Changeset 13071

Timestamp:

08/16/12 15:30:45 (13 years ago)

Author:

jschierm

Message:

NEW: More changes for python marshalling and running (plus corresponding matlab changes).

Location:

issm/trunk-jpl/src/m

Files:

• os/issmscpin.m (modified) (4 diffs)
• os/issmscpin.py (modified) (4 diffs)
• os/issmscpout.m (modified) (3 diffs)
• os/issmscpout.py (modified) (4 diffs)
• parameterization/parameterize.m (modified) (1 diff)
• solve/WriteData.py (modified) (8 diffs)
• solve/loadresultsfromcluster.py (modified) (3 diffs)
• solve/loadresultsfromdisk.py (modified) (2 diffs)
• solve/solve.py (modified) (2 diffs)
• solve/waitonlock.m (modified) (2 diffs)
• solve/waitonlock.py (modified) (2 diffs)

issm/trunk-jpl/src/m/os/issmscpin.m

@@ -1 @@
-function scpin(host, login,port,path, packages)
-%SCPIN get packages from host, using scp on unix, and pscp on windows
+function issmscpin(host, login,port,path, packages)
+%ISSMSCPIN get packages from host, using scp on unix, and pscp on windows
 %
-%   usage: scpin(host,packages,path)
+%   usage: issmscpin(host,packages,path)
 %
 %
@@ -35 +35 @@
                 [status,ISSM_DIR]=system('echo [%ISSM_DIR_WIN%]');
                 if status, 
-                        error('scpin error message: could not find ISSM_DIR_WIN environment variable');
+                        error('issmscpin error message: could not find ISSM_DIR_WIN environment variable');
                 end
                 ISSM_DIR=ISSM_DIR(2:end-2);
@@ -45 +45 @@
                         [status,result]=system([ISSM_DIR '/externalpackages/ssh/pscp.exe -l "' username '" -pw "' key '" ' host ':' path '/' packages{i} ' ./']);
                         if status, 
-                                error('scpin error message: could not call putty pscp');
+                                error('issmscpin error message: could not call putty pscp');
                         end
                 end
@@ -72 +72 @@
                 for i=1:numel(packages),
                         if ~exist(['./' packages{i}]),
-                                error('scpin error message: could not call scp on *nix system');
+                                error('issmscpin error message: could not call scp on *nix system');
                         end
                 end

issm/trunk-jpl/src/m/os/issmscpin.py

@@ -6 +6 @@
 from MatlabFuncs import *
 
-def scpin(host, login,port,path, packages):
+def issmscpin(host, login,port,path, packages):
         """
-        SCPIN get packages from host, using scp on unix, and pscp on windows
+        ISSMSCPIN get packages from host, using scp on unix, and pscp on windows
  
-           usage: scpin(host,packages,path)
+           usage: issmscpin(host,packages,path)
         """
 
@@ -42 +42 @@
                                 ISSM_DIR=os.environ['ISSM_DIR_WIN'][1:-2]
                         else:
-                                raise OSError("scpin error message: could not find ISSM_DIR_WIN environment variable.")
+                                raise OSError("issmscpin error message: could not find ISSM_DIR_WIN environment variable.")
 
                         username=raw_input('Username: (quoted string) ')
@@ -51 +51 @@
                                         subprocess.check_call('%s/externalpackages/ssh/pscp.exe -l "%s" -pw "%s" %s:%s %s' % (ISSM_DIR,username,key,host,os.path.join(path,package),os.getcwd()),shell=True)
                                 except CalledProcessError as e:
-                                        raise CalledProcessError("scpin error message: could not call putty pscp.")
+                                        raise CalledProcessError("issmscpin error message: could not call putty pscp.")
 
                 else:
@@ -73 +73 @@
                         for package in packages:
                                 if not os.path.exists(os.path.join('.',package)):
-                                        raise OSError("scpin error message: could not call scp on *nix system.")
+                                        raise OSError("issmscpin error message: could not call scp on *nix system.")
 

