| commit | author | age | ||
| 8ab985 | 1 | import configobj |
| SP | 2 | import xml.etree.ElementTree as ET |
| 3 | import base64 | |
| 4 | import zlib | |
| 5 | import sys,io | |
| 6 | import os | |
| 7 | from itertools import islice | |
| 8 | import mmap | |
| 9 | import shlex | |
| 10 | import psutil | |
| 11 | import time | |
| 12 | import datetime | |
| 13 | import subprocess | |
| 14 | import shutil | |
| 15 | ||
| 16 | # Process status | |
| 17 | TS_NOLOCK=0 # lock file does not exist | |
| 18 | TS_NONEXISTANT=0 # process is not in the list of processes | |
| 19 | TS_STOPPED=1 # the process is listed, but is in stopped state | |
| 20 | TS_RUNNING=2 # process is running | |
| 21 | TS_COMPLETED=3 #simulation is completed | |
| 22 | ||
| 23 | class FileContent: | |
| 24 | ''' | |
| 25 | Class is helpful for reading and writting the specific files. | |
| 26 | ''' | |
| 27 | def __init__(self,filename): | |
| 28 | ''' The instance is done by calling constructor FileContent(filename) | |
| 29 | ||
| 30 | The object then reads filename if it exists, otherwise the data is empty string. | |
| 31 | User may force to reread file by calling the readline() method of the class. | |
| 32 | ||
| 33 | Filename is stored in local variable for future file operations. | |
| 34 | ''' | |
| 35 | ||
| 36 | self.filename=filename | |
| 37 | self.readfile() | |
| 38 | ||
| 39 | def readfile(self): | |
| 40 | '''Force reread of the file and setting the data''' | |
| 41 | self.data="" | |
| 42 | try: | |
| 43 | with open (self.filename, "r") as myfile: | |
| 44 | self.data=myfile.read().replace('\n', '') #read the file and remove newline from the text | |
| 45 | except: | |
| 46 | pass # does nothing if error occurs | |
| 47 | ||
| 48 | ||
| 49 | def writefile(self, data, mode='w'): | |
| 50 | '''File may be updated by completely rewritting the file contents or appending the data to the end of the file. | |
| 51 | this is achieved by calling writefile(data, mode) method, where data is the string data to be written and | |
| 52 | mode can be 'a' for append and 'w' for writting the file anew. | |
| 53 | ''' | |
| 54 | with open (self.filename, mode) as myfile: | |
| 55 | myfile.write(data) | |
| 56 | ||
| 57 | def getText(self): | |
| 58 | ''' | |
| 59 | Method getText() or calling the object itself returns string of data | |
| 60 | ''' | |
| 61 | return self.data | |
| 62 | ||
| 63 | def __str__(self): | |
| 64 | ''' | |
| 65 | Method getText() or calling the object itself returns string of data | |
| 66 | ''' | |
| 67 | return self.getText() | |
| 68 | ||
| 69 | class Tape: | |
| 70 | ''' | |
| 71 | Special class that manages configuration of trisurf (commonly named tape). It can read and parse configuration from disk or parse it from string. | |
| 72 | ''' | |
| 73 | ||
| 74 | def __init__(self): | |
| 75 | '''The object is instatiated by calling Tape() constructor without parameters''' | |
| 76 | return | |
| 77 | ||
| 78 | def readTape(self, tape='tape'): | |
| 79 | ''' | |
| 80 | Tape is read and parsed by calling the readTape() method with optional tape parameter, which is full path to filename where the configuration is stored. | |
| 81 | If the tape cannot be read, it prints error and exits. | |
| 82 | ''' | |
| 83 | try: | |
| 84 | self.config=configobj.ConfigObj(tape) | |
| 85 | with open (tape, "r") as myfile: | |
| 86 | self.rawText=myfile.read() #read the file | |
| 87 | ||
| 88 | except: | |
