Index: /issm/trunk-jpl/src/m/classes/clusters/generic.py =================================================================== --- /issm/trunk-jpl/src/m/classes/clusters/generic.py (revision 26352) +++ /issm/trunk-jpl/src/m/classes/clusters/generic.py (revision 26353) @@ -6,5 +6,6 @@ from generic_settings import generic_settings except ImportError: - print('Warning generic_settings.py not found, default will be used') + #print('Warning: generic.py: generic_settings.py not found, default will be used') + pass from MatlabFuncs import * from IssmConfig import IssmConfig @@ -48,5 +49,6 @@ self = generic_settings(self) except NameError: - print('generic_settings.py not found, using default settings') + # print('generic_settings.py not found, using default settings') + pass # OK get other fields Index: /issm/trunk-jpl/src/m/classes/clusters/pfe.py =================================================================== --- /issm/trunk-jpl/src/m/classes/clusters/pfe.py (revision 26352) +++ /issm/trunk-jpl/src/m/classes/clusters/pfe.py (revision 26353) @@ -12,5 +12,6 @@ from pfe_settings import pfe_settings except ImportError: - print('You need pfe_settings.py to proceed, check presence and sys.path') + # print('You need pfe_settings.py to proceed, check presence and sys.path') + pass from QueueRequirements import QueueRequirements @@ -25,5 +26,5 @@ def __init__(self, *args): # {{{ - self.name = 'pfe' + self.name = '' self.login = '' self.modules = ['comp-intel/2016.2.181', 'mpi-sgi/mpt'] @@ -50,5 +51,6 @@ self = pfe_settings(self) except NameError: - print('pfe_settings.py not found, using default settings') + #print('pfe_settings.py not found, using default settings') + pass # OK get other fields Index: /issm/trunk-jpl/src/m/classes/issmsettings.py =================================================================== --- /issm/trunk-jpl/src/m/classes/issmsettings.py (revision 26352) +++ /issm/trunk-jpl/src/m/classes/issmsettings.py (revision 26353) @@ -21,21 +21,19 @@ self.solver_residue_threshold = 0 - #set defaults + # Set defaults self.setdefaultparameters() - #}}} def __repr__(self): # {{{ - string = " general issmsettings parameters:" - - string = "%s\n%s" % (string, fielddisplay(self, "results_on_nodes", "list of output for which results will be output for all the nodes of each element, Use 'all' for all output on nodes.")) - string = "%s\n%s" % (string, fielddisplay(self, "io_gather", "I / O gathering strategy for result outputs (default 1)")) - string = "%s\n%s" % (string, fielddisplay(self, "lowmem", "is the memory limited ? (0 or 1)")) - string = "%s\n%s" % (string, fielddisplay(self, "output_frequency", "frequency at which results are saved in all solutions with multiple time_steps")) - string = "%s\n%s" % (string, fielddisplay(self, "sb_coupling_frequency", "frequency at which StressBalance solver is coupled (default 1)")) - string = "%s\n%s" % (string, fielddisplay(self, "checkpoint_frequency", "frequency at which the runs are being recorded, allowing for a restart")) - string = "%s\n%s" % (string, fielddisplay(self, "waitonlock", "maximum number of minutes to wait for batch results, or return 0")) - string = "%s\n%s" % (string, fielddisplay(self, "solver_residue_threshold", "throw an error if solver residue exceeds this value (NaN to deactivate)")) - return string + s = " general issmsettings parameters:\n" + s += '{}\n'.format(fielddisplay(self, "results_on_nodes", "list of output for which results will be output for all the nodes of each element, Use 'all' for all output on nodes.")) + s += '{}\n'.format(fielddisplay(self, "io_gather", "I / O gathering strategy for result outputs (default 1)")) + s += '{}\n'.format(fielddisplay(self, "lowmem", "is the memory limited ? (0 or 1)")) + s += '{}\n'.format(fielddisplay(self, "output_frequency", "frequency at which results are saved in all solutions with multiple time_steps")) + s += '{}\n'.format(fielddisplay(self, "sb_coupling_frequency", "frequency at which StressBalance solver is coupled (default 1)")) + s += '{}\n'.format(fielddisplay(self, "checkpoint_frequency", "frequency at which the runs are being recorded, allowing for a restart")) + s += '{}\n'.format(fielddisplay(self, "waitonlock", "maximum number of minutes to wait for batch results, or return 0")) + s += '{}\n'.format(fielddisplay(self, "solver_residue_threshold", "throw an error if solver residue exceeds this value (NaN to deactivate)")) + return s #}}} Index: /issm/trunk-jpl/src/m/classes/model.py =================================================================== --- /issm/trunk-jpl/src/m/classes/model.py (revision 26352) +++ /issm/trunk-jpl/src/m/classes/model.py (revision 26353) @@ -37,7 +37,4 @@ from toolkits import toolkits from generic import generic -from pfe import pfe -from cyclone import cyclone -from saga import saga from balancethickness import balancethickness from stressbalance import stressbalance Index: /issm/trunk-jpl/src/m/classes/solidearthsettings.py =================================================================== --- /issm/trunk-jpl/src/m/classes/solidearthsettings.py (revision 26352) +++ /issm/trunk-jpl/src/m/classes/solidearthsettings.py (revision 26353) @@ -118,5 +118,5 @@ # A GRD computation has been requested, make some checks on the nature of the meshes provided if self.isgrd: - if md.mesh.__class__.__name__ is 'mesh3dsurface': + if md.mesh.__class__.__name__ == 'mesh3dsurface': if self.grdmodel == 2: raise RuntimeException('model requires a 2D mesh to run gia Ivins computations (change mesh from mesh3dsurface to mesh2d)') Index: /issm/trunk-jpl/src/m/coordsystems/gdaltransform.m =================================================================== --- /issm/trunk-jpl/src/m/coordsystems/gdaltransform.m (revision 26352) +++ /issm/trunk-jpl/src/m/coordsystems/gdaltransform.m (revision 26353) @@ -20,5 +20,5 @@ % +proj=stere +lat_0=90 +lat_ts=71 +lon_0=-39 +k=1 +x_0=0 +y_0=0 +a=6378273 +b=6356889.448564109 +units=m +no_defs % -% To get proj.4 string from EPSG, use gdalsrsinfo. Example: +% To get PROJ.4 string from EPSG, use gdalsrsinfo. Example: % gdalsrsinfo epsg:4326 | grep "PROJ.4" | sed "s/PROJ.4 : //" Index: /issm/trunk-jpl/src/m/dev/devpath.py =================================================================== --- /issm/trunk-jpl/src/m/dev/devpath.py (revision 26352) +++ /issm/trunk-jpl/src/m/dev/devpath.py (revision 26353) @@ -15,6 +15,6 @@ dirs.remove('.svn') for file in files: - if file.find(".py") != -1: - if file.find(".pyc") == -1: + if file.find('.py') != -1: + if file.find('.pyc') == -1: if root not in sys.path: sys.path.append(root) @@ -46,4 +46,4 @@ #c.InteractiveShellApp.exec_lines.append('print "Warning: disable autoreload in startup.py to improve performance." ') -print("\n ISSM development path correctly loaded") -print("Current path is {}\n\n".format(ISSM_DIR)) +# print("\n ISSM development path correctly loaded") +# print("Current path is {}\n\n".format(ISSM_DIR)) Index: /issm/trunk-jpl/src/m/miscellaneous/MatlabFuncs.py =================================================================== --- /issm/trunk-jpl/src/m/miscellaneous/MatlabFuncs.py (revision 26352) +++ /issm/trunk-jpl/src/m/miscellaneous/MatlabFuncs.py (revision 26353) @@ -104,4 +104,14 @@ #}}} +def isa(A, dataType): #{{{ + """FUNCTION