Index: /issm/trunk-jpl/externalpackages/gmsh/install-4-mac-python-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install-4-mac-python-static.sh (revision 25761) +++ /issm/trunk-jpl/externalpackages/gmsh/install-4-mac-python-static.sh (revision 25762) @@ -34,5 +34,5 @@ # Copy customized source and config files to 'src' directory -cp configs/4/mac/static/CMakeLists.txt src +cp configs/${VER}/mac/static/CMakeLists.txt src # Configure Index: /issm/trunk-jpl/jenkins/pine_island-mac-binaries-python =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-binaries-python (revision 25761) +++ /issm/trunk-jpl/jenkins/pine_island-mac-binaries-python (revision 25762) @@ -46,5 +46,4 @@ boost install-1.7-mac-static.sh dakota install-6.2-mac-static.sh - curl install-7.67-static.sh netcdf install-4.7-mac-parallel-static.sh proj install-6.2-static.sh @@ -75,5 +74,5 @@ # compilation # -NUMCPUS_INSTALL=4 +NUMCPUS_INSTALL=8 # Number of CPUs used in the nightly runs Index: /issm/trunk-jpl/scripts/py_to_pyc.sh =================================================================== --- /issm/trunk-jpl/scripts/py_to_pyc.sh (revision 25762) +++ /issm/trunk-jpl/scripts/py_to_pyc.sh (revision 25762) @@ -0,0 +1,24 @@ +#!/bin/bash + +################################################################################ +# Compiles all Python source files in a directory (recursively). +# +# Runs quietly if there are no errors. Otherwise, prints errors to console. +################################################################################ +COMPILE_LOG='./py_to_pyc.log' +TARGET='.' + +if [ "$#" -gt 0 ]; then + TARGET=$1 +fi + +echo "Compiling Python source files" +python -m compileall -q ${TARGET} > ${COMPILE_LOG} + +if [ -s ${COMPILE_LOG} ]; then + echo "Error(s) occured while compiling Python scripts!" + echo "--------------- start: ${COMPILE_LOG} ---------------" + cat ${COMPILE_LOG} + echo "---------------- end: ${COMPILE_LOG} ----------------" + exit 1 +fi Index: /issm/trunk-jpl/src/m/classes/clusters/local.py =================================================================== --- /issm/trunk-jpl/src/m/classes/clusters/local.py (revision 25761) +++ /issm/trunk-jpl/src/m/classes/clusters/local.py (revision 25762) @@ -48,5 +48,5 @@ #}}} - def checkconsistency: #{{{ + def checkconsistency(self, md, solution, analyses): #{{{ if cluster.np < 1: md.checkmessage('number of processors should be at least 1') Index: /issm/trunk-jpl/src/m/classes/spatiallinearbasalforcings.py =================================================================== --- /issm/trunk-jpl/src/m/classes/spatiallinearbasalforcings.py (revision 25761) +++ /issm/trunk-jpl/src/m/classes/spatiallinearbasalforcings.py (revision 25762) @@ -16,5 +16,5 @@ def __init__(self, *args): #{{{ - nargs = len(args): + nargs = len(args) if nargs == 0: self.groundedice_melting_rate = np.nan @@ -80,5 +80,5 @@ raise Exception('not implemented yet!') md = checkfield(md, 'fieldname', 'basalforcings.groundedice_melting_rate', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices]) - md = checkfield(md, x'fieldname', 'basalforcings.deepwater_melting_rate', '>=', 0, 'numel', 1) + md = checkfield(md, 'fieldname', 'basalforcings.deepwater_melting_rate', '>=', 0, 'numel', 1) md = checkfield(md, 'fieldname', 'basalforcings.deepwater_elevation', '<', 'basalforcings.upperwater_elevation', 'numel', 1) md = checkfield(md, 'fieldname', 'basalforcings.upperwater_elevation', '<=', 0, 'numel', 1) Index: /issm/trunk-jpl/src/m/geometry/AboveGround.py =================================================================== --- /issm/trunk-jpl/src/m/geometry/AboveGround.py (revision 25761) +++ /issm/trunk-jpl/src/m/geometry/AboveGround.py (revision 25762) @@ -1,5 +1,5 @@ import numpy as np -def function AboveGround(lat, long, r, height): #{{{ +def AboveGround(lat, long, r, height): #{{{ r = r + height x = r * np.cos(np.deg2rad(lat)) * np.cos(np.deg2rad(long)) Index: /issm/trunk-jpl/src/m/plot/plot_coastlines.py =================================================================== --- /issm/trunk-jpl/src/m/plot/plot_coastlines.py (revision 25761) +++ /issm/trunk-jpl/src/m/plot/plot_coastlines.py (revision 25762) @@ -1,3 +1,3 @@ -import matplotlib.patches.Polygon as mpl.Polygon +import