| 89 | print("Error reading or parsing tape file!\n") | |
| 90 | exit(1) | |
| 91 | ||
| 92 | def setTape(self, string): | |
| 93 | '''Method setTape(string) parses the string in memory that hold the tape contents.''' | |
| 94 | self.config=configobj.ConfigObj(io.StringIO(string)) | |
| 95 | self.rawText=string | |
| 96 | return | |
| 97 | ||
| 98 | def getValue(self,key): | |
| 99 | '''Method getValue(key) returns value of a single parsed setting named "key".''' | |
| 100 | ||
| 101 | return self.config[key] | |
| 102 | ||
| 103 | def __str__(self): | |
| 104 | '''Calling the object itself, it recreates the tape contents from parsed values in form of key=value.''' | |
| 105 | retval="" | |
| 106 | for key,val in self.config.iteritems(): | |
| 107 | retval=retval+str(key)+" = "+str(val)+"\n" | |
| 108 | return retval | |
| 109 | ||
| 110 | ||
| 111 | ||
| 112 | class Directory: | |
| 113 | ''' | |
| 114 | Class deals with the paths where the simulation is run and data is stored. | |
| 115 | ''' | |
| 116 | def __init__(self, maindir=".", simdir=""): | |
| 117 | '''Initialization Directory() takes two optional parameters, namely maindir and simdir. Defaults to current directory. It sets local variables maindir and simdir accordingly.''' | |
| 118 | self.maindir=maindir | |
| 119 | self.simdir=simdir | |
| 120 | return | |
| 121 | ||
| 122 | def fullpath(self): | |
| 123 | ''' | |
| 124 | Method returns string of path where the data is stored. It combines values of maindir and simdir as maindir/simdir on Unix. | |
| 125 | ''' | |
| 126 | return os.path.join(self.maindir,self.simdir) | |
| 127 | ||
| 128 | def exists(self): | |
| 129 | ''' Method checks whether the directory specified by fullpath() exists. It return True/False on completion.''' | |
| 130 | path=self.fullpath() | |
| 131 | if(os.path.exists(path)): | |
| 132 | return True | |
| 133 | else: | |
| 134 | return False | |
| 135 | ||
| 136 | def make(self): | |
| 137 | ''' Method make() creates directory. If it fails it exits the program with error message.''' | |
| 138 | try: | |
| 139 | os.makedirs(self.fullpath()) | |
| 140 | except: | |
| 141 | print("Cannot make directory "+self.fullpath()+"\n") | |
| 142 | exit(1) | |
| 143 | return | |
| 144 | ||
| 145 | def makeifnotexist(self): | |
| 146 | '''Method makeifnotexist() creates directory if it does not exist.''' | |
| 147 | if(self.exists()==0): | |
| 148 | self.make() | |
| 149 | return True | |
| 150 | else: | |
| 151 | return False | |
| 152 | ||
| 153 | def remove(self): | |
| 154 | '''Method remove() removes directory recursively. WARNING! No questions asked.''' | |
| 155 | if(self.exists()): | |
| 156 | try: | |
| 157 | os.rmdir(self.fullpath()) | |
| 158 | except: | |
| 159 | print("Cannot remove directory "+self.fullpath()+ "\n") | |
| 160 | exit(1) | |
| 161 | return | |
| 162 | ||
| 163 | def goto(self): | |
| 164 | ''' | |
| 165 | Method goto() moves current directory to the one specified by fullpath(). WARNING: when using the relative paths, do not call this function multiple times. | |
| 166 | ''' | |
| 167 | try: | |
| 168 | os.chdir(self.fullpath()) | |
| 169 | except: | |
| 170 | print("Cannot go to directory "+self.fullpath()+"\n") | |
| 171 | return | |
| 172 | ||
| 173 | ||
| 174 | class Statistics: | |
| 175 | ''' | |
| 176 | Class that deals with the statistics file from the simulations. | |
| 177 | File is generally large and not all data is needed, so it is dealt with in a specific way. | |