issm/trunk-jpl/src/m/os/issmscpout.m

@@ -1 +1 @@
 function issmscpout(host,path,login,port,packages)
-%SCPOUT send packages to a host, using scp on unix, and pscp on windows
+%ISSMSCPOUT send packages to a host, using scp on unix, and pscp on windows
 %
-%   usage: scpout(host,path,packages)
+%   usage: issmscpout(host,path,packages)
 %
 %
@@ -26 +26 @@
                 [status,ISSM_DIR]=system('echo [%ISSM_DIR_WIN%]');
                 if status, 
-                        error('scpout error message: could not find ISSM_DIR_WIN environment variable');
+                        error('issmscpout error message: could not find ISSM_DIR_WIN environment variable');
                 end
                 ISSM_DIR=ISSM_DIR(2:end-2);
@@ -36 +36 @@
                         [status,result]=system([ISSM_DIR '/externalpackages/ssh/pscp.exe -l "' username '" -pw "' key '" ' packages{i} ' ' host ':' path]);
                         if status, 
-                                error('scpout error message: could not call putty pscp');
+                                error('issmscpout error message: could not call putty pscp');
                         end
                 end

issm/trunk-jpl/src/m/os/issmscpout.py

@@ -3 +3 @@
 import subprocess
 import os
-import shutil
 from MatlabFuncs import *
 
 def issmscpout(host,path,login,port,packages):
         """
-        SCPOUT send packages to a host, using scp on unix, and pscp on windows
+        ISSMSCPOUT send packages to a host, using scp on unix, and pscp on windows
  
-           usage: scpout(host,path,packages)
+           usage: issmscpout(host,path,packages)
         """
-
-        print "host=",host
-        print "path=",path
-        print "login=",login
-        print "port=",port
-        print "packages=",packages
 
         #get hostname
@@ -28 +21 @@
                         here=os.getcwd()
                         os.chdir(path)
-                        shutil.rmtree(package)
+                        try:
+                                os.remove(package)
+                        except OSError as e:
+                                pass
                         subprocess.call('ln -s %s %s' % (os.path.join(here,package),path),shell=True)
                         os.chdir(here)
@@ -39 +35 @@
                                 ISSM_DIR=os.environ['ISSM_DIR_WIN'][1:-2]
                         else:
-                                raise OSError("scpout error message: could not find ISSM_DIR_WIN environment variable.")
+                                raise OSError("issmscpout error message: could not find ISSM_DIR_WIN environment variable.")
 
                         username=raw_input('Username: (quoted string) ')
@@ -48 +44 @@
                                         subprocess.check_call('%s/externalpackages/ssh/pscp.exe -l "%s" -pw "%s" %s %s:%s' % (ISSM_DIR,username,key,package,host,path),shell=True)
                                 except CalledProcessError as e:
-                                        raise CalledProcessError("scpout error message: could not call putty pscp.")
+                                        raise CalledProcessError("issmscpout error message: could not call putty pscp.")
 
                 else:

issm/trunk-jpl/src/m/parameterization/parameterize.m

@@ -56 +56 @@
 end
 md.miscellaneous.notes=['Model created by using parameter file: ' parametername ' on: ' datestr(now)];
+

issm/trunk-jpl/src/m/solve/WriteData.py

@@ -104 +104 @@
                         data=numpy.array([data])
                 if len(data.shape) == 1:
-                        data=data.reshape(numpy.size(data,0),1)
+                        data=data.reshape(1,numpy.size(data,0))
 
                 #Get size
@@ -124 +124 @@
                 for i in xrange(s[0]):
                         for j in xrange(s[1]):
-                                fid.write(struct.pack('i',data[i][j]))    #get to the "c" convention, hence the transpose
+                                fid.write(struct.pack('d',float(data[i][j])))    #get to the "c" convention, hence the transpose
                 # }}}
 
@@ -132 +132 @@
                         data=numpy.array([data])
                 if len(data.shape) == 1:
-                        data=data.reshape(numpy.size(data,0),1)
+                        data=data.reshape(1,numpy.size(data,0))
 
                 #Get size
@@ -152 +152 @@
                 for i in xrange(s[0]):
                         for j in xrange(s[1]):
-                                fid.write(struct.pack('i',data[i][j]))    #get to the "c" convention, hence the transpose
+                                fid.write(struct.pack('d',float(data[i][j])))    #get to the "c" convention, hence the transpose
                 # }}}
 
         elif strcmpi(format,'DoubleMat'):    # {{{
 
-                if isinstance(data,(int,long,float)):
+                if isinstance(data,(bool,int,long,float)):
                         data=numpy.array([data])
                 if len(data.shape) == 1:
-                        data=data.reshape(numpy.size(data,0),1)
+                        data=data.reshape(1,numpy.size(data,0))
 