matplotlib.patches.Polygon as Polygon import numpy as np @@ -9914,5 +9914,5 @@ # Plot else: - p = mpl.Polygon(np.hstack((x, y))) + p = Polygon(np.hstack((x, y))) # Plot if options.getfieldvalue('coordcent', 'atlantic') == 'pacific': Index: /issm/trunk-jpl/src/m/solvers/bcgsasmoptions.py =================================================================== --- /issm/trunk-jpl/src/m/solvers/bcgsasmoptions.py (revision 25761) +++ /issm/trunk-jpl/src/m/solvers/bcgsasmoptions.py (revision 25762) @@ -3,17 +3,12 @@ -from pairoptions import pairoptions - from collections import OrderedDict +def bcgsasmoptions(*args): - - def bcgsasmoptions(*args): - - #retrieve options provided in *args - options = pairoptions(*args) - solverOptions = OrderedDict() - solverOptions['toolkit'] = 'petsc' - solverOptions['mat_type'] = options.getfieldvalue('mat_type', 'mpiaij') - solverOptions['ksp_type'] = options.getfieldvalue('ksp_type', 'bcgs') - solverOptions['pc_type'] = options.getfieldvalue('pc_type', 'asm') - return solverOptions + #retrieve options provided in *args + options = pairoptions(*args) + solverOptions = OrderedDict() + solverOptions['toolkit'] = 'petsc' + solverOptions['mat_type'] = options.getfieldvalue('mat_type', 'mpiaij') + solverOptions['ksp_type'] = options.getfieldvalue('ksp_type', 'bcgs') + solverOptions['pc_type'] = options.getfieldvalue('pc_type', 'asm') return solverOptions Index: /issm/trunk-jpl/src/m/solvers/bcgsjacobioptions.py =================================================================== --- /issm/trunk-jpl/src/m/solvers/bcgsjacobioptions.py (revision 25761) +++ /issm/trunk-jpl/src/m/solvers/bcgsjacobioptions.py (revision 25762) @@ -3,17 +3,12 @@ -from pairoptions import pairoptions - from collections import OrderedDict +def bcgsjacobioptions(*args): + options = pairoptions(*args) + solverOptions = OrderedDict() + solverOptions['toolkit'] = 'petsc' + solverOptions['mat_type'] = options.getfieldvalue('mat_type', 'mpiaij') + solverOptions['ksp_type'] = options.getfieldvalue('ksp_type', 'bcgs') + solverOptions['pc_type'] = options.getfieldvalue('pc_type', 'jacobi') - def bcgsjacobioptions(*args): - - options = pairoptions(*args) - solverOptions = OrderedDict() - solverOptions['toolkit'] = 'petsc' - solverOptions['mat_type'] = options.getfieldvalue('mat_type', 'mpiaij') - solverOptions['ksp_type'] = options.getfieldvalue('ksp_type', 'bcgs') - solverOptions['pc_type'] = options.getfieldvalue('pc_type', 'jacobi') - - return solverOptions return solverOptions Index: /issm/trunk-jpl/src/m/solvers/cgnejacobioptions.py =================================================================== --- /issm/trunk-jpl/src/m/solvers/cgnejacobioptions.py (revision 25761) +++ /issm/trunk-jpl/src/m/solvers/cgnejacobioptions.py (revision 25762) @@ -3,18 +3,13 @@ -from pairoptions import pairoptions - from collections import OrderedDict +def cgnejacobioptions(*args): + #retrieve options provided in *args + options = pairoptions(*args) + solverOptions = OrderedDict() + solverOptions['toolkit'] = 'petsc' + solverOptions['mat_type'] = options.getfieldvalue('mat_type', 'mpiaij') + solverOptions['ksp_type'] = options.getfieldvalue('ksp_type', 'cgne') + solverOptions['pc_type'] = options.getfieldvalue('pc_type', 'jacobi') - def cgnejacobioptions(*args): - - #retrieve options provided in *args - options = pairoptions(*args) - solverOptions = OrderedDict() - solverOptions['toolkit'] = 'petsc' - solverOptions['mat_type'] = options.getfieldvalue('mat_type', 'mpiaij') - solverOptions['ksp_type'] = options.getfieldvalue('ksp_type', 'cgne') - solverOptions['pc_type'] = options.getfieldvalue('pc_type', 'jacobi') - - return solverOptions return solverOptions Index: /issm/trunk-jpl/src/m/solvers/conditionnumberoptions.py =================================================================== --- /issm/trunk-jpl/src/m/solvers/conditionnumberoptions.py (revision 25761) +++ /issm/trunk-jpl/src/m/solvers/conditionnumberoptions.py (revision 25762) @@ -3,9 +3,10 @@ -function cn = conditionnumberoptions(*args) - #MULTIGRIDOPTIONS - use Multigrid - # - # Usage: - # options = mgoptions +def conditionnumberoptions(*args): + """MULTIGRIDOPTIONS - use Multigrid + + Usage: + options = mgoptions + """ #retrieve options provided in *args