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issm/oecreview/Archive/24684-25833/ISSM-25299-25300.diff@
27235
| Last change on this file since 27235 was 25834, checked in by , 5 years ago | |
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../trunk-jpl/src/m/solve/loadresultfromdisk.py
1 import struct 2 3 import numpy as np 4 5 6 def loadresultfromdisk(filename, step, name, *args): # {{{ 7 """ 8 LOADRESULTFROMDISK - load specific result of solution sequence from disk 9 file "filename" 10 11 Usage: 12 variable = loadresultsfromdisk(filename, step, name) 13 14 TODO: 15 - Test this module against output of src/m/solve/loadresultsfromdisk.m 16 """ 17 print('Got hwrwefew') 18 exit() 19 # Open file 20 try: 21 fid = open(filename, 'rb') 22 except IOError as e: 23 raise IOError("loadresultsfromdisk error message: could not open {} for binary reading".format(filename)) 24 25 if len(args) == 4: 26 # Put the pointer on the right position in the file 27 fpos = args[0] 28 fid.seek(fpos) 29 30 while True: 31 # read field 32 fpos = tell(fid) 33 length = struct.unpack('i', fid.read(struct.calcsize('i')))[0] 34 35 fieldname = struct.unpack('{}s'.format(length), fid.read(length))[0][:-1] 36 fieldname = fieldname.decode() #strings are binaries when stored so need to be converted back 37 rtime = struct.unpack('d', fid.read(struct.calcsize('d')))[0] 38 rstep = struct.unpack('i', fid.read(struct.calcsize('i')))[0] 39 40 # TODO: Check number of characters unpacked and break if need be (see 41 # src/m/solve/loadresultfromdisk.py) 42 43 if (rstep == step) and (fieldname == name): 44 # ok, go read the result really 45 datatype = struct.unpack('i', fid.read(struct.calcsize('i')))[0] 46 M = struct.unpack('i', fid.read(struct.calcsize('i')))[0] 47 if datatype == 1: 48 field = np.array(struct.unpack('{}d'.format(M), fid.read(M * struct.calcsize('d'))), dtype=float) 49 elif datatype == 2: 50 field = struct.unpack('{}s'.format(M), fid.read(M))[0][:-1] 51 field = field.decode() 52 elif datatype == 3: 53 N = struct.unpack('i', fid.read(struct.calcsize('i')))[0] 54 field = np.zeros(shape=(M, N), dtype=float) 55 for i in range(M): 56 field[i, :] = struct.unpack('{}d'.format(N), fid.read(N * struct.calcsize('d'))) 57 elif datatype == 4: 58 N = struct.unpack('i', fid.read(struct.calcsize('i')))[0] 59 field = np.zeros(shape=(M, N), dtype=int) 60 for i in range(M): 61 field[i, :] = struct.unpack('{}i'.format(N), fid.read(N * struct.calcsize('i'))) 62 else: 63 raise TypeError("cannot read data of type {}".format(datatype)) 64 65 variable = field 66 break 67 else: 68 # just skim to next results 69 datatype = struct.unpack('i', fid.read(struct.calcsize('i')))[0] 70 M = struct.unpack('i', fid.read(struct.calcsize('i')))[0] 71 if datatype == 1: 72 fid.seek(M * 8, 1) 73 elif datatype == 2: 74 fid.seek(M, 1) 75 elif datatype == 3: 76 N = struct.unpack('i', fid.read(struct.calcsize('i')))[0] 77 fid.seek(N * M * 8, 1) 78 elif datatype == 4: 79 N = struct.unpack('i', fid.read(struct.calcsize('i')))[0] 80 fid.seek(N * M * 4, 1) 81 else: 82 raise TypeError("cannot read data of type {}".format(datatype)) 83 84 fid.close() 85 86 return (variable, fpos) 87 # }}} -
../trunk-jpl/src/m/solve/loadresultfromdisk.m
1 1 function [variable fpos]=loadresultfromdisk(filename,step,name,varargin) 2 %LOADRESULTFROMDISK - load specific result of solution sequence from disk file "filename" 2 %LOADRESULTFROMDISK - load specific result of solution sequence from disk file "filename" 3 3 % 4 4 % Usage: 5 5 % variable=loadresultfromdisk(filename,step,name); … … 11 11 end 12 12 13 13 if nargin==4, 14 %Put the pointer on the right position in the file: 14 15 fpos=varargin{1}; 15 16 fseek(fid,fpos,'bof'); 16 17 end 17 18 18 %Put the pointer on the right position in the file:19 19 while 1, 20 20 21 21 %read field -
../trunk-jpl/src/m/solve/loadresultsfromcluster.py
1 1 import os 2 import platform 2 3 import socket 3 import platform 4 5 from helpers import * 4 6 from loadresultsfromdisk import loadresultsfromdisk 5 from helpers import *6 7 7 8 8 9 def loadresultsfromcluster(md, runtimename=False): -
../trunk-jpl/src/m/solve/solve.py
136 136 filelist = [modelname + '.bin ', modelname + '.toolkits ', modelname + '.queue '] 137 137 if md.qmu.isdakota: 138 138 filelist.append(modelname + '.qmu.in') 139 139 140 140 if not restart: 141 141 cluster.UploadQueueJob(md.miscellaneous.name, md.private.runtimename, filelist) 142 142 … … 153 153 if md.verbose.solution: 154 154 print('loading results from cluster') 155 155 md = loadresultsfromcluster(md) 156 157 156 return md -
../trunk-jpl/src/m/classes/clusters/pfe.m
6 6 % cluster=pfe('np',3,'login','username'); 7 7 8 8 classdef pfe 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 9 properties (SetAccess=public) 10 % {{{ 11 name = 'pfe' 12 login = ''; 13 modules = {'comp-intel/2016.2.181' 'mpi-sgi/mpt'}; 14 numnodes = 20; 15 cpuspernode = 8; 16 port = 1025; 17 queue = 'long'; 18 time = 12*60; 19 processor = 'ivy'; 20 srcpath = ''; 21 codepath = ''; 22 executionpath = ''; 23 grouplist = 's1690'; 24 interactive = 0; 25 bbftp = 0; 26 numstreams = 8; 27 hyperthreading = 0; 28 end 29 %}}} 30 methods 31 function cluster=pfe(varargin) % {{{ 32 32 33 34 33 %initialize cluster using default settings if provided 34 if (exist('pfe_settings')==2), pfe_settings; end 35 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 36 %use provided options to change fields 37 cluster=AssignObjectFields(pairoptions(varargin{:}),cluster); 38 end 39 %}}} 40 function disp(cluster) % {{{ 41 % display the object 42 disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); 43 disp(sprintf(' name: %s',cluster.name)); 44 disp(sprintf(' login: %s',cluster.login)); 45 modules=''; for i=1:length(cluster.modules), modules=[modules