From 8574e5466f444145ef5d60eb9600e92ed38bf91f Mon Sep 17 00:00:00 2001
From: Wouter Peters <wouter.peters@wur.nl>
Date: Mon, 23 Jul 2012 15:50:05 +0000
Subject: [PATCH] TM5 now compiled before run
---
da/tm5/observationoperator.py | 91 +++++++++++++++++++++++++++++++++--
da/tools/pipeline.py | 4 +-
2 files changed, 89 insertions(+), 6 deletions(-)
diff --git a/da/tm5/observationoperator.py b/da/tm5/observationoperator.py
index ecabd520..6c110b33 100755
--- a/da/tm5/observationoperator.py
+++ b/da/tm5/observationoperator.py
@@ -26,6 +26,7 @@ import logging
import shutil
sys.path.append(os.getcwd())
+sys.path.append("../../")
identifier = 'TM5'
version = 'release 3.0'
@@ -79,13 +80,77 @@ class TM5ObservationOperator(ObservationOperator):
msg = 'Observation Operator initialized: %s (%s)'%(self.Identifier, self.Version,) ; logging.info(msg)
+ def Initialize(self ):
+ """
+ Execute all steps needed to prepare the ObsOperator for use inside CTDAS, only done at the very first cycle normally
+
+ """
+ from da.tools.general import CreateDirs
+
+
+ if self.DaCycle['time.restart'] == False :
+
+ msg = 'First time step, setting up and compiling the TM5 model before proceeding!' ; logging.info(msg)
+ # Modify the rc-file to reflect directory structure defined by CTDAS
+ NewItems = {
+ 'my.basedir' : self.DaCycle['dir.exec'] ,
+ }
+
+ self.ModifyRC(NewItems)
+
+ # Create the TM5 run directory to hold a copy of the modified rc-file
+
+ tm5compiledir = self.tm_settings[self.rundirkey]
+ dummy = CreateDirs(tm5compiledir)
+
+ self.RcFileName = self.WriteRc()
+
+ # Compile TM5 in the new directory, but only if this is a fresh start
+
+ self.CompileTM5()
+
+ return 0
+
+ def CompileTM5(self):
+ """
+ Compile TM5 model using setup_tm5 and the modified rc-file
+ """
+ import subprocess
+ from string import join
+
+ try:
+ os.chdir(self.DaCycle['da.obsoperator.home'])
+ except:
+
+ tm5_dir = os.path.split(self.DaCycle['da.obsoperator.rc'])[0]
+ msg = 'Guessing your TM5 root dir from the rc filename' ; logging.warning(msg)
+ msg = 'Try adding a key da.obsoperator.home to your da.rc' ; logging.warning(msg)
+ msg = 'Proceeding from guessed TM5 root dir (%s) '%tm5_dir ; logging.warning(msg)
+
+ os.chdir(tm5_dir)
+
+ cmd = ['python','setup_tm5','-q',self.RcFileName]
+
+ msg = 'Starting the external TM5 setup script' ; logging.info(msg)
+ msg = 'using command ... %s'% join(cmd) ; logging.info(msg)
+
+ retcode = subprocess.call(cmd)
+ os.chdir(self.DaCycle['dir.da_submit'])
+
+ if retcode != 0:
+ msg = 'Compilation failed, quitting CTDAS' ; logging.error(msg)
+ raise IOError
+ sys.exit(2)
+ else:
+ msg = 'Compilation successful, continuing' ; logging.info(msg)
+
def getid(self):
return identifier
def getversion(self):
return version
- def Initialize(self ):
+ def PrepareRun(self ):
"""
Prepare a forward model TM5 run, this consists of:
@@ -103,6 +168,7 @@ class TM5ObservationOperator(ObservationOperator):
dummy = self.LoadRc(self.RcFileName) # load the specified rc-file
dummy = self.ValidateRc() # validate the contents
+
# Create a link from TM5 to the rundirectory of the das system
sourcedir = self.tm_settings[self.rundirkey]
@@ -133,7 +199,7 @@ class TM5ObservationOperator(ObservationOperator):
self.ModifyRC(NewItems)
- self.WriteRc()
+ newrcfile = self.WriteRc()
#self.WriteRunRc() No longer needed with pycasso !
@@ -146,7 +212,8 @@ class TM5ObservationOperator(ObservationOperator):
"""
import da.tools.rcn as rc
- self.tm_settings = rc.read(RcFileName)
+ self.rcfile = rc.RcFile(RcFileName)
+ self.tm_settings = self.rcfile.values
self.RcFileName = RcFileName
self.Tm5RcLoaded = True
@@ -263,11 +330,13 @@ class TM5ObservationOperator(ObservationOperator):
"""
import da.tools.rc as rc
- tm5rcfilename = os.path.join(self.tm_settings[self.rundirkey],'tm5.rc')
+ tm5rcfilename = os.path.join(self.tm_settings[self.rundirkey],'tm5_ctdas_setup.rc')
dummy = rc.write(tm5rcfilename,self.tm_settings)
- msg = "Modified tm5.rc written (%s)" % tm5rcfilename ;logging.debug(msg)
+ msg = "Modified rc file for TM5 written (%s)" % tm5rcfilename ;logging.debug(msg)
+
+ return tm5rcfilename
def WriteRunRc(self):
"""
@@ -510,6 +579,15 @@ class TM5ObservationOperator(ObservationOperator):
if os.path.exists(okfile):
dummy = os.remove(okfile)
+ # Prepare a job for the current platform, this job needs to account for all job parameters such as
+ # runtime, queue request, number of processors, and other platform specific parameters
+
+ # It is easiest if all of these options are 'pre-configured' through the tm5.rc file that is used, then
+ # running the ObsOperator on all platforms simply becomes a matter of running the ./setup_tm5 script
+ # that was also used to compile TM5 when not actually running CTDAS. The first run of CTDAS
+ # then could be one where TM5 is actually compiled and run, the rest of the jobs would then *not* re-compile.
+ # An option would need to be added to force a re-compile of the TM5 code, for debugging purposes.
+
# file ID and names
jobid = 'tm5'
jobfile = os.path.join(targetdir,'jb.%s.jb'%jobid)
@@ -625,6 +703,8 @@ class TM5ObservationOperator(ObservationOperator):
if __name__ == "__main__":
+ sys.path.append('../../')
+
from da.tools.initexit import StartLogger
from da.tools.pipeline import JobStart
import datetime as dtm
@@ -641,6 +721,7 @@ if __name__ == "__main__":
DaCycle['time.sample.window'] = 0
tm=TM5ObservationOperator()
+ tm.Setup()
tm.Initialize()
tm.Run()
tm.SaveData()
diff --git a/da/tools/pipeline.py b/da/tools/pipeline.py
index 63da0bb4..a62f8e1c 100755
--- a/da/tools/pipeline.py
+++ b/da/tools/pipeline.py
@@ -79,6 +79,8 @@ def JobStart(DaCycle, DaSystem, DaPlatForm, StateVector, Samples, ObsOperator):
ObsOperator.DaCycle = DaCycle # also embed object in ObsOperator object so it can access cycle information for I/O etc
+ status = ObsOperator.Initialize() # Setup Observation Operator
+
return None
@@ -340,7 +342,7 @@ def RunForecastModel(DaCycle,ObsOperator):
submitting a string of jobs to the queue, or simply spawning a subprocess, or ...
"""
- status = ObsOperator.Initialize()
+ status = ObsOperator.PrepareRun()
status = ObsOperator.ValidateInput()
--
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