Load MERA-Files

The RAMSES simulation data can be stored and accessed from files in the JLD2 file format.

using Mera

Load the Data From Ramses

info = getinfo(300,  "../../testing/simulations/mw_L10");
gas  = gethydro(info, verbose=false, show_progress=false); 
part = getparticles(info, verbose=false, show_progress=false); 
grav = getgravity(info, verbose=false, show_progress=false); 
# the same applies for clump-data...

[Mera]: 2023-04-10T14:48:37.021

Code: RAMSES
output [300] summary:
mtime: 2023-04-09T05:34:09
ctime: 2023-04-10T08:08:14.488
=======================================================
simulation time: 445.89 [Myr]
boxlen: 48.0 [kpc]
ncpu: 640
ndim: 3
-------------------------------------------------------
amr:           true
level(s): 6 - 10 --> cellsize(s): 750.0 [pc] - 46.88 [pc]
-------------------------------------------------------
hydro:         true
hydro-variables:  7  --> (:rho, :vx, :vy, :vz, :p, :var6, :var7)
hydro-descriptor: (:density, :velocity_x, :velocity_y, :velocity_z, :pressure, :scalar_00, :scalar_01)
γ: 1.6667
-------------------------------------------------------
gravity:       true
gravity-variables: (:epot, :ax, :ay, :az)
-------------------------------------------------------
particles:     true
- Nstars:   5.445150e+05 
particle-variables: 7  --> (:vx, :vy, :vz, :mass, :family, :tag, :birth)
particle-descriptor: (:position_x, :position_y, :position_z, :velocity_x, :velocity_y, :velocity_z, :mass, :identity, :levelp, :family, :tag, :birth_time)
-------------------------------------------------------
rt:            false
clumps:           false
-------------------------------------------------------
namelist-file: ("&COOLING_PARAMS", "&SF_PARAMS", "&AMR_PARAMS", "&BOUNDARY_PARAMS", "&OUTPUT_PARAMS", "&POISSON_PARAMS", "&RUN_PARAMS", "&FEEDBACK_PARAMS", "&HYDRO_PARAMS", "&INIT_PARAMS", "&REFINE_PARAMS")
-------------------------------------------------------
timer-file:       true
compilation-file: false
makefile:         true
patchfile:        true
=======================================================

Store the Data Into JLD2 Files

The running number is taken from the original RAMSES outputs.

savedata(gas, "../../testing/simulations/JLD2_files/");

[Mera]: 2023-04-10T14:50:14.702


Not existing file: output_00300.jld2
Directory: /Users/mabe/Documents/codes/github/Mera.jl/tutorials/version_1/../../testing/simulations/mw_L10
-----------------------------------
merafile_version: 1.0  -  Simulation code: RAMSES
-----------------------------------
DataType: hydro  -  Data variables: (:level, :cx, :cy, :cz, :rho, :vx, :vy, :vz, :p, :var6, :var7)
-----------------------------------
I/O mode: nothing  -  Compression: nothing
-----------------------------------
-----------------------------------
Memory size: 2.321 GB (uncompressed)
-----------------------------------

<div class="alert alert-block alert-info"> <b>NOTE</b> The hydro data was not written into the file to prevent overwriting existing files.

The following argument is mandatory: fmode=:write </div>

savedata(gas, "../../testing/simulations/JLD2_files/", fmode=:write);

[Mera]: 2023-04-10T14:53:39.878


Create file: output_00300.jld2
Directory: /Users/mabe/Documents/codes/github/Mera.jl/tutorials/version_1/../../testing/simulations/mw_L10
-----------------------------------
merafile_version: 1.0  -  Simulation code: RAMSES
-----------------------------------
DataType: hydro  -  Data variables: (:level, :cx, :cy, :cz, :rho, :vx, :vy, :vz, :p, :var6, :var7)
-----------------------------------
I/O mode: write  -  Compression: CodecLz4.LZ4FrameCompressor(Base.RefValue{Ptr{CodecLz4.LZ4F_cctx}}(Ptr{CodecLz4.LZ4F_cctx} @0x0000000000000000), Base.RefValue{CodecLz4.LZ4F_preferences_t}(CodecLz4.LZ4F_preferences_t(CodecLz4.LZ4F_frameInfo_t(0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x0000000000000000, 0x00000000, 0x00000000), 0, 0x00000000, (0x00000000, 0x00000000, 0x00000000, 0x00000000))), TranscodingStreams.Memory(Ptr{UInt8} @0x000000011f192040, 0x0000000000000013), false)
-----------------------------------
CodecZlib  0.6.0
Mera  1.2.0   https://github.com/ManuelBehrendt/Mera.jl
CodecBzip2  0.7.2
JLD2  0.4.31
CodecLz4  0.4.0
-----------------------------------
Memory size: 2.321 GB (uncompressed)
Total file size: 1.276 GB
-----------------------------------

