[FLASH-USERS] Fatal error in PMPI_Waitall: See the MPI_ERROR field in MPI_Status for the error code

Fri Dec 6 23:53:33 EST 2019

Hi Guido,

I've seen FLASH crash with similar stdout due to insufficient memory many
times. Keep in mind that the more processors you use, the more memory the
run requires (since each processor has its own solution data array of
NUNK_VARSxNXBxNYBxNZBxMAXBLOCKS).

I was going to suggest reducing maxblocks since 3000 sounds to me rather
extreme. My simulations are happiest with MAXBLOCKS=200 (the default value).

Assuming static mesh refinement, you only need maxblocks to be ~1.02 *
num_blks_requested / num_procs (in your case, 1.02*97801/procs).

So, if you want to use more nodes, decrease maxblocks accordingly.

Best,
--------
Ryan

On Fri, Dec 6, 2019 at 8:42 PM guido <g.granda at irya.unam.mx> wrote:

> Hello,
> Thank you for replaying. I tried your suggestion and I still got the same
> errors. However, I tried increasing the number of nodes from 8 to 16 and
> the simulations runs. So, I guess the crash was due to lack of resources
> such as ram memory or sth similar. How can I check that it was the cause of
> the crash ?
>
> Cheers,
>
> On 12/6/19 6:13 PM, Eddie Hansen wrote:
>
> I haven't seen this error before, so I don't know if this is the solution,
> but here's something I noticed...
>
> You mentioned that you have loaded a version of hdf5 with parallel mode
> enabled, yet the IO unit that is loaded during setup is
> IO/IOMain/hdf5/serial. Try using the setup shortcut +hdf5typeio. This will
> load, by default, the parallel IO unit. Resetup, recompile, rerun, and see
> if you get the same error.
>
>
> On Fri, Dec 6, 2019 at 5:46 PM guido <g.granda at irya.unam.mx> wrote:
>
>> Hello Flash users,
>>
>> I’m having trouble running a simulation with FLASH 4.5. It compiled FLASH
>> 4.5 using:
>>
>> - hdf5-1.8.20 with parallel mode enabled
>>
>> - mpich-3.2.1
>>
>> - gcc-7.3.0
>>
>> The simulations run fine till I increase the maximum level of refinement
>> and the number of nodes used. For example, for simulation with lmax=9, it
>> runs slow but safe with 8 nodes. However, when I increase the number of
>> nodes to 10, the simulation crash trying to write the Coefficients in the
>> Taylor expansion into file.
>>
>> The log file is the following:
>>
>>
>> FLASH log file: 12-05-2019 12:01:48.640 Run number: 1
>>
>>
>> ==============================================================================
>>
>> Number of MPI tasks: 1
>>
>> MPI version: 3
>>
>> MPI subversion: 1
>>
>> Dimensionality: 3
>>
>> Max Number of Blocks/Proc: 3000
>>
>> Number x zones: 8
>>
>> Number y zones: 8
>>
>> Number z zones: 8
>>
>> Setup stamp: Wed Sep 18 16:44:51 2019
>>
>> Build stamp: Wed Sep 18 16:45:20 2019
>>
>> System info: Linux mouruka.crya.privado 2.6.32-504.16.2.el6.x86_64 #1 SMP
>> Wed Apr 22 06:48:29
>>
>> Version: FLASH 4.5_release
>>
>> Build directory: /home/guido/FLASH4.5/obj_mc
>>
>> Setup syntax: /home/guido/FLASH4.5/bin/setup.py magnetoHd/MC_evolution
>> -auto -3d -maxblocks=3000 -objdir=obj_mc -site=irya.guido
>> --without-unit=physics/Hydro/HydroMain/split/MHD_8Wave
>>
>> f compiler flags:
>> /home/guido/libraries/compiled_with_gcc-7.3.0/mpich-3.2.1/bin/mpif90 -g -c
