January 2010 - Nek5000-users - mailman3.cels.anl.gov

Restart
by nek5000-users＠lists.mcs.anl.gov 21 Jan '10

21 Jan '10

Hallo, I have some problems to restart my runs. I tried to do it like it's described in the "NEK5000 Primer" (to change the line in the .rea file). Here my new entry in the .rea file: 1 PRESOLVE/RESTART OPTIONS ***** channel_old.fld01 But it doesn't work. Here the last lines of the log-file: set initial conditions Checking restart options: channel_old.fld01 TIME=130.78383346949016 Reading checkpoint data 0 0 OPEN: channel_old.fld01 640 6 6 6 1.3078383E+0210000 X Y Z U P NELT,NX,NY,N 0.000 0.000 0.000 0.000 0.000 NONSTD HDR, parse_hdr, abort. call exitt: dying ... backtrace(): obtained 12 stack frames. ./nek5000 [0x4de05a] ./nek5000 [0x5da15d] ./nek5000 [0x46e248] ./nek5000 [0x46ceff] ./nek5000 [0x46d302] ./nek5000 [0x471df0] ./nek5000 [0x47577b] ./nek5000 [0x407db2] ./nek5000 [0x4074ca] ./nek5000 [0x60c9ac] /lib/libc.so.6(__libc_start_main+0xe6) [0x7ff0e9c101a6] ./nek5000 [0x4073e9] total elapsed time : 1.09375E+00 sec total solver time incl. I/O : 0.00000E+00 sec CPU seconds/timestep/DOF : 0.00000E+00 sec time/timestep : 0.00000E+00 sec real 0m1.107s user 0m0.996s sys 0m0.100s I tried it with different job names (same like the new, different to the new one...) and even with a channel_old.fld01 TIME=130.78383346949016 entry.. Do you know where might be the problem?? Thx a lot.. Greets, Fred

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Re: [Nek5000-users] **ERROR**: Failed in HMHOLTZ
by nek5000-users＠lists.mcs.anl.gov 19 Jan '10

19 Jan '10

Here my usr-file. For some tests I'm using a fixed driving force ffz and calculate my u_bar in every timestep (subroutine calc_ubar). The calculation also works if I'm only setting p94 to zero (projection of the velocity)... What do you mean by "what happens if you integrate for say 1 flow-through time"?? C----------------------------------------------------------------------- C nek5000 user-file template C C user specified routines: C - userbc : boundary conditions C - useric : initial conditions C - uservp : variable properties C - userf : local acceleration term for fluid C - userq : local source term for scalars C - userchk: general purpose routine for checking errors etc. C C----------------------------------------------------------------------- subroutine uservp (ix,iy,iz,eg) include 'SIZE' include 'TOTAL' include 'NEKUSE' integer e,f,eg c e = gllel(eg) udiff = 0.0 utrans = 0.0 return end c----------------------------------------------------------------------- subroutine userf (ix,iy,iz,eg) c c Note: this is an acceleration term, NOT a force! c Thus, ffx will subsequently be multiplied by rho(x,t). c include 'SIZE' include 'TOTAL' include 'NEKUSE' integer e,f,eg c e = gllel(eg) ffx = 0.0 ffy = 0.0 ffz = 0.05 return end c----------------------------------------------------------------------- subroutine userq (ix,iy,iz,eg) include 'SIZE' include 'TOTAL' include 'NEKUSE' integer e,f,eg c e = gllel(eg) qvol = 0.0 source = 0.0 return end c----------------------------------------------------------------------- subroutine userchk include 'SIZE' include 'TOTAL' include 'ZPER' ! for nelx,nely,nelz call calc_ubar(vz,1.0) return end c----------------------------------------------------------------------- subroutine userbc (ix,iy,iz,iside,ieg) include 'SIZE' include 'TOTAL' include 'NEKUSE' ux = 0.0 uy = 0.0 uz = 0.0 temp = 0.0 return end c----------------------------------------------------------------------- subroutine useric (ix,iy,iz,ieg) include 'SIZE' include 'TOTAL' include 'NEKUSE' ux = 0.0 uy = 0.0 uz = (1-(y-0.5)**2) temp = 0.0 return end c----------------------------------------------------------------------- subroutine usrdat ! This routine to modify element vertices include 'SIZE' include 'TOTAL' return end c----------------------------------------------------------------------- subroutine usrdat2 ! This routine to modify mesh coordinates include 'SIZE' include 'TOTAL' return end c----------------------------------------------------------------------- subroutine usrdat3 include 'SIZE' include 'TOTAL' return end c----------------------------------------------------------------------- subroutine calc_ubar(u,idir) ! driving force for Ubar = 1 include 'SIZE' include 'TOTAL' common /uforce/ utldo(ldim) n=nx1*ny1*nz1*nelv if (istep.eq.0) f_new=param(71) ! Update forcing for Ubar = 2 ubar = glsc2(u,bm1,n)/volvm1 open(unit=10,file='u_bar.out') write(10,*) ubar,ISTEP,TIME return end