Add/Append further datatypes:

savedata(part, "../../testing/simulations/JLD2_files/", fmode=:append);
savedata(grav, "../../testing/simulations/JLD2_files/", fmode=:append);

[Mera]: 2023-04-10T14:53:41.387


Create file: output_00300.jld2
Directory: /Users/mabe/Documents/codes/github/Mera.jl/tutorials/version_1/../../testing/simulations/mw_L10
-----------------------------------
merafile_version: 1.0  -  Simulation code: RAMSES
-----------------------------------
DataType: particles  -  Data variables: (:level, :x, :y, :z, :id, :family, :tag, :vx, :vy, :vz, :mass, :birth)
-----------------------------------
I/O mode: append  -  Compression: CodecLz4.LZ4FrameCompressor(Base.RefValue{Ptr{CodecLz4.LZ4F_cctx}}(Ptr{CodecLz4.LZ4F_cctx} @0x0000000000000000), Base.RefValue{CodecLz4.LZ4F_preferences_t}(CodecLz4.LZ4F_preferences_t(CodecLz4.LZ4F_frameInfo_t(0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x0000000000000000, 0x00000000, 0x00000000), 0, 0x00000000, (0x00000000, 0x00000000, 0x00000000, 0x00000000))), TranscodingStreams.Memory(Ptr{UInt8} @0x00000001198ff9a0, 0x0000000000000013), false)
-----------------------------------
CodecZlib  0.6.0
Mera  1.2.0   https://github.com/ManuelBehrendt/Mera.jl
CodecBzip2  0.7.2
JLD2  0.4.31
CodecLz4  0.4.0
-----------------------------------
Memory size: 38.451 MB (uncompressed)
Total file size: 1.306 GB
-----------------------------------

[Mera]: 2023-04-10T14:53:43.590


Create file: output_00300.jld2
Directory: /Users/mabe/Documents/codes/github/Mera.jl/tutorials/version_1/../../testing/simulations/mw_L10
-----------------------------------
merafile_version: 1.0  -  Simulation code: RAMSES
-----------------------------------
DataType: gravity  -  Data variables: (:level, :cx, :cy, :cz, :epot, :ax, :ay, :az)
-----------------------------------
I/O mode: append  -  Compression: CodecLz4.LZ4FrameCompressor(Base.RefValue{Ptr{CodecLz4.LZ4F_cctx}}(Ptr{CodecLz4.LZ4F_cctx} @0x0000000000000000), Base.RefValue{CodecLz4.LZ4F_preferences_t}(CodecLz4.LZ4F_preferences_t(CodecLz4.LZ4F_frameInfo_t(0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x0000000000000000, 0x00000000, 0x00000000), 0, 0x00000000, (0x00000000, 0x00000000, 0x00000000, 0x00000000))), TranscodingStreams.Memory(Ptr{UInt8} @0x000000011a600ec0, 0x0000000000000013), false)
-----------------------------------
CodecZlib  0.6.0
Mera  1.2.0   https://github.com/ManuelBehrendt/Mera.jl
CodecBzip2  0.7.2
JLD2  0.4.31
CodecLz4  0.4.0
-----------------------------------
Memory size: 1.688 GB (uncompressed)
Total file size: 2.159 GB
-----------------------------------

<div class="alert alert-block alert-info"> <b>NOTE</b> It is not possible to exchange stored data; only writing into a new file or appending is supported. </div>

Overview of Stored Data

vd = viewdata(300, "../../testing/simulations/JLD2_files/")

[Mera]: 2023-04-10T17:53:19.650

Mera-file output_00300.jld2 contains:

Datatype: particles
merafile_version: 1.0
Compression: CodecLz4.LZ4FrameCompressor(Base.RefValue{Ptr{CodecLz4.LZ4F_cctx}}(Ptr{CodecLz4.LZ4F_cctx} @0x0000000000000000), Base.RefValue{CodecLz4.LZ4F_preferences_t}(CodecLz4.LZ4F_preferences_t(CodecLz4.LZ4F_frameInfo_t(0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x0000000000000000, 0x00000000, 0x00000000), 0, 0x00000000, (0x00000000, 0x00000000, 0x00000000, 0x00000000))), TranscodingStreams.Memory(Ptr{UInt8} @0x0000000000000000, 0x0000000000000013), false)
CodecZlib: VersionNumber[v"0.6.0"]
merafile_version: 1.0
JLD2: VersionNumber[v"0.4.31"]
CodecBzip2: VersionNumber[v"0.7.2"]
JLD2compatible_versions: 0.1
CodecLz4: VersionNumber[v"0.4.0"]
Mera: Any[v"1.2.0", "https://github.com/ManuelBehrendt/Mera.jl"]
-------------------------
Memory: 38.4513635635376 MB (uncompressed)


Datatype: gravity
merafile_version: 1.0
Compression: CodecLz4.LZ4FrameCompressor(Base.RefValue{Ptr{CodecLz4.LZ4F_cctx}}(Ptr{CodecLz4.LZ4F_cctx} @0x0000000000000000), Base.RefValue{CodecLz4.LZ4F_preferences_t}(CodecLz4.LZ4F_preferences_t(CodecLz4.LZ4F_frameInfo_t(0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x0000000000000000, 0x00000000, 0x00000000), 0, 0x00000000, (0x00000000, 0x00000000, 0x00000000, 0x00000000))), TranscodingStreams.Memory(Ptr{UInt8} @0x0000000000000000, 0x0000000000000013), false)
CodecZlib: VersionNumber[v"0.6.0"]
merafile_version: 1.0
JLD2: VersionNumber[v"0.4.31"]
CodecBzip2: VersionNumber[v"0.7.2"]
JLD2compatible_versions: 0.1
CodecLz4: VersionNumber[v"0.4.0"]
Mera: Any[v"1.2.0", "https://github.com/ManuelBehrendt/Mera.jl"]
-------------------------
Memory: 1.6880846759304404 GB (uncompressed)


Datatype: hydro
merafile_version: 1.0
Compression: CodecLz4.LZ4FrameCompressor(Base.RefValue{Ptr{CodecLz4.LZ4F_cctx}}(Ptr{CodecLz4.LZ4F_cctx} @0x0000000000000000), Base.RefValue{CodecLz4.LZ4F_preferences_t}(CodecLz4.LZ4F_preferences_t(CodecLz4.LZ4F_frameInfo_t(0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x0000000000000000, 0x00000000, 0x00000000), 0, 0x00000000, (0x00000000, 0x00000000, 0x00000000, 0x00000000))), TranscodingStreams.Memory(Ptr{UInt8} @0x0000000000000000, 0x0000000000000013), false)
CodecZlib: VersionNumber[v"0.6.0"]
merafile_version: 1.0
JLD2: VersionNumber[v"0.4.31"]
CodecBzip2: VersionNumber[v"0.7.2"]
JLD2compatible_versions: 0.1
CodecLz4: VersionNumber[v"0.4.0"]
Mera: Any[v"1.2.0", "https://github.com/ManuelBehrendt/Mera.jl"]
-------------------------
Memory: 2.3211082834750414 GB (uncompressed)


-----------------------------------
convert stat: false
-----------------------------------
Total file size: 2.159 GB
-----------------------------------






Dict{Any, Any} with 4 entries:
  "particles" => Dict{Any, Any}("versions"=>Dict{Any, Any}("CodecZlib"=>Version…
  "FileSize"  => (2.159, "GB")
  "gravity"   => Dict{Any, Any}("versions"=>Dict{Any, Any}("CodecZlib"=>Version…
  "hydro"     => Dict{Any, Any}("versions"=>Dict{Any, Any}("CodecZlib"=>Version…

Information about the content, etc. is returned in a dictionary.

