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Changeset 25685
- Timestamp:
- 10/14/20 00:19:52 (5 years ago)
- Location:
- issm/trunk-jpl
- Files:
-
- 1 added
- 12 edited
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jenkins/jenkins.sh (modified) (3 diffs)
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src/m/classes/issmsettings.py (modified) (2 diffs)
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src/m/classes/qmu.py (modified) (1 diff)
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src/m/classes/qmustatistics.py (modified) (2 diffs)
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src/m/exp/contourlevelzero.m (modified) (1 diff)
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src/m/geometry/polyarea.py (modified) (1 diff)
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src/m/mesh/meshintersect3d.m (modified) (1 diff)
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src/m/plot/plot_coastlines.m (modified) (1 diff)
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src/m/plot/plot_coastlines.py (added)
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src/m/plot/processdata.py (modified) (2 diffs)
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src/m/qmu/postqmu.py (modified) (2 diffs)
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src/m/solve/loadresultsfromcluster.py (modified) (2 diffs)
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src/m/solve/loadresultsfromdisk.py (modified) (3 diffs)
Legend:
- Unmodified
- Added
- Removed
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issm/trunk-jpl/jenkins/jenkins.sh
r25301 r25685 58 58 59 59 #Install ISSM 60 #Determini g Installation type depending on svn changes{{{60 #Determining installation type depending on svn changes{{{ 61 61 echo "======================================================"; 62 62 echo " Determining Installation type " … … 153 153 NUMPACKAGES=$(($(echo ${EXTERNALPACKAGES} | wc -w ) / 2)) 154 154 155 #Jenkins xmlfiles for individual packages155 #Jenkins XML files for individual packages 156 156 EXTERNAL_TEST_FILE="$ISSM_DIR/nightlylog/results/external.xml" 157 157 mkdir -p $ISSM_DIR/nightlylog/results … … 183 183 echo "======================================================"; 184 184 185 ./$PACKAGEINST &> compil.log185 ./$PACKAGEINST $NUMCPUS_INSTALL &> compil.log 186 186 if [ $? -ne 0 ] && [ "$PACKAGENAME" != "boost" ]; then 187 187 cat compil.log -
issm/trunk-jpl/src/m/classes/issmsettings.py
r25637 r25685 1 from checkfield import checkfield 1 2 from fielddisplay import fielddisplay 2 from checkfield import checkfield3 3 from WriteData import WriteData 4 4 5 5 6 6 class issmsettings(object): 7 """ 8 ISSMSETTINGS class definition 7 """ISSMSETTINGS class definition 9 8 10 11 9 Usage: 10 issmsettings = issmsettings() 12 11 """ 13 12 … … 88 87 else: 89 88 WriteData(fid, prefix, 'name', 'md.settings.waitonlock', 'data', False, 'format', 'Boolean') 89 90 90 WriteData(fid, prefix, 'object', self, 'fieldname', 'solver_residue_threshold', 'format', 'Double') 91 91 # }}} -
issm/trunk-jpl/src/m/classes/qmu.py
r25649 r25685 206 206 WriteData(fid, prefix, 'data', False, 'name', 'md.qmu.mass_flux_segments_present', 'format', 'Boolean') 207 207 return 208 WriteData(fid, prefix, 'data', self.method.params.samples, 'name', 'md.qmu.method.params.samples', 'format', 'Integer') 208 209 WriteData(fid, prefix, 'object', self, 'fieldname', 'numberofresponses', 'format', 'Integer') 209 210 WriteData(fid, prefix, 'object', self, 'fieldname', 'variabledescriptors', 'format', 'StringArray') -
issm/trunk-jpl/src/m/classes/qmustatistics.py
r25649 r25685 1 # NOTE: Uncomment2 3 1 import numpy as np 4 2 … … 53 51 54 52 if self.method[0]['name'] == 'None': 55 return 53 return s 56 54 57 55 s += '{}\n'.format(fielddisplay(self, 'nfiles_per_directory', 'number of files per output directory')) -