cluster.modules{i} ',']; end; modules=modules(1:end-1); 46 disp(sprintf(' modules: %s',modules)); 47 disp(sprintf(' port: %i',cluster.port)); 48 disp(sprintf(' numnodes: %i',cluster.numnodes)); 49 disp(sprintf(' cpuspernode: %i',cluster.cpuspernode)); 50 disp(sprintf(' np: %i',cluster.cpuspernode*cluster.numnodes)); 51 disp(sprintf(' queue: %s',cluster.queue)); 52 disp(sprintf(' time: %i',cluster.time)); 53 disp(sprintf(' processor: %s',cluster.processor)); 54 disp(sprintf(' codepath: %s ($ISSM_DIR on pfe)',cluster.codepath)); 55 disp(sprintf(' executionpath: %s (directory containing issm.exe on pfe)',cluster.executionpath)); 56 disp(sprintf(' grouplist: %s',cluster.grouplist)); 57 disp(sprintf(' interactive: %i',cluster.interactive)); 58 disp(sprintf(' hyperthreading: %i',cluster.hyperthreading)); 59 end 60 %}}} 61 function numprocs=np(cluster) % {{{ 62 %compute number of processors 63 numprocs=cluster.numnodes*cluster.cpuspernode; 64 end 65 %}}} 66 function md = checkconsistency(cluster,md,solution,analyses) % {{{ 67 67 68 69 70 68 available_queues={'long','normal','debug','devel','alphatst@pbspl233'}; 69 queue_requirements_time=[5*24*60 8*60 2*60 2*60 24*60]; 70 queue_requirements_np=[2048 2048 150 150 2048]; 71 71 72 72 QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.np,cluster.time) 73 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 74 %now, check cluster.cpuspernode according to processor type 75 if strcmpi(cluster.processor,'wes'), 76 if cluster.hyperthreading, 77 if ((cluster.cpuspernode>24 ) | (cluster.cpuspernode<1)), 78 md = checkmessage(md,'cpuspernode should be between 1 and 24 for ''wes'' processors in hyperthreading mode'); 79 end 80 else 81 if ((cluster.cpuspernode>12 ) | (cluster.cpuspernode<1)), 82 md = checkmessage(md,'cpuspernode should be between 1 and 12 for ''wes'' processors'); 83 end 84 end 85 elseif strcmpi(cluster.processor,'ivy'), 86 if cluster.hyperthreading, 87 if ((cluster.cpuspernode>40 ) | (cluster.cpuspernode<1)), 88 md = checkmessage(md,'cpuspernode should be between 1 and 40 for ''ivy'' processors in hyperthreading mode'); 89 end 90 else 91 if ((cluster.cpuspernode>20 ) | (cluster.cpuspernode<1)), 92 md = checkmessage(md,'cpuspernode should be between 1 and 20 for ''ivy'' processors'); 93 end 94 end 95 elseif strcmpi(cluster.processor,'bro'), 96 if cluster.hyperthreading, 97 if ((cluster.cpuspernode>56 ) | (cluster.cpuspernode<1)), 98 md = checkmessage(md,'cpuspernode should be between 1 and 56 for ''bro'' processors in hyperthreading mode'); 99 end 100 else 101 if ((cluster.cpuspernode>28 ) | (cluster.cpuspernode<1)), 102 md = checkmessage(md,'cpuspernode should be between 1 and 28 for ''bro'' processors'); 103 end 104 end 105 elseif strcmpi(cluster.processor,'has'), 106 if cluster.hyperthreading, 107 if ((cluster.cpuspernode>48 ) | (cluster.cpuspernode<1)), 108 md = checkmessage(md,'cpuspernode should be between 1 and 48 for ''has'' processors in hyperthreading mode'); 109 end 110 else 111 if ((cluster.cpuspernode>24 ) | (cluster.cpuspernode<1)), 112 md = checkmessage(md,'cpuspernode should be between 1 and 24 for ''has'' processors'); 113 end 114 end 115 116 elseif strcmpi(cluster.processor,'san'), 117 if cluster.hyperthreading, 118 if ((cluster.cpuspernode>32 ) | (cluster.cpuspernode<1)), 119 md = checkmessage(md,'cpuspernode should be between 1 and 32 for ''san'' processors in hyperthreading mode'); 120 end 121 else 122 if ((cluster.cpuspernode>16 ) | (cluster.cpuspernode<1)), 123 md = checkmessage(md,'cpuspernode should be between 1 and 16 for ''san'' processors'); 124 end 125 end 126 126 127 128 129 127 else 128 md = checkmessage(md,'unknown processor type, should be ''wes'' or ''has'' or ''ivy'' or ''san'''); 129 end 130 130 131 %Miscelaneous132 133 134 135 136 131 %Miscellaneous 132 if isempty(cluster.login), md = checkmessage(md,'login empty'); end 133 if isempty(cluster.srcpath), md = checkmessage(md,'srcpath empty'); end 134 if isempty(cluster.codepath), md = checkmessage(md,'codepath empty'); end 135 if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end 136 if isempty(cluster.grouplist), md = checkmessage(md,'grouplist empty'); end 137 137 138 139 140 138 end 139 %}}} 140 function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ 141 141 142 142 if(isgprof), disp('gprof not supported by cluster, ignoring...'); end 143 143 144 145 146 147 148 149 150 151 152 153 144 executable='issm.exe'; 145 if isdakota, 146 version=IssmConfig('_DAKOTA_VERSION_'); version=str2num(version(1:3)); 147 if (version>=6), 148 executable='issm_dakota.exe'; 149 end 150 end 151 if isoceancoupling, 152 executable='issm_ocean.exe'; 153 end 154 154 155 156 157 158 % 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 155 %write queuing script 156 fid=fopen([modelname '.queue'],'w'); 157 fprintf(fid,'#PBS -S /bin/bash\n'); 158 % fprintf(fid,'#PBS -N %s\n',modelname); 159 fprintf(fid,'#PBS -l select=%i:ncpus=%i:model=%s\n',cluster.numnodes,cluster.cpuspernode,cluster.processor); 160 fprintf(fid,'#PBS -l walltime=%i\n',cluster.time*60); %walltime is in seconds. 161 fprintf(fid,'#PBS -q %s \n',cluster.queue); 162 fprintf(fid,'#PBS -W group_list=%s\n',cluster.grouplist); 163 fprintf(fid,'#PBS -m e\n'); 164 fprintf(fid,'#PBS -o %s.outlog \n',[cluster.executionpath '/' dirname '/' modelname]); 165 fprintf(fid,'#PBS -e %s.errlog \n\n',[cluster.executionpath '/' dirname '/' modelname]); 166 fprintf(fid,'. /usr/share/modules/init/bash\n\n'); 167 for i=1:numel(cluster.modules), fprintf(fid,['module load ' cluster.modules{i} '\n']); end 168 fprintf(fid,'export PATH="$PATH:."