1 1

Re: [Nek5000-users] **ERROR**: Failed in HMHOLTZ
by nek5000-users＠lists.mcs.anl.gov 19 Jan '10

19 Jan '10

I created the mesh with PRENEK. Yes, in x I hace periodic bcs, wall in y (top and bottom) and I also used periodic bcs in z. For USERBC I used the same like in the turbChannel example.

1 1

**ERROR**: Failed in HMHOLTZ
by nek5000-users＠lists.mcs.anl.gov 19 Jan '10

19 Jan '10

Here the useric subroutine (the flow direction is z) c----------------------------------------------------------------------- subroutine useric (ix,iy,iz,ieg) include 'SIZE' include 'TOTAL' include 'NEKUSE' ux = 0.0 uy = 0.0 uz = (1-(y-0.5)**2) temp = 0.0 return end c----------------------------------------------------------------------- the userbc subroutine: c----------------------------------------------------------------------- subroutine userbc (ix,iy,iz,iside,ieg) include 'SIZE' include 'TOTAL' include 'NEKUSE' ux = 0.0 uy = 0.0 uz = 0.0 temp = 0.0 return end c----------------------------------------------------------------------- Here the logfile (I stopped the run after step 8): /----------------------------------------------------------\\ | _ __ ______ __ __ ______ ____ ____ ____ | | / | / // ____// //_/ / ____/ / __ \\ / __ \\ / __ \\ | | / |/ // __/ / ,< /___ \\ / / / // / / // / / / | | / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / | | /_/ |_//_____//_/ |_|/_____/ \\____/ \\____/ \\____/ | | | |----------------------------------------------------------| | | | NEK5000: Open Source Spectal Element Solver | | COPYRIGHT (c) 2008 UCHICAGO ARGONNE, LLC | | Version: 1.0rc1 / SVN r369M | | Web: http://nek5000.mcs.anl.gov | | | \\----------------------------------------------------------/ Number of processors: 1 REAL wdsize : 8 INTEGER wdsize : 4 Beginning session: /home/folke/nek5_svn/runs/test_channel/channel.rea timer accuracy: 0.0000000E+00 sec read .rea file nelgt/nelgv/lelt: 640 640 643 lx1 /lx2 /lx3 : 6 4 4 mapping elements to processors 0 640 640 640 640 NELV RANK 0 IEG 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 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 67 68 69 70 71 72 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 done :: mapping elements to processors 0 objects found readat time 8.20312500000000000E-002 sec done :: read .rea file setup domain topology Right-handed check complete for 640 elements. OK. setvert3d: 6 6 6 setupds3d: 6 720 9040 41040 41040 41040 gs_setup: 0 unique labels shared gs_init time 5.0781E-02 seconds 6 640 138240 41040 0 8 max multiplicity done :: setup domain topology call usrdat done :: usrdat generate geomerty data vol_t,vol_v: 9.9999999999975824 9.9999999999975824 done :: generate geomerty data call usrdat2 done :: usrdat2 regenerate geomerty data 1 vol_t,vol_v: 9.9999999999980407 9.9999999999980407 done :: regenerate geomerty data 1 verify mesh topology -1.0000000000000002 1.0000000000000002 Xrange 0.0000000000000000 1.0000000000000002 Yrange 0.0000000000000000 5.0000000000000018 Zrange done :: verify mesh topology 103 Parameters from