                 #Get size
@@ -180 +180 @@
                 for i in xrange(s[0]):
                         for j in xrange(s[1]):
-                                fid.write(struct.pack('d',data[i][j]))    #get to the "c" convention, hence the transpose
+                                fid.write(struct.pack('d',float(data[i][j])))    #get to the "c" convention, hence the transpose
                 # }}}
 
@@ -188 +188 @@
                 recordlength=4+4    #number of records + code
                 for matrix in data:
+                        if isinstance(matrix,(bool,int,long,float)):
+                                matrix=numpy.array([matrix])
+                        if len(matrix.shape) == 1:
+                                matrix=matrix.reshape(1,numpy.size(matrix,0))
+
                         s=matrix.shape
                         recordlength+=4*2+s[0]*s[1]*8    #row and col of matrix + matrix of doubles
@@ -202 +207 @@
                 #write each matrix: 
                 for matrix in data:
+                        if isinstance(matrix,(bool,int,long,float)):
+                                matrix=numpy.array([matrix])
+                        if len(matrix.shape) == 1:
+                                matrix=matrix.reshape(1,numpy.size(matrix,0))
+
                         s=matrix.shape
                         fid.write(struct.pack('i',s[0])) 
@@ -207 +217 @@
                         for i in xrange(s[0]):
                                 for j in xrange(s[1]):
-                                        fid.write(struct.pack('d',matrix[i][j]))
+                                        fid.write(struct.pack('d',float(matrix[i][j])))
                 # }}}
 

issm/trunk-jpl/src/m/solve/loadresultsfromcluster.py

@@ -3 +3 @@
 import socket
 from MatlabFuncs import *
+from loadresultsfromdisk import *
 
 def loadresultsfromcluster(md,runtimename=False):
@@ -17 +18 @@
         if runtimename:
                 md.private.runtimename=runtimename
-        end
 
         #Download outputs from the cluster
@@ -28 +28 @@
                                 filelist.append('dakota_tabular.dat')
                 filelist.append(md.miscellaneous.name+'.outbin')
-        Download(cluster,md.private.runtimename,filelist)
+        cluster.Download(md.private.runtimename,filelist)
 
         #If we are here, no errors in the solution sequence, call loadresultsfromdisk.

issm/trunk-jpl/src/m/solve/loadresultsfromdisk.py

@@ -1 +1 @@
 import os
+from parseresultsfromdisk import *
 from EnumToString import EnumToString
 
@@ -28 +29 @@
                 if not len(structure):
                         raise RuntimeError("No result found in binary file '%s'. Check for solution crash." % filename)
-                end
                 md.results[structure[1]['SolutionType']]=structure;
 

issm/trunk-jpl/src/m/solve/solve.py

@@ -9 +9 @@
 from marshall import *
 from ispetsc import *
+from waitonlock import *
+from loadresultsfromcluster import *
 
 def solve(md,solutionenum,*args):
@@ -79 +81 @@
         marshall(md)                                           # bin file
         md.solver.PetscFile(md.miscellaneous.name+'.petsc')    # petsc file
-        cluster.BuildQueueScript(md.miscellaneous.name,md.private.runtimename,md.private.solution,md.settings.io_gather,md.debug.valgrind,md.debug.gprof)    # queue file
+        cluster.BuildQueueScript(md.private.runtimename,md.miscellaneous.name,md.private.solution,md.settings.io_gather,md.debug.valgrind,md.debug.gprof)    # queue file
 
         #we need to make sure we have PETSC support, otherwise, we run with only one cpu: 

issm/trunk-jpl/src/m/solve/waitonlock.m

@@ -1 @@
-function flag=waitonlock(md,executionpath,login,port)
+function flag=waitonlock(md)
 %WAITONLOCK - wait for a file
 %
@@ -6 +6 @@
 %
 %   Usage:
-%      flag=waitonlock(md,executionpath)
+%      flag=waitonlock(md)
 
 %Get filename (lock file) and options

issm/trunk-jpl/src/m/solve/waitonlock.py

@@ -4 +4 @@
 from MatlabFuncs import *
 
-def waitonlock(md,executionpath,login,port):
+def waitonlock(md):
         """
         WAITONLOCK - wait for a file
@@ -12 +12 @@
  
            Usage:
-              flag=waitonlock(md,executionpath)
+              flag=waitonlock(md)
         """