\n\n'); 169 fprintf(fid,'export MPI_LAUNCH_TIMEOUT=520\n'); 170 fprintf(fid,'export MPI_GROUP_MAX=64\n\n'); 171 fprintf(fid,'export ISSM_DIR="%s"\n',cluster.srcpath); %FIXME 172 fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); %FIXME 173 fprintf(fid,'export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$ISSM_DIR/externalpackages/petsc/install/lib"\n'); 174 fprintf(fid,'cd %s/%s/\n\n',cluster.executionpath,dirname); 175 if ~isvalgrind, 176 fprintf(fid,'/u/scicon/tools/bin/several_tries mpiexec -np %i /u/scicon/tools/bin/mbind.x -cs -n%i %s/%s %s %s %s\n',cluster.np,cluster.cpuspernode,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname); 177 else 178 fprintf(fid,'mpiexec -np %i valgrind --leak-check=full %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname); 179 end 180 if ~io_gather, %concatenate the output files: 181 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); 182 end 183 fclose(fid); 184 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 185 %in interactive mode, create a run file, and errlog and outlog file 186 if cluster.interactive, 187 fid=fopen([modelname '.run'],'w'); 188 if cluster.interactive==10, 189 fprintf(fid,'module unload mpi-mvapich2/1.4.1/gcc\n'); 190 fprintf(fid,'mpiexec -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[pwd() '/run'],modelname); 191 else 192 if ~isvalgrind, 193 fprintf(fid,'mpiexec -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/Interactive' num2str(cluster.interactive)],modelname); 194 else 195 fprintf(fid,'mpiexec -np %i valgrind --leak-check=full %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/Interactive' num2str(cluster.interactive)],modelname); 196 end 197 end 198 if ~io_gather, %concatenate the output files: 199 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); 200 end 201 fclose(fid); 202 fid=fopen([modelname '.errlog'],'w'); 203 fclose(fid); 204 fid=fopen([modelname '.outlog'],'w'); 205 fclose(fid); 206 end 207 end %}}} 208 function BuildQueueScriptMultipleModels(cluster,dirname,modelname,solution,dirnames,modelnames,nps) % {{{ 209 209 210 211 210 %some checks: 211 if isempty(modelname), error('BuildQueueScriptMultipleModels error message: need a non empty model name!');end 212 212 213 214 213 %what is the executable being called? 214 executable='issm_slr.exe'; 215 215 216 216 if ispc(), error('BuildQueueScriptMultipleModels not support yet on windows machines');end; 217 217 218 219 218 %write queuing script 219 fid=fopen([modelname '.queue'],'w'); 220 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 221 fprintf(fid,'#PBS -S /bin/bash\n'); 222 fprintf(fid,'#PBS -N %s\n',modelname); 223 fprintf(fid,'#PBS -l select=%i:ncpus=%i:model=%s\n',cluster.numnodes,cluster.cpuspernode,cluster.processor); 224 fprintf(fid,'#PBS -l walltime=%i\n',cluster.time*60); %walltime is in seconds. 225 fprintf(fid,'#PBS -q %s \n',cluster.queue); 226 fprintf(fid,'#PBS -W group_list=%s\n',cluster.grouplist); 227 fprintf(fid,'#PBS -m e\n'); 228 fprintf(fid,'#PBS -o %s.outlog \n',[cluster.executionpath '/' dirname '/' modelname]); 229 fprintf(fid,'#PBS -e %s.errlog \n\n',[cluster.executionpath '/' dirname '/' modelname]); 230 fprintf(fid,'. /usr/share/modules/init/bash\n\n'); 231 for i=1:numel(cluster.modules), fprintf(fid,['module load ' cluster.modules{i} '\n']); end 232 fprintf(fid,'export PATH="$PATH:."\n\n'); 233 fprintf(fid,'export MPI_GROUP_MAX=64\n\n'); 234 fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME 235 fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); %FIXME 236 fprintf(fid,'cd %s/%s/\n\n',cluster.executionpath,dirname); 237 237 238 239 238 %number of cpus: 239 mpistring=sprintf('mpiexec -np %i ',cluster.numnodes*cluster.cpuspernode); 240 240 241 242 241 %executable: 242 mpistring=[mpistring sprintf('%s/%s ',cluster.codepath,executable)]; 243 243 244 245 244 %solution name: 245 mpistring=[mpistring sprintf('%s ',solution)]; 246 246 247 248 247 %execution directory and model name: 248 mpistring=[mpistring sprintf('%s/%s %s',cluster.executionpath,dirname,modelname)]; 249 249 250 251 250 %inform main executable of how many icecaps, glaciers and earth models are being run: 251 mpistring=[mpistring sprintf(' %i ',length(dirnames))]; 252 252 253 254 255 256 253 %icecaps, glaciers and earth location, names and number of processors associated: 254 for i=1:length(dirnames), 255 mpistring=[mpistring sprintf(' %s/%s %s %i ',cluster.executionpath,dirnames{i},modelnames{i},nps{i})]; 256 end 257 257 258 259 260 258 %write this long string to disk: 259 fprintf(fid,mpistring); 260 fclose(fid); 261 261 262 263 262 if cluster.interactive, 263 fid=fopen([modelname '.run'],'w'); 264 264 265 266 265 %number of cpus: 266 mpistring=sprintf('mpiexec -np %i ',cluster.numnodes*cluster.cpuspernode); 267 267 268 269 268 %executable: 269 mpistring=[mpistring sprintf('%s/%s ',cluster.codepath,executable)]; 270 270 271 272 271 %solution name: 272 mpistring=[mpistring sprintf('%s ',solution)]; 273 273 274 275 274 %execution directory and model name: 275 mpistring=[mpistring sprintf('%s/%s %s',cluster.executionpath,dirname,modelname)]; 276 276 277 278 277 %inform main executable of how many icecaps, glaciers and earth models are being run: 278 mpistring=[mpistring sprintf(' %i ',length(dirnames))]; 279 279 280 281 282 283 280 %icecaps, glaciers and earth location, names and number of processors associated: 281 for i=1:length(dirnames), 282 mpistring=[mpistring sprintf(' %s/Interactive%i %s %i ',cluster.executionpath,cluster.interactive,modelnames{i},nps{i})]; 283 end 284 284 285 286 287 285 %write this long string to disk: 286 fprintf(fid,mpistring); 287 fclose(fid); 288 288 289 290 291 292 293 294 295 296 289 fid=fopen([modelname '.errlog'],'w'); 290 fclose(fid); 291 fid=fopen([modelname '.outlog'],'w'); 292 fclose(fid); 293 end 294 end 295 %}}} 296 function BuildKrigingQueueScript(cluster,modelname,solution,io_gather,isvalgrind,isgprof) % {{{ 297 297 298 298 if(isgprof), disp('gprof not supported by cluster, ignoring...'); end 299 299 300 301 302 303 %fprintf(fid,'#PBS -N %s\n',modelname);304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 300 %write queuing script 301 fid=fopen([modelname '.queue'],'w'); 302 fprintf(fid,'#PBS -S /bin/bash\n'); 303 % fprintf(fid,'#PBS -N %s\n',modelname); 304 fprintf(fid,'#PBS -l select=%i:ncpus=%i:model=%s\n',cluster.numnodes,cluster.cpuspernode,cluster.processor); 305 fprintf(fid,'#PBS -l walltime=%i\n',cluster.time*60); %walltime is in seconds. 