>> -O0 -fdefault-real-8 -fdefault-double-8 -ffree-line-length-none
>> -Wuninitialized -g -c -fdefault-real-8 -fdefault-double-8
>> -ffree-line-length-none -Wuninitialized -DMAXBLOCKS=3000 -DNXB=8 -DNYB=8
>> -DNZB=8 -DN_DIM=3
>>
>> c compiler flags:
>> /home/guido/libraries/compiled_with_gcc-7.3.0/mpich-3.2.1/bin/mpicc
>> -I/home/guido/libraries/compiled_with_gcc-7.3.0/hdf5-1.8.20/include
>> -DH5_USE_16_API -O0 -c -DMAXBLOCKS=3000 -DNXB=8 -DNYB=8 -DNZB=8 -DN_DIM=3
>>
>>
>> ==============================================================================
>>
>> Comment: MC evolution
>>
>>
>> ==============================================================================
>>
>> FLASH Units used:
>>
>> Driver/DriverMain/Split
>>
>> Driver/localAPI
>>
>> 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/source
>>
>>
>> Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/utilities/multigrid
>>
>> Grid/GridMain/paramesh/paramesh4/Paramesh4dev/flash_avoid_orrery
>>
>> Grid/GridSolvers/BHTree/Wunsch
>>
>> Grid/localAPI
>>
>> IO/IOMain/hdf5/serial/PM
>>
>> IO/localAPI
>>
>> PhysicalConstants/PhysicalConstantsMain
>>
>> RuntimeParameters/RuntimeParametersMain
>>
>> Simulation/SimulationMain/magnetoHD/MC_evolution
>>
>> 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/Gravity/GravityMain/Poisson/BHTree
>>
>> physics/Hydro/HydroMain/split/Bouchut/Bouchut3
>>
>> physics/Hydro/localAPI
>>
>> physics/sourceTerms/Polytrope/PolytropeMain
>>
>>
>> ==============================================================================
>>
>> RuntimeParameters:
>>
>>
>> ==============================================================================
>>
>> bndpriorityone = 1
>>
>> bndprioritythree = 3
>>
>> bndprioritytwo = 2
>>
>> checkpointfileintervalstep = 1000000 [CHANGED]
>>
>> checkpointfilenumber = 0
>>
>> dr_abortpause = 2
>>
>> dr_dtminbelowaction = 1
>>
>> dr_numposdefvars = 4
>>
>> drift_break_inst = 0
>>
>> drift_trunc_mantissa = 2
>>
>> drift_verbose_inst = 0
>>
>> eos_entrelescalechoice = 6
>>
>> eos_loglevel = 700
>>
>> fileformatversion = 9
>>
>> forcedplotfilenumber = 0
>>
>> gr_bhtwmaxqueuesize = 10000
>>
>> 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 = 0
>>
>> gr_pmrpmaxblocks = -1
>>
>> gr_pmrpmflags = 1
>>
>> gr_pmrpnboundaries = 6
>>
>> gr_pmrpndim = 3
>>
>> 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 = 3 [CHANGED]
>>
>> gr_sanitizeverbosity = 5
>>
>> grv_bhewaldfieldnxv42 = 32
>>
>> grv_bhewaldfieldnyv42 = 32
>>
>> grv_bhewaldfieldnzv42 = 32
>>
>> grv_bhewaldnper = 32
>>
>> grv_bhewaldnrefv42 = -1
>>
>> grv_bhewaldseriesn = 10
>>
>> grv_bhmpdegree = 2
>>
>> iprocs = 1
>>
>> interpol_order = 2
>>
>> irenorm = 0
>>
>> jprocs = 1
>>
>> kprocs = 1
>>
>> lrefine_del = 0
>>
>> lrefine_max = 9 [CHANGED]
>>
>> lrefine_min = 3 [CHANGED]
>>
>> 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 = 1000000 [CHANGED]
>>
>> nrefs = 2
>>
>> nsteptotalsts = 5
>>
>> outputsplitnum = 1
>>
>> plotfileintervalstep = 1000000 [CHANGED]
>>
>> plotfilenumber = 0
>>
>> refine_var_count = 4
>>
>> rolling_checkpoint = 10000
>>
>> sim_refine = 9 [CHANGED]
>>
>> sweeporder = 123
>>
>> wr_integrals_freq = 1
>>
>> cfl = 0.800E+00
>>
>> checkpointfileintervaltime = 0.316E+14 [CHANGED]
>>