issm/trunk-jpl/src/m/exp/contourlevelzero.m
r25636 r25685 1 1 function contours=contourlevelzero(md,mask,level) 2 %CONTOURLEVELZERO - figure out the zero level (or offset thereof, specified by the level value)3 % of a vectorial mask, and vectorialize it into an exp or shp compatible4 % structure.2 %CONTOURLEVELZERO - figure out the zero level (or offset thereof, specified by 3 %the level value) of a vectorial mask, and vectorialize it into an exp or shp 4 %compatible structure. 5 5 % 6 6 % Usage: -
issm/trunk-jpl/src/m/geometry/polyarea.py
r25455 r25685 5 5 6 6 def polyarea(x, y): #{{{ 7 """ 8 POLYAREA - returns the area of the 2-D polygon defined by the vertices in 7 """POLYAREA - returns the area of the 2-D polygon defined by the vertices in 9 8 lists x and y 10 9 -
issm/trunk-jpl/src/m/mesh/meshintersect3d.m
r24779 r25685 1 1 function indices=meshintersect3d(x,y,z,xs,ys,zs,varargin) 2 %MESHINTERSECT - return indices (into x,y and z) of common values between (x,y,z) and (xs,ys,zs). 3 % i.e: x(index)=xs; y(index)=ys; 2 %MESHINTERSECT - return indices (into x,y and z) of common values between 3 %(x,y,z) and (xs,ys,zs). 4 % i.e: x(index)=xs; y(index)=ys; 4 5 % 5 6 -
issm/trunk-jpl/src/m/plot/plot_coastlines.m
r25627 r25685 3 3 %define coastline: {{{ 4 4 coast=[-90 -180; ... 5 5 -83.83 -180 ;... 6 6 -84.33 -178 ;... 7 7 -84.5 -174 ;... -
issm/trunk-jpl/src/m/plot/processdata.py
r24261 r25685 3 3 4 4 def processdata(md, data, options): 5 """ 6 PROCESSDATA - process data to be plotted 5 """PROCESSDATA - process data to be plotted 7 6 8 7 datatype = 1 -> elements … … 16 15 See also: PLOTMODEL, PROCESSMESH 17 16 """ 18 # {{{ Initiali sation and grabbing auxiliaries17 # {{{ Initialization and grabbing auxiliaries 19 18 # check format 20 19 if (len(data) == 0 or (len(data) == 1 and not isinstance(data, dict) and np.isnan(data).all())): -
issm/trunk-jpl/src/m/qmu/postqmu.py
r25632 r25685 45 45 dakotaresults.dresp_dat = dresp_dat 46 46 47 if md.qmu.output :48 if md.qmu.method.method == 'nond_sampling' and md.qmu.statistics.method[0].name == 'None':47 if md.qmu.output and md.qmu.statistics.method[0]['name'] == 'None': 48 if md.qmu.method.method == 'nond_sampling': 49 49 dakotaresults.modelresults = [] 50 50 md2 = copy.deepcopy(md) … … 55 55 dakotaresults.modelresults.append(md2.results) 56 56 57 # TODO: Uncomment the following once qmustatistics class is translated 58 # if md.qmu.statistics.method[0].name != 'None': 59 # md.qmu.isdakota = 0 60 # md = loadresultsfromdisk(md, [md.miscellaneous.name,'.stats']) 61 # md.qmu.isdakota = 1 57 if md.qmu.statistics.method[0]['name'] != 'None': 58 md.qmu.isdakota = 0 59 md = loadresultsfromdisk(md, [md.miscellaneous.name,'.stats']) 60 md.qmu.isdakota = 1 62 61 63 62 # put dakotaresults in their right location. -
issm/trunk-jpl/src/m/solve/loadresultsfromcluster.py
r25300 r25685 5 5 from helpers import * 6 6 from loadresultsfromdisk import loadresultsfromdisk 7 from MatlabFuncs import ispc 8 from pairoptions import pairoptions 7 9 8 10 9 def loadresultsfromcluster(md, runtimename=False): 10 ''' 11 LOADRESULTSFROMCLUSTER - load results of solution sequence from cluster 11 def remove(filename): 12 try: 13 os.remove(filename) 14 except OSError: 15 print(('WARNING: ' + filename + ' does not exist')) 12 16 13 Usage: 14 md = loadresultsfromcluster(md, runtimename) 15 ''' 17 def loadresultsfromcluster(md, *args): 18 """LOADRESULTSFROMCLUSTER - load results of solution sequence from cluster 16 19 17 #retrieve cluster, to be able to call its methods 20 Usage: 21 md = loadresultsfromcluster(md, runtimename) 22 """ 23 24 # Process options 25 options = pairoptions(*args) 26 nolog = options.getfieldvalue('nolog', 0) 27 