306 fprintf(fid,'#PBS -q %s \n',cluster.queue); 307 fprintf(fid,'#PBS -W group_list=%s\n',cluster.grouplist); 308 fprintf(fid,'#PBS -m e\n'); 309 fprintf(fid,'#PBS -o %s.outlog \n',modelname); 310 fprintf(fid,'#PBS -e %s.errlog \n\n',modelname); 311 fprintf(fid,'. /usr/share/modules/init/bash\n\n'); 312 for i=1:numel(cluster.modules), fprintf(fid,['module load ' cluster.modules{i} '\n']); end 313 fprintf(fid,'export PATH="$PATH:."\n'); 314 fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME 315 fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); %FIXME 316 fprintf(fid,'export MPI_GROUP_MAX=64\n\n'); 317 fprintf(fid,'cd %s/%s/\n\n',cluster.executionpath,modelname); 318 fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s\n',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname); %FIXME 319 if ~io_gather, %concatenate the output files: 320 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); 321 end 322 fclose(fid); 323 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 324 %in interactive mode, create a run file, and errlog and outlog file 325 if cluster.interactive, 326 fid=fopen([modelname '.run'],'w'); 327 if ~isvalgrind, 328 fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s\n',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname); 329 else 330 fprintf(fid,'mpiexec -np %i valgrind --leak-check=full %s/kriging.exe %s %s\n',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname); 331 end 332 if ~io_gather, %concatenate the output files: 333 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); 334 end 335 fclose(fid); 336 fid=fopen([modelname '.errlog'],'w'); 337 fclose(fid); 338 fid=fopen([modelname '.outlog'],'w'); 339 fclose(fid); 340 end 341 end %}}} 342 function BuildOceanQueueScript(np,cluster,modelname) % {{{ 343 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 % 364 % 365 % 366 344 %write queuing script 345 fid=fopen([modelname '.queue'],'w'); 346 fprintf(fid,'#PBS -S /bin/bash\n'); 347 fprintf(fid,'#PBS -l select=1:ncpus=%i:model=%s\n',np,cluster.processor); 348 fprintf(fid,'#PBS -l walltime=%i\n',cluster.time*60); %walltime is in seconds. 349 fprintf(fid,'#PBS -q %s \n',cluster.queue); 350 fprintf(fid,'#PBS -W group_list=%s\n',cluster.grouplist); 351 fprintf(fid,'#PBS -m e\n'); 352 fprintf(fid,'#PBS -o %s.outlog \n',modelname); 353 fprintf(fid,'#PBS -e %s.errlog \n\n',modelname); 354 fprintf(fid,'. /usr/share/modules/init/bash\n\n'); 355 %for i=1:numel(cluster.modules), fprintf(fid,['module load ' cluster.modules{i} '\n']); end %FIXME: should use this! 356 fprintf(fid,'module load comp-intel/2016.2.181\n'); 357 fprintf(fid,'module load netcdf/4.4.1.1_mpt\n'); 358 fprintf(fid,'module load mpi-sgi/mpt.2.15r20\n'); 359 fprintf(fid,'export PATH="$PATH:."\n'); 360 fprintf(fid,'export MPI_GROUP_MAX=64\n\n'); 361 fprintf(fid,['cd ' pwd() ' \n\n']); 362 fprintf(fid,'mpiexec -np %i ./mitgcmuv\n',np); 363 % if ~io_gather, %concatenate the output files: 364 % fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); 365 % end 366 fclose(fid); 367 367 368 369 370 371 372 373 374 375 376 377 378 379 368 %in interactive mode, create a run file, and errlog and outlog file 369 if cluster.interactive, 370 fid=fopen([modelname '.run'],'w'); 371 fprintf(fid,'module load mpi-sgi/mpt.2.15r20\n'); 372 fprintf(fid,['mpiexec -np %i ./mitgcmuv \n'],np); 373 fprintf(fid,['touch ' modelname '.lock %s\n']); 374 fclose(fid); 375 fid=fopen([modelname '.errlog'],'w'); 376 fclose(fid); 377 fid=fopen([modelname '.outlog'],'w'); 378 fclose(fid); 379 end 380 380 381 382 381 end %}}} 382 function UploadQueueJob(cluster,modelname,dirname,filelist)% {{{ 383 383 384 385 386 387 388 389 390 391 392 384 %compress the files into one zip. 385 compressstring=['tar -zcf ' dirname '.tar.gz ']; 386 for i=1:numel(filelist), 387 compressstring = [compressstring ' ' filelist{i}]; 388 end 389 if cluster.interactive, 390 compressstring = [compressstring ' ' modelname '.run ' modelname '.errlog ' modelname '.outlog ']; 391 end 392 system(compressstring); 393 393 394 395 396 397 398 399 400 401 394 disp('uploading input file and queueing script'); 395 if cluster.interactive==10, 396 directory=[pwd() '/run/']; 397 elseif cluster.interactive, 398 directory=[cluster.executionpath '/Interactive' num2str(cluster.interactive)]; 399 else 400 directory=cluster.executionpath; 401 end 402 402 403 404 405 406 407 403 if ~cluster.bbftp, 404 issmscpout(cluster.name,directory,cluster.login,cluster.port,{[dirname '.tar.gz']}); 405 else 406 issmbbftpout(cluster.name,directory,cluster.login,cluster.port,cluster.numstreams,{[dirname '.tar.gz']}); 407 end 408 408 409 410 411 409 end 410 %}}} 411 function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{ 412 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 413 %lauch command, to be executed via ssh 414 if ~cluster.interactive, 415 if ~isempty(restart) 416 launchcommand=['cd ' cluster.executionpath ' && cd ' dirname ' && qsub ' modelname '.queue ']; 417 else 418 launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ... 