On Jan 8, 2008 3:40 PM, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > > On 1/8/2008 8:49 AM, Rod wrote: > > On Jan 8, 2008 12:41 PM, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > >> > >> Rod wrote: > >> > Hello, > >> > > >> > I have a memory problem when I run package WinBUGS with R (2.6.1). > >> > Until now I have been using a Pentium IV 3.2Ghz computer with 512Mb of > >> > RAM memory (with Windows XP Pro SP2), and I hadn't had any problem. > >> > Now I have a new computer with the following characteristics: Intel > >> > Core 2 duo 2.33Ghz and 3Gb of RAM memory (with Windows XP Pro SP2) and > >> > when I am running the same R syntax I receive the following error > >> > message: > >> > > >> > "Error: cannot allocate vector of size 216.0 Mb". > >> > > >> > This is an extract of my R syntax: > >> > > >> > > >> >> memory.limit(4000) > >> >> > >> > NULL > >> > > >> >> simu.BYM<-bugs(data, inits, parameters, model.file="Modelo.txt", > >> >> n.chains=3, n.iter=200000, n.burnin=20000, n.thin=180, debug=FALSE, > >> >> DIC=FALSE, digits=5, codaPkg=FALSE, bugs.directory="c:/Archivos de > >> >> programa/WinBUGS14", working.directory=NULL) > >> >> > >> > Error: cannot allocate vector of size 216.0 Mb > >> > > >> > I have tried: > >> > -Change size of virtual memory inside Windows XP > >> > -change the R memory settings > >> > -run from DOS (R CMD BATCH...) > >> > -reviewed the R Windows FAQ and R-Help. > >> > > >> > but I haven't be able to find a solution ! > >> Could you try R-patched? I recently fixed a minor bug that could have > >> symptoms like this. Under certain conditions it would miscalculate the > >> amount of available memory. You can download a copy from > >> cran.r-project.org/bin/windows/base/rpatched.html. > >> > >> Duncan Murdoch > >> > > > > Dear Duncan, > > > > Thank for your advice. But, the patched version produce the same error. > > In that case, you are probably really running out of memory. It's hard > to see why this would happen on the larger machine and not the smaller > one, but perhaps the code tries to adapt itself to available resources. > You are likely to have a bit of work diagnosing the problem. > > The tools to use are memory.size(), memory.limit() (which report on what > is available); memory.profile() (which gives more detail on usage). > Rprofmem() would also be nice, but it's not enabled in the standard > Windows build. > > Duncan Murdoch >
Dear Duncan, I have tried to run the same syntax in another pc (with exactly the same mark and model as mine) and I have obtained the same error. Then we can rule out that it is a problem with the hardware of my pc. I have tried to change the memory with command --max-mem-size=4000M ("c:\...\Rgui.exe" --max-mem-size=4000Mb) but I obtain this alert: WARNING: --max-mem-size=4000M: too large and taken as 2047 Here I show you the parameters of memory that I obtain before and after I run my syntax, and the gc() results obtained during the process. Perhaps this values can help you. thank you, Rodrigo ############# Memory values before I run the syntax############### > memory.limit() [1] 1535.875 > memory.size() [1] 29.42623 > memory.profile() NULL symbol pairlist closure environment promise 1 9368 407965 12045 2013 7091 language special builtin char logical integer 107052 269 2397 11503 13032 8429 double complex character ... any list 11122 17 122950 1 0 7535 expression bytecode externalptr weakref raw 1 0 1341 359 1 > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 727690 19.5 1166886 31.2 984024 26.3 Vcells 282062 2.2 786432 6.0 519695 4.0 ############# Memory values after I run the syntax############### > memory.limit() [1] 4000 > memory.size() [1] 1417.948 > memory.profile() NULL symbol pairlist closure environment promise 1 9921 466736 12211 2013 7091 language special builtin char logical integer 114491 269 2397 14534 13341 46991 double complex character ... any list 35508 17 131349 1 0 14663 expression bytecode externalptr weakref raw 1 0 1324 342 1 > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 876371 23.5 1835812 49.1 1835812 49.1 Vcells 1247398 9.6 121622414 928.0 180932899 1380.5 > memory.size(TRUE) [1] 1541.688 ############# gc() values during the process############### Garbage collection 330 = 271+30+29 (level 2) ... 