| 178 | ''' | |
| 179 | ||
| 180 | def __init__(self,path,filename="statistics.csv"): | |
| 181 | ''' | |
| 182 | At the initialization call it receives optional filename parameter specifying the path and filename of the statistics file. | |
| 183 | ||
| 184 | The local variables path, filename, fullname (joined path and filename) and private check if the file exists are stored. | |
| 185 | ''' | |
| 186 | self.path=path | |
| 187 | self.filename=filename | |
| 188 | self.fullname=os.path.join(path,filename) | |
| 189 | return | |
| 190 | ||
| 191 | def exists(self): | |
| 192 | '''Method check if the statistics file exists.''' | |
| 193 | if(os.path.isfile(self.fullname)): | |
| 194 | return True | |
| 195 | else: | |
| 196 | return False | |
| 197 | ||
| 5795ac | 198 | def lineCount(self): |
| 8ab985 | 199 | ''' |
| SP | 200 | Internal method for determining the number of the lines in the most efficient way. Is it really the most efficient? |
| 201 | ''' | |
| 202 | f = open(self.fullname, "r+") | |
| 203 | try: | |
| 204 | buf = mmap.mmap(f.fileno(), 0) | |
| 205 | lines = 0 | |
| 206 | readline = buf.readline | |
| 207 | while readline(): | |
| 208 | lines += 1 | |
| 209 | f.close() | |
| 210 | except: | |
| 211 | lines=0 | |
| 212 | f.close() | |
| 213 | return lines | |
| 214 | ||
| 5795ac | 215 | def tail(self): |
| SP | 216 | with open(self.fullname,'r') as myfile: |
| 8ab985 | 217 | lines=myfile.readlines() |
| SP | 218 | return [lines[len(lines)-2].replace('\n',''),lines[len(lines)-1].replace('\n','')] |
| 219 | ||
| 5795ac | 220 | def checkFileValidity(self): |
| 8ab985 | 221 | try: |
| 5795ac | 222 | lines=self.tail() |
| 8ab985 | 223 | except: |
| SP | 224 | return(False) |
| 225 | if len(lines)<2: | |
| 226 | return(False) | |
| 5795ac | 227 | return(True) |
| SP | 228 | |
| 229 | def getSimulationDeltaTime(self): | |
| 230 | try: | |
| 231 | lines=self.tail() | |
| 232 | except: | |
| 233 | return 0 | |
| 234 | ||
| 8ab985 | 235 | fields=shlex.split(lines[0]) |
| SP | 236 | epoch1=fields[0] |
| 237 | n1=fields[1] | |
| 238 | ||
| 239 | fields=shlex.split(lines[1]) | |
| 240 | epoch2=fields[0] | |
| 241 | n2=fields[1] | |
| 242 | try: | |
| 5795ac | 243 | dT=int(epoch2)-int(epoch1) |
| 8ab985 | 244 | except: |
| 5795ac | 245 | return 0 |
| SP | 246 | return dT |
| 247 | ||
| 248 | def getLastIterationInStatistics(self): | |
| 249 | try: | |
| 250 | lines=self.tail() | |
| 251 | except: | |
| 252 | return 0 | |
| 253 | ||
| 254 | fields=shlex.split(lines[0]) | |
| 255 | epoch1=fields[0] | |
| 256 | n1=fields[1] | |
| 257 | ||
| 258 | fields=shlex.split(lines[1]) | |
| 259 | epoch2=fields[0] | |
| 260 | return (fields[1]) | |
| 99bb43 | 261 | |
| SP | 262 | def getColumn(self,n=0): |
| 263 | lines=self.readText().splitlines() | |
| 264 | col=[] | |
| 265 | name=lines[0].split()[n] | |
| 266 | for line in lines: | |
| 267 | col.append(line.split()[n]) | |
| 268 | return col[2:],name | |
| 269 | ||
| 270 | def getTable(self): | |
| 271 | lines=self.readText().splitlines() | |
| 272 | keys=lines[0].split() | |
| 273 | table={} | |
| 274 | def num(s): | |
| 275 | try: | |
| 276 | return int(s) | |
| 277 | except ValueError: | |
| 278 | return float(s) | |
| 279 | for key in keys: | |
| 280 | table[key]=[] | |
| 281 | for line in lines: | |
| 282 | fields=line.split() | |
| f0131d | 283 | for i in range(0,len(keys)): |
| 99bb43 | 284 | try: |
| SP | 285 | value=num(fields[i]) |