ISA + + NOTE: + - Takes a type as its second argument (in contrast to the MATLAB function + that it replicates, which takes a string representing the name of a type) + """ + return type(A) == dataType +#}}} + def isfile(fileName): #{{{ import os Index: /issm/trunk-jpl/src/m/plot/googlemaps.m =================================================================== --- /issm/trunk-jpl/src/m/plot/googlemaps.m (revision 26352) +++ /issm/trunk-jpl/src/m/plot/googlemaps.m (revision 26353) @@ -175,8 +175,8 @@ delete('temp.png'); -%If not gdal, exit +%If not GDAL, exit if status~=0, disp(result); - disp('googlemaps info: gdal not found or not working properly, the Google image will not be transformed'); + disp('googlemaps info: GDAL not found or not working properly, the Google image will not be transformed'); [gX gY]=meshgrid(ulx:ulx+size(final,2)-1,uly:-1:uly-size(final,1)+1); [LAT LON]=pixelstolatlon(gX,gY, zoom); @@ -204,5 +204,5 @@ if ~isempty(strfind(result,'ERROR')), disp(result); - disp(' ');disp('googlemaps info: gdal not working properly (missing proj.4 library?), Google image will not be transformed'); + disp(' ');disp('googlemaps info: GDAL not working properly (missing PROJ.4 library?), Google image will not be transformed'); disp(result); [gX gY]=meshgrid(ulx:ulx+size(final,2)-1,uly:-1:uly-size(final,1)+1); Index: /issm/trunk-jpl/src/m/plot/plot_manager.py =================================================================== --- /issm/trunk-jpl/src/m/plot/plot_manager.py (revision 26352) +++ /issm/trunk-jpl/src/m/plot/plot_manager.py (revision 26353) @@ -3,5 +3,5 @@ overlaysupport = True except ImportError: - print('osgeo/gdal for python not installed, overlay plots are not enabled') + print('OSGeo/GDAL for Python not installed, overlay plots are not enabled') overlaysupport = False @@ -20,6 +20,5 @@ def plot_manager(md, options, fig, axgrid, gridindex): - ''' - PLOT_MANAGER - distribute the plots called by plotmodel + """PLOT_MANAGER - distribute the plots called by plotmodel 'fig' is a handle to the figure instance created by plotmodel. @@ -35,5 +34,5 @@ See also: PLOTMODEL, PLOT_UNIT - ''' + """ #parse options and get a structure of options options = checkplotoptions(md, options) @@ -46,4 +45,5 @@ # TODO: Check why we are doing this and if it is absolutely necessary (see # also src/m/plot/plot_mesh.py, src/m/plot/applyoptions.py) + # options.addfielddefault('ticklabels', 'on') Index: /issm/trunk-jpl/src/m/plot/plot_overlay.py =================================================================== --- /issm/trunk-jpl/src/m/plot/plot_overlay.py (revision 26352) +++ /issm/trunk-jpl/src/m/plot/plot_overlay.py (revision 26353) @@ -11,5 +11,5 @@ from osgeo import gdal except ImportError: - print('osgeo/gdal for python not installed, plot_overlay is disabled') + print('OSGeo/GDAL for python not installed, plot_overlay is disabled') from processdata import processdata @@ -19,6 +19,5 @@ def plot_overlay(md, data, options, ax): - ''' - Function for plotting a georeferenced image. Called from plot_manager by + """Function for plotting a georeferenced image. Called from plot_manager by call to plotmodel. @@ -27,5 +26,5 @@ See also: PLOTMODEL - ''' + """ x, y, z, elements, is2d, isplanet = processmesh(md, [], options) Index: /issm/trunk-jpl/src/m/plot/radarpower.m =================================================================== --- /issm/trunk-jpl/src/m/plot/radarpower.m (revision 26352) +++ /issm/trunk-jpl/src/m/plot/radarpower.m (revision 26353) @@ -29,5 +29,5 @@ d = getfieldvalue(options,'overlay_adjust_d',1); -%find gdal coordinates +%find GDAL coordinates