md.private.runtimename = options.getfieldvalue('runtimename', md.private.runtimename) 28 29 # Retrieve cluster, to be able to call its methods 18 30 cluster = md.cluster 19 31 20 if runtimename:21 md.private.runtimename = runtimename22 23 #Download outputs from the cluster24 filelist = [md.miscellaneous.name + '.outlog', md.miscellaneous.name + '.errlog']32 # Download outputs from the cluster 33 if not nolog: 34 filelist = [md.miscellaneous.name + '.outlog', md.miscellaneous.name + '.errlog'] 35 else: 36 filelist = [] 25 37 if md.qmu.isdakota: 26 38 filelist.append(md.miscellaneous.name + '.qmu.err') … … 29 41 if md.qmu.params.tabular_graphics_data: 30 42 filelist.append('dakota_tabular.dat') 43 if md.qmu.output and md.qmu.statistics.method[0]['name'] == 'None': 44 if md.qmu.method.method == 'nond_sampling': 45 for i in range(len(md.qmu.method.params.samples)): 46 filelist.append(md.miscellaneous.name + '.outbin' + str(i)) 47 if md.qmu.statistics.method[0]['name'] != 'None': 48 filelist.append(md.miscellaneous.name + '.stats') 31 49 else: 32 50 filelist.append(md.miscellaneous.name + '.outbin') 33 51 cluster.Download(md.private.runtimename, filelist) 34 52 35 #If we are here, no errors in the solution sequence, call loadresultsfromdisk. 36 if os.path.exists(md.miscellaneous.name + '.outbin'): 37 if os.path.getsize(md.miscellaneous.name + '.outbin') > 0: 38 md = loadresultsfromdisk(md, md.miscellaneous.name + '.outbin') 39 else: 40 print(('WARNING, outbin file is empty for run ' + md.miscellaneous.name)) 41 elif not md.qmu.isdakota: 42 print(('WARNING, outbin file does not exist ' + md.miscellaneous.name)) 53 # If we are here, no errors in the solution sequence, call loadresultsfromdisk 54 md = loadresultsfromdisk(md, md.miscellaneous.name + '.outbin') 43 55 44 #erase the log and output files 45 if md.qmu.isdakota: 46 #filename = os.path.join('qmu' + str(os.getpid()), md.miscellaneous.name) 47 filename = md.miscellaneous.name 56 # Erase the log and output files 57 for i in range(len(filelist)): 58 filename = filelist[i] 59 remove(filename) 60 if not ispc(): 61 remove(md.private.runtimename + '.tar.gz') 48 62 49 # this will not work like normal as dakota doesn't generate outbin files, 50 # instead calls postqmu to store results directly in the model 51 # at md.results.dakota via dakota_out_parse 52 md = loadresultsfromdisk(md, md.miscellaneous.name + '.outbin') 53 else: 54 filename = md.miscellaneous.name 55 TryRem('.outbin', filename) 56 if not platform.system() == 'Windows': 57 TryRem('.tar.gz', md.private.runtimename) 58 59 TryRem('.errlog', filename) 60 TryRem('.outlog', filename) 61 62 #erase input file if run was carried out on same platform. 63 # Erase input file if run was carried out on same platform 63 64 hostname = socket.gethostname() 64 65 if hostname == cluster.name: 66 remove(md.miscellaneous.name + '.bin') 67 remove(md.miscellaneous.name + '.toolkits') 65 68 if md.qmu.isdakota: 66 #filename = os.path.join('qmu' + str(os.getpid()), md.miscellaneous.name)67 filename = md.miscellaneous.name68 TryRem('.queue', filename)69 remove(md.miscellaneous.name + '.qmu.in') 70 if not ispc(): 71 remove(md.miscellaneous.name + '.queue') 69 72 else: 70 filename = md.miscellaneous.name 71 TryRem('.toolkits', filename) 72 if not platform.system() == 'Windows': 73 TryRem('.queue', filename) 74 else: 75 TryRem('.bat', filename) 76 77 # remove this for bin file debugging 78 TryRem('.bin', filename) 73 remove(md.miscellaneous.name + '.bat') 79 74 80 75 return md 81 82 def TryRem(extension, filename):83 try:84 os.remove(filename + extension)85 except OSError:86 print(('WARNING, no ' + extension + ' is present for run ' + filename)) -
issm/trunk-jpl/src/m/solve/loadresultsfromdisk.py