23.6 Mbytes of cons cells used (48%) 9.9 Mbytes of vectors used (8%) Garbage collection 331 = 271+30+30 (level 2) ... 23.6 Mbytes of cons cells used (48%) 117.8 Mbytes of vectors used (49%) Garbage collection 332 = 271+30+31 (level 2) ... 23.6 Mbytes of cons cells used (48%) 225.8 Mbytes of vectors used (64%) Garbage collection 333 = 271+30+32 (level 2) ... 23.6 Mbytes of cons cells used (48%) 333.8 Mbytes of vectors used (72%) Garbage collection 334 = 272+30+32 (level 0) ... 23.6 Mbytes of cons cells used (48%) 441.9 Mbytes of vectors used (95%) Garbage collection 335 = 272+31+32 (level 1) ... 23.7 Mbytes of cons cells used (48%) 441.9 Mbytes of vectors used (95%) Garbage collection 336 = 272+31+33 (level 2) ... 23.8 Mbytes of cons cells used (48%) 226.0 Mbytes of vectors used (49%) Garbage collection 337 = 273+31+33 (level 0) ... 23.8 Mbytes of cons cells used (48%) 226.0 Mbytes of vectors used (49%) Garbage collection 338 = 274+31+33 (level 0) ... 24.1 Mbytes of cons cells used (49%) 288.7 Mbytes of vectors used (62%) Garbage collection 339 = 274+31+34 (level 2) ... 24.1 Mbytes of cons cells used (49%) 351.1 Mbytes of vectors used (55%) Garbage collection 340 = 274+31+35 (level 2) ... 24.1 Mbytes of cons cells used (49%) 476.1 Mbytes of vectors used (72%) Garbage collection 341 = 274+31+36 (level 2) ... 24.1 Mbytes of cons cells used (49%) 406.1 Mbytes of vectors used (58%) Garbage collection 342 = 275+31+36 (level 0) ... 24.1 Mbytes of cons cells used (49%) 550.1 Mbytes of vectors used (79%) Garbage collection 343 = 275+31+37 (level 2) ... 24.1 Mbytes of cons cells used (49%) 298.2 Mbytes of vectors used (41%) Garbage collection 344 = 275+31+38 (level 2) ... 24.1 Mbytes of cons cells used (49%) 406.1 Mbytes of vectors used (53%) Garbage collection 345 = 275+31+39 (level 2) ... 24.1 Mbytes of cons cells used (49%) 576.6 Mbytes of vectors used (71%) Garbage collection 346 = 275+31+40 (level 2) ... 24.1 Mbytes of cons cells used (49%) 639.1 Mbytes of vectors used (68%) Garbage collection 347 = 275+31+41 (level 2) ... 24.1 Mbytes of cons cells used (49%) 764.1 Mbytes of vectors used (78%) Garbage collection 348 = 275+31+42 (level 2) ... 24.1 Mbytes of cons cells used (49%) 694.0 Mbytes of vectors used (67%) Garbage collection 349 = 276+31+42 (level 0) ... 24.1 Mbytes of cons cells used (49%) 869.3 Mbytes of vectors used (84%) Garbage collection 350 = 276+31+43 (level 2) ... 24.1 Mbytes of cons cells used (49%) 576.6 Mbytes of vectors used (56%) Garbage collection 351 = 277+31+43 (level 0) ... 24.1 Mbytes of cons cells used (49%) 826.6 Mbytes of vectors used (80%) Garbage collection 352 = 277+32+43 (level 1) ... 24.1 Mbytes of cons cells used (49%) 694.0 Mbytes of vectors used (67%) Garbage collection 353 = 278+32+43 (level 0) ... 24.1 Mbytes of cons cells used (49%) 838.4 Mbytes of vectors used (81%) Garbage collection 354 = 278+33+43 (level 1) ... 24.1 Mbytes of cons cells used (49%) 694.5 Mbytes of vectors used (67%) Garbage collection 355 = 279+33+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 802.6 Mbytes of vectors used (78%) Garbage collection 356 = 280+33+43 (level 0) ... 24.4 Mbytes of cons cells used (50%) 803.7 Mbytes of vectors used (78%) Garbage collection 357 = 281+33+43 (level 0) ... 24.4 Mbytes of cons cells used (50%) 803.7 Mbytes of vectors used (78%) Garbage collection 358 = 282+33+43 (level 0) ... 24.4 Mbytes of cons cells used (50%) 803.8 Mbytes of vectors used (78%) Garbage collection 359 = 283+33+43 (level 0) ... 24.4 Mbytes of cons cells used (50%) 803.8 Mbytes of vectors used (78%) Garbage collection 360 = 284+33+43 (level 0) ... 