file:/home/folke/nek5_svn/runs/test_channel/channel.rea 1 1.00000 DENSITY 2 -1000.00 VISCOS 7 1.00000 RHOCP 8 1.00000 CONDUCT 11 10.00000 NSTEPS 12 0.500000 DT 13 20.0000 IOCOMM 18 -20.0000 GRID 19 -1.00000 INTYPE 20 5.00000 NORDER 21 1.00000E-05 DIVERGENCE 22 1.000000E-08 HELMHOLTZ 24 0.100000E-01 TOLREL 25 0.100000E-01 TOLABS 26 0.250000 COURANT 27 2.00000 TORDER 28 0.00000 49 0.00000 65 1.00000 new file each dump (1) # P065 number of I 67 0.00000 read format # P067 Read format 68 1 iostep for avg_all (if ^= 0, else = iostep) # P068 averaging f 71 0.0021 initial ffx # P071 not used 93 20.000 Number of pressure sol'ns saved # P093 if >0, numb 94 5.00000 start saving pressure soln's after this # P094 if >0, star 95 5.00000 start saving pressure soln's after this # P095 if >0, star 99 4.000000E+00 p99 = 3 --> dealias turned on # P099 dealiasing: 101 1.000000E+00 p101 = # of addl filter modes # P101 number of a 102 1.00000 Dump out divergence at each time step # P102 ????? 103 -1 0.010 # P103 filter weight for last mode (<0: disabled) IFTRAN = T IFFLOW = T IFHEAT = F IFSPLIT = F IFLOMACH = F IFUSERVP = F IFUSERMV = F IFSTRS = F IFCHAR = F IFCYCLIC = F IFAXIS = F IFMVBD = F IFMELT = F IFMODEL = F IFKEPS = F IFMOAB = F IFSYNC = F IFVCOR = T IFINTQ = F IFCWUZ = F IFSWALL = F IFGEOM = F IFSURT = F IFWCNO = F IFTMSH for field 1 = F IFADVC for field 1 = T IFNONL for field 1 = F Estimated eigenvalues EIGAA = 4.2439298924684223 EIGGA = 89413.331884118597 EIGAE = 0.39478417604357408 EIGAS = 7.75193798449612132E-003 EIGGE = 89413.331884118597 EIGGS = 2.0000000000000000 verify mesh topology -1.0000000000000002 1.0000000000000002 Xrange 0.0000000000000000 1.0000000000000002 Yrange 0.0000000000000000 5.0000000000000018 Zrange done :: verify mesh topology E-solver strategy: 1 0 estrat 1 10 0.0000000000000000 itr mg_nx: 1 3 5 mg_ny: 1 3 5 mg_nz: 1 3 5 setvert3d: 2 2 2 gs_setup: 0 unique labels shared gs_init time 1.5625E-02 seconds 2 640 5120 720 1 setvert3d: 4 4 4 setupds3d: 4 720 4880 12880 12880 12880 gs_setup: 0 unique labels shared gs_init time 1.5625E-02 seconds 4 640 40960 12880 2 setvert3d: 4 4 4 setupds3d: 4 720 4880 12880 12880 12880 gs_setup: 0 unique labels shared gs_init time 2.3438E-02 seconds 4 640 40960 12880 3 setvert3d: 6 6 6 setupds3d: 6 720 9040 41040 41040 41040 gs_setup: 0 unique labels shared gs_init time 7.0313E-02 seconds 6 640 138240 41040 4 setup h1 coarse grid setvert3d: 2 2 2 gs_setup: 0 unique labels shared gs_setup: 0 unique labels shared set_up_h1_crs time: 0.20703125000000000 seconds done :: setup h1 coarse grid call usrdat3 done :: usrdat3 set initial conditions call nekuic for vel xyz min -1.0000 0.0000 0.0000 uvwpt min 0.86087E-20 0.86087E-20 0.75000 0.0000 0.86087E-20 PS min 0.99000E+22 xyz max 1.0000 1.0000 5.0000 uvwpt max 0.80000E-19 0.80000E-19 1.0000 0.0000 0.80000E-19 PS max -0.99000E+22 done :: set initial conditions call userchk done :: userchk dofs: 78000 40960 7760 Initialization successfully completed 2.6484 sec Starting time loop ... DT/DTCFL/DTFS/DTINIT 0.147E-01 