r25168 r25685 1 1 import os 2 from results import results 2 3 from helpers import fieldnames 3 4 from parseresultsfromdisk import parseresultsfromdisk 4 5 from postqmu import postqmu 6 from results import results 5 7 6 8 7 9 def loadresultsfromdisk(md, filename): 8 '''9 LOADRESULTSFROMDISK - load results of solution sequence from disk file"filename"10 """LOADRESULTSFROMDISK - load results of solution sequence from disk file 11 "filename" 10 12 11 Usage: 12 md = loadresultsfromdisk(md=False,filename=False); 13 ''' 14 #check number of inputs/outputs 13 Usage: 14 md = loadresultsfromdisk(md=False, filename=False) 15 """ 16 17 # Check number of inputs/outputs 15 18 if not md or not filename: 16 19 raise ValueError("loadresultsfromdisk: error message.") … … 18 21 if not md.qmu.isdakota: 19 22 20 # Check that file exists23 # Check that file exists 21 24 if not os.path.exists(filename): 22 raise OSError("binary file '{}' not found.".format(filename)) 25 err_msg = '============================================================\n' 26 err_msg += ' Binary file {} not found \n'.format(filename) 27 err_msg += ' \n' 28 err_msg += ' This typically happens when the run crashed. \n' 29 err_msg += ' Please check for error messages above or in the outlog \n' 30 err_msg += '============================================================\n' 23 31 24 #initialize md.results if not a structure yet 32 raise OSError(err_msg) 33 34 # Initialize md.results if not a structure yet 25 35 if not isinstance(md.results, results): 26 36 md.results = results() 27 37 28 # load results onto model38 # Load results onto model 29 39 structure = parseresultsfromdisk(md, filename, not md.settings.io_gather) 30 if not len(structure):40 if not structure: 31 41 raise RuntimeError("No result found in binary file '{}'. Check for solution crash.".format(filename)) 32 42 if not structure[0].SolutionType: 43 if structure[-1].SolutionType: 44 structure[0].SolutionType = structure[-1].SolutionType 45 else: 46 print('Cannot find a solution type in the results! Ascribing one: \'NoneSolution\'.') 47 structure[0].SolutionType = 'NoneSolution' 33 48 setattr(md.results, structure[0].SolutionType, structure) 34 49 35 # recover solution_type from results50 # Recover solution_type from results 36 51 md.private.solution = structure[0].SolutionType 37 52 38 # read log files onto fields53 # Read log files onto fields 39 54 if os.path.exists(md.miscellaneous.name + '.errlog'): 40 55 with open(md.miscellaneous.name + '.errlog', 'r') as f: 41 56 setattr(getattr(md.results, structure[0].SolutionType)[0], 'errlog', [line[:-1] for line in f]) 42 57 else: 43 setattr(getattr(md.results, structure[0].SolutionType)[0], 'errlog', [])58 setattr(getattr(md.results, structure[0].SolutionType)[0], 'errlog', '') 44 59 45 60 if os.path.exists(md.miscellaneous.name + '.outlog'): … … 47 62 setattr(getattr(md.results, structure[0].SolutionType)[0], 'outlog', [line[:-1] for line in f]) 48 63 else: 49 setattr(getattr(md.results, structure[0].SolutionType)[0], 'outlog', [])64 setattr(getattr(md.results, structure[0].SolutionType)[0], 'outlog', '') 50 65 51 if len(getattr(md.results, structure[0].SolutionType)[0].errlog):66 if getattr(md.results, structure[0].SolutionType)[0].errlog: 52 67 print("loadresultsfromcluster info message: error during solution. Check your errlog and outlog model fields.") 53 68 54 # if only one solution, extract it from list for user friendliness69 # If only one solution, extract it from list for user friendliness 55 70 if len(structure) == 1 and structure[0].SolutionType != 'TransientSolution': 56 71 setattr(md.results, structure[0].SolutionType, structure[0]) 57 72 58 # post processes qmuresults if necessary73 # Post processes QMU results if necessary 59 74 else: 60 75 md = postqmu(md)
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