24.4 Mbytes of cons cells used (50%) 803.8 Mbytes of vectors used (78%) Garbage collection 361 = 285+33+43 (level 0) ... 24.4 Mbytes of cons cells used (50%) 803.9 Mbytes of vectors used (78%) Garbage collection 362 = 286+33+43 (level 0) ... 24.4 Mbytes of cons cells used (50%) 803.9 Mbytes of vectors used (78%) Garbage collection 363 = 287+33+43 (level 0) ... 24.4 Mbytes of cons cells used (50%) 803.9 Mbytes of vectors used (78%) Garbage collection 364 = 288+33+43 (level 0) ... 24.4 Mbytes of cons cells used (50%) 804.0 Mbytes of vectors used (78%) Garbage collection 365 = 288+34+43 (level 1) ... 24.2 Mbytes of cons cells used (49%) 803.5 Mbytes of vectors used (78%) Garbage collection 366 = 289+34+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.6 Mbytes of vectors used (78%) Garbage collection 367 = 290+34+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.6 Mbytes of vectors used (78%) Garbage collection 368 = 291+34+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.7 Mbytes of vectors used (78%) Garbage collection 369 = 292+34+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.7 Mbytes of vectors used (78%) Garbage collection 370 = 293+34+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.8 Mbytes of vectors used (78%) Garbage collection 371 = 294+34+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.8 Mbytes of vectors used (78%) Garbage collection 372 = 295+34+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.9 Mbytes of vectors used (78%) Garbage collection 373 = 296+34+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.9 Mbytes of vectors used (78%) Garbage collection 374 = 297+34+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.0 Mbytes of vectors used (78%) Garbage collection 375 = 298+34+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.0 Mbytes of vectors used (78%) Garbage collection 376 = 299+34+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.1 Mbytes of vectors used (78%) Garbage collection 377 = 300+34+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.1 Mbytes of vectors used (78%) Garbage collection 378 = 301+34+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.2 Mbytes of vectors used (78%) Garbage collection 379 = 302+34+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.2 Mbytes of vectors used (78%) Garbage collection 380 = 303+34+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.3 Mbytes of vectors used (78%) Garbage collection 381 = 304+34+43 (level 0) ... 24.3 Mbytes of cons cells used (49%) 804.3 Mbytes of vectors used (78%) Garbage collection 382 = 305+34+43 (level 0) ... 24.3 Mbytes of cons cells used (49%) 804.4 Mbytes of vectors used (78%) Garbage collection 383 = 306+34+43 (level 0) ... 24.3 Mbytes of cons cells used (49%) 804.4 Mbytes of vectors used (78%) Garbage collection 384 = 307+34+43 (level 0) ... 24.3 Mbytes of cons cells used (49%) 804.5 Mbytes of vectors used (78%) Garbage collection 385 = 308+34+43 (level 0) ... 24.3 Mbytes of cons cells used (49%) 804.5 Mbytes of vectors used (78%) Garbage collection 386 = 308+35+43 (level 1) ... 24.2 Mbytes of cons cells used (49%) 803.6 Mbytes of vectors used (78%) Garbage collection 387 = 309+35+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.7 Mbytes of vectors used (78%) Garbage collection 388 = 310+35+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.7 Mbytes of vectors used (78%) Garbage collection 389 = 311+35+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.8 Mbytes of vectors used (78%) Garbage collection 390 = 312+35+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.9 Mbytes of vectors used (78%) Garbage collection 391 = 313+35+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.9 Mbytes of vectors used (78%) Garbage collection 392 = 314+35+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.0 Mbytes of vectors used (78%) Garbage collection 