Index: /issm/trunk-jpl/src/m/solvers/mumpsnoneoptions.py =================================================================== --- /issm/trunk-jpl/src/m/solvers/mumpsnoneoptions.py (revision 25761) +++ /issm/trunk-jpl/src/m/solvers/mumpsnoneoptions.py (revision 25762) @@ -3,5 +3,5 @@ -function mumps = mumpsoptions(*args) +def mumpsoptions(*args): #MUMPSOPTIONS - return MUMPS direct solver petsc options # @@ -16,5 +16,5 @@ PETSC_MAJOR = IssmConfig('_PETSC_MAJOR_') PETSC_MINOR = IssmConfig('_PETSC_MINOR_') - if PETSC_MAJOR == 2., + if PETSC_MAJOR == 2: mumps.toolkit = 'petsc' mumps.mat_type = getfieldvalue(options, 'mat_type', 'aijmumps') @@ -24,12 +24,12 @@ end - if PETSC_MAJOR == 3., + if PETSC_MAJOR == 3: mumps.toolkit = 'petsc' mumps.mat_type = getfieldvalue(options, 'mat_type', 'mpiaij') mumps.ksp_type = getfieldvalue(options, 'ksp_type', 'preonly') mumps.pc_type = getfieldvalue(options, 'pc_type', 'lu') - if PETSC_MINOR > 8 + if PETSC_MINOR > 8: mumps.pc_factor_mat_solver_type = getfieldvalue(options, 'pc_factor_mat_solver_type', 'mumps') - else + else: mumps.pc_factor_mat_solver_package = getfieldvalue(options, 'pc_factor_mat_solver_package', 'mumps') end Index: /issm/trunk-jpl/test/NightlyRun/GetIds.py =================================================================== --- /issm/trunk-jpl/test/NightlyRun/GetIds.py (revision 25761) +++ /issm/trunk-jpl/test/NightlyRun/GetIds.py (revision 25762) @@ -6,23 +6,20 @@ def GetIds(ids_names): - """ - GetIds - output ids from a given array of IDs and test names + """GETIDS - Output ids from a given array of IDs and test names - the test names can be any string or sub - string present - in the test's name (first line of corresponding file) + The test names can be any string or substring present in the test's name + (first line of corresponding file). Test names are case sensitive. - test names are case sensitive - - Usage: - ids = GetIds(101) - ids = GetIds('Dakota') - ids = GetIds([101, 102...]) - ids = GetIds([\'Dakota\', \'Slr\'...]) - ids = GetIds([[101, 102...], [\'Dakota\', \'Slr\'...]]) + Usage: + ids = GetIds(101) + ids = GetIds('Dakota') + ids = GetIds([101, 102...]) + ids = GetIds([\'Dakota\', \'Slr\'...]) + ids = GetIds([[101, 102...], [\'Dakota\', \'Slr\'...]]) """ ids = [] - # 1 input, either an id or a test name + # Non-list input: either an ID or a test name if type(ids_names) == str: ids = IdFromString(ids_names) @@ -32,4 +29,5 @@ #raise RuntimeError('runme.py: GetIds.py: No tests with names matching "' + ids_names + '" were found. Note that name checking is case sensitive. Test names are in the first line of a given test eg: "Square" would include test101.py: "SquareShelfConstrainedStressSSA2d"') + # Non-list input: ID if type(ids_names) == int: ids = [ids_names] @@ -39,10 +37,10 @@ #raise RuntimeError('runme.py: GetIds.py: No tests with ids matching "' + ids_names + '" were found. Check that there is a test file named "test' + str(ids_names) + '.py"') - # many inputs of either ids or test names + # many inputs of either ids or test names if type(ids_names) == list and len(ids_names) > 0: # is everything a string or int? if np.array([type(i) == int for i in ids_names]).all(): ids = ids_names - if np.array([type(i) == np.int64 for i in ids_names]).all(): + elif np.array([type(i) == np.int64 for i in ids_names]).all(): ids = ids_names elif np.array([type(i) == str for i in ids_names]).all(): @@ -51,10 +49,24 @@ raise RuntimeError('runme.py: GetIds.py: No tests with names matching "' + ids_names + '" were found. Note that name checking is case sensitive.') - # many inputs of both ids and test names - # ids_names[0] -> ids_names by id - # ids_names[1] -> ids_names by test name + # many inputs of both ids and test names + # ids_names[0] -> ids_names by id + # ids_names[1] -> ids_names by test name + # + # NOTE: ID inclusion/exclusion lists will always hit this condition + # becasue of the way their respective arguments are gathered at the + # end of __main__ in the call to function runme. if type(ids_names) == list and len(ids_names) == 2: - if type(ids_names[0]) == list and len(ids_names[0]) > 0 and type(ids_names[0][0]) == int: - ids = np.concatenate([ids, ids_names[0]]) + if type(ids_names[0]) == list and len(ids_names[0]) > 