0.147E-01 0.000E+00 0.500E+00 Step 1, t= 1.4684042E-02, DT= 1.4684042E-02, C= 0.250 1.2500E-01 1.2500E-01 Solving for fluid 1.00000000000000002E-008 p22 1 1 1 1 Helmholtz VELX F: 1.2365E-19 1.0000E-08 1.0000E-03 6.8101E+01 1 Hmholtz VELX: 0 1.2365E-19 1.2365E-19 1.0000E-08 1.00000000000000002E-008 p22 1 1 1 1 Helmholtz VELY F: 1.2365E-19 1.0000E-08 1.0000E-03 6.8101E+01 1 Hmholtz VELY: 0 1.2365E-19 1.2365E-19 1.0000E-08 1.00000000000000002E-008 p22 1 1 1 1 Helmholtz VELZ F: 2.5258E+00 1.0000E-08 1.0000E-03 6.8101E+01 1 2 Helmholtz VELZ F: 3.3988E-01 1.0000E-08 1.0000E-03 6.8101E+01 1 3 Helmholtz VELZ F: 5.4135E-02 1.0000E-08 1.0000E-03 6.8101E+01 1 4 Helmholtz VELZ F: 8.7135E-03 1.0000E-08 1.0000E-03 6.8101E+01 1 5 Helmholtz VELZ F: 7.5232E-04 1.0000E-08 1.0000E-03 6.8101E+01 1 6 Helmholtz VELZ F: 1.6707E-04 1.0000E-08 1.0000E-03 6.8101E+01 1 7 Helmholtz VELZ F: 3.8786E-05 1.0000E-08 1.0000E-03 6.8101E+01 1 8 Helmholtz VELZ F: 4.9937E-06 1.0000E-08 1.0000E-03 6.8101E+01 1 9 Helmholtz VELZ F: 7.4701E-07 1.0000E-08 1.0000E-03 6.8101E+01 1 10 Helmholtz VELZ F: 1.2222E-07 1.0000E-08 1.0000E-03 6.8101E+01 1 11 Helmholtz VELZ F: 2.4478E-08 1.0000E-08 1.0000E-03 6.8101E+01 1 12 Helmholtz VELZ F: 4.5145E-09 1.0000E-08 1.0000E-03 6.8101E+01 1 Hmholtz VELZ: 11 4.5145E-09 2.5258E+00 1.0000E-08 1 1.00000E-05 3.17251E-10 3.99951E-10 7.93224E-01 1 Divergence 1 U-Pres gmres: 1 3.1725E-10 1.0000E-05 3.9995E-10 1.4063E-01 1 DNORM, DIVEX 3.17250961806725983E-010 3.17251059854635242E-010 1 1.4684E-02 1.1133E+00 Fluid done schfile:/home/folke/nek5_svn/runs/test_channel/channel.sch Step 2, t= 2.9368085E-02, DT= 1.4684042E-02, C= 0.250 2.2695E+00 2.1445E+00 Solving for fluid 1.00000000000000002E-008 p22 2 1 2 Hmholtz VELX: 0 8.4698E-11 8.4698E-11 1.0000E-08 1.00000000000000002E-008 p22 2 1 2 Hmholtz VELY: 0 3.3881E-10 3.3881E-10 1.0000E-08 1.00000000000000002E-008 p22 2 1 2 Hmholtz VELZ: 9 9.0588E-09 2.4120E+00 1.0000E-08 2 U-Pres gmres: 1 4.2967E-10 1.0000E-05 6.2883E-10 1.7578E-01 2 DNORM, DIVEX 4.29672058094189053E-010 4.29672004136921625E-010 2 2.9368E-02 9.3359E-01 Fluid done Step 3, t= 4.4052127E-02, DT= 1.4684042E-02, C= 0.250 3.8945E+00 1.6250E+00 Solving for fluid 1.00000000000000002E-008 p22 3 1 3 Hmholtz VELX: 0 2.0686E-10 2.0686E-10 1.0000E-08 1.00000000000000002E-008 p22 3 1 3 Hmholtz VELY: 0 7.3369E-10 7.3369E-10 1.0000E-08 1.00000000000000002E-008 p22 3 1 3 Hmholtz VELZ: 9 6.0801E-09 1.5993E+00 1.0000E-08 3 U-Pres gmres: 1 2.1081E-10 1.0000E-05 5.6586E-10 1.2500E-01 3 DNORM, DIVEX 2.10806427110722163E-010 2.10806458332255450E-010 3 4.4052E-02 7.9688E-01 Fluid done Step 4, t= 5.8736169E-02, DT= 1.4684042E-02, C= 0.250 5.2461E+00 1.3516E+00 Solving for fluid 1.00000000000000002E-008 p22 4 1 4 Hmholtz VELX: 0 2.3711E-10 2.3711E-10 1.0000E-08 1.00000000000000002E-008 p22 4 1 4 Hmholtz VELY: 0 1.0978E-09 1.0978E-09 1.0000E-08 1.00000000000000002E-008 p22 4 1 4 Hmholtz VELZ: 9 4.1584E-09 1.0849E+00 1.0000E-08 4 U-Pres gmres: 1 1.2092E-10 1.0000E-05 2.0354E-10 1.3672E-01 4 DNORM, DIVEX 1.20917860593520714E-010 