[FLASH-USERS] How to generate big checkpoint files in FLASH
Zheng Yuan
zhengyuan2014 at u.northwestern.edu
Tue Mar 1 11:15:45 EST 2016
Dear all,
My goal is to run FLASH using 1K MPI processes and get large checkpoint
files (500 GB each. These large checkpoint files will be used as the
test data of a parallel data compression algorithm proposed by our
group.). Does anybody know how to set the parameters to run FLASH in
large scale and get large checkpoint files?
Currently, I am trying to run FLASH/Sedov to generate large checkpoint
files. However, FLASH reports an error when I increase the dimension of
the grid.
I configured FLASH using:
./setup Sedov -auto +pnetcdf -objdir=sedov_2d
-parfile=sedov_io_69b_2d.par -2d -nxb=64 -nyb=64 -maxblocks=200
To run more iterations, I changed the 'nend' parameter to 10 in
sedov_2d/flash.par and make sedov_2d
I run flash using command:
mpirun -n 4 ./flash4
FLASH terminate at the third iteration. The error is:
-------------------------------------------------
.....
*** Wrote checkpoint file to sedov_2d_6lev_ncmpi_chk_0002 ****
*** Wrote plotfile to sedov_2d_6lev_ncmpi_plt_cnt_0003 ****
3 1.0000E-04 2.5000E-05 ( 5.139E-01, 4.988E-01, 0.000E+00) |
6.407E-07
*** Wrote checkpoint file to sedov_2d_6lev_ncmpi_chk_0003 ****
Nonconvergence in subroutine rieman
Zone index = 30
Zone center = 0.51245117187500000
Iterations tried = 12
Pressure error = 1.38898716088727185E-005
rieman_tol = 1.00000000000000008E-005
.....
Terminating execution.
DRIVER_ABORT: Nonconvergence in subroutine rieman
....
Terminating execution.
Driver_abort called. See log file for details.
Error message is Nonconvergence in subroutine rieman
Calling MPI_Abort() for shutdown in 2 seconds!
(I attached the output, the log file and the flash.par.)
-------------------------------------------------
The parameter -nxb and -nyb controls the size of checkpoint file. If
-nxb=32 -nyb=32, FLASH works well. I don't know why -nxb=64 -nyb=64 does
not work. I just want to get large checkpoint files. If Sedov cannot
generate large checkpoint file size, using other routines is also fine.
Best
Zheng Yuan
-------------- next part --------------
RuntimeParameters_read: ignoring unknown parameter "packMeshPlotWriteHDF5"...
RuntimeParameters_read: ignoring unknown parameter "packMeshChkWriteHDF5"...
RuntimeParameters_read: ignoring unknown parameter "packMeshChkReadHDF5"...
RuntimeParameters_read: ignoring unknown parameter "asyncMeshPlotWritePnet"...
RuntimeParameters_read: ignoring unknown parameter "asyncMeshChkWritePnet"...
RuntimeParameters_read: ignoring unknown parameter "asyncMeshChkReadPnet"...
RuntimeParameters_read: ignoring unknown parameter "particleFileIntervalStep"...
MaterialProperties initialized
Cosmology initialized
Source terms initialized
iteration, no. not moved = 0 0
refined: total leaf blocks = 1
refined: total blocks = 1
INFO: Grid_fillGuardCells is ignoring masking.
iteration, no. not moved = 0 0
refined: total leaf blocks = 4
refined: total blocks = 5
iteration, no. not moved = 0 0
refined: total leaf blocks = 16
refined: total blocks = 21
iteration, no. not moved = 0 0
refined: total leaf blocks = 28
refined: total blocks = 37
iteration, no. not moved = 0 2
iteration, no. not moved = 1 0
refined: total leaf blocks = 40
refined: total blocks = 53
iteration, no. not moved = 0 7
iteration, no. not moved = 1 0
refined: total leaf blocks = 52
refined: total blocks = 69
Finished with Grid_initDomain, no restart
Ready to call Hydro_init
Info: Hydro_init has set hy_specialFluxVars to 3
Hydro initialized
Gravity initialized
Initial dt verified
*** Wrote checkpoint file to sedov_2d_6lev_ncmpi_chk_0000 ****
*** Wrote plotfile to sedov_2d_6lev_ncmpi_plt_cnt_0000 ****
Initial plotfile written
Driver init all done
*** Wrote plotfile to sedov_2d_6lev_ncmpi_plt_cnt_0001 ****
n t dt ( x, y, z) | dt_hydro
1 2.0000E-10 2.5000E-05 ( 4.993E-01, 4.875E-01, 0.000E+00) | 1.265E-05
*** Wrote checkpoint file to sedov_2d_6lev_ncmpi_chk_0001 ****
*** Wrote plotfile to sedov_2d_6lev_ncmpi_plt_cnt_0002 ****
2 5.0000E-05 2.5000E-05 ( 5.134E-01, 5.017E-01, 0.000E+00) | 8.673E-06
*** Wrote checkpoint file to sedov_2d_6lev_ncmpi_chk_0002 ****
*** Wrote plotfile to sedov_2d_6lev_ncmpi_plt_cnt_0003 ****
3 1.0000E-04 2.5000E-05 ( 5.139E-01, 4.988E-01, 0.000E+00) | 6.407E-07
*** Wrote checkpoint file to sedov_2d_6lev_ncmpi_chk_0003 ****
Nonconvergence in subroutine rieman
Zone index = 30
Zone center = 0.51245117187500000
Iterations tried = 12
Pressure error = 1.38898716088727185E-005
rieman_tol = 1.00000000000000008E-005
pL = 333.48471777529863 pR = 1.00000000000000004E-010
uL = 11.503265312380062 uR = -1.44440110346356202E+028
cL = 16.833268337161257 cR = 1.18321595661992316E-010
gamma_eL = 1.3999999999999999 gamma_eR = 1.3999999999999999
gamma_cL = 1.3999999999999999 gamma_cR = 1.3999999999999999
Iteration history:
n p*
1 0.170903843337E+19
2 0.206846782834E+33
3 0.227560710287E+40
4 0.755009425342E+43
5 0.442176204670E+45
6 0.370411584433E+46
7 0.116770949481E+47
8 0.201508288303E+47
9 0.242187016811E+47
10 0.249925783066E+47
11 0.250345435163E+47
12 0.250348912477E+47
Terminating execution.
DRIVER_ABORT: Nonconvergence in subroutine rieman
Nonconvergence in subroutine rieman
Zone index = 39
Zone center = 0.48559570312500000
Iterations tried = 12
Pressure error = 1.99750620179465857E-005
rieman_tol = 1.00000000000000008E-005
pL = 1.00000000000000004E-010 pR = 192096058.35865149
uL = 2.37381854747597564E+029 uR = 1.03278389927049904E+020
cL = 1.18321595661992316E-010 cR = 271664851.00921851
gamma_eL = 1.3999999999999999 gamma_eR = 1.3999999999999999
gamma_cL = 1.3999999999999999 gamma_cR = 1.3999999999999999
Iteration history:
n p*
1 0.280873998227E+20
2 0.137814181347E+35
3 0.305270694707E+42
4 0.143705352884E+46
5 0.999925802682E+47
6 0.908873863104E+48
7 0.299989680773E+49
8 0.533178306863E+49
9 0.650904254583E+49
10 0.674771187290E+49
11 0.676188223833E+49
12 0.676201731005E+49
Terminating execution.
DRIVER_ABORT: Nonconvergence in subroutine rieman
Nonconvergence in subroutine rieman
Zone index = 21
Zone center = 0.50805664062500000
Iterations tried = 12
Pressure error = 1.10480408485796593E-005
rieman_tol = 1.00000000000000008E-005
pL = 390.01492358876504 pR = 1.00000000000000004E-010
uL = 10.890052704970055 uR = -2.73398548595714679E+027
cL = 21.836454516391196 cR = 1.18321595661992316E-010
gamma_eL = 1.3999999999999999 gamma_eR = 1.3999999999999999
gamma_cL = 1.3999999999999999 gamma_cR = 1.3999999999999999
Iteration history:
n p*
1 0.323489525213E+18
2 0.170338293335E+32
3 0.123605667824E+39
4 0.333090697670E+42
5 0.176113137384E+44
6 0.140546185976E+45
7 0.430983822756E+45
8 0.730681219742E+45
9 0.870130120688E+45
10 0.895625974979E+45
11 0.896932087028E+45
12 0.896941996480E+45
Terminating execution.