Get a detailed tree-view of the data-file:

vd = viewdata(300, "../../testing/simulations/JLD2_files/", showfull=true)

[Mera]: 2023-04-10T17:54:10.300

Mera-file output_00300.jld2 contains:

 ├─📂 hydro
 │  ├─🔢 data
 │  ├─🔢 info
 │  └─📂 information
 │     ├─🔢 compression
 │     ├─🔢 comments
 │     ├─🔢 storage
 │     ├─🔢 memory
 │     └─📂 versions
 │        ├─🔢 merafile_version
 │        ├─🔢 JLD2compatible_versions
 │        ├─🔢 CodecZlib
 │        ├─🔢 Mera
 │        ├─🔢 CodecBzip2
 │        ├─🔢 JLD2
 │        └─🔢 CodecLz4
 ├─📂 particles
 │  ├─🔢 data
 │  ├─🔢 info
 │  └─📂 information
 │     ├─🔢 compression
 │     ├─🔢 comments
 │     ├─🔢 storage
 │     ├─🔢 memory
 │     └─📂 versions
 │        ├─🔢 merafile_version
 │        ├─🔢 JLD2compatible_versions
 │        ├─🔢 CodecZlib
 │        ├─🔢 Mera
 │        ├─🔢 CodecBzip2
 │        ├─🔢 JLD2
 │        └─🔢 CodecLz4
 └─📂 gravity
    ├─🔢 data
    ├─🔢 info
    └─📂 information
       ├─🔢 compression
       ├─🔢 comments
       ├─🔢 storage
       ├─🔢 memory
       └─📂 versions
          ├─🔢 merafile_version
          ├─🔢 JLD2compatible_versions
          ├─🔢 CodecZlib
          ├─🔢 Mera
          ├─🔢 CodecBzip2
          ├─🔢 JLD2
          └─🔢 CodecLz4

Datatype: particles
merafile_version: 1.0
Compression: CodecLz4.LZ4FrameCompressor(Base.RefValue{Ptr{CodecLz4.LZ4F_cctx}}(Ptr{CodecLz4.LZ4F_cctx} @0x0000000000000000), Base.RefValue{CodecLz4.LZ4F_preferences_t}(CodecLz4.LZ4F_preferences_t(CodecLz4.LZ4F_frameInfo_t(0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x0000000000000000, 0x00000000, 0x00000000), 0, 0x00000000, (0x00000000, 0x00000000, 0x00000000, 0x00000000))), TranscodingStreams.Memory(Ptr{UInt8} @0x0000000000000000, 0x0000000000000013), false)
CodecZlib: VersionNumber[v"0.6.0"]
merafile_version: 1.0
JLD2: VersionNumber[v"0.4.31"]
CodecBzip2: VersionNumber[v"0.7.2"]
JLD2compatible_versions: 0.1
CodecLz4: VersionNumber[v"0.4.0"]
Mera: Any[v"1.2.0", "https://github.com/ManuelBehrendt/Mera.jl"]
-------------------------
Memory: 38.4513635635376 MB (uncompressed)


Datatype: gravity
merafile_version: 1.0
Compression: CodecLz4.LZ4FrameCompressor(Base.RefValue{Ptr{CodecLz4.LZ4F_cctx}}(Ptr{CodecLz4.LZ4F_cctx} @0x0000000000000000), Base.RefValue{CodecLz4.LZ4F_preferences_t}(CodecLz4.LZ4F_preferences_t(CodecLz4.LZ4F_frameInfo_t(0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x0000000000000000, 0x00000000, 0x00000000), 0, 0x00000000, (0x00000000, 0x00000000, 0x00000000, 0x00000000))), TranscodingStreams.Memory(Ptr{UInt8} @0x0000000000000000, 0x0000000000000013), false)
CodecZlib: VersionNumber[v"0.6.0"]
merafile_version: 1.0
JLD2: VersionNumber[v"0.4.31"]
CodecBzip2: VersionNumber[v"0.7.2"]
JLD2compatible_versions: 0.1
CodecLz4: VersionNumber[v"0.4.0"]
Mera: Any[v"1.2.0", "https://github.com/ManuelBehrendt/Mera.jl"]
-------------------------
Memory: 1.6880846759304404 GB (uncompressed)