>> checkpointfileintervalz = 0.180+309
>>
>> derefine_cutoff_1 = 0.300E+00 [CHANGED]
>>
>> derefine_cutoff_2 = 0.200E+00
>>
>> derefine_cutoff_3 = 0.200E+00
>>
>> derefine_cutoff_4 = 0.200E+00
>>
>> dr_dtmincontinue = 0.000E+00
>>
>> dr_posdefdtfactor = 0.100E+01
>>
>> dr_tstepslowstartfactor = 0.100E+00
>>
>> dtinit = 0.316E+11 [CHANGED]
>>
>> dtmax = 0.316E+13 [CHANGED]
>>
>> dtmin = 0.316E+10 [CHANGED]
>>
>> eintswitch = 0.100E-03 [CHANGED]
>>
>> eos_singlespeciesa = 0.100E+01
>>
>> eos_singlespeciesz = 0.100E+01
>>
>> gamma = 0.167E+01
>>
>> gr_bhtreelimangle = 0.500E+00
>>
>> gr_bhtreemaxcellmass = 0.100+100
>>
>> gr_bhtreemincellmass = 0.100E-98
>>
>> gr_bhtreesafebox = 0.120E+01
>>
>> 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
>>
>> grv_bhaccerr = 0.100E+00
>>
>> grv_bhextrnpotcenterx = 0.000E+00
>>
>> grv_bhextrnpotcentery = 0.000E+00
>>
>> grv_bhextrnpotcenterz = 0.000E+00
>>
>> grv_bhnewton = -0.100E+01
>>
>> hall_parameter = 0.000E+00
>>
>> hyperresistivity = 0.000E+00
>>
>> nusts = 0.100E+00
>>
>> plotfileintervaltime = 0.316E+13 [CHANGED]
>>
>> plotfileintervalz = 0.180+309
>>
>> point_mass = 0.000E+00
>>
>> point_mass_rsoft = 0.000E+00
>>
>> polytropedens1 = 0.212E-24 [CHANGED]
>>
>> polytropedens2 = 0.100+100
>>
>> polytropedens3 = 0.100+100
>>
>> polytropedens4 = 0.100+100
>>
>> polytropedens5 = 0.100+100
>>
>> polytropegamma1 = 0.100E+01
>>
>> polytropegamma2 = 0.100E+01
>>
>> polytropegamma3 = 0.100E+01
>>
>> polytropegamma4 = 0.100E+01
>>
>> polytropegamma5 = 0.100E+01
>>
>> polytropekonst = 0.400E+09 [CHANGED]
>>
>> refine_cutoff_1 = 0.700E+00 [CHANGED]
>>
>> 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
>>
>> rss_limit = -0.100E+01
>>
>> sim_bx = 0.710E-05 [CHANGED]
>>
>> sim_by = 0.000E+00
>>
>> sim_bz = 0.000E+00
>>
>> sim_cs = 0.200E+05 [CHANGED]
>>
>> sim_delta = 0.463E+19 [CHANGED]
>>
>> sim_mu_mol = 0.127E+01
>>
>> sim_pert = 0.150E+01 [CHANGED]
>>
>> sim_rho = 0.212E-21 [CHANGED]
>>
>> sim_sigma = 0.250E+00 [CHANGED]
>>
>> sim_vx = 0.000E+00
>>
>> sim_vy = 0.000E+00
>>
>> sim_vz = 0.000E+00
>>
>> sim_x_cent = 0.000E+00
>>
>> sim_y_cent = 0.000E+00
>>
>> sim_z_cent = 0.000E+00
>>
>> small = 0.100E-39 [CHANGED]
>>
>> smalle = 0.100E-09
>>
>> smallp = 0.100E-21 [CHANGED]
>>
>> smallt = 0.100E+01 [CHANGED]
>>
>> smallu = 0.100E-39 [CHANGED]
>>
>> smallx = 0.100E-09
>>
>> smlrho = 0.100E-39 [CHANGED]
>>
>> tinitial = 0.000E+00
>>
>> tmax = 0.252E+15 [CHANGED]
>>
>> tstep_change_factor = 0.200E+01
>>
>> wall_clock_checkpoint = 0.432E+05
>>
>> wall_clock_time_limit = 0.605E+06
>>
>> x_refine_center = 0.000E+00
>>
>> xmax = 0.154E+20 [CHANGED]
>>
>> xmin = -0.154E+20 [CHANGED]
>>
>> y_refine_center = 0.000E+00
>>
>> ymax = 0.154E+20 [CHANGED]
>>
>> ymin = -0.154E+20 [CHANGED]
>>
>> zfinal = 0.000E+00
>>
>> zinitial = -0.100E+01
>>
>> z_refine_center = 0.000E+00
>>
>> zmax = 0.154E+20 [CHANGED]
>>
>> zmin = -0.154E+20 [CHANGED]
>>
>> unitsystem = CGS [CHANGED]
>>
>> basenm = mc_evolution_ [CHANGED]
>>
>> dr_posdefvar_1 = none
>>
>> dr_posdefvar_2 = none
>>
>> dr_posdefvar_3 = none
>>
>> dr_posdefvar_4 = none
>>
>> eosmode = dens_ie
>>
>> eosmodeinit = dens_ie
>>
>> geometry = cartesian
>>
>> gr_pmrpoutputdir = ./
>>
>> grav_boundary_type = periodic [CHANGED]