419 ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz && qsub ' modelname '.queue ']; 420 end 421 else 422 if ~isempty(restart) 423 launchcommand=['cd ' cluster.executionpath '/Interactive' num2str(cluster.interactive)]; 424 else 425 if cluster.interactive==10, 426 launchcommand=['cd ' pwd() '/run && tar -zxf ' dirname '.tar.gz']; 427 else 428 launchcommand=['cd ' cluster.executionpath '/Interactive' num2str(cluster.interactive) ' && tar -zxf ' dirname '.tar.gz']; 429 end 430 end 431 end 432 432 433 434 435 436 437 433 disp('launching solution sequence on remote cluster'); 434 issmssh(cluster.name,cluster.login,cluster.port,launchcommand); 435 end 436 %}}} 437 function Download(cluster,dirname,filelist)% {{{ 438 438 439 440 441 442 443 444 445 446 439 %copy files from cluster to current directory 440 if cluster.interactive==10, 441 directory=[pwd() '/run/']; 442 elseif ~cluster.interactive, 443 directory=[cluster.executionpath '/' dirname '/']; 444 else 445 directory=[cluster.executionpath '/Interactive' num2str(cluster.interactive) '/']; 446 end 447 447 448 449 450 451 452 448 if ~cluster.bbftp, 449 issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist); 450 else 451 issmbbftpin(cluster.name, cluster.login, cluster.port, cluster.numstreams, directory, filelist); 452 end 453 453 454 454 end %}}} 455 455 end 456 456 end -
../trunk-jpl/src/m/classes/clusters/pfe.py
31 31 self.queue = 'long' 32 32 self.time = 12 * 60 33 33 self.processor = 'wes' 34 self.srcpath = '' 34 35 self.codepath = '' 35 36 self.executionpath = '' 36 37 self.grouplist = 's1010' … … 60 61 s = "%s\n%s" % (s, fielddisplay(self, 'cpuspernode', 'number of nodes per CPUs')) 61 62 s = "%s\n%s" % (s, fielddisplay(self, 'np', 'number of CPUs')) 62 63 s = "%s\n%s" % (s, fielddisplay(self, 'port', 'machine access port')) 63 s = "%s\n%s" % (s, fielddisplay(self, 'codepath', 'code path on the cluster'))64 s = "%s\n%s" % (s, fielddisplay(self, 'executionpath', 'execution path on the cluster'))65 64 s = "%s\n%s" % (s, fielddisplay(self, 'queue', 'name of the queue')) 66 65 s = "%s\n%s" % (s, fielddisplay(self, 'time', 'walltime requested')) 67 66 s = "%s\n%s" % (s, fielddisplay(self, 'processor', 'type of processor')) 67 s = "%s\n%s" % (s, fielddisplay(self, 'codepath', '$ISSM_DIR on pfe')) 68 s = "%s\n%s" % (s, fielddisplay(self, 'executionpath', 'directory containing issm.exe on pfe')) 68 69 s = "%s\n%s" % (s, fielddisplay(self, 'grouplist', 'name of the group')) 69 70 s = "%s\n%s" % (s, fielddisplay(self, 'interactive', '')) 70 71 s = "%s\n%s" % (s, fielddisplay(self, 'bbftp', '')) … … 112 113 else: 113 114 md = md.checkmessage('unknown processor type, should be ''neh'', ''wes'' or ''har'' or ''ivy''') 114 115 115 #Miscelaneous116 #Miscellaneous 116 117 if not self.login: 117 118 md = md.checkmessage('login empty') 119 if not self.srcpath: 120 md = md.checkmessage('srcpath empty') 118 121 if not self.codepath: 119 122 md = md.checkmessage('codepath empty') 120 123 if not self.executionpath: … … 152 155 fid.write('module load mpi-sgi/mpt.2.11r13\n') 153 156 fid.write('export PATH="$PATH:."\n\n') 154 157 fid.write('export MPI_GROUP_MAX=64\n\n') 155 fid.write('export ISSM_DIR="%s /../ "\n' % self.codepath)158 fid.write('export ISSM_DIR="%s"\n' % self.srcpath) 156 159 fid.write('source $ISSM_DIR/etc/environment.sh\n') 160 fid.write('export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$ISSM_DIR/externalpackages/petsc/install/lib"\n') 157 161 fid.write('cd %s/%s/ \n\n' % (self.executionpath, dirname)) 158 162 fid.write('mpiexec - np %i %s/%s %s %s/%s %s\n' % (self.nprocs(), self.codepath, executable, str(solution), self.executionpath, dirname, modelname)) 159 163 -
../trunk-jpl/src/m/classes/fourierlove.py
64 64 self.frequencies = [0] #Hz 65 65 self.sh_nmax = 256 # .35 degree, 40 km at the equator. 66 66 self.sh_nmin = 1 67 self.g0 = 10 # m /s^268 self.r0 = 637 8e3#m69 self.mu0 = 1e11 67 self.g0 = 9.81 # m/s^2 68 self.r0 = 6371e3 #m 69 self.mu0 = 1e11 # Pa 70 70 self.allow_layer_deletion = 1 71 71 self.love_kernels = 0 72 72 self.forcing_type = 11 -
../trunk-jpl/test/Par/GiaIvinsBenchmarksAB.py
11 11 from verbose import * 12 12 from SetIceSheetBC import * 13 13 14 14 15 rad = 600000. 15 16 nv = md.mesh.numberofvertices 16 17 if (np.isnan(md.geometry.thickness)): … … 20 21 if (dist <= rad): 21 22 md.geometry.thickness[i] = 2000.0 22 23 else: 23 md.geometry.thickness[i] = 1.0 # non-zero thickness24 md.geometry.thickness[i] = 0 24 25 25 26 md.geometry.thickness = md.geometry.thickness.reshape(-1, 1) 26 27 md.geometry.base = np.zeros((md.mesh.numberofvertices, 1)) -
../trunk-jpl/test/Par/GiaIvinsBenchmarksCD.py
1 1 #Geometry specific to Experiments C and D 2 3 2 import inspect 4 3 import os.path 5 4 … … 22 21 if (dist <= rad): 23 22 md.geometry.thickness[i] = 3000.0 24 23 else: 25 md.geometry.thickness[i] = 1.0 # non - zero thickness24 md.geometry.thickness[i] = 0 26 25 27 26 md.geometry.thickness = md.geometry.thickness.reshape(-1, 1) 28 27 md.geometry.base = np.zeros((md.mesh.numberofvertices, 1)) -
../trunk-jpl/test/NightlyRun/test2001.py
31 31 #Define loading history (see test2001.m for the description) 32 32 md.timestepping.start_time = 2400000 # 2, 400 kyr 33 33 md.timestepping.final_time = 2500000 # 2, 500 kyr 34 md.geometry.thickness = np.vstack((np.hstack((md.geometry.thickness * 0.0, 0.0)), 35 np.hstack((md.geometry.thickness / 2.0, 0.1)), 36 np.hstack((md.geometry.thickness, 0.2)), 37 np.hstack((md.geometry.thickness, 1.0)), 38 np.hstack((md.geometry.thickness, md.timestepping.start_time)))).T 34 md.geometry.thickness = np.array([ 35 np.append(md.geometry.thickness * 0.0, 0.0), 36 np.append(md.geometry.thickness / 2.0, 0.1), 37 np.append(md.geometry.thickness, 0.2), 38 np.append(md.geometry.thickness, 1.0), 39 np.append(md.geometry.thickness, md.timestepping.start_time) 40 ]).T 39 41 40 42 #Solve for GIA deflection 41 43 md.cluster = generic('name', gethostname(), 'np', 3) -