DRIVER_ABORT: Nonconvergence in subroutine rieman
Nonconvergence in subroutine rieman
Zone index = 53
Zone center = 0.49243164062500000
Iterations tried = 12
Pressure error = 1.10480408482670228E-005
rieman_tol = 1.00000000000000008E-005
pL = 1.00000000000000004E-010 pR = 390.01492358877618
uL = 2.73398548595211267E+027 uR = -10.890052704973192
cL = 1.18321595661992316E-010 cR = 21.836454516391907
gamma_eL = 1.3999999999999999 gamma_eR = 1.3999999999999999
gamma_cL = 1.3999999999999999 gamma_cR = 1.3999999999999999
Iteration history:
n p*
1 0.323489525213E+18
2 0.170338293334E+32
3 0.123605667824E+39
4 0.333090697669E+42
5 0.176113137384E+44
6 0.140546185976E+45
7 0.430983822755E+45
8 0.730681219739E+45
9 0.870130120684E+45
10 0.895625974976E+45
11 0.896932087025E+45
12 0.896941996477E+45
Terminating execution.
Driver_abort called. See log file for details.
Error message is Nonconvergence in subroutine rieman
Calling MPI_Abort() for shutdown in 2 seconds!
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 28605 RUNNING AT bigdata.eecs.northwestern.edu
= EXIT CODE: 1
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
-------------- next part --------------
FLASH log file: 03-01-2016 09:11:40.420 Run number: 1
==============================================================================
Number of MPI tasks: 4
MPI version: 3
MPI subversion: 0
Dimensionality: 2
Max Number of Blocks/Proc: 200
Number x zones: 64
Number y zones: 64
Number z zones: 1
Setup stamp: Tue Mar 1 09:08:39 2016
Build stamp: Tue Mar 1 09:11:02 2016
System info: Linux bigdata.eecs.northwestern.edu 2.6.32-573.18.1.el6.x86_64 #1 SMP Wed Jan 6
Version: FLASH 4.2.1_release
Build directory: /home/zys133/FLASH/FLASH4.2.1/sedov_2d
Setup syntax: /home/zys133/FLASH/FLASH4.2.1/bin/setup.py Sedov -auto +pnetcdf -objdir=sedov_2d -parfile=sedov_io_69b_2d.par -2d -nxb=64 -nyb=64 -maxblocks=200
f compiler flags: /usr/local//bin/mpif90 -ggdb -c -O2 -fdefault-real-8 -fdefault-double-8 -Wuninitialized -DMAXBLOCKS=200 -DNXB=64 -DNYB=64 -DNZB=1 -DN_DIM=2
c compiler flags: /usr/local//bin/mpicc -I/home/wkliao/PnetCDF/include -ggdb -c -O2 -Wuninitialized -D_FORTIFY_SOURCE=2 -DMAXBLOCKS=200 -DNXB=64 -DNYB=64 -DNZB=1 -DN_DIM=2
==============================================================================
Comment: 2D Sedov explosion, from t=0 with sim_rInit = 3.5dx_min
==============================================================================
FLASH Units used:
Driver/DriverMain/Split
Grid/GridBoundaryConditions
Grid/GridMain/paramesh/interpolation/Paramesh4/prolong
Grid/GridMain/paramesh/interpolation/prolong
Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/headers
Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/mpi_source
Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/source
Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/utilities/multigrid
Grid/localAPI
IO/IOMain/pnetcdf/explicitCopy
IO/localAPI
PhysicalConstants/PhysicalConstantsMain
RuntimeParameters/RuntimeParametersMain
Simulation/SimulationMain/Sedov
flashUtilities/contiguousConversion
flashUtilities/general
flashUtilities/interpolation/oneDim
flashUtilities/nameValueLL
flashUtilities/sorting/quicksort
flashUtilities/system/memoryUsage/legacy
monitors/Logfile/LogfileMain
monitors/Timers/TimersMain/MPINative
physics/Eos/EosMain/Gamma
physics/Eos/localAPI
physics/Hydro/HydroMain/split/PPM/PPMKernel
==============================================================================
RuntimeParameters:
==============================================================================
bndpriorityone = 1
bndprioritythree = 3
bndprioritytwo = 2
checkpointfileintervalstep = 1 [CHANGED]
checkpointfilenumber = 0
dr_abortpause = 2
drift_break_inst = 0
drift_trunc_mantissa = 2
drift_verbose_inst = 0
eos_entrelescalechoice = 6
fileformatversion = 9
forcedplotfilenumber = 0
gr_lrefmaxtimevalue_1 = -1
gr_lrefmaxtimevalue_10 = -1
gr_lrefmaxtimevalue_11 = -1
gr_lrefmaxtimevalue_12 = -1
gr_lrefmaxtimevalue_13 = -1
gr_lrefmaxtimevalue_14 = -1
gr_lrefmaxtimevalue_15 = -1
gr_lrefmaxtimevalue_16 = -1
gr_lrefmaxtimevalue_17 = -1
gr_lrefmaxtimevalue_18 = -1
gr_lrefmaxtimevalue_19 = -1
gr_lrefmaxtimevalue_2 = -1
gr_lrefmaxtimevalue_20 = -1
gr_lrefmaxtimevalue_3 = -1
gr_lrefmaxtimevalue_4 = -1
gr_lrefmaxtimevalue_5 = -1
gr_lrefmaxtimevalue_6 = -1
gr_lrefmaxtimevalue_7 = -1
gr_lrefmaxtimevalue_8 = -1
gr_lrefmaxtimevalue_9 = -1
gr_pmrpdivergencefree = 1
gr_pmrpifaceoff = 0
gr_pmrpl2p5d = -1
gr_pmrpmaxblocks = -1
gr_pmrpmflags = 1
gr_pmrpnboundaries = 4
gr_pmrpndim = 2
gr_pmrpnedgevar1 = -1
gr_pmrpnfacevar = -1
gr_pmrpnfielddivf = -1
gr_pmrpnfluxvar = -1
gr_pmrpnguard = -1
gr_pmrpnguardwork = -1
gr_pmrpnvar = -1
gr_pmrpnvarwork = 1
gr_pmrpnvarcorn = 0
gr_pmrpnvaredge = 0
gr_pmrpnxb = -1
gr_pmrpnyb = -1
gr_pmrpnzb = 1
gr_restrictallmethod = 3
gr_sanitizedatamode = 1
gr_sanitizeverbosity = 5
iprocs = 1
igodu = 0
interpol_order = 2
iplm = 0
irenorm = 0
jprocs = 1
kprocs = 1
lrefine_del = 0
lrefine_max = 6 [CHANGED]
lrefine_min = 1
lrefine_min_init = 1
max_particles_per_blk = 100
memory_stat_freq = 100000
meshcopycount = 1
min_particles_per_blk = 1
nbegin = 1
nblockx = 1
nblocky = 1
nblockz = 1
nend = 6 [CHANGED]
nrefs = 2
nriem = 10
nsteptotalsts = 5
outputsplitnum = 1
plotfileintervalstep = 1 [CHANGED]
plotfilenumber = 0
ppmeintcompfluxconstructionmeth = 0
ppmeintfluxconstructionmeth = 0
ppmenercompfluxconstructionmeth = 0
ppmenerfluxconstructionmeth = 0
refine_var_count = 4
rolling_checkpoint = 10000
sim_nsubzones = 7
sweeporder = 123
wr_integrals_freq = 1
cfl = 0.800E+00
checkpointfileintervaltime = 0.100E+01
checkpointfileintervalz = 0.180+309
cvisc = 0.100E+00
derefine_cutoff_1 = 0.200E+00
derefine_cutoff_2 = 0.200E+00
derefine_cutoff_3 = 0.200E+00
derefine_cutoff_4 = 0.200E+00
dp_sh = 0.330E+00
dp_sh_md = 0.330E+00