>>
>> grav_boundary_type_x = periodic [CHANGED]
>>
>> grav_boundary_type_y = periodic [CHANGED]
>>
>> grav_boundary_type_z = periodic [CHANGED]
>>
>> grv_bhewaldfname = ewald_coeffs
>>
>> grv_bhewaldfnameaccv42 = ewald_field_acc
>>
>> grv_bhewaldfnamepotv42 = ewald_field_pot
>>
>> grv_bhextrnpotfile = external_potential.dat
>>
>> grv_bhextrnpottype = planez
>>
>> grv_bhmac = ApproxPartialErr
>>
>> log_file = mc_evolution.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 = magz [CHANGED]
>>
>> plot_var_11 = none
>>
>> plot_var_12 = none
>>
>> plot_var_13 = none
>>
>> plot_var_14 = none
>>
>> plot_var_15 = none
>>
>> plot_var_16 = none
>>
>> plot_var_17 = none
>>
>> plot_var_18 = none
>>
>> plot_var_2 = pres [CHANGED]
>>
>> plot_var_3 = none
>>
>> plot_var_4 = eint [CHANGED]
>>
>> plot_var_5 = velx [CHANGED]
>>
>> plot_var_6 = vely [CHANGED]
>>
>> plot_var_7 = velz [CHANGED]
>>
>> plot_var_8 = magx [CHANGED]
>>
>> plot_var_9 = magy [CHANGED]
>>
>> prof_file = profile.dat
>>
>> refine_var_1 = dens [CHANGED]
>>
>> refine_var_2 = none
>>
>> refine_var_3 = none
>>
>> refine_var_4 = none
>>
>> refine_var_thresh = dens [CHANGED]
>>
>> run_comment = MC evolution [CHANGED]
>>
>> run_number = 1
>>
>> stats_file = mc.dat [CHANGED]
>>
>> xl_boundary_type = periodic
>>
>> xr_boundary_type = periodic
>>
>> yl_boundary_type = periodic
>>
>> yr_boundary_type = periodic
>>
>> zl_boundary_type = periodic
>>
>> zr_boundary_type = periodic
>>
>> allowdtstsdominate = F
>>
>> alwayscomputeuservars = T
>>
>> alwaysrestrictcheckpoint = T
>>
>> chkguardcellsinput = F
>>
>> chkguardcellsoutput = F
>>
>> converttoconsvdformeshcalls = F
>>
>> converttoconsvdinmeshinterp = T
>>
>> corners = F
>>
>> dr_printtsteploc = T
>>
>> dr_shortenlaststepbeforetmax = F
>>
>> dr_useposdefcomputedt = F
>>
>> drift_tuples = F
>>
>> eachprocwritesownabortlog = F
>>
>> eachprocwritessummary = F
>>
>> earlyblockdistadjustment = T
>>
>> enablemaskedgcfill = F
>>
>> flux_correct = T
>>
>> geometryoverride = F
>>
>> gr_bcenableapplymixedgds = T
>>
>> gr_bhphysmaccomm = F
>>
>> gr_bhphysmactw = F
>>
>> gr_bhuseunifiedtw = F [CHANGED]
>>
>> 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
>>
>> grav_temporal_extrp = F
>>
>> grav_unjunkpden = T
>>
>> grv_bhewaldalwaysgenerate = T
>>
>> grv_bhlinearinterpolonlyv42 = T
>>
>> grv_bhuserelaccerr = F
>>
>> grv_useexternalpotential = F
>>
>> grv_usepoissonpotential = T
>>
>> ignoreforcedplot = F
>>
>> io_writemscalarintegrals = F
>>
>> killdivb = T [CHANGED]
>>
>> plotfilegridquantitydp = F
>>
>> plotfilemetadatadp = F
>>
>> reducegcellfills = F
>>
>> refine_on_particle_count = F
>>
>> restart = F
>>
>> summaryoutputonly = F
>>
>> threadblocklistbuild = F
>>
>> threaddriverblocklist = F
>>
>> threaddriverwithinblock = F
>>
>> threadeoswithinblock = F
>>
>> threadhydroblocklist = F
>>
>> threadhydrowithinblock = F
>>
>> threadraytracebuild = F
>>
>> threadwithinblockbuild = F
>>
>> typematchedxfer = T
>>
>> unbiased_geometry = F
>>
>> updategravity = T
>>
>> updatehydrofluxes = T
>>
>> useburn = F
>>
>> usecollectivehdf5 = T
>>
>> useconductivity = F
>>
>> usecool = F
>>
>> usecosmology = F
>>
>> usedeleptonize = F
>>
>> usediffuse = F
>>
>> usediffusecomputedtspecies = F