../trunk-jpl/test/NightlyRun/test2051.m
23 23 24 24 % find out elements that have zero loads throughout the loading history. 25 25 pos = find(sum(abs(md.geometry.thickness(1:end-1,:)),2)==0); 26 md.mask.ice_levelset(pos)=1; % no -ice.26 md.mask.ice_levelset(pos)=1; % no ice 27 27 28 28 md.cluster=generic('name',oshostname(),'np',3); 29 29 md.verbose=verbose('1111111'); … … 37 37 38 38 %Test Name: GiaIvinsBenchmarksAB2dA2 39 39 %% different evaluation time. {{{ 40 md.timestepping.start_time=2005100; % after 5 kyr of deglaciation 41 md.geometry.thickness(end,end) = md.timestepping.start_time; 40 md.timestepping.start_time=2005100; % after 5 kyr of deglaciation 41 md.geometry.thickness(end,end) = md.timestepping.start_time; 42 42 43 43 md=solve(md,'Gia'); 44 44 -
../trunk-jpl/test/NightlyRun/test2053.m
8 8 md.gia.cross_section_shape=2; % for elliptical edge 9 9 10 10 % evaluation time (termed start_time) 11 md.timestepping.start_time=0.3; % for t \approx 0 kyr : to get el eastic response!11 md.timestepping.start_time=0.3; % for t \approx 0 kyr : to get elastic response! 12 12 md.timestepping.final_time=2500000; % 2,500 kyr 13 13 14 14 %% define loading history {{{ … … 22 22 23 23 % find out elements that have zero loads throughout the loading history. 24 24 pos = find(sum(abs(md.geometry.thickness(1:end-1,:)),2)==0); 25 md.mask.ice_levelset(pos)=1; % no -ice.25 md.mask.ice_levelset(pos)=1; % no ice 26 26 27 27 md.cluster=generic('name',oshostname(),'np',3); 28 28 md.verbose=verbose('1111111'); -
../trunk-jpl/test/NightlyRun/test2051.py
1 #Test Name: GiaIvinsBenchmarksAB2dA 11 #Test Name: GiaIvinsBenchmarksAB2dA 2 2 from socket import gethostname 3 3 4 4 import numpy as np … … 16 16 md = parameterize(md, '../Par/GiaIvinsBenchmarksAB.py') 17 17 18 18 # indicate what you want to compute 19 md.gia.cross_section_shape = 1 # for square-edged x -section19 md.gia.cross_section_shape = 1 # for square-edged x-section 20 20 21 # define loading history21 # evaluation time (termed start_time) 22 22 md.timestepping.start_time = 2002100 # after 2 kyr of deglaciation 23 md.timestepping.final_time = 2500000 # 2, 500 kyr 24 md.geometry.thickness = np.array([np.append(md.geometry.thickness * 0.0, 0.0), 25 np.append(md.geometry.thickness, 1000), 26 np.append(md.geometry.thickness, 2000000), 27 np.append(md.geometry.thickness * 0.0, 2000100), 28 np.append(md.geometry.thickness * 0.0, md.timestepping.start_time)]).T 23 md.timestepping.final_time = 2500000 # 2,500 kyr 29 24 30 # solve for GIA deflection 25 # define loading history 26 md.geometry.thickness = np.array([ 27 np.append(md.geometry.thickness * 0.0, 0.0), 28 np.append(md.geometry.thickness, 1000), 29 np.append(md.geometry.thickness, 2000000), 30 np.append(md.geometry.thickness * 0.0, 2000100), 31 np.append(md.geometry.thickness * 0.0, md.timestepping.start_time) 32 ]).T 33 34 # find out the elements that have zero loads throughout the loading history 35 pos = np.where(np.abs(md.geometry.thickness[0:-2, :].sum(axis=1)) == 0)[0] 36 md.mask.ice_levelset[pos] = 1 # no ice 37 31 38 md.cluster = generic('name', gethostname(), 'np', 3) 32 39 md.verbose = verbose('1111111') 40 41 # solve for GIA deflection 33 42 md = solve(md, 'Gia') 34 43 35 #Fields and tolerances to track changes 36 field_names = ['UGia', 'UGiaRate'] 37 field_tolerances = [1e-13, 1e-13] 38 field_values = [md.results.GiaSolution.UGia, md.results.GiaSolution.UGiaRate] 44 # Test Name: GiaIvinsBenchmarksAB2dA1 45 U_AB2dA1 = md.results.GiaSolution.UGia 46 URate_AB2dA1 = md.results.GiaSolution.UGiaRate 47 48 # Test Name: GiaIvinsBenchmarksAB2dA2 49 # different evaluation time # {{{ 50 md.timestepping.start_time = 2005100 # after 5 kyr of deglaciation 51 md.geometry.thickness[-1, -1] = md.timestepping.start_time 52 53 md = solve(md, 'Gia') 54 55 U_AB2dA2 = md.results.GiaSolution.UGia 56 URate_AB2dA2 = md.results.GiaSolution.UGiaRate 57 # }}} 58 59 # Test Name: GiaIvinsBenchmarksAB2dA3 60 # different evaluation time # {{{ 61 md.timestepping.start_time = 2010100 # after 10 kyr of deglaciation 62 md.geometry.thickness[-1, -1] = md.timestepping.start_time 63 64 md = solve(md, 'Gia') 65 66 U_AB2dA3 = md.results.GiaSolution.UGia 67 URate_AB2dA3 = md.results.GiaSolution.UGiaRate 68 # }}} 69 70 # Fields and tolerances to track changes 71 field_names = ['U_AB2dA1','URate_AB2dA1','U_AB2dA2','URate_AB2dA2','U_AB2dA3','URate_AB2dA3'] 72 field_tolerances = [1e-13, 1e-13, 1e-13, 1e-13, 1e-13, 1e-13] 73 field_values = [U_AB2dA1, URate_AB2dA1, U_AB2dA2, URate_AB2dA2, U_AB2dA3, URate_AB2dA3] -
../trunk-jpl/test/NightlyRun/test2052.py
1 #Test Name: GiaIvinsBenchmarksAB2dC 11 #Test Name: GiaIvinsBenchmarksAB2dC 2 2 from socket import gethostname 3 3 4 4 import numpy as np … … 10 10 from triangle import * 11 11 12 12 13 # Benchmark experiments (Figure A2cIvins and James, 1999, Geophys. J. Int.)14 md = triangle(model(), '../Exp/RoundFrontEISMINT.exp', 200000 )13 # Benchmark experiments (Figure A2a Ivins and James, 1999, Geophys. J. Int.) 14 md = triangle(model(), '../Exp/RoundFrontEISMINT.exp', 200000.) 15 15 md = setmask(md, '', '') 16 16 md = parameterize(md, '../Par/GiaIvinsBenchmarksCD.py') 17 17 18 # indicate what you want to compute18 # indicate what you want to compute 19 19 md.gia.cross_section_shape = 1 # for square-edged x-section 20 20 21 # define loading history22 md.timestepping.start_time = 0.3 # for t \approx 0 kyr : to get el eastic response!21 # evaluation time (termed start_time) 22 md.timestepping.start_time = 0.3 # for t \approx 0 kyr : to get elastic response! 