0: + ids_expanded = [] + for i in ids_names[0]: + # Handle case where list element follows MATLAB range syntax + if ':' in i: + i_range = i.split(':') + for j in range(int(i_range[0]), int(i_range[1])): + ids_expanded.append(j) + else: + ids_expanded.append(int(i)) + unique_ids = list(set(ids_expanded)) + ids += unique_ids if type(ids_names[1]) == list and len(ids_names[1]) > 0 and type(ids_names[1][0]) == str: ids = np.concatenate([ids, np.concatenate([IdFromString(i) for i in ids_names[1]])]) @@ -62,5 +74,5 @@ raise RuntimeError('runme.py: GetIds.py: No tests with names matching "' + ids_names + '" were found. Note that name checking is case sensitive.') - # no recognizable ids or id formats + # no recognizable ids or id formats if np.size(ids) == 0 and not np.all(np.equal(ids_names, None)): raise RuntimeError('runme.py: GetIds.py: include and exclude options (-i/--id; -in/--include_name; -e/--exclude; -en/--exclude_name) options must follow GetIds usage format:\n' + GetIds.__doc__) Index: /issm/trunk-jpl/test/NightlyRun/runme.py =================================================================== --- /issm/trunk-jpl/test/NightlyRun/runme.py (revision 25761) +++ /issm/trunk-jpl/test/NightlyRun/runme.py (revision 25762) @@ -22,14 +22,14 @@ """RUNME - test deck for ISSM nightly runs - In a test deck directory (tests/Vertification / NightlyRun for example) the - following command will launch all the existing tests: - - >> ./runme.py - - To run the tests 101 and 102: - - >> ./runme.py -i [101, 102] - - Available options: + In a test deck directory (test/NightlyRun for example), the following + command will launch all the existing tests, + + ./runme.py + + To run tests 101 and 102: + + ./runme.py -i [101, 102] + + Options: -i/--id followed by the list of ids or (parts of) test names requested NOTE: runs all tests by default @@ -144,5 +144,5 @@ erroredtest_list = [] for id in test_ids: - print(("----------------starting:{}----------------------- ".format(id))) + print(("----------------starting:{}-----------------------".format(id))) try: #Execute test @@ -218,5 +218,5 @@ fid = open(os.path.join(ISSM_DIR, 'nightlylog', 'pythonerror.log'), 'a') fid.write('%s' % message) - fid.write('\n------------------------------------------------------------------ \n') + fid.write('\n------------------------------------------------------------------\n') fid.close() print(('FAILURE difference: N/A test id: {} test name: {} field: {}'.format(id, id_string, fieldname))) @@ -231,5 +231,5 @@ fid = open(os.path.join(ISSM_DIR, 'nightlylog', 'pythonerror.log'), 'a') fid.write('%s' % message) - fid.write('\n------------------------------------------------------------------ \n') + fid.write('\n------------------------------------------------------------------\n') fid.close() print(('FAILURE difference: N/A test id: {} test name: {} field: {}'.format(id, id_string, 'N/A'))) @@ -238,5 +238,5 @@ raise RuntimeError(message) - print(("---------------- finished:{}----------------------- ".format(id))) + print(("----------------finished:{}-----------------------".format(id))) if errorcount > 0: @@ -244,9 +244,7 @@ return - if __name__ == '__main__': if 'PYTHONSTARTUP' in os.environ: PYTHONSTARTUP = os.environ['PYTHONSTARTUP'] -#print 'PYTHONSTARTUP = ', PYTHONSTARTUP if os.path.exists(PYTHONSTARTUP): try: @@ -258,7 +256,7 @@ parser = argparse.ArgumentParser(description='RUNME - test deck for ISSM nightly runs') - parser.add_argument('-i', '--id', nargs='*', type=int, help='followed by the list of ids requested', default=[]) + parser.add_argument('-i', '--id', nargs='*', type=str, help='followed by the list of ids requested', default=[]) parser.add_argument('-in', '--include_name', nargs='*', type=str, help='followed by the list of test names requested', default=[]) - parser.add_argument('-e', '--exclude', nargs='+', type=int, help='ids to be excluded from the test', default=[]) + parser.add_argument('-e', '--exclude', nargs='+', type=str, help='ids to be excluded from the test', default=[]) parser.add_argument('-en', '--exclude_name', nargs='+', type=str, help='test names to be excluded from the test', default=[]) parser.add_argument('-b', '--benchmark', help='nightly/ismip/eismint/thermal/mesh/...', default='nightly')