ArepoVTK
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Published
20 hours ago •
dnelson86
dnelson86
No png produced
I tried the install instructions of the README. I'm running ArchLinux with the "libpng-1.6.37-3" package installed with pacman. After following the README instructions, skipping the part for installing libpng since I already have it installed, I get
$ ./ArepoRT tests/config_2.txt
___ ___ ___ ___ ___ ___ ___
/\ \ /\ \ /\ \ /\ \ /\ \ /\ \ /\ \
/::\ \ /::\ \ /::\ \ /::\ \ /::\ \ /::\ \ \:\ \
/:/\:\ \ /:/\:\ \ /:/\:\ \ /:/\:\ \ /:/\:\ \ /:/\:\ \ \:\ \
/::\~\:\ \ /::\~\:\ \ /::\~\:\ \ /::\~\:\ \ /:/ \:\ \ /::\~\:\ \ /::\ \
/:/\:\ \:\__\ /:/\:\ \:\__\ /:/\:\ \:\__\ /:/\:\ \:\__\ /:/__/ \:\__\ /:/\:\ \:\__\ /:/\:\__\
\/__\:\/:/ / \/_|::\/:/ / \:\~\:\ \/__/ \/__\:\/:/ / \:\ \ /:/ / \/_|::\/:/ / /:/ \/__/
\::/ / |:|::/ / \:\ \:\__\ \::/ / \:\ /:/ / |:|::/ / /:/ /
/:/ / |:|\/__/ \:\ \/__/ \/__/ \:\/:/ / |:|\/__/ \/__/
/:/ / |:| | \:\__\ \::/ / |:| |
\/__/ \|__| \/__/ \/__/ \|__|
v0.44 (Aug 10 2021). Author: Dylan Nelson ([email protected])
Reading Configuration File [tests/config_2.txt].
AREPO ENABLED. (OpenMP NThreads = 1, MPI NTask = 1, ThisTask = 0)
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
and no png is produced. Any idea what the issue might be ? I tried
unset I_MPI_HYDRA_BOOTSTRAP
unset I_MPI_PMI_LIBRARY
as suggested in the README but it didn't help.
Is there any other output? Perhaps turn verbose = True in the parameter file. Likely there is an error coming from Arepo, rather than ArepoVTK.
Thanks for your reply, here is the output with verbose = true:
./ArepoRT tests/config_2.txt
___ ___ ___ ___ ___ ___ ___
/\ \ /\ \ /\ \ /\ \ /\ \ /\ \ /\ \
/::\ \ /::\ \ /::\ \ /::\ \ /::\ \ /::\ \ \:\ \
/:/\:\ \ /:/\:\ \ /:/\:\ \ /:/\:\ \ /:/\:\ \ /:/\:\ \ \:\ \
/::\~\:\ \ /::\~\:\ \ /::\~\:\ \ /::\~\:\ \ /:/ \:\ \ /::\~\:\ \ /::\ \
/:/\:\ \:\__\ /:/\:\ \:\__\ /:/\:\ \:\__\ /:/\:\ \:\__\ /:/__/ \:\__\ /:/\:\ \:\__\ /:/\:\__\
\/__\:\/:/ / \/_|::\/:/ / \:\~\:\ \/__/ \/__\:\/:/ / \:\ \ /:/ / \/_|::\/:/ / /:/ \/__/
\::/ / |:|::/ / \:\ \:\__\ \::/ / \:\ /:/ / |:|::/ / /:/ /
/:/ / |:|\/__/ \:\ \/__/ \/__/ \:\/:/ / |:|\/__/ \/__/
/:/ / |:| | \:\__\ \::/ / |:| |
\/__/ \|__| \/__/ \/__/ \|__|
v0.44 (Aug 10 2021). Author: Dylan Nelson ([email protected])
Reading Configuration File [tests/config_2.txt].