23 23 md.timestepping.final_time = 2500000 # 2,500 kyr 24 md.geometry.thickness = np.array([np.append(md.geometry.thickness * 0.0, 0.0),25 np.append(md.geometry.thickness / 2.0, 0.1),26 np.append(md.geometry.thickness, 0.2),27 np.append(md.geometry.thickness, md.timestepping.start_time)]).T28 24 29 #solve for GIA deflection 25 # define loading history 26 md.geometry.thickness = np.array([ 27 np.append(md.geometry.thickness * 0.0, 0.0), 28 np.append(md.geometry.thickness / 2.0, 0.1), 29 np.append(md.geometry.thickness, 0.2), 30 np.append(md.geometry.thickness, md.timestepping.start_time) 31 ]).T 32 33 # find out elements that have zero loads throughout the loading history 34 pos = np.where(np.abs(md.geometry.thickness[0:-2, :].sum(axis=1)) == 0)[0] 35 md.mask.ice_levelset[pos] = 1 # no ice 36 30 37 md.cluster = generic('name', gethostname(), 'np', 3) 31 38 md.verbose = verbose('1111111') 39 40 # solve for GIA deflection 32 41 md = solve(md, 'Gia') 33 42 34 #Fields and tolerances to track changes 35 field_names = ['UGia', 'UGiaRate'] 36 field_tolerances = [1e-13, 1e-13] 37 field_values = [md.results.GiaSolution.UGia, md.results.GiaSolution.UGiaRate] 43 # Test Name: GiaIvinsBenchmarksAB2dC1 44 U_AB2dC1 = md.results.GiaSolution.UGia 45 URate_AB2dC1 = md.results.GiaSolution.UGiaRate 46 47 # Test Name: GiaIvinsBenchmarksAB2dC2 48 # different evaluation time # {{{ 49 md.timestepping.start_time = 1000.3 # for t \approx 1 kyr 50 md.geometry.thickness[-1, -1] = md.timestepping.start_time 51 52 md = solve(md, 'Gia') 53 54 U_AB2dC2 = md.results.GiaSolution.UGia 55 URate_AB2dC2 = md.results.GiaSolution.UGiaRate 56 # }}} 57 58 # Test Name: GiaIvinsBenchmarksAB2dC3 59 # different evaluation time # {{{ 60 md.timestepping.start_time = 2400000 # for t \approx \infty 61 md.geometry.thickness[-1, -1] = md.timestepping.start_time 62 63 md = solve(md, 'Gia') 64 65 U_AB2dC3 = md.results.GiaSolution.UGia 66 URate_AB2dC3 = md.results.GiaSolution.UGiaRate 67 # }}} 68 69 # Fields and tolerances to track changes 70 field_names = ['U_AB2dC1', 'URate_AB2dC1', 'U_AB2dC2', 'URate_AB2dC2', 'U_AB2dC3', 'URate_AB2dC3'] 71 field_tolerances = [1e-13, 1e-13, 1e-13, 1e-13, 1e-13, 1e-13] 72 field_values = [U_AB2dC1, URate_AB2dC1, U_AB2dC2, URate_AB2dC2, U_AB2dC3, URate_AB2dC3] -
../trunk-jpl/test/NightlyRun/test2053.py
1 #Test Name: GiaIvinsBenchmarksAB2dD 11 #Test Name: GiaIvinsBenchmarksAB2dD 2 2 from socket import gethostname 3 3 4 4 import numpy as np … … 10 10 from triangle import * 11 11 12 12 13 # Benchmark experiments (Figure A2cIvins and James, 1999, Geophys. J. Int.)13 # Benchmark experiments (Figure A2a Ivins and James, 1999, Geophys. J. Int.) 14 14 md = triangle(model(), '../Exp/RoundFrontEISMINT.exp', 200000) 15 15 md = setmask(md, '', '') 16 16 md = parameterize(md, '../Par/GiaIvinsBenchmarksCD.py') 17 17 18 # indicate what you want to compute19 md.gia.cross_section_shape = 2 # for square-edged x - section18 # indicate what you want to compute 19 md.gia.cross_section_shape = 2 # for elliptical edge 20 20 21 #define loading history 22 md.timestepping.start_time = 0.3 # for t \approx 0 kyr : to get eleastic response! 23 md.timestepping.final_time = 2500000 # 2, 500 kyr 24 md.geometry.thickness = np.array([np.append(md.geometry.thickness * 0.0, 0.0), 25 np.append(md.geometry.thickness / 2.0, 0.1), 26 np.append(md.geometry.thickness, 0.2), 27 np.append(md.geometry.thickness, md.timestepping.start_time)]).T 21 # evaluation time (termed start_time) 22 md.timestepping.start_time = 0.3 # for t \approx 0 kyr : to get elastic response! 23 md.timestepping.final_time = 2500000 # 2,500 kyr 28 24 29 #solve for GIA deflection 25 # define loading history 26 md.geometry.thickness = np.array([ 27 np.append(md.geometry.thickness * 0.0, 0.0), 28 np.append(md.geometry.thickness / 2.0, 0.1), 29 np.append(md.geometry.thickness, 0.2), 30 np.append(md.geometry.thickness, md.timestepping.start_time) 31 ]).T 32 33 # find out elements that have zero loads throughout the loading history 34 pos = np.where(np.abs(md.geometry.thickness[0:-2, :].sum(axis=1)) == 0)[0] 35 md.mask.ice_levelset[pos] = 1 # no ice 36 30 37 md.cluster = generic('name', gethostname(), 'np', 3) 31 38 md.verbose = verbose('1111111') 39 40 # solve for GIA deflection 32 41 md = solve(md, 'Gia') 33 42 34 #Fields and tolerances to track changes 35 field_names = ['UGia', 'UGiaRate'] 36 field_tolerances = [1e-13, 1e-13] 37 field_values = [md.results.GiaSolution.UGia, md.results.GiaSolution.UGiaRate] 43 # Test Name: GiaIvinsBenchmarksAB2dD1 44 U_AB2dD1 = md.results.GiaSolution.UGia 45 URate_AB2dD1 = md.results.GiaSolution.UGiaRate 46 47 # Test Name: GiaIvinsBenchmarksAB2dD2 48 # different evaluation time # {{{ 49 md.timestepping.start_time = 1000.3 # for t \approx 1 kyr 50 md.geometry.thickness[-1, -1] = md.timestepping.start_time 51 52 md = solve(md, 'Gia') 53 54 U_AB2dD2 = md.results.GiaSolution.UGia 55 URate_AB2dD2 = md.results.GiaSolution.UGiaRate 56 # }}} 57 58 # Test Name: GiaIvinsBenchmarksAB2dD3 59 # different evaluation time # {{{ 60 md.timestepping.start_time = 2400000 # for t \approx \infty 61 md.geometry.thickness[-1, -1] = md.timestepping.start_time 62 63 md = solve(md, 'Gia') 64 65 U_AB2dD3 = md.results.GiaSolution.UGia 66 URate_AB2dD3 = md.results.GiaSolution.UGiaRate 67 # }}} 68 69 # Fields and tolerances to track changes 70 field_names = ['U_AB2dD1', 'URate_AB2dD1', 'U_AB2dD2', 'URate_AB2dD2', 'U_AB2dD3', 'URate_AB2dD3'] 71 field_tolerances = [1e-13, 1e-13, 1e-13, 1e-13, 1e-13, 1e-13] 72 field_values = [U_AB2dD1, URate_AB2dD1, U_AB2dD2, URate_AB2dD2, U_AB2dD3, URate_AB2dD3] 73 -
../trunk-jpl/src/m/solve/WriteData.py