dr_tstepslowstartfactor = 0.100E+00
dtinit = 0.100E-09
dtmax = 0.250E-04 [CHANGED]
dtmin = 0.250E-04 [CHANGED]
eintswitch = 0.100E-03 [CHANGED]
eos_singlespeciesa = 0.100E+01
eos_singlespeciesz = 0.100E+01
epsiln = 0.330E+00
gamma = 0.140E+01 [CHANGED]
gr_lrefinemaxredlogbase = 0.100E+02
gr_lrefinemaxredradiusfact = 0.000E+00
gr_lrefinemaxredtref = 0.000E+00
gr_lrefinemaxredtimescale = 0.100E+01
gr_lrefmaxtime_1 = -0.100E+01
gr_lrefmaxtime_10 = -0.100E+01
gr_lrefmaxtime_11 = -0.100E+01
gr_lrefmaxtime_12 = -0.100E+01
gr_lrefmaxtime_13 = -0.100E+01
gr_lrefmaxtime_14 = -0.100E+01
gr_lrefmaxtime_15 = -0.100E+01
gr_lrefmaxtime_16 = -0.100E+01
gr_lrefmaxtime_17 = -0.100E+01
gr_lrefmaxtime_18 = -0.100E+01
gr_lrefmaxtime_19 = -0.100E+01
gr_lrefmaxtime_2 = -0.100E+01
gr_lrefmaxtime_20 = -0.100E+01
gr_lrefmaxtime_3 = -0.100E+01
gr_lrefmaxtime_4 = -0.100E+01
gr_lrefmaxtime_5 = -0.100E+01
gr_lrefmaxtime_6 = -0.100E+01
gr_lrefmaxtime_7 = -0.100E+01
gr_lrefmaxtime_8 = -0.100E+01
gr_lrefmaxtime_9 = -0.100E+01
nusts = 0.100E+00
omg1 = 0.750E+00
omg2 = 0.100E+02
plotfileintervaltime = 0.100E+01
plotfileintervalz = 0.180+309
refine_cutoff_1 = 0.800E+00
refine_cutoff_2 = 0.800E+00
refine_cutoff_3 = 0.800E+00
refine_cutoff_4 = 0.800E+00
refine_filter_1 = 0.100E-01
refine_filter_2 = 0.100E-01
refine_filter_3 = 0.100E-01
refine_filter_4 = 0.100E-01
rieman_tol = 0.100E-04
rss_limit = -0.100E+01
sim_expenergy = 0.100E+01
sim_pambient = 0.100E-04
sim_rinit = 0.137E-01 [CHANGED]
sim_rhoambient = 0.100E+01
sim_xctr = 0.500E+00
sim_yctr = 0.500E+00
sim_zctr = 0.500E+00
small = 0.100E-09
smalle = 0.100E-09
smallp = 0.100E-09
smallt = 0.100E-09
smallu = 0.100E-09
smallx = 0.100E-09
smlrho = 0.100E-09
tinitial = 0.000E+00
tmax = 0.500E-01 [CHANGED]
tstep_change_factor = 0.200E+01
vgrid = 0.000E+00
wall_clock_checkpoint = 0.432E+05
wall_clock_time_limit = 0.605E+06
x_refine_center = 0.000E+00
xmax = 0.100E+01
xmin = 0.000E+00
y_refine_center = 0.000E+00
ymax = 0.100E+01
ymin = 0.000E+00
zfinal = 0.000E+00
zinitial = -0.100E+01
z_refine_center = 0.000E+00
zmax = 0.100E+01
zmin = 0.000E+00
unitsystem = none
basenm = sedov_2d_6lev_ [CHANGED]
eosmode = dens_ie
eosmodeinit = dens_ie
geometry = cartesian
gr_pmrpoutputdir = ./
grav_boundary_type = isolated
hy_eosmodeafter = dens_ie
hy_fluxrepresentation = fluxes
log_file = sedov_2d_6lev.log [CHANGED]
output_directory =
pc_unitsbase = CGS
plot_grid_var_1 = none
plot_grid_var_10 = none
plot_grid_var_11 = none
plot_grid_var_12 = none
plot_grid_var_2 = none
plot_grid_var_3 = none
plot_grid_var_4 = none
plot_grid_var_5 = none
plot_grid_var_6 = none
plot_grid_var_7 = none
plot_grid_var_8 = none
plot_grid_var_9 = none
plot_var_1 = dens [CHANGED]
plot_var_10 = none
plot_var_11 = none
plot_var_12 = none
plot_var_2 = pres [CHANGED]
plot_var_3 = temp [CHANGED]
plot_var_4 = none
plot_var_5 = none
plot_var_6 = none
plot_var_7 = none
plot_var_8 = none
plot_var_9 = none
prof_file = profile.dat
refine_var_1 = dens [CHANGED]
refine_var_2 = pres [CHANGED]
refine_var_3 = none
refine_var_4 = none
run_comment = 2D Sedov explosion, from t=0 w [CHANGED]
run_number = 1
stats_file = flash.dat
xl_boundary_type = outflow [CHANGED]
xr_boundary_type = outflow [CHANGED]
yl_boundary_type = outflow [CHANGED]
yr_boundary_type = outflow [CHANGED]
zl_boundary_type = outflow [CHANGED]
zr_boundary_type = outflow [CHANGED]
allowdtstsdominate = F
alwayscomputeuservars = T
alwaysrestrictcheckpoint = T
bytepack = F
charlimiting = T
chkguardcellsinput = F
chkguardcellsoutput = F
converttoconsvdformeshcalls = F
converttoconsvdinmeshinterp = T
corners = F
dr_printtsteploc = T
dr_shortenlaststepbeforetmax = F
drift_tuples = F
eachprocwritesownabortlog = F
eachprocwritessummary = F
earlyblockdistadjustment = T
enablemaskedgcfill = F
flux_correct = T
geometryoverride = F
gr_bcenableapplymixedgds = T
gr_lrefinemaxbytime = F
gr_lrefinemaxreddobylogr = F
gr_lrefinemaxreddobytime = F
gr_pmrpadvancealllevels = F
gr_pmrpamrerrorchecking = F
gr_pmrpcartesianpm = F
gr_pmrpconserve = F
gr_pmrpconsvfluxdensities = T
gr_pmrpconsvfluxes = F
gr_pmrpcurvilinear = F
gr_pmrpcurvilinearconserve = F
gr_pmrpcylindricalpm = F
gr_pmrpdiagonals = T
gr_pmrpedgevalue = T
gr_pmrpedgevalueinteg = F
gr_pmrpemptycells = F
gr_pmrpforceconsistency = T
gr_pmrplsingularline = F
gr_pmrpnopermanentguardcells = F
gr_pmrppolarpm = F
gr_pmrppredcorr = F
gr_pmrpsphericalpm = F
gr_pmrptimingmpi = F
gr_pmrptimingmpix = F
gr_pmrpvardt = F
hybrid_riemann = F
ignoreforcedplot = F
io_writemscalarintegrals = F
leveque = F
plotfilegridquantitydp = F
plotfilemetadatadp = F
ppm_modifystates = F
reducegcellfills = F
refine_on_particle_count = F
restart = F
summaryoutputonly = F
threadblocklistbuild = F
threaddelepblocklist = F
threaddelepwithinblock = F
threaddriverblocklist = F
threaddriverwithinblock = F
threadeoswithinblock = F
threadhydroblocklist = F
threadhydrowithinblock = F
threadraytracebuild = F
threadwithinblockbuild = F
typematchedxfer = T
unbiased_geometry = F
updatehydrofluxes = T
useburn = F
usecollectivehdf5 = T
useconductivity = F
usecool = F
usecosmology = F
usedeleptonize = F
usediffuse = F
useenergydeposition = F
useflame = F
usegravity = F
useheat = F
useheatexchange = F
usehydro = T
useionize = F
uselegacylabels = T
usemagneticresistivity = F
usemassdiffusivity = F
useopacity = F
useparticles = F
usepolytrope = F
useprimordialchemistry = F
useradtrans = F
usests = F
usestsfordiffusion = F
usestir = F
usetreecol = F
useturb = T
useviscosity = F
use_cma_advection = F
use_cma_flattening = F
use_cma_steepening = F
use_steepening = T
writestatsummary = T
==============================================================================
WARNING: Ignored Parameters :
These parameters were found in the flash.par file, but they were
not declared in any Config file for the simulation!