1.20917830212450389E-010 4 5.8736E-02 8.7109E-01 Fluid done Step 5, t= 7.3420211E-02, DT= 1.4684042E-02, C= 0.250 6.6484E+00 1.4023E+00 Solving for fluid this is mprev: 20 20 alpha1: 2.09756734094134443E-010 9.9999999999980407 138240 binvm1: 360000.00000000384 0.12500000000000000 -5.93354375460066903E-021 5 2.0976E-10 2.0976E-10 1.0000E+00 0 alph1x 5 halpha 0 5 Hmholtz VELX: 0 2.0976E-10 2.0976E-10 1.0000E-08 5 9.3816E-10 9.3816E-10 1.0000E+00 0 alph1x 5 halpha 0 5 Hmholtz VELY: 0 9.3816E-10 9.3816E-10 1.0000E-08 5 8.0549E-01 8.0549E-01 1.0000E+00 0 alph1x 5 halpha 0 5 Hmholtz VELZ: 9 2.7499E-09 8.0549E-01 1.0000E-08 5 U-Pres gmres: 1 2.8336E-10 1.0000E-05 3.9384E-10 1.0547E-01 5 DNORM, DIVEX 2.83364732567017946E-010 2.83364756720865127E-010 5 7.3420E-02 1.1406E+00 Fluid done Step 6, t= 8.8104254E-02, DT= 1.4684042E-02, C= 0.250 8.4688E+00 1.8203E+00 Solving for fluid 6 1.9617E-10 NaN NaN 1 alph1x 6 halpha 1 NaN 6 5000 **ERROR**: Failed in HMHOLTZ: VELX NaN NaN 1.0000E-08 6 8.1680E-10 NaN NaN 1 alph1x 6 halpha 1 NaN 6 5000 **ERROR**: Failed in HMHOLTZ: VELY NaN NaN 1.0000E-08 6 6.5525E-01 1.3376E-01 4.8988E+00 1 alph1x 6 halpha 1 1.9191E-01 6 Hmholtz VELZ: 8 9.0843E-09 1.3376E-01 1.0000E-08 6 1 alpha: NaN 6 1 NaN NaN NaN alph12 6 U-Pres gmres: 120 NaN 1.0000E-05 NaN 1.3609E+01 6 DNORM, DIVEX NaN NaN 6 8.8104E-02 2.5375E+02 Fluid done Step 7, t= 1.0572510E-01, DT= 1.7620851E-02, C=******* 2.6286E+02 2.5439E+02 Solving for fluid 7 NaN NaN NaN 0 alph1x 7 halpha 0 7 5000 **ERROR**: Failed in HMHOLTZ: VELX NaN NaN 1.0000E-08 7 NaN NaN NaN 2 alph1x 7 halpha 2 NaN NaN 7 5000 **ERROR**: Failed in HMHOLTZ: VELY NaN NaN 1.0000E-08 7 NaN NaN NaN 2 alph1x 7 halpha 2 NaN NaN 7 5000 **ERROR**: Failed in HMHOLTZ: VELZ NaN NaN 1.0000E-08 reorthogo: 2 7 1 alpha: NaN 7 1 NaN NaN NaN alph12 7 U-Pres gmres: 120 NaN 1.0000E-05 NaN 1.4965E+01 7 DNORM, DIVEX NaN NaN 7 1.0573E-01 3.4402E+02 Fluid done Step 8, t= 1.2687013E-01, DT= 2.1145021E-02, C=******* 6.0731E+02 3.4445E+02 Solving for fluid 8 NaN NaN NaN 0 alph1x 8 halpha 0 8 5000 **ERROR**: Failed in HMHOLTZ: VELX NaN NaN 1.0000E-08 8 NaN NaN NaN 3 alph1x 8 halpha 3 NaN NaN NaN 8 5000 **ERROR**: Failed in HMHOLTZ: VELY NaN NaN 1.0000E-08 8 NaN NaN NaN 3 alph1x 8 halpha 3 NaN NaN NaN 8 5000 **ERROR**: Failed in HMHOLTZ: VELZ NaN NaN 1.0000E-08 reorthogo: 2 8 1 alpha: NaN 8 1 NaN NaN NaN alph12 8 U-Pres gmres: 120 NaN 1.0000E-05 NaN 1.3871E+01 8 DNORM, DIVEX NaN NaN 8 1.2687E-01 3.5561E+02 Fluid done Output: -1 8 1.2687E-01 Write checkpoint: 8 1.2687E-01 OPEN: channel.fld01 call nek_end runtime statistics: 0 opcount 336739039360.00000 TOTAL OPCOUNT 336739039360.00000 opnode 0 subcl4 0.000000 opnode 0 ascol5 0.000000 0 opnode 0 vlsum 0.000000 0 opnode 0 inver2 1105920. 8 opnode 0 vsqrt 3317760. 24 opnode 0 invcl1 3317760. 24 opnode 0 opcolv 3317760. 8 opnode 0 sub2 4408320. 34 opnode 0 subcl3 6635520. 24 opnode 0 opa2cl 6635520. 8 opnode 0 invcl2 6635520. 48 opnode 0 add3s2 9953280. 