>>
>> usediffusecomputedttherm = F
>>
>> usediffusecomputedtvisc = F
>>
>> usediffusecomputedtmagnetic = F
>>
>> useenergydeposition = F
>>
>> useflame = F
>>
>> usegravity = T
>>
>> useheat = F
>>
>> useheatexchange = F
>>
>> usehydro = T
>>
>> useincompns = F
>>
>> useionize = F
>>
>> uselegacylabels = T
>>
>> usemagneticresistivity = F
>>
>> usemassdiffusivity = F
>>
>> useopacity = F
>>
>> useparticles = F
>>
>> useplasmastate = F
>>
>> usepolytrope = T [CHANGED]
>>
>> useprimordialchemistry = F
>>
>> useprotonemission = F
>>
>> useprotonimaging = F
>>
>> useradtrans = F
>>
>> useraytrace = F
>>
>> usests = F
>>
>> usestsfordiffusion = F
>>
>> usestir = F
>>
>> usethomsonscattering = F
>>
>> usetreeray = F
>>
>> useturb = T
>>
>> useviscosity = F
>>
>> usexrayimaging = F
>>
>> use_cma_advection = F
>>
>> use_cma_flattening = F
>>
>> use_flash_surr_blks_fill = T
>>
>> use_reduced_orrery = T
>>
>> 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!
>>
>>
>> energyFix
>>
>>
>>
>> ==============================================================================
>>
>>
>> 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 1.16045E+07 K
>>
>> -----------End of Units--------------------
>>
>>
>> Known physical constants:
>>
>>
>> Constant Name Constant Value cm s g K esu mol
>>
>> 1 Newton 6.67408E-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 8.31446E+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 5.67037E-05 0.0 -3.0 1.0 -4.0 0.0 0.0
>>
>> 13 Radiation Constant 7.56572E-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
>>
>>
>>
>> ==============================================================================
>>
>> [ 12-05-2019 12:02:26.975 ] [gr_initGeometry] checking BCs for idir: 1
>>
>> [ 12-05-2019 12:02:26.976 ] [gr_initGeometry] checking BCs for idir: 2
>>
>> [ 12-05-2019 12:02:26.976 ] [gr_initGeometry] checking BCs for idir: 3
>>
>> [ 12-05-2019 12:02:27.074 ] [GRID amr_refine_derefine]: initiating
>> refinement
>>
>> [ 12-05-2019 12:02:27.302 ] [GRID amr_refine_derefine]: redist. phase.
>> tot blks requested: 9
>>
>> [GRID amr_refine_derefine] min blks 0 max blks 1 tot blks 9
>>
>> [GRID amr_refine_derefine] min leaf blks 0 max leaf blks 1 tot leaf blks 8
>>
>> [ 12-05-2019 12:02:27.543 ] [GRID amr_refine_derefine]: refinement
>> complete
>>
>> [ 12-05-2019 12:02:27.968 ] [GRID gr_expandDomain]: iteration=1, create
>> level=3
>>
>> INFO: Grid_fillGuardCells is ignoring masking.
>>
>> [ 12-05-2019 12:02:28.078 ] [mpi_amr_comm_setup]: buffer_dim_send=74785,
>> buffer_dim_recv=1
>>
>> [ 12-05-2019 12:02:28.157 ] [GRID amr_refine_derefine]: initiating
>> refinement
>>
>> [ 12-05-2019 12:02:29.011 ] [GRID amr_refine_derefine]: redist. phase.
>> tot blks requested: 73
>>
>> [GRID amr_refine_derefine] min blks 0 max blks 1 tot blks 73
>>
>> [GRID amr_refine_derefine] min leaf blks 0 max leaf blks 1 tot leaf blks
>> 64
>>
>> [ 12-05-2019 12:02:29.440 ] [GRID amr_refine_derefine]: refinement
>> complete
>>
>> [ 12-05-2019 12:02:29.833 ] [GRID gr_expandDomain]: iteration=2, create
>> level=4
>>
>> [ 12-05-2019 12:02:30.253 ] [GRID amr_refine_derefine]: initiating
>> refinement
>>
>> [ 12-05-2019 12:02:30.322 ] [GRID amr_refine_derefine]: redist. phase.