1 from copy import deepcopy 1 2 from struct import pack, error 2 3 import numpy as np 3 4 import pairoptions … … 38 39 # data = full(data) 39 40 # end 40 41 42 # Always make a copy of the the data so that we do not accidently overwrite 43 # any model fields. 44 data = deepcopy(data) 45 41 46 #Scale data if necesarry 42 47 if options.exist('scale'): 43 48 data = np.array(data) … … 147 152 # }}} 148 153 149 154 elif datatype == 'DoubleMat': # {{{ 150 151 155 if isinstance(data, (bool, int, float)): 152 156 data = np.array([data]) 153 157 elif isinstance(data, (list, tuple)): … … 170 174 try: 171 175 fid.write(pack('q', recordlength)) 172 176 except error as Err: 173 raise ValueError('Field {} can not be marshaled, {}, with "number" the leng htof the record.'.format(name, Err))177 raise ValueError('Field {} can not be marshaled, {}, with "number" the length of the record.'.format(name, Err)) 174 178 175 179 #write data code and matrix type: 176 180 fid.write(pack('i', FormatToCode(datatype))) -
../trunk-jpl/src/m/solve/parseresultsfromdisk.py
17 17 try: 18 18 fid = open(filename, 'rb') 19 19 except IOError as e: 20 raise IOError(" loadresultsfromdisk error message: could not open '{}' for binary reading.".format(filename))20 raise IOError("parseresultsfromdisk error message: could not open {} for binary reading".format(filename)) 21 21 22 22 #initialize results: 23 23 saveres = [] … … 242 242 nlayer = md.materials.numlayers 243 243 degmax = md.love.sh_nmax 244 244 nfreq = md.love.nfreq 245 #for numpy 1.8 + only 246 #temp_field = np.full((degmax + 1, nfreq, nlayer + 1, 6), 0.0) 245 r0 = md.love.r0 246 g0 = md.love.g0 247 mu0 = md.love.mu0 248 rr = md.materials.radius 249 rho = md.materials.density 250 rho_avg = (rho * np.diff(np.power(rr, 3), n=1, axis=0)) / np.diff(np.power(rr, 3).sum()).sum() 247 251 temp_field = np.empty((degmax + 1, nfreq, nlayer + 1, 6)) 248 252 temp_field.fill(0.0) 249 253 for ii in range(degmax + 1): 250 254 for jj in range(nfreq): 251 255 for kk in range(nlayer + 1): 252 ll = ii * (nlayer + 1) * 6 + (kk * 6 + 1) 253 for mm in range(6): 254 temp_field[ii, jj, kk, mm] = field[ll + mm - 1, jj] 256 if kk < nlayer + 1: 257 ll = ii * (nlayer + 1) * 6 + (kk * 6 + 1) + 3 258 temp_field[ii, jj, kk, 0] = field[ll + (1 - 1), jj] * r0 # mm = 4 259 temp_field[ii, jj, kk, 1] = field[ll + (2 - 1), jj] * mu0 # mm = 5 260 temp_field[ii, jj, kk, 2] = field[ll + (3 - 1), jj] * r0 # mm = 6 261 temp_field[ii, jj, kk, 3] = field[ll + (4 - 1), jj] * mu0 # mm = 1 262 temp_field[ii, jj, kk, 4] = field[ll + (5 - 1), jj] * r0 * g0 # mm = 2 263 temp_field[ii, jj, kk, 5] = field[ll + (6 - 1), jj] * g0 # mm = 3 264 print(temp_field) 265 else: # surface 266 ll = ii * (nlayer + 1) * 6 - 2 267 temp_field[ii, jj, kk, 0] = field[ll + (1 - 1), jj] * r0 268 temp_field[ii, jj, kk, 2] = field[ll + (2 - 1), jj] * r0 269 temp_field[ii, jj, kk, 4] = field[ll + (3 - 1), jj] * r0 * g0 270 # surface BC 271 temp_field[ii, jj, kk, 3] = 0 272 if md.love.forcing_type == 9: 273 temp_field[ii, jj, kk, 1] = 0 274 temp_field[ii, jj, kk, 5] = (2 * ii - 1) / r0 - ii * field[ll + (3 - 1), jj] * g0 275 elif md.love.forcing_type == 11: 276 temp_field[ii, jj, kk, 1] = -(2 * (ii - 1) + 1) * rho_avg / 3 277 temp_field[ii, jj, kk, 5] = (2 * ii - 1) / r0 - ii * field[ll + (3 - 1), jj] * g0 255 278 field = temp_field 256 279 257 280 if time != -9999: -
../trunk-jpl/src/m/solve/parseresultsfromdisk.m
270 270 end 271 271 result.step=step; 272 272 result.field=field; 273 274 273 end 275 274 % }}} 276 275 function result=ReadDataDimensions(fid) % {{{ -
../trunk-jpl/src/m/solve/marshall.py
5 5 ''' 6 6 MARSHALL - outputs a compatible binary file from @model md, for certain solution type. 7 7 8 The routine creates a compatible binary file from @model md9 This binary file will be used for parallel runs in JPL -package8 The routine creates a compatible binary file from @model md 9 This binary file will be used for parallel runs in JPL-package 10 10 11 Usage:12 marshall(md)11 Usage: 12 marshall(md) 13 13 ''' 14 14 if md.verbose.solution: 15 15 print("marshalling file {}.bin".format(md.miscellaneous.name)) -
../trunk-jpl/src/m/classes/geometry.m
89 89 90 90 end % }}} 91 91 function marshall(self,prefix,md,fid) % {{{ 92 disp(md.geometry.thickness) 92 93 WriteData(fid,prefix,'object',self,'fieldname','surface','format','DoubleMat','mattype',1); 93 94 WriteData(fid,prefix,'object',self,'fieldname','thickness','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); 95 disp(md.geometry.thickness) 96 pause 94 97 WriteData(fid,prefix,'object',self,'fieldname','base','format','DoubleMat','mattype',1); 95 98 WriteData(fid,prefix,'object',self,'fieldname','bed','format','DoubleMat','mattype',1); 96 99 WriteData(fid,prefix,'object',self,'fieldname','hydrostatic_ratio','format','DoubleMat','mattype',1); -
../trunk-jpl/test/NightlyRun/test2052.m
8 8 md.gia.cross_section_shape=1; % for square-edged x-section 9 9 10 10 % evaluation time (termed start_time) 11 md.timestepping.start_time=0.3; % for t \approx 0 kyr : to get eleastic response!11 md.timestepping.start_time=0.3; % for t \approx 0 kyr: to get elastic response! 12 12 md.timestepping.final_time=2500000; % 2,500 kyr 13 13 14 14 %% define loading history {{{ … … 22 22 23 23 % find out elements that have zero loads throughout the loading history. 24 24 pos = find(sum(abs(md.geometry.thickness(1:end-1,:)),2)==0); 25 md.mask.ice_levelset(pos)=1; % no -ice.25 md.mask.ice_levelset(pos)=1; % no ice 26 26 27 27 md.cluster=generic('name',oshostname(),'np',3); 28 28 md.verbose=verbose('1111111'); … … 30 30 %% solve for GIA deflection 31 31 md=solve(md,'Gia'); 32 32 33 pause 34 33 35 %Test Name: GiaIvinsBenchmarksAB2dC1 34 36 U_AB2dC1 = md.results.GiaSolution.UGia; 35 URate_AB2dC1 = md.results.GiaSolution.UGiaRate; 37 URate_AB2dC1 = md.results.GiaSolution.UGiaRate; 36 38 37 39 %Test Name: GiaIvinsBenchmarksAB2dC2 38 40 %% different evaluation time. {{{
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