packMeshPlotWriteHDF5
packMeshChkWriteHDF5
packMeshChkReadHDF5
asyncMeshPlotWritePnet
asyncMeshChkWritePnet
asyncMeshChkReadPnet
particleFileIntervalStep
==============================================================================
Known units of measurement:
Unit CGS Value Base Unit
1 cm 1.0000 cm
2 s 1.0000 s
3 g 1.0000 g
4 K 1.0000 K
5 esu 1.0000 esu
6 mol 1.0000 mol
7 m 100.00 cm
8 km 1.00000E+05 cm
9 pc 3.08568E+18 cm
10 kpc 3.08568E+21 cm
11 Mpc 3.08568E+24 cm
12 Gpc 3.08568E+27 cm
13 Rsun 6.96000E+10 cm
14 AU 1.49598E+13 cm
15 yr 3.15569E+07 s
16 Myr 3.15569E+13 s
17 Gyr 3.15569E+16 s
18 kg 1000.0 g
19 Msun 1.98892E+33 g
20 amu 1.66054E-24 g
21 eV 11605. K
22 C 2.99792E+09 esu
23 LFLY 3.08568E+24 cm
24 TFLY 2.05759E+17 s
25 MFLY 9.88470E+45 g
26 clLength 3.08568E+24 cm
27 clTime 3.15569E+16 s
28 clMass 1.98892E+48 g
29 clTemp 1.16044E+07 K
-----------End of Units--------------------
Known physical constants:
Constant Name Constant Value cm s g K esu mol
1 Newton 6.67428E-08 3.0 -2.0 -1.0 0.0 0.0 0.0
2 speed of light 2.99792E+10 1.0 -1.0 0.0 0.0 0.0 0.0
3 Planck 6.62607E-27 2.0 -1.0 1.0 0.0 0.0 0.0
4 electron charge 4.80320E-10 0.0 0.0 0.0 0.0 1.0 0.0
5 electron mass 9.10938E-28 0.0 0.0 1.0 0.0 0.0 0.0
6 proton mass 1.67262E-24 0.0 0.0 1.0 0.0 0.0 0.0
7 fine-structure 7.29735E-03 0.0 0.0 0.0 0.0 0.0 0.0
8 Avogadro 6.02214E+23 0.0 0.0 0.0 0.0 0.0 -1.0
9 Boltzmann 1.38065E-16 2.0 -2.0 1.0 -1.0 0.0 0.0
10 ideal gas constant 8.31447E+07 2.0 -2.0 1.0 -1.0 0.0 -1.0
11 Wien 0.28978 1.0 0.0 0.0 1.0 0.0 0.0
12 Stefan-Boltzmann 5.67040E-05 0.0 -3.0 1.0 -4.0 0.0 0.0
13 Radiation Constant 7.56577E-15 -1.0 -2.0 1.0 -4.0 0.0 0.0
14 pi 3.1416 0.0 0.0 0.0 0.0 0.0 0.0
15 e 2.7183 0.0 0.0 0.0 0.0 0.0 0.0
16 Euler 0.57722 0.0 0.0 0.0 0.0 0.0 0.0
==============================================================================
Multifluid database: not configured in
==============================================================================
[ 03-01-2016 09:11:40.512 ] [gr_initGeometry] checking BCs for idir: 1
[ 03-01-2016 09:11:40.512 ] [gr_initGeometry] checking BCs for idir: 2
[ 03-01-2016 09:11:40.516 ] [GRID amr_refine_derefine]: initiating refinement
[ 03-01-2016 09:11:40.516 ] [GRID amr_refine_derefine]: redist. phase. tot blks requested: 1
[GRID amr_refine_derefine] min blks 0 max blks 1 tot blks 1
[GRID amr_refine_derefine] min leaf blks 0 max leaf blks 1 tot leaf blks 1
[ 03-01-2016 09:11:40.517 ] [GRID amr_refine_derefine]: refinement complete
[ 03-01-2016 09:11:40.519 ] [GRID gr_expandDomain]: iteration=1, create level=2
INFO: Grid_fillGuardCells is ignoring masking.
[ 03-01-2016 09:11:40.564 ] [mpi_amr_comm_setup]: buffer_dim_send=1, buffer_dim_recv=1
[ 03-01-2016 09:11:40.567 ] [GRID amr_refine_derefine]: initiating refinement
[ 03-01-2016 09:11:40.567 ] [GRID amr_refine_derefine]: redist. phase. tot blks requested: 5
[GRID amr_refine_derefine] min blks 1 max blks 2 tot blks 5
[GRID amr_refine_derefine] min leaf blks 1 max leaf blks 1 tot leaf blks 4
[ 03-01-2016 09:11:40.568 ] [GRID amr_refine_derefine]: refinement complete
[ 03-01-2016 09:11:40.568 ] [GRID gr_expandDomain]: iteration=2, create level=3
[ 03-01-2016 09:11:40.617 ] [mpi_amr_comm_setup]: buffer_dim_send=128629, buffer_dim_recv=5515
[ 03-01-2016 09:11:40.622 ] [GRID amr_refine_derefine]: initiating refinement
[ 03-01-2016 09:11:40.623 ] [GRID amr_refine_derefine]: redist. phase. tot blks requested: 21
[GRID amr_refine_derefine] min blks 5 max blks 6 tot blks 21
[GRID amr_refine_derefine] min leaf blks 4 max leaf blks 4 tot leaf blks 16
[ 03-01-2016 09:11:40.623 ] [GRID amr_refine_derefine]: refinement complete
[ 03-01-2016 09:11:40.624 ] [GRID gr_expandDomain]: iteration=3, create level=4
[ 03-01-2016 09:11:40.785 ] [mpi_amr_comm_setup]: buffer_dim_send=139419, buffer_dim_recv=16305
[ 03-01-2016 09:11:40.797 ] [GRID amr_refine_derefine]: initiating refinement
[ 03-01-2016 09:11:40.797 ] [GRID amr_refine_derefine]: redist. phase. tot blks requested: 37
[GRID amr_refine_derefine] min blks 9 max blks 10 tot blks 37
[GRID amr_refine_derefine] min leaf blks 7 max leaf blks 7 tot leaf blks 28
[ 03-01-2016 09:11:40.800 ] [GRID amr_refine_derefine]: refinement complete
[ 03-01-2016 09:11:40.801 ] [GRID gr_expandDomain]: iteration=4, create level=5
[ 03-01-2016 09:11:41.077 ] [mpi_amr_comm_setup]: buffer_dim_send=150209, buffer_dim_recv=27095
[ 03-01-2016 09:11:41.101 ] [GRID amr_refine_derefine]: initiating refinement
[ 03-01-2016 09:11:41.102 ] [GRID amr_refine_derefine]: redist. phase. tot blks requested: 53
[GRID amr_refine_derefine] min blks 13 max blks 14 tot blks 53
[GRID amr_refine_derefine] min leaf blks 10 max leaf blks 10 tot leaf blks 40
[ 03-01-2016 09:11:41.104 ] [GRID amr_refine_derefine]: refinement complete
[ 03-01-2016 09:11:41.105 ] [GRID gr_expandDomain]: iteration=5, create level=6
[ 03-01-2016 09:11:41.386 ] [mpi_amr_comm_setup]: buffer_dim_send=160999, buffer_dim_recv=37885
[ 03-01-2016 09:11:41.408 ] [GRID amr_refine_derefine]: initiating refinement
[ 03-01-2016 09:11:41.409 ] [GRID amr_refine_derefine]: redist. phase. tot blks requested: 69
[GRID amr_refine_derefine] min blks 17 max blks 18 tot blks 69
[GRID amr_refine_derefine] min leaf blks 13 max leaf blks 13 tot leaf blks 52
[ 03-01-2016 09:11:41.411 ] [GRID amr_refine_derefine]: refinement complete
[ 03-01-2016 09:11:41.412 ] [GRID gr_expandDomain]: iteration=6, create level=6
[ 03-01-2016 09:11:41.688 ] [mpi_amr_comm_setup]: buffer_dim_send=171789, buffer_dim_recv=48675
[ 03-01-2016 09:11:41.717 ] [GRID gr_expandDomain]: iteration=7, create level=6
[ 03-01-2016 09:11:42.022 ] [GRID gr_expandDomain]: iteration=8, create level=6
[ 03-01-2016 09:11:42.284 ] memory: /proc vsize (MB): 543.27 (min) 544.58 (max) 543.66 (avg)
[ 03-01-2016 09:11:42.284 ] memory: /proc rss (MB): 101.91 (min) 103.50 (max) 102.38 (avg)
[ 03-01-2016 09:11:42.284 ] memory: /proc vsize (MB): 543.27 (min) 544.58 (max) 543.66 (avg)
[ 03-01-2016 09:11:42.285 ] memory: /proc rss (MB): 101.94 (min) 103.54 (max) 102.41 (avg)
[ 03-01-2016 09:11:42.288 ] memory: /proc vsize (MB): 543.27 (min) 544.58 (max) 543.66 (avg)
[ 03-01-2016 09:11:42.289 ] memory: /proc rss (MB): 101.95 (min) 103.55 (max) 102.42 (avg)
[ 03-01-2016 09:11:42.322 ] [IO_writeCheckpoint] open: type=checkpoint name=sedov_2d_6lev_ncmpi_chk_0000