| 286 | table[keys[i]].append(value) | |
| 287 | except: | |
| 288 | pass | |
| 289 | return table | |
| 5795ac | 290 | |
| 8ab985 | 291 | |
| SP | 292 | def readText(self): |
| 293 | with open(self.fullname, 'r+') as fin: | |
| 294 | cont=fin.read() | |
| 295 | return cont | |
| 296 | ||
| 297 | def __str__(self): | |
| 298 | ''' | |
| 299 | Prints the full path with filename of the statistics.csv file | |
| 300 | ''' | |
| 301 | return(str(self.fullname)) | |
| 302 | ||
| 303 | ||
| 304 | ||
| 305 | class Runner: | |
| 306 | ''' | |
| 307 | Class Runner consists of a single running or terminated instance of the trisurf. It manages starting, stopping, verifying the running process and printing the reports of the configured instances. | |
| 308 | ''' | |
| 309 | ||
| 310 | @property | |
| 311 | def Dir(self): | |
| 312 | return Directory(maindir=self.maindir,simdir=self.subdir) | |
| 313 | ||
| 314 | ||
| 315 | @property | |
| 316 | def Statistics(self): | |
| 317 | return Statistics(self.Dir.fullpath(), "statistics.csv") | |
| 318 | ||
| 319 | def __init__(self, subdir='run0', tape=None, snapshot=None, runArgs=[]): | |
| 320 | self.subdir=subdir | |
| 321 | self.runArgs=runArgs | |
| 322 | self.isFromSnapshot=False | |
| 323 | if(tape!=None): | |
| 324 | self.initFromTape(tape) | |
| 325 | if(snapshot!=None): | |
| 326 | self.initFromSnapshot(snapshot) | |
| 327 | return | |
| 328 | ||
| 329 | ||
| 330 | def initFromTape(self, tape): | |
| 331 | self.Tape=Tape() | |
| 332 | self.Tape.readTape(tape) | |
| 333 | self.tapeFilename=tape | |
| 334 | ||
| 335 | def initFromSnapshot(self, snapshotfile): | |
| 336 | try: | |
| 337 | tree = ET.parse(snapshotfile) | |
| 338 | except: | |
| 339 | print("Error reading snapshot file") | |
| 340 | exit(1) | |
| 341 | self.isFromSnapshot=True | |
| 342 | self.snapshotFile=snapshotfile | |
| 343 | root = tree.getroot() | |
| 344 | tapetxt=root.find('tape') | |
| 345 | version=root.find('trisurfversion') | |
| 346 | self.Tape=Tape() | |
| 347 | self.Tape.setTape(tapetxt.text) | |
| 348 | ||
| 349 | def getPID(self): | |
| 350 | try: | |
| 351 | fp = open(os.path.join(self.Dir.fullpath(),'.lock')) | |
| 352 | except IOError as e: | |
| 353 | return 0 #file probably does not exist. e==2?? | |
| 354 | pid=fp.readline() | |
| 355 | fp.close() | |
| 356 | return int(pid) | |
| 357 | ||
| 358 | def getLastIteration(self): | |
| 359 | try: | |
| 360 | fp = open(os.path.join(self.Dir.fullpath(),'.status')) | |
| 361 | except IOError as e: | |
| 362 | return -1 #file probably does not exist. e==2?? | |
| 363 | status=fp.readline() | |
| 364 | fp.close() | |
| 365 | return int(status) | |
| 366 | ||
| 367 | def isCompleted(self): | |
| 368 | if int(self.Tape.getValue("iterations"))+int(self.Tape.getValue("inititer"))==self.getLastIteration()+1: | |
| 369 | return True | |
| 370 | else: | |
| 371 | return False | |
| 5795ac | 372 | |
| SP | 373 | |
| 374 | def getStartTime(self): | |
| 375 | try: | |
| 376 | return os.path.getmtime(os.path.join(self.Dir.fullpath(),'.lock')) | |
| 377 | except: | |
| 378 | return -1 | |
| 8ab985 | 379 | |
| SP | 380 | def getStatus(self): |
| 381 | pid=self.getPID() | |
| 382 | if(self.isCompleted()): | |
| 383 | return TS_COMPLETED | |
| 384 | if(pid==0): | |
| 385 | return TS_NOLOCK | |
| 386 | if(psutil.pid_exists(int(pid))): | |
| 387 | proc= psutil.Process(int(pid)) | |
| 388 | #psutil.__version__ == '3.4.2' requires name() and status(), some older versions reguire name, status | |