24 opnode 0 opcv3c 0.1244160E+08 15 opnode 0 cadd 0.1560576E+08 381 opnode 0 glsc2 0.4501504E+08 445 opnode 0 invcl3 0.5363712E+08 388 opnode 0 addcl3 0.2012774E+09 1520664 opnode 0 opbinv 0.2145485E+09 388 opnode 0 VLSC2 0.6090650E+09 7404 opnode 0 ADD3 0.5553428E+10 25708808 opnode 0 cmult 0.5555005E+10 25708818 opnode 0 col3 0.5773681E+10 3081917 opnode 0 ADD2 0.5945682E+10 27230464 opnode 0 add2s1 0.1108104E+11 40079 opnode 0 VLSC3 0.1662364E+11 40084 opnode 0 addcl4 0.1663940E+11 40122 opnode 0 glsc3 0.1664233E+11 40134 opnode 0 col2 0.2255086E+11 78922456 opnode 0 add2s2 0.2278993E+11 87891 opnode 0 mxm 0.2063871E+12 250425600 total time 967.00390625000000 964.35546884999997 copy time 0 0.0000000000000000 0.0000000000000000 mxmf time 0 0.0000000000000000 0.0000000000000000 inv3 time 388 0.65234375000000000 6.76455696132385745E-004 invc time 48 7.03125000000000000E-002 7.29113923975026546E-005 mltd time 1188 6.8515625000000000 7.10481012584553671E-003 cdtp time 1188 9.1953125000000000 9.53518987242895841E-003 eslv time 8 43.132812500000000 4.47270886029569117E-002 pres time 8 43.765625000000000 4.53832911345344314E-002 crsl time 365 0.44921875000000000 4.65822784761822542E-004 crsl min 0.44921875000000000 crsl max 0.44921875000000000 crsl avg 0.44921875000000000 hmhz time 12 911.79687500000000 0.94549873407917062 usbc time 9 0.32031250000000000 3.32151898699734353E-004 axhm time 40189 394.10937500000000 0.40867645565382432 advc time 1112775117 6.61060408125804329E-202 6.85494539595573689E-205 gop time 81651 1.9687500000000000 2.04151898713007427E-003 gop min 1.9687500000000000 gop max 1.9687500000000000 gop avg 1.9687500000000000 vdss time 389 2.5820312500000000 2.67746835415273634E-003 vdss min 2.5820312500000000 vdss max 2.5820312500000000 vdss avg 2.5820312500000000 dsum time 41263 86.929687500000000 9.01427848007791271E-002 dsum min 86.929687500000000 dsum max 86.929687500000000 dsum avg 86.929687500000000 gsum time 0 0.0000000000000000 0.0000000000000000 dsnd time 0 0.0000000000000000 0.0000000000000000 dadd time 0 1.8984375000000000 1.96860759473257161E-003 dsmx time 0 7.81250000000000000E-002 8.10126582194474015E-005 dsmn time 0 0.0000000000000000 0.0000000000000000 slvb time 0 0.0000000000000000 0.0000000000000000 ddsl time 365 17.832031250000000 1.84911392385888676E-002 solv time 365 3.0937500000000000 3.20810126549011696E-003 sett time 0 0.0000000000000000 0.0000000000000000 prep time 8 1.0703125000000000 1.10987341760642941E-003 bsol time 0 0.0000000000000000 0.0000000000000000 bso2 time 0 0.0000000000000000 0.0000000000000000 # nid tusbc tdadd tcrsl tvdss tdsum tgop qqq 0 3.2031E-01 1.8984E+00 4.4922E-01 2.5820E+00 8.6930E+01 1.9688E+00 qqq Simulation successfully completed call exitt: dying ... backtrace(): obtained 5 stack frames. ./nek5000 [0x4de05a] ./nek5000 [0x5da15d] ./nek5000 [0x60c9ac] /lib/libc.so.6(__libc_start_main+0xe6) [0x7f7ee3cc71a6] ./nek5000 [0x4073e9] total elapsed time : 9.67008E+02 sec total solver time incl. I/O : 6.07313E+02 sec CPU seconds/timestep/DOF : 5.49147E-04 sec time/timestep : 7.59141E+01 sec real 16m7.038s user 13m48.072s sys 0m2.980s