393 = 315+35+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.1 Mbytes of vectors used (78%) Garbage collection 394 = 316+35+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.1 Mbytes of vectors used (78%) Garbage collection 395 = 317+35+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.2 Mbytes of vectors used (78%) Garbage collection 396 = 318+35+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.2 Mbytes of vectors used (78%) Garbage collection 397 = 319+35+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.2 Mbytes of vectors used (78%) Garbage collection 398 = 320+35+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.3 Mbytes of vectors used (78%) Garbage collection 399 = 321+35+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.4 Mbytes of vectors used (78%) Garbage collection 400 = 322+35+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.4 Mbytes of vectors used (78%) Garbage collection 401 = 323+35+43 (level 0) ... 24.3 Mbytes of cons cells used (49%) 804.5 Mbytes of vectors used (78%) Garbage collection 402 = 324+35+43 (level 0) ... 24.3 Mbytes of cons cells used (49%) 804.5 Mbytes of vectors used (78%) Garbage collection 403 = 325+35+43 (level 0) ... 24.3 Mbytes of cons cells used (49%) 804.6 Mbytes of vectors used (78%) Garbage collection 404 = 326+35+43 (level 0) ... 24.3 Mbytes of cons cells used (49%) 804.7 Mbytes of vectors used (78%) Garbage collection 405 = 327+35+43 (level 0) ... 24.3 Mbytes of cons cells used (49%) 804.7 Mbytes of vectors used (78%) Garbage collection 406 = 328+35+43 (level 0) ... 24.3 Mbytes of cons cells used (49%) 804.8 Mbytes of vectors used (78%) Garbage collection 407 = 328+36+43 (level 1) ... 24.2 Mbytes of cons cells used (49%) 803.6 Mbytes of vectors used (78%) Garbage collection 408 = 329+36+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.7 Mbytes of vectors used (78%) Garbage collection 409 = 330+36+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.7 Mbytes of vectors used (78%) Garbage collection 410 = 331+36+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.8 Mbytes of vectors used (78%) Garbage collection 411 = 332+36+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.9 Mbytes of vectors used (78%) Garbage collection 412 = 333+36+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 803.9 Mbytes of vectors used (78%) Garbage collection 413 = 334+36+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.0 Mbytes of vectors used (78%) Garbage collection 414 = 335+36+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.1 Mbytes of vectors used (78%) Garbage collection 415 = 336+36+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.2 Mbytes of vectors used (78%) Garbage collection 416 = 337+36+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.2 Mbytes of vectors used (78%) Garbage collection 417 = 338+36+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.3 Mbytes of vectors used (78%) Garbage collection 418 = 339+36+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.3 Mbytes of vectors used (78%) Garbage collection 419 = 340+36+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.4 Mbytes of vectors used (78%) Garbage collection 420 = 341+36+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.5 Mbytes of vectors used (78%) Garbage collection 421 = 342+36+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.5 Mbytes of vectors used (78%) Garbage collection 422 = 343+36+43 (level 0) ... 24.2 Mbytes of cons cells used (49%) 804.6 Mbytes of vectors used (78%) Garbage collection 423 = 344+36+43 (level 0) ... 24.3 Mbytes of cons cells used (49%) 804.7 Mbytes of vectors used (78%) Garbage collection 424 = 345+36+43 (level 0) ... 24.3 Mbytes of cons cells used (49%) 804.8 Mbytes of vectors used (78%) Garbage collection 425 = 346+36+43 (level 0) ... 24.3 Mbytes of cons cells used (49%) 804.9 Mbytes of vectors used (78%) Garbage collection 426 = 347+36+43 (level 0) ... 