| 389 | if(psutil.__version__>='2.0.0'): | |
| 390 | procname=proc.name() | |
| 391 | procstat=proc.status() | |
| 392 | else: | |
| 393 | procname=proc.name | |
| 394 | procstat=proc.status | |
| 395 | if procname=="trisurf": | |
| 396 | if procstat=="stopped": | |
| 397 | return TS_STOPPED | |
| 398 | else: | |
| 399 | return TS_RUNNING | |
| 400 | else: | |
| 401 | return TS_NONEXISTANT | |
| 402 | else: | |
| 403 | return TS_NONEXISTANT | |
| 404 | ||
| 405 | def start(self): | |
| 406 | if(self.getStatus()==0 or self.getStatus()==TS_COMPLETED): | |
| 407 | #check if executable exists | |
| 408 | if(shutil.which('trisurf')==None): | |
| 409 | print("Error. Trisurf executable not found in PATH. Please install trisurf prior to running trisurf manager.") | |
| 410 | exit(1) | |
| 411 | #Symlinks tape file to the directory or create tape file from snapshot in the direcory... | |
| 412 | if(self.Dir.makeifnotexist()): | |
| 413 | if(self.isFromSnapshot==False): | |
| 414 | try: | |
| 415 | os.symlink(os.path.abspath(self.tapeFilename), self.Dir.fullpath()+"/tape") | |
| 416 | except: | |
| 417 | print("Error while symlinking "+os.path.abspath(self.tapeFilename)+" to "+self.Dir.fullpath()+"/tape") | |
| 418 | exit(1) | |
| 419 | else: | |
| 420 | try: | |
| 421 | with open (os.path.join(self.Dir.fullpath(),"tape"), "w") as myfile: | |
| 422 | #myfile.write("#This is automatically generated tape file from snapshot") | |
| 423 | myfile.write(str(self.Tape.rawText)) | |
| 424 | except: | |
| 425 | print("Error -- cannot make tapefile "+ os.path.join(self.Dir.fullpath(),"tape")+" from the snapshot in the running directory") | |
| 426 | exit(1) | |
| 427 | try: | |
| 428 | os.symlink(os.path.abspath(self.snapshotFile), os.path.join(self.Dir.fullpath(),"initial_snapshot.vtu")) | |
| 429 | except: | |
| 430 | print("Error while symlinking "+os.path.abspath(self.snapshotFile)+" to "+os.path.join(self.Dir.fullpath(),self.snapshotFile)) | |
| 431 | ||
| 432 | #check if the simulation has been completed. in this case notify user and stop executing. | |
| 433 | if(self.isCompleted() and ("--force-from-tape" not in self.runArgs) and ("--reset-iteration-count" not in self.runArgs)): | |
| 434 | print("The simulation was completed. Not starting executable in "+self.Dir.fullpath()) | |
| 435 | return | |
| 436 | ||
| 437 | cwd=Directory(maindir=os.getcwd()) | |
| 438 | lastVTU=self.getLastVTU() #we get last VTU file in case we need to continue the simulation from last snapshot. Need to be done before the Dir.goto() call. | |
| 439 | self.Dir.goto() | |
| 440 | print("Starting trisurf-ng executable in "+self.Dir.fullpath()) | |
| 441 | if(self.isFromSnapshot==True): | |
| 442 | #here we try to determine whether we should continue the simulation or start from last known VTU snapshot. | |
| 443 | if(lastVTU==None): | |
| 444 | initSnap="initial_snapshot.vtu" | |
| 445 | else: | |
| 446 | initSnap=lastVTU | |
| 447 | print("WARNING: Not using initial snapshot as starting point, but selecting "+initSnap+" as a starting vesicle") | |
| 448 | params=["trisurf", "--restore-from-vtk",initSnap]+self.runArgs | |
| 449 | print("InitSnap is: "+initSnap) | |
| 450 | else: | |
| 451 | #veify if dump exists. If not it is a first run and shoud be run with --force-from-tape | |
| 452 | if(os.path.isfile("dump.bin")==False): | |
| 453 | self.runArgs.append("--force-from-tape") | |
| 454 | params=["trisurf"]+self.runArgs | |