x0=min(xlim); x1=max(xlim); y0=min(ylim); y1=max(ylim); Index: /issm/trunk-jpl/src/m/solve/solve.m =================================================================== --- /issm/trunk-jpl/src/m/solve/solve.m (revision 26352) +++ /issm/trunk-jpl/src/m/solve/solve.m (revision 26353) @@ -173,5 +173,5 @@ end elseif md.settings.waitonlock>0, - %we wait for the done file + %wait for done file done=waitonlock(md); if md.verbose.solution, Index: /issm/trunk-jpl/src/m/solve/solve.py =================================================================== --- /issm/trunk-jpl/src/m/solve/solve.py (revision 26352) +++ /issm/trunk-jpl/src/m/solve/solve.py (revision 26353) @@ -141,5 +141,5 @@ if md.qmu.isdakota: filelist.append(modelname + '.qmu.in') - + if not restart: cluster.UploadQueueJob(md.miscellaneous.name, md.private.runtimename, filelist) @@ -150,11 +150,11 @@ # Wait on lock if md.settings.waitonlock > 0: - islock = waitonlock(md) - if islock == 0: # no results to be loaded - print('The results must be loaded manually with md = loadresultsfromcluster(md).') - else: # load results - if md.verbose.solution: - print('loading results from cluster') - md = loadresultsfromcluster(md) + # Wait for done file + done = waitonlock(md) + if md.verbose.solution: + print('loading results from cluster') + md = loadresultsfromcluster(md) + elif md.settings.waitonlock == 0: + print('Model results must be loaded manually with md = loadresultsfromcluster(md).') return md Index: /issm/trunk-jpl/src/m/solve/waitonlock.m =================================================================== --- /issm/trunk-jpl/src/m/solve/waitonlock.m (revision 26352) +++ /issm/trunk-jpl/src/m/solve/waitonlock.m (revision 26353) @@ -5,4 +5,5 @@ % disk. Also check for outlog file be cause it might be written several % seconds after the lock file. +% % If the time limit given in input is exceeded, return 0 % Index: /issm/trunk-jpl/src/m/solve/waitonlock.py =================================================================== --- /issm/trunk-jpl/src/m/solve/waitonlock.py (revision 26352) +++ /issm/trunk-jpl/src/m/solve/waitonlock.py (revision 26353) @@ -2,5 +2,9 @@ import sys import time +from generic import * +from generic_static import * +# from localpfe import * from MatlabFuncs import * +from pfe import * def waitonlock(md): @@ -15,4 +19,8 @@ Usage: flag = waitonlock(md) + + TODO: + - Uncomment import of localpfe and check on cluster type once localpfe.py + has been translated from localpfe.m. """ @@ -22,14 +30,10 @@ cluster = md.cluster - """ - NOTE: We check cluster.name against string as cluster classes are not - defined globally and we do not have to import them all - """ - if cluster.name == 'pfe' and cluster.interactive > 1: + if isa(cluster, pfe) and cluster.interactive > 1: lockfilename = '{}/Interactive{}/{}.lock'.format(executionpath, cluster.interactive, md.miscellaneous.name) logfilename = '{}/Interactive{}/{}.outlog'.format(executionpath, cluster.interactive, md.miscellaneous.name) - elif cluster.name == 'localpfe': - lockfilename = '{}/{}.lock'.format(executionpath, md.miscellaneous.name) - logfilename = '{}/{}.outlog'.format(executionpath, md.miscellaneous.name) + # elif isa(cluster, localpfe): + # lockfilename = '{}/{}.lock'.format(executionpath, md.miscellaneous.name) + # logfilename = '{}/{}.outlog'.format(executionpath, md.miscellaneous.name) else: lockfilename = '{}/{}/{}.lock'.format(executionpath, md.private.runtimename, md.miscellaneous.name) @@ -37,5 +41,5 @@ # If we are using the generic cluster in interactive mode, job is already complete - if (cluster.name == 'generic' and cluster.interactive) or (cluster.name == 'generic_static'): + if (isa(cluster, generic) and cluster.interactive) or (isa(cluster, generic_static)): # We are in interactive mode, no need to check for job completion return 1 @@ -73,9 +77,10 @@ subproc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) outs, errs = subproc.communicate() # NOTE: Need to consume output before checking return code + # TODO: Debug the following check under Linux (exits after first iteration with errs = "b") # UPDATE: Works in testing under Debian Linux system. Leaving comment for now so that it is easier to backtrace this issue if someone else encounters it. # if errs != '': - raise Exception("waitonlock: check for existence of files failed: {}".format(errs)) + raise Exception('waitonlock: check for existence of files failed: {}'.format(errs)) ispresent = not subproc.returncode if ispresent: Index: /issm/trunk-jpl/test/NightlyRun/runme.py =================================================================== --- /issm/trunk-jpl/test/NightlyRun/runme.py (revision 26352) +++ /issm/trunk-jpl/test/NightlyRun/runme.py (revision 26353) @@ -10,12 +10,13 @@ try: - from parallelrange import parallelrange -except ImportError: #we don't have issm code in path, just get it + from arch import archread +except: # ISSM_DIR is not on path import devpath - from parallelrange import parallelrange + from arch import archread from arch import archwrite from GetIds import * from IdToName import IdToName +from parallelrange import parallelrange @@ -33,22 +34,23 @@ Options: - -i/--id followed by the list of ids or (parts of) test names requested - NOTE: runs all tests by default - -e/--exclude ids or (parts of) test names to be excluded (same format as id) - NOTE: exclude does nothing if 'id' is specified with different values - -b/--benchmark 'all' : (all of the tests) - 'nightly' : (nightly run/daily run) - 'validation' : (validation) - 'adolc' : validation of adolc tests - 'eismint' : validation of eismint tests - 'ismip' : validation of ismip-hom tests - 'mesh' : validation of mesh tests - 'qmu' : validation of qmu tests - 'referential' : validation of referential tests - 'slc' : validation of slc tests - 'thermal' : validation of thermal tests - 'tranforcing' : validation of transient forcing tests - -p/--procedure 'check' : run the test (default) - 'update' : update the archive + -i/--id Followed by the list of ids or (parts of) test names + requested + -e/--exclude Ids or (parts of) test names to be excluded (same + format as id). Does nothing if 'id' is specified with + different values. + -b/--benchmark 'all' : (all of the tests) + 'nightly' : (nightly run/daily run) + 'validation' : (validation) + 'adolc' : validation of adolc tests + 'eismint' : validation of eismint tests + 'ismip' : validation of ismip-hom tests + 'mesh' : validation of mesh tests + 'qmu' : validation of qmu tests + 'referential' : validation of referential tests + 'slc' : validation of slc tests + 'thermal' : validation of thermal tests + 'tranforcing' : validation of transient forcing tests + -p/--procedure 'check' : run the test (default) + 'update' : update the archive Usage: @@ -103,5 +105,5 @@ #GET ids {{{ flist = glob('test*.py') #File name must start with 'test' and must end by '.py' and must be different than 'test.py' - list_ids = [int(re.search(r'\d+',file.split('.')[0]).group()) for file in flist if not file == 'test.py'] #Keep test id only (skip 'test' and '.py') + list_ids = [int(re.search(r'\d+',file.split('.')[0]).group()) for file in flist if not file == 'test.py'] # Keep test id only (skip 'test' and '.py') i1, i2 = parallelrange(rank, numprocs, len(list_ids)) #Get tests for this cpu only