[ 03-01-2016 09:11:42.497 ] [IO_writeCheckpoint] close: type=checkpoint name=sedov_2d_6lev_ncmpi_chk_0000
[ 03-01-2016 09:11:42.498 ] [IO_writePlotfile] open: type=plotfile name=sedov_2d_6lev_ncmpi_plt_cnt_0000
[ 03-01-2016 09:11:42.541 ] [IO_writePlotfile] close: type=plotfile name=sedov_2d_6lev_ncmpi_plt_cnt_0000
[ 03-01-2016 09:11:42.541 ] memory: /proc vsize (MB): 568.47 (min) 568.73 (max) 568.60 (avg)
[ 03-01-2016 09:11:42.541 ] memory: /proc rss (MB): 103.70 (min) 107.05 (max) 105.09 (avg)
[ 03-01-2016 09:11:42.541 ] [Driver_evolveFlash]: Entering evolution loop
[ 03-01-2016 09:11:42.541 ] step: n=1 t=0.000000E+00 dt=1.000000E-10
[ 03-01-2016 09:11:43.425 ] [IO_writePlotfile] open: type=plotfile name=sedov_2d_6lev_ncmpi_plt_cnt_0001
[ 03-01-2016 09:11:43.455 ] [IO_writePlotfile] close: type=plotfile name=sedov_2d_6lev_ncmpi_plt_cnt_0001
[ 03-01-2016 09:11:43.458 ] [IO_writeCheckpoint] open: type=checkpoint name=sedov_2d_6lev_ncmpi_chk_0001
[ 03-01-2016 09:11:43.574 ] [IO_writeCheckpoint] close: type=checkpoint name=sedov_2d_6lev_ncmpi_chk_0001
[ 03-01-2016 09:11:43.574 ] step: n=2 t=2.000000E-10 dt=2.500000E-05
[ 03-01-2016 09:11:44.197 ] [IO_writePlotfile] open: type=plotfile name=sedov_2d_6lev_ncmpi_plt_cnt_0002
[ 03-01-2016 09:11:44.227 ] [IO_writePlotfile] close: type=plotfile name=sedov_2d_6lev_ncmpi_plt_cnt_0002
[ 03-01-2016 09:11:44.283 ] [IO_writeCheckpoint] open: type=checkpoint name=sedov_2d_6lev_ncmpi_chk_0002
[ 03-01-2016 09:11:44.398 ] [IO_writeCheckpoint] close: type=checkpoint name=sedov_2d_6lev_ncmpi_chk_0002
[ 03-01-2016 09:11:44.398 ] step: n=3 t=5.000020E-05 dt=2.500000E-05
[ 03-01-2016 09:11:45.023 ] [IO_writePlotfile] open: type=plotfile name=sedov_2d_6lev_ncmpi_plt_cnt_0003
[ 03-01-2016 09:11:45.053 ] [IO_writePlotfile] close: type=plotfile name=sedov_2d_6lev_ncmpi_plt_cnt_0003
[ 03-01-2016 09:11:45.056 ] [IO_writeCheckpoint] open: type=checkpoint name=sedov_2d_6lev_ncmpi_chk_0003
[ 03-01-2016 09:11:45.172 ] [IO_writeCheckpoint] close: type=checkpoint name=sedov_2d_6lev_ncmpi_chk_0003
[ 03-01-2016 09:11:45.173 ] step: n=4 t=1.000002E-04 dt=2.500000E-05
[ 03-01-2016 09:11:45.768 ] [DRIVER_ABORT]: Driver_abort() called by PE 0
[ 03-01-2016 09:11:45.768 ] abort_message: Nonconvergence in subroutine rieman
FLASH log file: 03-01-2016 09:40:54.705 Run number: 1
==============================================================================
Number of MPI tasks: 4
MPI version: 3
MPI subversion: 0
Dimensionality: 2
Max Number of Blocks/Proc: 200
Number x zones: 64
Number y zones: 64
Number z zones: 1
Setup stamp: Tue Mar 1 09:08:39 2016
Build stamp: Tue Mar 1 09:11:02 2016
System info: Linux bigdata.eecs.northwestern.edu 2.6.32-573.18.1.el6.x86_64 #1 SMP Wed Jan 6
Version: FLASH 4.2.1_release
Build directory: /home/zys133/FLASH/FLASH4.2.1/sedov_2d
Setup syntax: /home/zys133/FLASH/FLASH4.2.1/bin/setup.py Sedov -auto +pnetcdf -objdir=sedov_2d -parfile=sedov_io_69b_2d.par -2d -nxb=64 -nyb=64 -maxblocks=200
f compiler flags: /usr/local//bin/mpif90 -ggdb -c -O2 -fdefault-real-8 -fdefault-double-8 -Wuninitialized -DMAXBLOCKS=200 -DNXB=64 -DNYB=64 -DNZB=1 -DN_DIM=2
c compiler flags: /usr/local//bin/mpicc -I/home/wkliao/PnetCDF/include -ggdb -c -O2 -Wuninitialized -D_FORTIFY_SOURCE=2 -DMAXBLOCKS=200 -DNXB=64 -DNYB=64 -DNZB=1 -DN_DIM=2
==============================================================================
Comment: 2D Sedov explosion, from t=0 with sim_rInit = 3.5dx_min
==============================================================================
FLASH Units used:
Driver/DriverMain/Split
Grid/GridBoundaryConditions
Grid/GridMain/paramesh/interpolation/Paramesh4/prolong
Grid/GridMain/paramesh/interpolation/prolong
Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/headers
Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/mpi_source
Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/source
Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/utilities/multigrid
Grid/localAPI
IO/IOMain/pnetcdf/explicitCopy
IO/localAPI
PhysicalConstants/PhysicalConstantsMain
RuntimeParameters/RuntimeParametersMain
Simulation/SimulationMain/Sedov
flashUtilities/contiguousConversion
flashUtilities/general
flashUtilities/interpolation/oneDim
flashUtilities/nameValueLL
flashUtilities/sorting/quicksort
flashUtilities/system/memoryUsage/legacy
monitors/Logfile/LogfileMain
monitors/Timers/TimersMain/MPINative
physics/Eos/EosMain/Gamma
physics/Eos/localAPI
physics/Hydro/HydroMain/split/PPM/PPMKernel
==============================================================================
RuntimeParameters:
==============================================================================
bndpriorityone = 1
bndprioritythree = 3
bndprioritytwo = 2
checkpointfileintervalstep = 1 [CHANGED]
checkpointfilenumber = 0
dr_abortpause = 2
drift_break_inst = 0
drift_trunc_mantissa = 2
drift_verbose_inst = 0
eos_entrelescalechoice = 6
fileformatversion = 9
forcedplotfilenumber = 0
gr_lrefmaxtimevalue_1 = -1
gr_lrefmaxtimevalue_10 = -1
gr_lrefmaxtimevalue_11 = -1
gr_lrefmaxtimevalue_12 = -1
gr_lrefmaxtimevalue_13 = -1
gr_lrefmaxtimevalue_14 = -1
gr_lrefmaxtimevalue_15 = -1
gr_lrefmaxtimevalue_16 = -1
gr_lrefmaxtimevalue_17 = -1
gr_lrefmaxtimevalue_18 = -1
gr_lrefmaxtimevalue_19 = -1
gr_lrefmaxtimevalue_2 = -1
gr_lrefmaxtimevalue_20 = -1
gr_lrefmaxtimevalue_3 = -1
gr_lrefmaxtimevalue_4 = -1
gr_lrefmaxtimevalue_5 = -1
gr_lrefmaxtimevalue_6 = -1
gr_lrefmaxtimevalue_7 = -1
gr_lrefmaxtimevalue_8 = -1
gr_lrefmaxtimevalue_9 = -1
gr_pmrpdivergencefree = 1
gr_pmrpifaceoff = 0
gr_pmrpl2p5d = -1
gr_pmrpmaxblocks = -1
gr_pmrpmflags = 1
gr_pmrpnboundaries = 4
gr_pmrpndim = 2
gr_pmrpnedgevar1 = -1
gr_pmrpnfacevar = -1
gr_pmrpnfielddivf = -1
gr_pmrpnfluxvar = -1
gr_pmrpnguard = -1
gr_pmrpnguardwork = -1
gr_pmrpnvar = -1
gr_pmrpnvarwork = 1
gr_pmrpnvarcorn = 0
gr_pmrpnvaredge = 0
gr_pmrpnxb = -1
gr_pmrpnyb = -1
gr_pmrpnzb = 1
gr_restrictallmethod = 3
gr_sanitizedatamode = 1
gr_sanitizeverbosity = 5
iprocs = 1
igodu = 0
interpol_order = 2
iplm = 0
irenorm = 0
jprocs = 1
kprocs = 1
lrefine_del = 0
lrefine_max = 6 [CHANGED]
lrefine_min = 1
lrefine_min_init = 1
max_particles_per_blk = 100
memory_stat_freq = 100000
meshcopycount = 1
min_particles_per_blk = 1
nbegin = 1
nblockx = 1
nblocky = 1
nblockz = 1
nend = 6 [CHANGED]
nrefs = 2
nriem = 10
nsteptotalsts = 5
outputsplitnum = 1
plotfileintervalstep = 1 [CHANGED]