1 2

**ERROR**: Failed in HMHOLTZ
by nek5000-users＠lists.mcs.anl.gov 19 Jan '10

19 Jan '10

Hello, when I run my simulation (periodic open-channel flow) I got the following error message at timestep 6: Step 6, t= 1.0043885E-01, DT= 2.1145021E-02, C= 0.203 1.7406E+01 3.5078E+00 Solving for fluid 6 6.1565E-10 6.1565E-10 1.0000E+00 0 alph1x 6 halpha 0 6 Hmholtz VELX: 1 4.3435E-10 6.1565E-10 1.0000E-08 6 2.6858E-09 NaN NaN 1 alph1x 6 halpha 1 NaN 6 5000 **ERROR**: Failed in HMHOLTZ: VELY NaN NaN 1.0000E-08 6 6.2743E+00 8.5949E-01 7.3000E+00 1 alph1x 6 halpha 1 2.0336E+00 6 Hmholtz VELZ: 76 8.4969E-09 8.5949E-01 1.0000E-08 reorthogo: 1 6 1 alpha: NaN 6 1 NaN NaN NaN alph12 6 U-Pres gmres: 120 NaN 1.0000E-05 NaN 1.5230E+01 6 DNORM, DIVEX NaN NaN 6 1.0044E-01 1.2954E+02 Fluid done In the rea-file the parameter 94 and 95 are set to: P94 = 5.0 P95 = 5.0 If I set P94=0.0 the simulation is running without stopping at timestep 6. I tried to decrease P21 (DIVERGENCE) and P22 (HELMHOLTZ) similar to the turbChannel example, but without succes. May you help me with this problem? Thanks a lot. Best regards, Fred

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Re: [Nek5000-users] Writing data files with lower lx during runtim e
by nek5000-users＠lists.mcs.anl.gov 16 Jan '10