24.3 Mbytes of cons cells used (49%) 804.9 Mbytes of vectors used (78%) Garbage collection 427 = 348+36+43 (level 0) ... 24.3 Mbytes of cons cells used (49%) 805.0 Mbytes of vectors used (78%) Garbage collection 428 = 348+36+44 (level 2) ... 24.2 Mbytes of cons cells used (49%) 515.0 Mbytes of vectors used (50%) Garbage collection 429 = 349+36+44 (level 0) ... 24.2 Mbytes of cons cells used (49%) 515.1 Mbytes of vectors used (50%) Garbage collection 430 = 350+36+44 (level 0) ... 24.2 Mbytes of cons cells used (49%) 515.1 Mbytes of vectors used (50%) Garbage collection 431 = 351+36+44 (level 0) ... 24.2 Mbytes of cons cells used (49%) 515.2 Mbytes of vectors used (50%) Garbage collection 432 = 352+36+44 (level 0) ... 24.2 Mbytes of cons cells used (49%) 515.3 Mbytes of vectors used (50%) Garbage collection 433 = 353+36+44 (level 0) ... 24.2 Mbytes of cons cells used (49%) 515.3 Mbytes of vectors used (50%) Garbage collection 434 = 354+36+44 (level 0) ... 24.2 Mbytes of cons cells used (49%) 515.4 Mbytes of vectors used (50%) Garbage collection 435 = 355+36+44 (level 0) ... 24.2 Mbytes of cons cells used (49%) 515.5 Mbytes of vectors used (50%) Garbage collection 436 = 356+36+44 (level 0) ... 24.2 Mbytes of cons cells used (49%) 515.6 Mbytes of vectors used (50%) Garbage collection 437 = 357+36+44 (level 0) ... 24.2 Mbytes of cons cells used (49%) 515.7 Mbytes of vectors used (50%) Garbage collection 438 = 358+36+44 (level 0) ... 24.2 Mbytes of cons cells used (49%) 515.8 Mbytes of vectors used (50%) Garbage collection 439 = 359+36+44 (level 0) ... 24.2 Mbytes of cons cells used (49%) 515.9 Mbytes of vectors used (50%) Garbage collection 440 = 360+36+44 (level 0) ... 24.2 Mbytes of cons cells used (49%) 516.0 Mbytes of vectors used (50%) Garbage collection 441 = 361+36+44 (level 0) ... 24.2 Mbytes of cons cells used (49%) 516.0 Mbytes of vectors used (50%) Garbage collection 442 = 362+36+44 (level 0) ... 24.3 Mbytes of cons cells used (49%) 516.1 Mbytes of vectors used (50%) Garbage collection 443 = 363+36+44 (level 0) ... 24.3 Mbytes of cons cells used (49%) 516.2 Mbytes of vectors used (50%) Garbage collection 444 = 364+36+44 (level 0) ... 24.3 Mbytes of cons cells used (49%) 516.2 Mbytes of vectors used (50%) Garbage collection 445 = 365+36+44 (level 0) ... 24.3 Mbytes of cons cells used (49%) 516.3 Mbytes of vectors used (50%) Garbage collection 446 = 366+36+44 (level 0) ... 24.3 Mbytes of cons cells used (49%) 516.4 Mbytes of vectors used (50%) Garbage collection 447 = 367+36+44 (level 0) ... 24.3 Mbytes of cons cells used (49%) 516.4 Mbytes of vectors used (50%) Garbage collection 448 = 368+36+44 (level 0) ... 24.3 Mbytes of cons cells used (49%) 516.5 Mbytes of vectors used (50%) Garbage collection 449 = 368+37+44 (level 1) ... 24.2 Mbytes of cons cells used (49%) 515.0 Mbytes of vectors used (50%) Garbage collection 450 = 369+37+44 (level 0) ... 24.2 Mbytes of cons cells used (49%) 839.2 Mbytes of vectors used (81%) Garbage collection 451 = 369+38+44 (level 1) ... 24.2 Mbytes of cons cells used (49%) 893.2 Mbytes of vectors used (87%) Garbage collection 452 = 369+38+45 (level 2) ... 24.2 Mbytes of cons cells used (49%) 731.1 Mbytes of vectors used (67%) Garbage collection 453 = 369+38+46 (level 2) ... 24.2 Mbytes of cons cells used (49%) 947.2 Mbytes of vectors used (77%) Garbage collection 454 = 369+38+47 (level 2) ... 24.2 Mbytes of cons cells used (49%) 1217.2 Mbytes of vectors used (91%) Garbage collection 455 = 369+38+48 (level 2) ... 24.2 Mbytes of cons cells used (49%) 1325.1 Mbytes of vectors used (91%) Garbage collection 456 = 369+38+49 (level 2) ... 24.4 Mbytes of cons cells used (50%) 1380.4 Mbytes of vectors used (82%) Garbage collection 457 = 370+38+49 (level 0) ... 24.4 Mbytes of cons cells used (50%) 1380.4 Mbytes of vectors used (82%) Error: cannot allocate vector of size 216.0 Mb ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.