>> tot blks requested: 585
>>
>> [GRID amr_refine_derefine] min blks 2 max blks 4 tot blks 585
>>
>> [GRID amr_refine_derefine] min leaf blks 1 max leaf blks 3 tot leaf blks
>> 512
>>
>> [ 12-05-2019 12:02:32.046 ] [GRID amr_refine_derefine]: refinement
>> complete
>>
>> [ 12-05-2019 12:02:32.564 ] [GRID gr_expandDomain]: iteration=3, create
>> level=5
>>
>> [ 12-05-2019 12:02:32.684 ] [mpi_amr_comm_setup]: buffer_dim_send=233185,
>> buffer_dim_recv=135889
>>
>> [ 12-05-2019 12:02:33.443 ] [GRID amr_refine_derefine]: initiating
>> refinement
>>
>> [ 12-05-2019 12:02:34.807 ] [GRID amr_refine_derefine]: redist. phase.
>> tot blks requested: 3033
>>
>> [GRID amr_refine_derefine] min blks 11 max blks 14 tot blks 3033
>>
>> [GRID amr_refine_derefine] min leaf blks 9 max leaf blks 11 tot leaf blks
>> 2654
>>
>> [ 12-05-2019 12:02:35.561 ] [GRID amr_refine_derefine]: refinement
>> complete
>>
>> [ 12-05-2019 12:02:35.977 ] [GRID gr_expandDomain]: iteration=4, create
>> level=6
>>
>> [ 12-05-2019 12:02:36.173 ] [mpi_amr_comm_setup]: buffer_dim_send=575965,
>> buffer_dim_recv=351529
>>
>> [ 12-05-2019 12:02:37.611 ] [GRID amr_refine_derefine]: initiating
>> refinement
>>
>> [ 12-05-2019 12:02:40.401 ] [GRID amr_refine_derefine]: redist. phase.
>> tot blks requested: 6297
>>
>> [GRID amr_refine_derefine] min blks 24 max blks 26 tot blks 6297
>>
>> [GRID amr_refine_derefine] min leaf blks 20 max leaf blks 23 tot leaf
>> blks 5510
>>
>> [ 12-05-2019 12:02:41.154 ] [GRID amr_refine_derefine]: refinement
>> complete
>>
>> [ 12-05-2019 12:02:41.544 ] [GRID gr_expandDomain]: iteration=5, create
>> level=7
>>
>> [ 12-05-2019 12:02:41.815 ] [mpi_amr_comm_setup]: buffer_dim_send=540997,
>> buffer_dim_recv=411109
>>
>> [ 12-05-2019 12:02:44.513 ] [GRID amr_refine_derefine]: initiating
>> refinement
>>
>> [ 12-05-2019 12:02:46.394 ] [GRID amr_refine_derefine]: redist. phase.
>> tot blks requested: 16185
>>
>> [GRID amr_refine_derefine] min blks 62 max blks 65 tot blks 16185
>>
>> [GRID amr_refine_derefine] min leaf blks 54 max leaf blks 57 tot leaf
>> blks 14162
>>
>> [ 12-05-2019 12:02:47.277 ] [GRID amr_refine_derefine]: refinement
>> complete
>>
>> [ 12-05-2019 12:02:47.696 ] [GRID gr_expandDomain]: iteration=6, create
>> level=8
>>
>> [ 12-05-2019 12:02:48.106 ] [mpi_amr_comm_setup]: buffer_dim_send=881329,
>> buffer_dim_recv=699133
>>
>> [ 12-05-2019 12:02:50.281 ] [GRID amr_refine_derefine]: initiating
>> refinement
>>
>> [ 12-05-2019 12:02:51.436 ] [GRID amr_refine_derefine]: redist. phase.
>> tot blks requested: 89497
>>
>> [GRID amr_refine_derefine] min blks 348 max blks 351 tot blks 89497
>>
>> [GRID amr_refine_derefine] min leaf blks 304 max leaf blks 308 tot leaf
>> blks 78310
>>
>> [ 12-05-2019 12:02:53.153 ] [GRID amr_refine_derefine]: refinement
>> complete
>>
>> [ 12-05-2019 12:02:53.443 ] [GRID gr_expandDomain]: iteration=7, create
>> level=9
>>
>> [ 12-05-2019 12:02:56.118 ] [mpi_amr_comm_setup]:
>> buffer_dim_send=1952545, buffer_dim_recv=1773109
>>
>> [ 12-05-2019 12:03:03.333 ] [GRID amr_refine_derefine]: initiating
>> refinement
>>
>> [ 12-05-2019 12:03:07.980 ] [GRID amr_refine_derefine]: redist. phase.