Datatype: hydro
merafile_version: 1.0
Compression: CodecLz4.LZ4FrameCompressor(Base.RefValue{Ptr{CodecLz4.LZ4F_cctx}}(Ptr{CodecLz4.LZ4F_cctx} @0x0000000000000000), Base.RefValue{CodecLz4.LZ4F_preferences_t}(CodecLz4.LZ4F_preferences_t(CodecLz4.LZ4F_frameInfo_t(0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x0000000000000000, 0x00000000, 0x00000000), 0, 0x00000000, (0x00000000, 0x00000000, 0x00000000, 0x00000000))), TranscodingStreams.Memory(Ptr{UInt8} @0x0000000000000000, 0x0000000000000013), false)
CodecZlib: VersionNumber[v"0.6.0"]
merafile_version: 1.0
JLD2: VersionNumber[v"0.4.31"]
CodecBzip2: VersionNumber[v"0.7.2"]
JLD2compatible_versions: 0.1
CodecLz4: VersionNumber[v"0.4.0"]
Mera: Any[v"1.2.0", "https://github.com/ManuelBehrendt/Mera.jl"]
-------------------------
Memory: 2.3211082834750414 GB (uncompressed)


-----------------------------------
convert stat: false
-----------------------------------
Total file size: 2.159 GB
-----------------------------------






Dict{Any, Any} with 4 entries:
  "particles" => Dict{Any, Any}("versions"=>Dict{Any, Any}("CodecZlib"=>Version…
  "FileSize"  => (2.159, "GB")
  "gravity"   => Dict{Any, Any}("versions"=>Dict{Any, Any}("CodecZlib"=>Version…
  "hydro"     => Dict{Any, Any}("versions"=>Dict{Any, Any}("CodecZlib"=>Version…

Get Info

The following function infodata is comparable to getinfo() used for the RAMSES files and loads detailed information about the simulation output:

info = infodata(300, "../../testing/simulations/JLD2_files/");

[Mera]: 2023-04-10T17:56:08.095

Use datatype: hydro
Code: RAMSES
output [300] summary:
mtime: 2023-04-09T05:34:09
ctime: 2023-04-10T08:08:14.488
=======================================================
simulation time: 445.89 [Myr]
boxlen: 48.0 [kpc]
ncpu: 640
ndim: 3
-------------------------------------------------------
amr:           true
level(s): 6 - 10 --> cellsize(s): 750.0 [pc] - 46.88 [pc]
-------------------------------------------------------
hydro:         true
hydro-variables:  7  --> (:rho, :vx, :vy, :vz, :p, :var6, :var7)
hydro-descriptor: (:density, :velocity_x, :velocity_y, :velocity_z, :pressure, :scalar_00, :scalar_01)
γ: 1.6667
-------------------------------------------------------
gravity:       true
gravity-variables: (:epot, :ax, :ay, :az)
-------------------------------------------------------
particles:     true
- Nstars:   5.445150e+05 
particle-variables: 7  --> (:vx, :vy, :vz, :mass, :family, :tag, :birth)
particle-descriptor: (:position_x, :position_y, :position_z, :velocity_x, :velocity_y, :velocity_z, :mass, :identity, :levelp, :family, :tag, :birth_time)
-------------------------------------------------------
rt:            false
clumps:           false
-------------------------------------------------------
namelist-file: ("&COOLING_PARAMS", "&HYDRO_PARAMS", "&SF_PARAMS", "&AMR_PARAMS", "&BOUNDARY_PARAMS", "&OUTPUT_PARAMS", "&POISSON_PARAMS", "&INIT_PARAMS", "&RUN_PARAMS", "&FEEDBACK_PARAMS", "&REFINE_PARAMS")
-------------------------------------------------------
timer-file:       true
compilation-file: false
makefile:         true
patchfile:        true
=======================================================

In this case, it loaded the InfoDataType from the hydro data. Choose a different stored datatype to get the info from:

info = infodata(300, "../../testing/simulations/JLD2_files/", :particles);