plotfilenumber = 0
ppmeintcompfluxconstructionmeth = 0
ppmeintfluxconstructionmeth = 0
ppmenercompfluxconstructionmeth = 0
ppmenerfluxconstructionmeth = 0
refine_var_count = 4
rolling_checkpoint = 10000
sim_nsubzones = 7
sweeporder = 123
wr_integrals_freq = 1
cfl = 0.800E+00
checkpointfileintervaltime = 0.100E+01
checkpointfileintervalz = 0.180+309
cvisc = 0.100E+00
derefine_cutoff_1 = 0.200E+00
derefine_cutoff_2 = 0.200E+00
derefine_cutoff_3 = 0.200E+00
derefine_cutoff_4 = 0.200E+00
dp_sh = 0.330E+00
dp_sh_md = 0.330E+00
dr_tstepslowstartfactor = 0.100E+00
dtinit = 0.100E-09
dtmax = 0.250E-04 [CHANGED]
dtmin = 0.250E-04 [CHANGED]
eintswitch = 0.100E-03 [CHANGED]
eos_singlespeciesa = 0.100E+01
eos_singlespeciesz = 0.100E+01
epsiln = 0.330E+00
gamma = 0.140E+01 [CHANGED]
gr_lrefinemaxredlogbase = 0.100E+02
gr_lrefinemaxredradiusfact = 0.000E+00
gr_lrefinemaxredtref = 0.000E+00
gr_lrefinemaxredtimescale = 0.100E+01
gr_lrefmaxtime_1 = -0.100E+01
gr_lrefmaxtime_10 = -0.100E+01
gr_lrefmaxtime_11 = -0.100E+01
gr_lrefmaxtime_12 = -0.100E+01
gr_lrefmaxtime_13 = -0.100E+01
gr_lrefmaxtime_14 = -0.100E+01
gr_lrefmaxtime_15 = -0.100E+01
gr_lrefmaxtime_16 = -0.100E+01
gr_lrefmaxtime_17 = -0.100E+01
gr_lrefmaxtime_18 = -0.100E+01
gr_lrefmaxtime_19 = -0.100E+01
gr_lrefmaxtime_2 = -0.100E+01
gr_lrefmaxtime_20 = -0.100E+01
gr_lrefmaxtime_3 = -0.100E+01
gr_lrefmaxtime_4 = -0.100E+01
gr_lrefmaxtime_5 = -0.100E+01
gr_lrefmaxtime_6 = -0.100E+01
gr_lrefmaxtime_7 = -0.100E+01
gr_lrefmaxtime_8 = -0.100E+01
gr_lrefmaxtime_9 = -0.100E+01
nusts = 0.100E+00
omg1 = 0.750E+00
omg2 = 0.100E+02
plotfileintervaltime = 0.100E+01
plotfileintervalz = 0.180+309
refine_cutoff_1 = 0.800E+00
refine_cutoff_2 = 0.800E+00
refine_cutoff_3 = 0.800E+00
refine_cutoff_4 = 0.800E+00
refine_filter_1 = 0.100E-01
refine_filter_2 = 0.100E-01
refine_filter_3 = 0.100E-01
refine_filter_4 = 0.100E-01
rieman_tol = 0.100E-04
rss_limit = -0.100E+01
sim_expenergy = 0.100E+01
sim_pambient = 0.100E-04
sim_rinit = 0.137E-01 [CHANGED]
sim_rhoambient = 0.100E+01
sim_xctr = 0.500E+00
sim_yctr = 0.500E+00
sim_zctr = 0.500E+00
small = 0.100E-09
smalle = 0.100E-09
smallp = 0.100E-09
smallt = 0.100E-09
smallu = 0.100E-09
smallx = 0.100E-09
smlrho = 0.100E-09
tinitial = 0.000E+00
tmax = 0.500E-01 [CHANGED]
tstep_change_factor = 0.200E+01
vgrid = 0.000E+00
wall_clock_checkpoint = 0.432E+05
wall_clock_time_limit = 0.605E+06
x_refine_center = 0.000E+00
xmax = 0.100E+01
xmin = 0.000E+00
y_refine_center = 0.000E+00
ymax = 0.100E+01
ymin = 0.000E+00
zfinal = 0.000E+00
zinitial = -0.100E+01
z_refine_center = 0.000E+00
zmax = 0.100E+01
zmin = 0.000E+00
unitsystem = none
basenm = sedov_2d_6lev_ [CHANGED]
eosmode = dens_ie
eosmodeinit = dens_ie
geometry = cartesian
gr_pmrpoutputdir = ./
grav_boundary_type = isolated
hy_eosmodeafter = dens_ie
hy_fluxrepresentation = fluxes
log_file = sedov_2d_6lev.log [CHANGED]
output_directory =
pc_unitsbase = CGS
plot_grid_var_1 = none
plot_grid_var_10 = none
plot_grid_var_11 = none
plot_grid_var_12 = none
plot_grid_var_2 = none
plot_grid_var_3 = none
plot_grid_var_4 = none
plot_grid_var_5 = none
plot_grid_var_6 = none
plot_grid_var_7 = none
plot_grid_var_8 = none
plot_grid_var_9 = none
plot_var_1 = dens [CHANGED]
plot_var_10 = none
plot_var_11 = none
plot_var_12 = none
plot_var_2 = pres [CHANGED]
plot_var_3 = temp [CHANGED]
plot_var_4 = none
plot_var_5 = none
plot_var_6 = none
plot_var_7 = none
plot_var_8 = none
plot_var_9 = none
prof_file = profile.dat
refine_var_1 = dens [CHANGED]
refine_var_2 = pres [CHANGED]
refine_var_3 = none
refine_var_4 = none
run_comment = 2D Sedov explosion, from t=0 w [CHANGED]
run_number = 1
stats_file = flash.dat
xl_boundary_type = outflow [CHANGED]
xr_boundary_type = outflow [CHANGED]
yl_boundary_type = outflow [CHANGED]
yr_boundary_type = outflow [CHANGED]
zl_boundary_type = outflow [CHANGED]
zr_boundary_type = outflow [CHANGED]
allowdtstsdominate = F
alwayscomputeuservars = T
alwaysrestrictcheckpoint = T
bytepack = F
charlimiting = T
chkguardcellsinput = F
chkguardcellsoutput = F
converttoconsvdformeshcalls = F
converttoconsvdinmeshinterp = T
corners = F
dr_printtsteploc = T
dr_shortenlaststepbeforetmax = F
drift_tuples = F
eachprocwritesownabortlog = F
eachprocwritessummary = F
earlyblockdistadjustment = T
enablemaskedgcfill = F
flux_correct = T
geometryoverride = F
gr_bcenableapplymixedgds = T
gr_lrefinemaxbytime = F
gr_lrefinemaxreddobylogr = F
gr_lrefinemaxreddobytime = F
gr_pmrpadvancealllevels = F
gr_pmrpamrerrorchecking = F
gr_pmrpcartesianpm = F
gr_pmrpconserve = F
gr_pmrpconsvfluxdensities = T
gr_pmrpconsvfluxes = F
gr_pmrpcurvilinear = F
gr_pmrpcurvilinearconserve = F
gr_pmrpcylindricalpm = F
gr_pmrpdiagonals = T
gr_pmrpedgevalue = T
gr_pmrpedgevalueinteg = F
gr_pmrpemptycells = F
gr_pmrpforceconsistency = T
gr_pmrplsingularline = F
gr_pmrpnopermanentguardcells = F
gr_pmrppolarpm = F
gr_pmrppredcorr = F
gr_pmrpsphericalpm = F
gr_pmrptimingmpi = F
gr_pmrptimingmpix = F
gr_pmrpvardt = F
hybrid_riemann = F
ignoreforcedplot = F
io_writemscalarintegrals = F
leveque = F
plotfilegridquantitydp = F
plotfilemetadatadp = F
ppm_modifystates = F
reducegcellfills = F
refine_on_particle_count = F
restart = F
summaryoutputonly = F
threadblocklistbuild = F
threaddelepblocklist = F
threaddelepwithinblock = F
threaddriverblocklist = F
threaddriverwithinblock = F
threadeoswithinblock = F
threadhydroblocklist = F
threadhydrowithinblock = F
threadraytracebuild = F
threadwithinblockbuild = F
typematchedxfer = T
unbiased_geometry = F
updatehydrofluxes = T
useburn = F
usecollectivehdf5 = T
useconductivity = F
usecool = F
usecosmology = F
usedeleptonize = F
usediffuse = F
useenergydeposition = F
useflame = F
usegravity = F
useheat = F
useheatexchange = F
usehydro = T
useionize = F
uselegacylabels = T
usemagneticresistivity = F
usemassdiffusivity = F
useopacity = F
useparticles = F
usepolytrope = F
useprimordialchemistry = F
useradtrans = F
usests = F
usestsfordiffusion = F
usestir = F
usetreecol = F
useturb = T
useviscosity = F
use_cma_advection = F
use_cma_flattening = F
use_cma_steepening = F
use_steepening = T
writestatsummary = T
==============================================================================
WARNING: Ignored Parameters :
These parameters were found in the flash.par file, but they were
not declared in any Config file for the simulation!