16 Jan '10

Hi, To dump out files on a coarser GLL mesh during runtime, I modified subroutine mfo_outfld in prepost.f (find attached), and use map_m_to_n to interpolate. Then I add these lines to usrchk: common lxnew integer useriostep,lxnew lxnew=8 c--- If lxnew is common, integer and > 2, and if param(66)=6, and ifreguo=.false., a modification in subroutine mfo_outfld(prefix) c--- in prepost.f will be activated when dumping data (either through iostep, outpost or prepost) that maps all fields onto a coarser c--- GLL mesh where lxnew-1 is the new polynomial order. useriostep=10 !Delta time step for interpolated output param(66)=6 c-----Parameters for IO, etc. if ((modulo(istep,useriostep).eq.0.).and.(istep.gt.1.)) then if (istep.gt.useriostep) ifxyo = .false. ! Turn off xyz output ifreguo= .false. ! Maintain GLL mesh for later (spectral) post processing. ! dump results into file call prepost(.true.,'coa') ! endif c-----The following is done for the last dump iostep = param(11) ! Dump on original grid at very last time step (to have a restart solution) ifxyo = .true. !To ensure that geometry is dumped with restart file after last time step param(66)=4. !To output last file on uncoarsened grid The last 3 lines will ensure that at the end of the run, a data file is dumped with the "original"/fine resolution to serve as a restarting point. The attached pictures show a comparison of the stagnation region of an internal flow (temperature contour and velocity vectors) on the original and a coarser (lx1=8 instead of 14) grid. The vectors are interpolated on an evenly spaced grid in both cases by VisIt. As far as the motivation for this goes, I'd like to give some background info on what we intend to do ("we" is Dr. Andrew Duggleby's research group (FT2L) at Texas A&M). We are running simulations of high Reynolds number, high free stream turbulence intensity flow in complex geometries (turbine blades) with heat transfer. The grid size for my problem is about 250 Mio points. In order to analyze the data, we have a set of in house proper orthogonal decomposition routines. They all require time correlations of snapshots (up to 1000 data samples), to be read into memory multiple times. Since we only look at the lower order representation, a coarser grid than the simulation is running on supposedly suffices for that and makes these many file reading operations feasible on the resources we have. Since I intend to do the post processing with Nek, I wanted to maintain the GLL mesh distribution. I would be happy to hear any comments, Markus Schwaenen http://www1.mengr.tamu.edu/FT2L

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Re: [Nek5000-users] Writing data files with lower lx during runtim e
by nek5000-users＠lists.mcs.anl.gov 14 Jan '10

14 Jan '10

Hi Markus, Let me check if I understand: You want to dump your data onto a GLL mesh with a lower polynomial order than N=LX1-1 during the simulation, right? Stefan --- original message --- From: "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov> Subject: [Nek5000-users] Writing data files with lower lx during runtime Date: 14th January 2010 Time: 1:47:00 am Hi, in order to facilitate some "lower order" post processing on data files of a rather big simulation, I would like to write out data files with lower polynomial order on a GLL mesh during runtime. I have figured out how to do that onto a regular grid (ifreguo=.true.), but it would be nice to keep the ability to use nek5000 for post processing (on the smaller mesh). Is there a way to do that? Thanks, Markus _______________________________________________ Nek5000-users mailing list Nek5000-users(a)lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

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Writing data files with lower lx during runtime
by nek5000-users＠lists.mcs.anl.gov 13 Jan '10

13 Jan '10

Hi, in order to facilitate some "lower order" post processing on data files of a rather big simulation, I would like to write out data files with lower polynomial order on a GLL mesh during runtime. I have figured out how to do that onto a regular grid (ifreguo=.true.), but it would be nice to keep the ability to use nek5000 for post processing (on the smaller mesh). Is there a way to do that? Thanks, Markus

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Flow past a sphere
by nek5000-users＠lists.mcs.anl.gov 11 Jan '10

11 Jan '10

Hello, I have some problems with the PRENEK tool. I would like to simulate the flow past a sphere with NEK5000. But I have some problems to set up this case with PRENEK. When I defined a straight open-channel with some element (lets say Nx * Ny * Nz = 2 * 2 * 4, whereas x is the transverse, y the vertical and z the flow direction). To put a sphere into the channel, I'm using the CURVE SIDES > SPHERICAL MESH tool. I'm typing the following w (whole sphere) 0 1 2 (coordinates of sphere center) ("center of the channel") n (no prolate spheroid) s (spherical shell) 0.5 (radius) c (extend to cartesian box) 1.0 (minimal distance to box) Then I'm defining the elements of the sphere as "Wall", but I also have to define all the sides of the cartesian box... And how should I do this, because this box just should be a part of the channel... Thanking you in anticipation.. Best regards, Fred

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