[Mera]: 2023-04-10T17:58:12.353

Use datatype: particles
Code: RAMSES
output [300] summary:
mtime: 2023-04-09T05:34:09
ctime: 2023-04-10T08:08:14.488
=======================================================
simulation time: 445.89 [Myr]
boxlen: 48.0 [kpc]
ncpu: 640
ndim: 3
-------------------------------------------------------
amr:           true
level(s): 6 - 10 --> cellsize(s): 750.0 [pc] - 46.88 [pc]
-------------------------------------------------------
hydro:         true
hydro-variables:  7  --> (:rho, :vx, :vy, :vz, :p, :var6, :var7)
hydro-descriptor: (:density, :velocity_x, :velocity_y, :velocity_z, :pressure, :scalar_00, :scalar_01)
γ: 1.6667
-------------------------------------------------------
gravity:       true
gravity-variables: (:epot, :ax, :ay, :az)
-------------------------------------------------------
particles:     true
- Nstars:   5.445150e+05 
particle-variables: 7  --> (:vx, :vy, :vz, :mass, :family, :tag, :birth)
particle-descriptor: (:position_x, :position_y, :position_z, :velocity_x, :velocity_y, :velocity_z, :mass, :identity, :levelp, :family, :tag, :birth_time)
-------------------------------------------------------
rt:            false
clumps:           false
-------------------------------------------------------
namelist-file: ("&COOLING_PARAMS", "&HYDRO_PARAMS", "&SF_PARAMS", "&AMR_PARAMS", "&BOUNDARY_PARAMS", "&OUTPUT_PARAMS", "&POISSON_PARAMS", "&INIT_PARAMS", "&RUN_PARAMS", "&FEEDBACK_PARAMS", "&REFINE_PARAMS")
-------------------------------------------------------
timer-file:       true
compilation-file: false
makefile:         true
patchfile:        true
=======================================================

Load The Data from JLD2

Full Data

gas = loaddata(300, "../../testing/simulations/JLD2_files/", :hydro);

[Mera]: 2023-04-10T17:59:17.292

Open Mera-file output_00300.jld2:

domain:
xmin::xmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
ymin::ymax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
zmin::zmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]

Memory used for data table :2.321107776835561 GB
-------------------------------------------------------

typeof(gas)

HydroDataType

part = loaddata(300, "../../testing/simulations/JLD2_files/", :particles);

[Mera]: 2023-04-10T17:59:53.847

Open Mera-file output_00300.jld2:

domain:
xmin::xmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
ymin::ymax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
zmin::zmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]

Memory used for data table :38.45084476470947 MB
-------------------------------------------------------

typeof(part)

PartDataType

Data Range

Complete data is loaded, and the selected subregion is returned:

gas = loaddata(300, "../../testing/simulations/JLD2_files/", :hydro,
                    xrange=[-10,10], 
                    yrange=[-10,10], zrange=[-2,2],
                    center=[:boxcenter], 
                    range_unit=:kpc);

[Mera]: 2023-04-10T18:02:11.639

Open Mera-file output_00300.jld2:

center: [0.5, 0.5, 0.5] ==> [24.0 [kpc] :: 24.0 [kpc] :: 24.0 [kpc]]

domain:
xmin::xmax: 0.2916667 :: 0.7083333  	==> 14.0 [kpc] :: 34.0 [kpc]
ymin::ymax: 0.2916667 :: 0.7083333  	==> 14.0 [kpc] :: 34.0 [kpc]
zmin::zmax: 0.4583333 :: 0.5416667  	==> 22.0 [kpc] :: 26.0 [kpc]

Memory used for data table :587.3237018585205 MB
-------------------------------------------------------

Convert RAMSES Output Into JLD2

Existing AMR, hydro, gravity, particle, and clump data is sequentially stored in a JLD2 file. The individual loading/writing processes are timed, and the memory usage is returned in a dictionary:

Full Data

cvd = convertdata(300, path="../../testing/simulations/mw_L10",
                  fpath="../../testing/simulations/JLD2_files/");

[Mera]: 2023-04-10T18:06:14.413

Requested datatypes: [:hydro, :gravity, :particles, :clumps]

domain:
xmin::xmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
ymin::ymax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
zmin::zmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]


reading/writing lmax: 10 of 10
-----------------------------------
Compression: CodecLz4.LZ4FrameCompressor(Base.RefValue{Ptr{CodecLz4.LZ4F_cctx}}(Ptr{CodecLz4.LZ4F_cctx} @0x0000000000000000), Base.RefValue{CodecLz4.LZ4F_preferences_t}(CodecLz4.LZ4F_preferences_t(CodecLz4.LZ4F_frameInfo_t(0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x0000000000000000, 0x00000000, 0x00000000), 0, 0x00000000, (0x00000000, 0x00000000, 0x00000000, 0x00000000))), TranscodingStreams.Memory(Ptr{UInt8} @0x000000011f291c50, 0x0000000000000013), false)
-----------------------------------
- hydro
Reading data...