| 455 | subprocess.Popen (params, stdout=subprocess.DEVNULL) | |
| 456 | cwd.goto() | |
| 457 | else: | |
| 458 | print("Process in "+self.Dir.fullpath()+" already running. Not starting.") | |
| 459 | return | |
| 460 | ||
| 461 | ||
| 462 | def setMaindir(self,prefix,variables): | |
| 463 | maindir="" | |
| 464 | for p,v in zip(prefix,variables): | |
| 465 | if(v=="xk0"): | |
| 466 | tv=str(round(float(self.Tape.config[v]))) | |
| 467 | if sys.version_info<(3,0): | |
| 468 | tv=str(int(float(self.Tape.config[v]))) | |
| 469 | else: | |
| 470 | tv=self.Tape.config[v] | |
| 471 | maindir=maindir+p+tv | |
| 472 | self.maindir=maindir | |
| 473 | return | |
| 474 | ||
| 475 | def setSubdir(self, subdir="run0"): | |
| 476 | self.subdir=subdir | |
| 477 | return | |
| 478 | ||
| 479 | def getStatistics(self, statfile="statistics.csv"): | |
| 480 | self.Comment=FileContent(os.path.join(self.Dir.fullpath(),".comment")) | |
| 481 | pid=self.getPID() | |
| 482 | status=self.getStatus() | |
| 5795ac | 483 | if(self.Statistics.checkFileValidity()): |
| SP | 484 | ETA=str(datetime.timedelta(microseconds=(int(self.Tape.config['iterations'])-int(self.Statistics.getLastIterationInStatistics()))*self.Statistics.getSimulationDeltaTime())*1000000) |
| 8ab985 | 485 | if(status==TS_NONEXISTANT or status==TS_NOLOCK): |
| SP | 486 | statustxt="Not running" |
| 487 | pid="" | |
| 488 | ETA="" | |
| 489 | elif status==TS_STOPPED: | |
| 490 | statustxt="Stopped" | |
| 491 | ETA="N/A" | |
| 492 | elif status==TS_COMPLETED: | |
| 493 | statustxt="Completed" | |
| 494 | pid="" | |
| 495 | ETA="" | |
| 496 | else: | |
| 497 | statustxt="Running" | |
| 498 | ||
| 5795ac | 499 | if(self.Statistics.checkFileValidity()): |
| SP | 500 | report=[time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(int(self.getStartTime()))),ETA, statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()] |
| 8ab985 | 501 | else: |
| SP | 502 | report=["N/A","N/A",statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()] |
| 503 | return report | |
| 504 | ||
| 505 | ||
| 506 | def stop(self): | |
| 507 | try: | |
| 508 | p=psutil.Process(self.getPID()) | |
| 509 | p.kill() | |
| 510 | except: | |
| 511 | print("Could not stop the process. Is the process running? Do you have sufficient privileges?") | |
| 512 | ||
| 513 | ||
| 514 | def writeComment(self, data, mode='w'): | |
| 515 | self.Comment=FileContent(os.path.join(self.Dir.fullpath(),".comment")) | |
| 516 | self.Comment.writefile(data,mode=mode) | |
| 517 | ||
| 518 | ||
| f49271 | 519 | def getLastVTUold(self): |
| 8ab985 | 520 | vtuidx=self.getLastIteration()-int(self.Tape.getValue("inititer")) |
| SP | 521 | if vtuidx<0: |
| 522 | return None | |
| 523 | else: | |
| 524 | return 'timestep_{:06d}.vtu'.format(vtuidx) | |
| 525 | ||
| f49271 | 526 | def getLastVTU(self): |
| SP | 527 | flist=[] |
| 528 | for file in os.listdir(self.Dir.fullpath()): | |
| 529 | if file.endswith(".vtu"): | |
| 530 | flist.append(file) | |
| 52e871 | 531 | flist.sort() |
| SP | 532 | if(len(flist)==0): |
| 533 | return -1 | |
| 534 | else: | |
| 535 | return(flist[-1]) | |
| f49271 | 536 | |
| 8ab985 | 537 | def __str__(self): |
| SP | 538 | if(self.getStatus()==0): |
| 539 | str=" not running." | |
| 540 | else: | |
| 541 | str=" running." | |
| 542 | return(self.Dir.fullpath()+str) | |
| 543 | ||
| 57b1a6 | 544 | def __repr__(self): |
| SP | 545 | return("Instance of trisurf in "+self.Dir.fullpath()) |