packMeshPlotWriteHDF5
packMeshChkWriteHDF5
packMeshChkReadHDF5
asyncMeshPlotWritePnet
asyncMeshChkWritePnet
asyncMeshChkReadPnet
particleFileIntervalStep
==============================================================================
Known units of measurement:
Unit CGS Value Base Unit
1 cm 1.0000 cm
2 s 1.0000 s
3 g 1.0000 g
4 K 1.0000 K
5 esu 1.0000 esu
6 mol 1.0000 mol
7 m 100.00 cm
8 km 1.00000E+05 cm
9 pc 3.08568E+18 cm
10 kpc 3.08568E+21 cm
11 Mpc 3.08568E+24 cm
12 Gpc 3.08568E+27 cm
13 Rsun 6.96000E+10 cm
14 AU 1.49598E+13 cm
15 yr 3.15569E+07 s
16 Myr 3.15569E+13 s
17 Gyr 3.15569E+16 s
18 kg 1000.0 g
19 Msun 1.98892E+33 g
20 amu 1.66054E-24 g
21 eV 11605. K
22 C 2.99792E+09 esu
23 LFLY 3.08568E+24 cm
24 TFLY 2.05759E+17 s
25 MFLY 9.88470E+45 g
26 clLength 3.08568E+24 cm
27 clTime 3.15569E+16 s
28 clMass 1.98892E+48 g
29 clTemp 1.16044E+07 K
-----------End of Units--------------------
Known physical constants:
Constant Name Constant Value cm s g K esu mol
1 Newton 6.67428E-08 3.0 -2.0 -1.0 0.0 0.0 0.0
2 speed of light 2.99792E+10 1.0 -1.0 0.0 0.0 0.0 0.0
3 Planck 6.62607E-27 2.0 -1.0 1.0 0.0 0.0 0.0
4 electron charge 4.80320E-10 0.0 0.0 0.0 0.0 1.0 0.0
5 electron mass 9.10938E-28 0.0 0.0 1.0 0.0 0.0 0.0
6 proton mass 1.67262E-24 0.0 0.0 1.0 0.0 0.0 0.0
7 fine-structure 7.29735E-03 0.0 0.0 0.0 0.0 0.0 0.0
8 Avogadro 6.02214E+23 0.0 0.0 0.0 0.0 0.0 -1.0
9 Boltzmann 1.38065E-16 2.0 -2.0 1.0 -1.0 0.0 0.0
10 ideal gas constant 8.31447E+07 2.0 -2.0 1.0 -1.0 0.0 -1.0
11 Wien 0.28978 1.0 0.0 0.0 1.0 0.0 0.0
12 Stefan-Boltzmann 5.67040E-05 0.0 -3.0 1.0 -4.0 0.0 0.0
13 Radiation Constant 7.56577E-15 -1.0 -2.0 1.0 -4.0 0.0 0.0
14 pi 3.1416 0.0 0.0 0.0 0.0 0.0 0.0
15 e 2.7183 0.0 0.0 0.0 0.0 0.0 0.0
16 Euler 0.57722 0.0 0.0 0.0 0.0 0.0 0.0
==============================================================================
Multifluid database: not configured in
==============================================================================
[ 03-01-2016 09:40:54.781 ] [gr_initGeometry] checking BCs for idir: 1
[ 03-01-2016 09:40:54.781 ] [gr_initGeometry] checking BCs for idir: 2
[ 03-01-2016 09:40:54.784 ] [GRID amr_refine_derefine]: initiating refinement
[ 03-01-2016 09:40:54.784 ] [GRID amr_refine_derefine]: redist. phase. tot blks requested: 1
[GRID amr_refine_derefine] min blks 0 max blks 1 tot blks 1
[GRID amr_refine_derefine] min leaf blks 0 max leaf blks 1 tot leaf blks 1
[ 03-01-2016 09:40:54.785 ] [GRID amr_refine_derefine]: refinement complete
[ 03-01-2016 09:40:54.787 ] [GRID gr_expandDomain]: iteration=1, create level=2
INFO: Grid_fillGuardCells is ignoring masking.
[ 03-01-2016 09:40:54.833 ] [mpi_amr_comm_setup]: buffer_dim_send=1, buffer_dim_recv=1
[ 03-01-2016 09:40:54.835 ] [GRID amr_refine_derefine]: initiating refinement
[ 03-01-2016 09:40:54.835 ] [GRID amr_refine_derefine]: redist. phase. tot blks requested: 5
[GRID amr_refine_derefine] min blks 1 max blks 2 tot blks 5
[GRID amr_refine_derefine] min leaf blks 1 max leaf blks 1 tot leaf blks 4
[ 03-01-2016 09:40:54.836 ] [GRID amr_refine_derefine]: refinement complete
[ 03-01-2016 09:40:54.837 ] [GRID gr_expandDomain]: iteration=2, create level=3
[ 03-01-2016 09:40:54.886 ] [mpi_amr_comm_setup]: buffer_dim_send=128629, buffer_dim_recv=5515
[ 03-01-2016 09:40:54.892 ] [GRID amr_refine_derefine]: initiating refinement
[ 03-01-2016 09:40:54.892 ] [GRID amr_refine_derefine]: redist. phase. tot blks requested: 21
[GRID amr_refine_derefine] min blks 5 max blks 6 tot blks 21
[GRID amr_refine_derefine] min leaf blks 4 max leaf blks 4 tot leaf blks 16
[ 03-01-2016 09:40:54.893 ] [GRID amr_refine_derefine]: refinement complete
[ 03-01-2016 09:40:54.894 ] [GRID gr_expandDomain]: iteration=3, create level=4
[ 03-01-2016 09:40:55.057 ] [mpi_amr_comm_setup]: buffer_dim_send=139419, buffer_dim_recv=16305
[ 03-01-2016 09:40:55.068 ] [GRID amr_refine_derefine]: initiating refinement
[ 03-01-2016 09:40:55.068 ] [GRID amr_refine_derefine]: redist. phase. tot blks requested: 37
[GRID amr_refine_derefine] min blks 9 max blks 10 tot blks 37
[GRID amr_refine_derefine] min leaf blks 7 max leaf blks 7 tot leaf blks 28
[ 03-01-2016 09:40:55.070 ] [GRID amr_refine_derefine]: refinement complete
[ 03-01-2016 09:40:55.071 ] [GRID gr_expandDomain]: iteration=4, create level=5
[ 03-01-2016 09:40:55.313 ] [mpi_amr_comm_setup]: buffer_dim_send=150209, buffer_dim_recv=27095
[ 03-01-2016 09:40:55.327 ] [GRID amr_refine_derefine]: initiating refinement
[ 03-01-2016 09:40:55.327 ] [GRID amr_refine_derefine]: redist. phase. tot blks requested: 53
[GRID amr_refine_derefine] min blks 13 max blks 14 tot blks 53
[GRID amr_refine_derefine] min leaf blks 10 max leaf blks 10 tot leaf blks 40
[ 03-01-2016 09:40:55.329 ] [GRID amr_refine_derefine]: refinement complete
[ 03-01-2016 09:40:55.329 ] [GRID gr_expandDomain]: iteration=5, create level=6
[ 03-01-2016 09:40:55.546 ] [mpi_amr_comm_setup]: buffer_dim_send=160999, buffer_dim_recv=37885
[ 03-01-2016 09:40:55.566 ] [GRID amr_refine_derefine]: initiating refinement
[ 03-01-2016 09:40:55.566 ] [GRID amr_refine_derefine]: redist. phase. tot blks requested: 69
[GRID amr_refine_derefine] min blks 17 max blks 18 tot blks 69
[GRID amr_refine_derefine] min leaf blks 13 max leaf blks 13 tot leaf blks 52
[ 03-01-2016 09:40:55.568 ] [GRID amr_refine_derefine]: refinement complete
[ 03-01-2016 09:40:55.569 ] [GRID gr_expandDomain]: iteration=6, create level=6
[ 03-01-2016 09:40:55.849 ] [mpi_amr_comm_setup]: buffer_dim_send=171789, buffer_dim_recv=48675
[ 03-01-2016 09:40:55.876 ] [GRID gr_expandDomain]: iteration=7, create level=6
[ 03-01-2016 09:40:56.183 ] [GRID gr_expandDomain]: iteration=8, create level=6
[ 03-01-2016 09:40:56.451 ] memory: /proc vsize (MB): 543.27 (min) 544.58 (max) 543.66 (avg)
[ 03-01-2016 09:40:56.451 ] memory: /proc rss (MB): 101.94 (min) 103.50 (max) 102.40 (avg)
[ 03-01-2016 09:40:56.452 ] memory: /proc vsize (MB): 543.27 (min) 544.58 (max) 543.66 (avg)
[ 03-01-2016 09:40:56.452 ] memory: /proc rss (MB): 101.97 (min) 103.54 (max) 102.44 (avg)
[ 03-01-2016 09:40:56.454 ] memory: /proc vsize (MB): 543.27 (min) 544.58 (max) 543.66 (avg)
[ 03-01-2016 09:40:56.454 ] memory: /proc rss (MB): 101.98 (min) 103.54 (max) 102.45 (avg)