>> tot blks requested: 626345
>>
>> [GRID amr_refine_derefine] min blks 2445 max blks 2449 tot blks 626345
>>
>> [GRID amr_refine_derefine] min leaf blks 2139 max leaf blks 2142 tot leaf
>> blks 548052
>>
>> [ 12-05-2019 12:03:13.985 ] [GRID amr_refine_derefine]: refinement
>> complete
>>
>> [ 12-05-2019 12:03:14.055 ] [GRID gr_expandDomain]: iteration=8, create
>> level=9
>>
>> [ 12-05-2019 12:03:25.399 ] [mpi_amr_comm_setup]:
>> buffer_dim_send=6183577, buffer_dim_recv=5623945
>>
>> [ 12-05-2019 12:03:55.420 ] [GRID amr_refine_derefine]: initiating
>> refinement
>>
>> [ 12-05-2019 12:03:58.377 ] [GRID amr_refine_derefine]: redist. phase.
>> tot blks requested: 97801
>>
>> [GRID amr_refine_derefine] min blks 381 max blks 384 tot blks 97801
>>
>> [GRID amr_refine_derefine] min leaf blks 333 max leaf blks 336 tot leaf
>> blks 85576
>>
>> [ 12-05-2019 12:04:01.822 ] [GRID amr_refine_derefine]: refinement
>> complete
>>
>> [ 12-05-2019 12:04:01.849 ] [GRID gr_expandDomain]: iteration=9, create
>> level=9
>>
>> [ 12-05-2019 12:04:03.709 ] [mpi_amr_comm_setup]:
>> buffer_dim_send=2129845, buffer_dim_recv=1958629
>>
>> [ 12-05-2019 12:04:11.340 ] [GRID amr_refine_derefine]: initiating
>> refinement
>>
>> [ 12-05-2019 12:04:15.464 ] [GRID amr_refine_derefine]: redist. phase.
>> tot blks requested: 626345
>>
>> [GRID amr_refine_derefine] min blks 2445 max blks 2449 tot blks 626345
>>
>> [GRID amr_refine_derefine] min leaf blks 2139 max leaf blks 2142 tot leaf
>> blks 548052
>>
>> [ 12-05-2019 12:04:24.519 ] [GRID amr_refine_derefine]: refinement
>> complete
>>
>> [ 12-05-2019 12:04:24.588 ] [GRID gr_expandDomain]: iteration=10, create
>> level=9
>>
>> [ 12-05-2019 12:04:35.959 ] [mpi_amr_comm_setup]:
>> buffer_dim_send=6183577, buffer_dim_recv=5623945
>>
>> [ 12-05-2019 12:05:06.370 ] [GRID amr_refine_derefine]: initiating
>> refinement
>>
>> [ 12-05-2019 12:05:09.335 ] [GRID amr_refine_derefine]: redist. phase.
>> tot blks requested: 97801
>>
>> [GRID amr_refine_derefine] min blks 381 max blks 384 tot blks 97801
>>
>> [GRID amr_refine_derefine] min leaf blks 333 max leaf blks 336 tot leaf
>> blks 85576
>>
>> [ 12-05-2019 12:05:12.763 ] [GRID amr_refine_derefine]: refinement
>> complete
>>
>> [ 12-05-2019 12:05:12.790 ] [GRID gr_expandDomain]: iteration=11, create
>> level=9
>>
>> [ 12-05-2019 12:05:14.289 ] [gr_ensureValidNeighborInfo] found
>> mpi_pattern_id: -10
>>
>> [ 12-05-2019 12:05:14.317 ] [mpi_amr_comm_setup]: buffer_dim_send=73525,
>> buffer_dim_recv=62437
>>
>> [ 12-05-2019 12:05:14.806 ] memory: /proc vsize (MiB): 2918.54 (min)
>> 3030.76 (max) 2946.03 (avg)
>>
>> [ 12-05-2019 12:05:14.807 ] memory: /proc rss (MiB): 1798.14 (min)
>> 1883.50 (max) 1830.61 (avg)
>>
>> [ 12-05-2019 12:05:14.808 ] memory: /proc vsize (MiB): 2918.54 (min)
>> 3030.76 (max) 2946.03 (avg)
>>
>> [ 12-05-2019 12:05:14.809 ] memory: /proc rss (MiB): 1798.18 (min)
>> 1883.53 (max) 1830.67 (avg)
>>
>> [ 12-05-2019 12:05:17.553 ] [BHTree]: Coefficients in the Taylor
>> expansion written into file
>>
>>
>>
>> The error file says:
>>
>>
>> Fatal error in PMPI_Waitall: See the MPI_ERROR field in MPI_Status for
>> the error code
>>
>>
>> The out file says:
>>
>>
>> RuntimeParameters_read: ignoring unknown parameter "energyFix"...
