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userguide/diagnosticfiles.md
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......@@ -21,18 +21,18 @@ Table of contents
# Diagnostic output
Arepo will not only output the simulation snapshot and reduced data via
the halo-finder files, but also a number of (mostly ascii) diagnostic log-
files which contain important information about the code performance and
runtime behavior.
In practice, to quickly check the performance of large
production runs, it is useful to check the ``timebins.txt``
and ``cpu.txt`` files. The former will give information how many simulation
elements are on which timestep, i.e. characteristics of the system
simulated, the latter provides information about the computational
time spent in each part of the code, which can be influenced to some
degree by the values of the code parameters.
Arepo will not only output the simulation snapshot and reduced data
via the halo-finder files, but also a number of (mostly ascii)
diagnostic log- files which contain important information about the
code performance and runtime behavior.
In practice, to quickly check the performance of large production
runs, it is useful to check the ``timebins.txt`` and ``cpu.txt``
files. The former will give information how many simulation elements
are evolved with which timestep sizes, i.e. characteristics of the
system simulated, the latter provides information about the
computational time spent in each part of the code, which can be
influenced to some degree by the values of the code parameters.
For ongoing simulations, these can be checked via
......@@ -43,18 +43,18 @@ For ongoing simulations, these can be checked via
stdout
======
The standard output contains general information about the simulation status
and many of the main routines will print general information in it.
The output itself is mainly relevant for reconstructing what the simulation
did, which is needed e.g. for debugging purposes.
The standard output contains general information about the simulation
status and many of the main routines will print general information in
it. The output itself is mainly relevant for reconstructing what the
simulation did, which is needed e.g. for debugging purposes.
balance.txt
===========
Output of fractional cpu time used in each individual step, optimized to be
machine readable (while cpu.txt is more human readable).
Output of fractional cpu time used in each individual step, optimized
to be machine readable (while cpu.txt is more human readable).
Symbol key:
Symbol key
total = '-' / '-'
treegrav = 'a' / ')'
......@@ -116,21 +116,24 @@ example:
cpu.txt
=======
Each sync-point, such a block is written. This file
reports the result of the different timers built into Arepo. Each
computationally expensive operation has a different timer attached to it and
this way allows to closely monitor what the computational time is spent on.
Some of the timers (e.g. treegrav) have sub-timers for individual operations.
This is denoted by the indentation hierarchy in the first column.
The distribution of these timings is highly problem dependent, but it is
possible to identify inefficient parts of the overall algorithm and optimize
only the most time-consuming parts of the code. There is the option
``OUTPUT_CPU_CSV`` which also returns this data as a ``cpu.csv`` file.
The different columns are:
name; wallclock time (in s) this step; percentage this step; wallclock time
(in s) cumulative; percentage up to this step. A typical block of cpu.txt looks
the following (here a gravity-only, tree-only run):
For each sync-point, such a block is written. This file reports
measurements of the different timers built into Arepo. Each
computationally expensive operation has a different timer attached to
it, thus allowing to closely monitor where the computational time is
spent. Some of the timers (e.g. treegrav) have sub-timers for
individual operations. This is denoted by the indentation hierarchy
in the first column. The fraction of time spent in different code
parts, as well as the absolute amount, is highly problem
dependent. The timers make it possible to identify inefficient parts
of the overall algorithm and concentrate on the most time-consuming
parts of the code. There is also the option ``OUTPUT_CPU_CSV`` which
returns thes same data as a more easily machine-readable ``cpu.csv``
file.
The different columns are: name; wallclock time (in s) this step;
percentage this step; wallclock time (in s) cumulative; percentage up
to this step. A typical block of cpu.txt looks the following (here a
gravity-only, tree-only run):
Step 131, Time: 0.197266, CPUs: 1, MultiDomains: 8, HighestActiveTim
eBin: 20
......@@ -180,13 +183,13 @@ the following (here a gravity-only, tree-only run):
misc 0.00 0.0% 0.02 0.0%
domain.txt
domain.txt
==========
The load-balancing (cpu work and memory) both in gravity and hydro calculation
are reported for each timebin individually. Reported every sync-point.
Ideally balanced runs have the value 1, the higher the value, the more
imbalanced the simulation.
The load-balancing (cpu work and memory) both for gravity and hydro
calculations is reported for each timebin individually. Reported every
sync-point. Ideally balanced runs have a value 1, the higher the
value, the more imbalanced the simulation.
DOMAIN BALANCE, Sync-Point 13314, Time: 0.997486
Timebins: Gravity Hydro cumulative grav-balance
......@@ -204,15 +207,15 @@ imbalanced the simulation.
--------------------------------------------------------------------
-----------------
energy.txt
energy.txt
==========
In specified intervals (in simulation time, specified by the parameter
`TimeBetStatistics`) the total energy and its components are computed and
written into `energy.txt`. This file also contains the cumulative energy
that had to be injected into the system to ensure positivity in thermal energy.
All output in code units. Note: this only works with up to 6 particle types.
The columns are
In specified intervals (in simulation time, specified by the parameter
`TimeBetStatistics`) the total energy and its components are computed
and written into the file `energy.txt`. This file also contains the
cumulative energy that had to be injected into the system to ensure
positivity in thermal energy. All output is in code units. Note: this
only works with up to 6 particle types. The columns are
1. simulation time/ scalefactor
2. total thermal energy
......@@ -245,7 +248,7 @@ The columns are
29. total injected energy due to positivity enforcement of thermal e
nergy
Two example lines
Two example lines:
0.96967 3.29069e+06 0 4.27406e+07 3.29069e+06 0 1.65766e+06 0 0 3.93
02e+07 0 0 0 0 0 0 0 0 1.78097e+06 0 0 0 503.489 3047.89 0 0 65.5756
......@@ -254,11 +257,11 @@ Two example lines
4203e+07 0 0 0 0 0 0 0 0 1.76774e+06 0 0 0 503.306 3047.89 0 0 65.75
86 0 7.71477
info.txt
info.txt
========
Every sync-point, the time-bins, time, timestep and number of active particles
are written into this file, e.g.
