaryFile(suffix='.py', dir=ezdefaults['tmpdir'])
     file.write(''.join(src(func)))
     file.write('FUNC = %s\n' % func.func_name)
@@ -100 +100 @@
               'python' : '`which mpipython.exe`' ,
               'nodes' : '1',
-              'progargs' : ''
+              'progargs' : '',
+              'tmpdir' : '.'
             }
 
@@ -109 +110 @@
     import dill as pickle
     import tempfile
-    file = tempfile.NamedTemporaryFile(suffix=suffix, dir='.')
+    file = tempfile.NamedTemporaryFile(suffix=suffix, dir=ezdefaults['tmpdir'])
     pickle.dump(arglist, file)
     file.flush()
@@ -132 +133 @@
   - queue -- string name of selected queue (e.g. 'normal')
 """
+    import dill as pickle
+    import os.path, tempfile, os
     # mapper = None (allow for use of default mapper)
     if kwds.has_key('mapper'):
@@ -146 +149 @@
     if kwds.has_key('launcher'): launcher = kwds['launcher']
     else: launcher = mpirun_launcher  #XXX: default = non_mpi?
-
-    import dill as pickle
-    import os.path, tempfile, os
+    # set scratch directory (most often required for queue launcher)
+    if kwds.has_key('tmpdir'): ezdefaults['tmpdir'] = kwds['tmpdir']
+    else:
+        if launcher in [torque_launcher]:
+            ezdefaults['tmpdir'] = os.path.expanduser("~")
+
     modfile = func_pickle(func)
     argfile = arg_pickle(arglist)
-    resfilename = tempfile.mktemp(dir='.')
+    resfilename = tempfile.mktemp(dir=ezdefaults['tmpdir'])
     modname = os.path.splitext(os.path.basename(modfile.name))[0] 
-    ezdefaults['progargs'] = ' '.join([modname, argfile.name, resfilename])
+    ezdefaults['progargs'] = ' '.join([modname, argfile.name, resfilename, \
+                                       ezdefaults['tmpdir']])
     #HOLD.append(modfile)
     #HOLD.append(argfile)
 
     if launcher == torque_launcher:
-        jobfilename = tempfile.mktemp(dir='.')
-        outfilename = tempfile.mktemp(dir='.')
-        errfilename = tempfile.mktemp(dir='.')
+        jobfilename = tempfile.mktemp(dir=ezdefaults['tmpdir'])
+        outfilename = tempfile.mktemp(dir=ezdefaults['tmpdir'])
+        errfilename = tempfile.mktemp(dir=ezdefaults['tmpdir'])
         ezdefaults['jobfile'] = jobfilename
         ezdefaults['outfile'] = outfilename
@@ -194 +201 @@
 same functionality as ez_map, however function 'func' and arguments 'arglist'
 are stored and sent as pickled strings."""
+    import dill as pickle
+    import os.path, tempfile, os
     # mapper = None (allow for use of default mapper)
     if kwds.has_key('mapper'):
@@ -208 +217 @@
     if kwds.has_key('launcher'): launcher = kwds['launcher']
     else: launcher = mpirun_launcher  #XXX: default = non_mpi?
-
-    import dill as pickle
-    import os.path, tempfile, os
+    # set scratch directory (most often required for queue launcher)
+    if kwds.has_key('tmpdir'): ezdefaults['tmpdir'] = kwds['tmpdir']
+    else:
+        if launcher in [torque_launcher]:
+            ezdefaults['tmpdir'] = os.path.expanduser("~")
+
     modfile = func_pickle2(func)
     argfile = arg_pickle(arglist)
-    resfilename = tempfile.mktemp(dir='.')
-    ezdefaults['progargs'] = ' '.join([modfile.name, argfile.name, resfilename])
+    resfilename = tempfile.mktemp(dir=ezdefaults['tmpdir'])
+    ezdefaults['progargs'] = ' '.join([modfile.name,argfile.name,resfilename, \
+                                       ezdefaults['tmpdir']])
     #HOLD.append(modfile)
     #HOLD.append(argfile)
 
     if launcher == torque_launcher:
-        jobfilename = tempfile.mktemp(dir='.')
-        outfilename = tempfile.mktemp(dir='.')
-        errfilename = tempfile.mktemp(dir='.')
+        jobfilename = tempfile.mktemp(dir=ezdefaults['tmpdir'])
+        outfilename = tempfile.mktemp(dir=ezdefaults['tmpdir'])
+        errfilename = tempfile.mktemp(dir=ezdefaults['tmpdir'])
         ezdefaults['jobfile'] = jobfilename
         ezdefaults['outfile'] = outfilename

pyina/pyina/launchers.py

@@ -16 +16 @@
     if error: raise IOError, "launch failed"
     return error
+
     
+def tasks(nodes):
+    """ compute # of tasks from node string of pattern = N[:TYPE][:ppn=P]
+    For example, tasks("3:core4:ppn=2") yields 6 """
+    nodestr = str(nodes)
+    nodelst = nodestr.split(":")
+    n = int(nodelst[0])
+    nodelst = nodestr.split("ppn=")
+    if len(nodelst) > 1:
+        ppn = nodelst[1]
+        ppn = int(ppn.split(":")[0])
+    else: ppn = 1
+    tasks =  n*ppn
+    return tasks
+
 
 def serial_launcher(kdict={}):
@@ -53 +68 @@
     mydict = defaults.copy()
     mydict.update(kdict)
-    str = """ echo \"mpirun -np %(nodes)s %(python)s %(file)s %(progargs)s\" | qsub -l nodes=%(nodes)s -l walltime=%(timelimit)s -o %(outfile)s -e %(errfile)s -q %(queue)s &> %(jobfile)s""" % mydict
-    #XXX: would be nice to allow "-l nodes=x:ppn=y" in qsub
+    mydict['tasks'] = tasks(mydict['nodes'])
+    str = """ echo \"mpirun -np %(tasks)s %(python)s %(file)s %(progargs)s\" | qsub -l nodes=%(nodes)s -l walltime=%(timelimit)s -o %(outfile)s -e %(errfile)s -q %(queue)s &> %(jobfile)s""" % mydict
     return str