[ 03-01-2016 09:40:56.480 ] [IO_writeCheckpoint] open: type=checkpoint name=sedov_2d_6lev_ncmpi_chk_0000
[ 03-01-2016 09:40:56.597 ] [IO_writeCheckpoint] close: type=checkpoint name=sedov_2d_6lev_ncmpi_chk_0000
[ 03-01-2016 09:40:56.599 ] [IO_writePlotfile] open: type=plotfile name=sedov_2d_6lev_ncmpi_plt_cnt_0000
[ 03-01-2016 09:40:56.628 ] [IO_writePlotfile] close: type=plotfile name=sedov_2d_6lev_ncmpi_plt_cnt_0000
[ 03-01-2016 09:40:56.628 ] memory: /proc vsize (MB): 568.47 (min) 568.73 (max) 568.60 (avg)
[ 03-01-2016 09:40:56.628 ] memory: /proc rss (MB): 103.71 (min) 105.14 (max) 104.14 (avg)
[ 03-01-2016 09:40:56.628 ] [Driver_evolveFlash]: Entering evolution loop
[ 03-01-2016 09:40:56.628 ] step: n=1 t=0.000000E+00 dt=1.000000E-10
[ 03-01-2016 09:40:57.244 ] [IO_writePlotfile] open: type=plotfile name=sedov_2d_6lev_ncmpi_plt_cnt_0001
[ 03-01-2016 09:40:57.274 ] [IO_writePlotfile] close: type=plotfile name=sedov_2d_6lev_ncmpi_plt_cnt_0001
[ 03-01-2016 09:40:57.282 ] [IO_writeCheckpoint] open: type=checkpoint name=sedov_2d_6lev_ncmpi_chk_0001
[ 03-01-2016 09:40:57.397 ] [IO_writeCheckpoint] close: type=checkpoint name=sedov_2d_6lev_ncmpi_chk_0001
[ 03-01-2016 09:40:57.397 ] step: n=2 t=2.000000E-10 dt=2.500000E-05
[ 03-01-2016 09:40:58.015 ] [IO_writePlotfile] open: type=plotfile name=sedov_2d_6lev_ncmpi_plt_cnt_0002
[ 03-01-2016 09:40:58.045 ] [IO_writePlotfile] close: type=plotfile name=sedov_2d_6lev_ncmpi_plt_cnt_0002
[ 03-01-2016 09:40:58.105 ] [IO_writeCheckpoint] open: type=checkpoint name=sedov_2d_6lev_ncmpi_chk_0002
[ 03-01-2016 09:40:58.220 ] [IO_writeCheckpoint] close: type=checkpoint name=sedov_2d_6lev_ncmpi_chk_0002
[ 03-01-2016 09:40:58.220 ] step: n=3 t=5.000020E-05 dt=2.500000E-05
[ 03-01-2016 09:40:58.839 ] [IO_writePlotfile] open: type=plotfile name=sedov_2d_6lev_ncmpi_plt_cnt_0003
[ 03-01-2016 09:40:58.868 ] [IO_writePlotfile] close: type=plotfile name=sedov_2d_6lev_ncmpi_plt_cnt_0003
[ 03-01-2016 09:40:58.876 ] [IO_writeCheckpoint] open: type=checkpoint name=sedov_2d_6lev_ncmpi_chk_0003
[ 03-01-2016 09:40:58.990 ] [IO_writeCheckpoint] close: type=checkpoint name=sedov_2d_6lev_ncmpi_chk_0003
[ 03-01-2016 09:40:58.991 ] step: n=4 t=1.000002E-04 dt=2.500000E-05
[ 03-01-2016 09:40:59.579 ] [DRIVER_ABORT]: Driver_abort() called by PE 0
[ 03-01-2016 09:40:59.579 ] abort_message: Nonconvergence in subroutine rieman
-------------- next part --------------
# Runtime parameters for the Sedov explosion problem.
#
# ----------------------------------------------------------------------
# This parameter file is designed to be used for I/O
# benchmarks and not science. It is based upon test_paramesh_2d.par.
# It will cause FLASH to run 4 time steps and output
# a checkpoint file and plot file each and every time step.
#
# Setup lines:
# ./setup Sedov -auto +pm4dev -maxblocks=200 -2d -nxb=16 -nyb=16
# --with-unit=IO/IOMain/pnetcdf/PM_argonne -parfile=sedov_io_69b_2d.par
# -objdir=flash_pnet
#
# ./setup Sedov -auto +pm4dev -maxblocks=200 -2d -nxb=16 -nyb=16
# --with-unit=IO/IOMain/hdf5/parallel/PM_argonne -parfile=sedov_io_69b_2d.par
# -objdir=flash_hdf5
#
# Tunable I/O parameters:
#
# Parameter name Library Valid values
# fileFormatVersion HDF5 & Pnetcdf 9, 10
# useCollectiveHDF5 HDF5 .true., .false.
# packMeshPlotWriteHDF5 HDF5 .true., .false.
# packMeshChkWriteHDF5 HDF5 .true., .false.
# packMeshChkReadHDF5 HDF5 .true., .false.
# asyncMeshPlotWritePnet Pnetcdf .true., .false.
# asyncMeshChkWritePnet Pnetcdf .true., .false.
# asyncMeshChkReadPnet Pnetcdf .true., .false.
#
# fileFormat version 9 indicates standard FLASH I/O format where each
# mesh variable (e.g. dens, pres) is written to a separate dataset in
# the output file. fileFormat version 10 indicates all mesh variables
# are written to the same dataset in the output file.
#
# useCollectiveHDF5 is a switch for independent or collective HDF5.
#
# packMeshPlotWriteHDF5, packMeshChkWriteHDF5, packMeshChkReadHDF5 are
# used to pack mesh data into a new buffer using the mesh MPI datatypes
# with the MPI_Pack and MPI_Unpack functions. It is a useful option
# for plotfiles where a type conversion (double precision in memory to
# single precision in file) prevents HDF5 collective I/O optimizations.
# I would expect that the only useful parameter is packMeshPlotWriteHDF5,
# the other parameters, packMeshChkWriteHDF5 and packMeshChkReadHDF5
# are only provided for completeness.
#
# asyncMeshPlotWritePnet, asyncMeshChkWritePnet, asyncMeshChkReadPnet
# are used to replace ncmpi_put_vara_all, ncmpi_get_vara_all library
# calls with ncmpi_iput_vara, ncmpi_iget_vara. I would expect it is
# most useful when used in conjunction with fileFormatVersion = 9 as
# here the N mesh variables (and so N library calls) are transferred
# asynchronously.
#
fileFormatVersion = 9
useCollectiveHDF5 = .true.
packMeshPlotWriteHDF5 = .false.
packMeshChkWriteHDF5 = .false.
packMeshChkReadHDF5 = .false.
asyncMeshPlotWritePnet = .false.
asyncMeshChkWritePnet = .false.
asyncMeshChkReadPnet = .false.
eachProcWritesSummary = .false.
# ----------------------------------------------------------------------
# Parameters for initial model
# Ambient pressure and density, explosion energy, initial
# radius of perturbation, and location of explosion center
sim_pAmbient = 1.E-5
sim_rhoAmbient = 1.
sim_expEnergy = 1.
sim_rInit = 0.013671875
sim_xctr = 0.5
sim_yctr = 0.5
sim_zctr = 0.5
# Gas ratio of specific heats
gamma = 1.4
# Size of computational volume
xmin = 0.
xmax = 1.
ymin = 0.
ymax = 1.
zmin = 0.
zmax = 1.
# Boundary conditions
xl_boundary_type = "outflow"
xr_boundary_type = "outflow"
yl_boundary_type = "outflow"
yr_boundary_type = "outflow"
zl_boundary_type = "outflow"
zr_boundary_type = "outflow"
# Simulation (grid, time, I/O) parameters
cfl = 0.8
lrefine_max = 6
refine_var_1 = "dens"
refine_var_2 = "pres"
basenm = "sedov_2d_6lev_"
restart = .false.
checkpointFileIntervalStep = 1
plotFileIntervalStep = 1
particleFileIntervalStep = 1
plot_var_1 = "dens"
plot_var_2 = "pres"
plot_var_3 = "temp"
nend = 6
tmax = 0.05
dtmin = 2.5D-5
dtmax = 2.5D-5
run_comment = "2D Sedov explosion, from t=0 with sim_rInit = 3.5dx_min"
log_file = "sedov_2d_6lev.log"
eintSwitch = 1.e-4
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