Every sync-point, the time-bins, time, timestep and number of active
particles are written into this file, e.g.
Sync-Point 13327, TimeBin=16, Time: 0.999408, Redshift: 0.000592464,
Systemstep: 0.000147974, Dloga: 0.000148072, Nsync-grv: 17679,
......@@ -267,14 +270,15 @@ are written into this file, e.g.
memory.txt
==========
Arepo internally uses an own memory manager. This means that one large chunk of
memory is reserved initially for Arepo (specified by the parameter
`MaxMemSize`) and allocation for individual arrays is handled internally.
The reason for introducing this was to avoid memory fragmentation during
runtime on some machines, but also to have detailed information about how much
memory Arepo actually needs and to terminate if this exceeds a pre-defined
threshold. ``memory.txt`` reports this internal memory usage, and how much memory
is actually needed by the simulation.
Arepo uses its own internal memory manager. This means that one large
chunk of memory is reserved initially for Arepo (specified by the
parameter `MaxMemSize`), and the allocation for individual arrays is
then handled internally from this pool. The reason for introducing
this was to avoid memory fragmentation during runtime on some
machines, but also to have detailed information about how much memory
Arepo actually needs and to terminate if this exceeds a pre-defined
threshold. ``memory.txt`` reports this internal memory usage, and how
much memory is actually needed by the simulation.
MEMORY: Largest Allocation = 816.742 Mbyte | Largest Allocation W
ithout Generic = 132.938 Mbyte
......@@ -462,41 +466,45 @@ is actually needed by the simulation.
sfr.txt
=======
In case ``USE_SFR`` is active, Arepo will create a ``sfr.txt`` file, which reports
the stars created in every call of the star-formation routine.
In case ``USE_SFR`` is active, Arepo will create a ``sfr.txt`` file,
which reports the stars created in every call of the star-formation
routine.
The individual columns are:
* time (code units or scale factor)
* total stellar mass to be formed in timestepo prior to stochastic sampling (code units),
* total stellar mass to be formed in timestepo prior to stochastic
sampling (code units),
* instantaneous star formation rate of all cells (Msun/yr),
* instantaneous star formation rate of active cells (Msun/yr),
* total mass in stars formed in this timestep (after sampling) (code units),
* cumulative stellar mass formed (code units).
Example:
Example:
4.373019e-01 9.714635e-03 1.100743e+02 1.405136e+02 2.2809
41e-02 2.752464e+01
4.373667e-01 4.007455e-04 1.104648e+02 5.795346e+00 0.0000
00e+00 2.752464e+01
4.374315e-01 2.009357e-02 1.104276e+02 2.905270e+02 0.0000
00e+00 2.752464e+01
4.374962e-01 3.904148e-04 1.103389e+02 5.643836e+00 0.0000
00e+00 2.752464e+01
4.373019e-01 9.714635e-03 1.100743e+02 1.405136e+02 2.2809
41e-02 2.752464e+01
4.373667e-01 4.007455e-04 1.104648e+02 5.795346e+00 0.0000
00e+00 2.752464e+01
4.374315e-01 2.009357e-02 1.104276e+02 2.905270e+02 0.0000
00e+00 2.752464e+01
4.374962e-01 3.904148e-04 1.103389e+02 5.643836e+00 0.0000
00e+00 2.752464e+01
timebins.txt
============
Arepo is optimized for time-integrating both hydrodynamical as well as
gravitational interactions on the largest possible timestep that is allowed by
the timestep criterion and allowed by the binary hierarchy of time steps.
Each for each timestep, a linked list of particles on this particular
integration step exists, and their statistics are reported in `timebins.txt`.
In this file, the number of gas cells and collisionless particles in each
timebin (i.e. integration timestep) is reported for each sync-point, as well
as the cpu time and fraction spent on each timebin. A typical bock looks like
Arepo is optimized for time-integrating both hydrodynamical as well as
gravitational interactions on the largest possible timestep that is
allowed by the timestep criterion and allowed by the binary hierarchy
of time steps. For each timestep, a linked list of particles on this
particular integration step exists, and their statistics are reported
in `timebins.txt`. In this file, the number of gas cells and
collisionless particles in each timebin (i.e. integration timestep) is
reported for each sync-point, as well as the cpu time and the fraction
of the total cost contributed by each timebin. A typical block looks
like
Sync-Point 2658, Time: 0.307419, Redshift: 2.25289, Systemstep: 9.10
27e-05, Dloga: 0.000296144
......@@ -513,12 +521,13 @@ as the cpu time and fraction spent on each timebin. A typical bock looks like
------------------------
Total active: 185 143
timings.txt
timings.txt
===========
The performance of the gravitational tree algorithm is reported in
`timings.txt` for each sync-point. An example of a single sync-point looks
the following:
The performance of the gravitational tree algorithm is reported in
`timings.txt` for each sync-point. An example of a single sync-point
looks like the following
Step(*): 372, t: 0.0455302, dt: 0.000215226, highest active timebin:
19 (lowest active: 19, highest occupied: 19)
......@@ -529,3 +538,5 @@ the following:
maximum number of nodes: 31091, filled: 0.677246
avg times: all=0.519064 tree1=0.515797 tree2=0 commwait=1.0013
6e-05 sec