>>
>> Grid_init: resolution based on runtime params:
>>
>> lrefine dx dy dz
>>
>> 3 9.643E+17 9.643E+17 9.643E+17
>>
>> 4 4.821E+17 4.821E+17 4.821E+17
>>
>> 5 2.411E+17 2.411E+17 2.411E+17
>>
>> 6 1.205E+17 1.205E+17 1.205E+17
>>
>> 7 6.027E+16 6.027E+16 6.027E+16
>>
>> 8 3.013E+16 3.013E+16 3.013E+16
>>
>> 9 1.507E+16 1.507E+16 1.507E+16
>>
>> MaterialProperties initialized
>>
>> Cosmology initialized
>>
>> Initializing Polytropic Equation of State
>>
>> Source terms initialized
>>
>> iteration, no. not moved = 0 0
>>
>> refined: total leaf blocks = 8
>>
>> refined: total blocks = 9
>>
>> [amr_morton_process]: Initializing surr_blks using standard orrery
>> implementation
>>
>> INFO: Grid_fillGuardCells is ignoring masking.
>>
>> iteration, no. not moved = 0 6
>>
>> iteration, no. not moved = 1 0
>>
>> refined: total leaf blocks = 64
>>
>> refined: total blocks = 73
>>
>> iteration, no. not moved = 0 46
>>
>> iteration, no. not moved = 1 2
>>
>> iteration, no. not moved = 2 0
>>
>> refined: total leaf blocks = 512
>>
>> refined: total blocks = 585
>>
>> iteration, no. not moved = 0 459
>>
>> iteration, no. not moved = 1 58
>>
>> iteration, no. not moved = 2 0
>>
>> refined: total leaf blocks = 2654
>>
>> refined: total blocks = 3033
>>
>> iteration, no. not moved = 0 2675
>>
>> iteration, no. not moved = 1 765
>>
>> iteration, no. not moved = 2 0
>>
>> refined: total leaf blocks = 5510
>>
>> refined: total blocks = 6297
>>
>> iteration, no. not moved = 0 5642
>>
>> iteration, no. not moved = 1 1146
>>
>> iteration, no. not moved = 2 0
>>
>> refined: total leaf blocks = 14162
>>
>> refined: total blocks = 16185
>>
>> iteration, no. not moved = 0 15209
>>
>> iteration, no. not moved = 1 1503
>>
>> iteration, no. not moved = 2 0
>>
>> refined: total leaf blocks = 78310
>>
>> refined: total blocks = 89497
>>
>> iteration, no. not moved = 0 79298
>>
>> iteration, no. not moved = 1 4927
>>
>> iteration, no. not moved = 2 0
>>
>> refined: total leaf blocks = 548052
>>
>> refined: total blocks = 626345
>>
>> iteration, no. not moved = 0 91484
>>
>> iteration, no. not moved = 1 36351
>>
>> iteration, no. not moved = 2 0
>>
>> refined: total leaf blocks = 85576
>>
>> refined: total blocks = 97801
>>
>> iteration, no. not moved = 0 89804
>>
>> iteration, no. not moved = 1 6879
>>
>> iteration, no. not moved = 2 0
>>
>> refined: total leaf blocks = 548052
>>
>> refined: total blocks = 626345
>>
>> iteration, no. not moved = 0 91447
>>
>> iteration, no. not moved = 1 36080
>>
>> iteration, no. not moved = 2 0
>>
>> refined: total leaf blocks = 85576
>>
>> refined: total blocks = 97801
>>
>> NSIZE = 4 1
>>
>> Tree solver initialized
>>
>> Finished with Grid_initDomain, no restart
>>
>> Ready to call Hydro_init
>>
>> Hydro initialized
>>
>> Gravity initialized
>>
>> Initial dt verified
>>
>>
>> I’m not sure what is the reason for this kind of crash, have you ever
>> experienced something similar?
>>
>> My guess is that it is a communication problem due to the use of
>> mpich-3.2.1 but i’m not sure.
>>
>>
>> Cheers,
>>
>>
>
> --
> Eddie Hansen, PhD
> Postdoctoral Scholar
> University of Chicago
> 607-341-6126 | Flash Center
>
>
>
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