CONFIGURATION PARAMETERS USED:
addTF_01 = constant_table Density idl_33_blue-red 0.5 20
cameraFOV = 0.0
cameraLookAt = 0.5 0.5 0.5
cameraPosition = 0.5 0.5 1e-2
cameraUp = 0.0 1.0 0.0
convertUthermToKelvin = false
drawBBox = true
drawTetra = false
drawVoronoi = true
dumpMeshCells = false
filename = tests/grid_2
imageFile = frame2.png
imageXPixels = 600
imageYPixels = 600
maskFileBase = mask
maskPadFac = 0.0
nCores = 2
nTasks = 40
numFrames = 1
openWindow = false
paramFilename = tests/param.txt
projColDens = false
quickRender = false
rayMaxT = 0.0
recenterBoxCoords = -1 -1 -1
rgbAbsorb = 0.0 0.0 0.0
rgbLine = 0.6 0.6 0.6
rgbTetra = 0.02 0.0 0.0
rgbVoronoi = 0.02 0.02 0.02
swScale = 0.52
timePerFrame = 1.0
totNumJobs = 0
verbose = true
viStepSize = 0
AREPO ENABLED. (OpenMP NThreads = 1, MPI NTask = 1, ThisTask = 0)
Obtaining parameters from file 'tests/param.txt':
InitCondFile ./dummy
OutputDir ./output
SnapshotFileBase snap
OutputListFilename output_list.txt
ICFormat 3
SnapFormat 3
TimeLimitCPU 81000
CpuTimeBetRestartFile 7200
ResubmitOn 0
ResubmitCommand my-scriptfile
MaxMemSize 500
MultipleDomains 1
TopNodeFactor 5
ActivePartFracForNewDomainDecomp 0.1
CellShapingFactor 0.2
CellShapingSpeed 0.5
TimeBegin 0
TimeMax 1
BoxSize 1
ComovingIntegrationOn 0
PeriodicBoundariesOn 1
CoolingOn 0
StarformationOn 0
Omega0 0
OmegaLambda 0
OmegaBaryon 0
HubbleParam 1
OutputListOn 0
TimeBetSnapshot 0.1
TimeOfFirstSnapshot 0
TimeBetStatistics 0.01
NumFilesPerSnapshot 1
NumFilesWrittenInParallel 1
TypeOfTimestepCriterion 0
ErrTolIntAccuracy 0.025
CourantFac 0.4
MaxSizeTimestep 0.01
MinSizeTimestep 1e-10
MinimumDensityOnStartUp 1e-20
LimitUBelowThisDensity 1e-20
LimitUBelowCertainDensityToThisValue 1
InitGasTemp 0
MinGasTemp 0
MinEgySpec 0
TypeOfOpeningCriterion 1
ErrTolTheta 0.7
ErrTolForceAcc 0.0025
DesNumNgb 32
MaxNumNgbDeviation 2
UnitLength_in_cm 1
UnitMass_in_g 1
UnitVelocity_in_cm_per_s 1
GravityConstantInternal 0
GasSoftFactor 1.5
SofteningComovingType0 1
SofteningComovingType1 0
SofteningComovingType2 0
SofteningComovingType3 0
SofteningComovingType4 0
SofteningComovingType5 0
SofteningMaxPhysType0 1
SofteningMaxPhysType1 0
SofteningMaxPhysType2 0
SofteningMaxPhysType3 0
SofteningMaxPhysType4 0
SofteningMaxPhysType5 0
SofteningTypeOfPartType0 0
SofteningTypeOfPartType1 1
SofteningTypeOfPartType2 1
SofteningTypeOfPartType3 1
SofteningTypeOfPartType4 1
SofteningTypeOfPartType5 1
On node 'XPS15-arch-blegat', we have 1 MPI ranks and at most 0 MB available. This is not enough space for MaxMemSize = 500 MB
BEGRUN: Size of particle structure 96 [bytes]
BEGRUN: Size of sph particle structure 168 [bytes]
BEGRUN: Size of gravity tree node 80 [bytes]
BEGRUN: Hubble (internal units) = 3.24078e-18
BEGRUN: G (internal units) = 6.6738e-08
BEGRUN: UnitMass_in_g = 1
BEGRUN: UnitTime_in_s = 1
BEGRUN: UnitVelocity_in_cm_per_s = 1
BEGRUN: UnitDensity_in_cgs = 1
BEGRUN: UnitEnergy_in_cgs = 1
BEGRUN: MinEgySpec set to 0 based on MinGasTemp=0
INIT: 5/5 Gradients used.
Custom load with only [1] job, not using mask file.
Reading total of [9] particles across all files.
ALLOCATE: initial allocation for MaxPart = 10
ALLOCATE: initial allocation for MaxPartSph = 10
File [0: tests/grid_2.hdf5] loading [9] particles.
TERMINATE: ******!!!!!****** Code termination on task=0, function drift_particle(), file src/time_integration/predict.c, line 370: no prediction into past allowed: time0=1066192077 time1=0
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
This
On node 'XPS15-arch-blegat', we have 1 MPI ranks and at most 0 MB available.
seems bad. This is coming from the report_comittable_memory function in arepo/system/utils.c, which tries to get information from the operating system about the node. If you run
cat /proc/meminfo
on this computer, does it have valid information?