Progress: 100%|█████████████████████████████████████████| Time: 0:00:24


- gravity
Reading data...


Progress: 100%|█████████████████████████████████████████| Time: 0:00:19


- particles

Total datasize:
- total folder: 5.682 GB
- selected: 5.68 GB
- used: 4.047 GB
- new on disc: 2.159 GB

Timer

Get a view of the timers:

using TimerOutputs

cvd

Dict{Any, Any} with 3 entries:
  "viewdata"     => Dict{Any, Any}("particles"=>Dict{Any, Any}("versions"=>Dict…
  "size"         => Dict{Any, Any}("folder"=>Any[6101105264, "Bytes"], "selecte…
  "TimerOutputs" => Dict{Any, Any}("writing"=> ──────────────────────────…

cvd["TimerOutputs"]["reading"]

 ──────────────────────────────────────────────────────────────────────
                              Time                    Allocations      
                     ───────────────────────   ────────────────────────
  Tot / % measured:        324s /  16.9%           45.4GiB /  72.9%    

 Section     ncalls     time    %tot     avg     alloc    %tot      avg
 ──────────────────────────────────────────────────────────────────────
 hydro            1    30.4s   55.4%   30.4s   18.7GiB   56.5%  18.7GiB
 gravity          1    24.0s   43.7%   24.0s   14.1GiB   42.6%  14.1GiB
 particles        1    503ms    0.9%   503ms    309MiB    0.9%   309MiB
 ──────────────────────────────────────────────────────────────────────

cvd["TimerOutputs"]["writing"]

 ──────────────────────────────────────────────────────────────────────
                              Time                    Allocations      
                     ───────────────────────   ────────────────────────
  Tot / % measured:        327s /   1.0%           45.4GiB /  22.6%    

 Section     ncalls     time    %tot     avg     alloc    %tot      avg
 ──────────────────────────────────────────────────────────────────────
 hydro            1    1.89s   55.4%   1.89s   5.92GiB   57.6%  5.92GiB
 gravity          1    1.34s   39.3%   1.34s   4.23GiB   41.2%  4.23GiB
 particles        1    181ms    5.3%   181ms    129MiB    1.2%   129MiB
 ──────────────────────────────────────────────────────────────────────

# prep timer
to = TimerOutput();

@timeit to "MERA" begin
    @timeit to "hydro"     gas = loaddata(300, "../../testing/simulations/JLD2_files/", :hydro, )
    @timeit to "particles" part= loaddata(300, "../../testing/simulations/JLD2_files/", :particles)
end;

[Mera]: 2023-04-10T18:13:05.133

Open Mera-file output_00300.jld2:

domain:
xmin::xmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
ymin::ymax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
zmin::zmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]

Memory used for data table :2.321107776835561 GB
-------------------------------------------------------

[Mera]: 2023-04-10T18:13:11.371

Open Mera-file output_00300.jld2:

domain:
xmin::xmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
ymin::ymax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
zmin::zmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]

Memory used for data table :38.45084476470947 MB
-------------------------------------------------------

to

 ────────────────────────────────────────────────────────────────────────
                                Time                    Allocations      
                       ───────────────────────   ────────────────────────
   Tot / % measured:        80.3s /   8.1%           7.23GiB /  99.8%    

 Section       ncalls     time    %tot     avg     alloc    %tot      avg
 ────────────────────────────────────────────────────────────────────────
 MERA               3    6.50s  100.0%   2.17s   7.22GiB  100.0%  2.41GiB
   hydro            3    6.36s   97.8%   2.12s   7.10GiB   98.4%  2.37GiB
   particles        1    140ms    2.1%   140ms    121MiB    1.6%   121MiB
 ────────────────────────────────────────────────────────────────────────

<div class="alert alert-block alert-info"> <b>NOTE</b> The reading from JLD2 files is multiple times faster than from the original RAMSES files. </div>

Used Memory

cvd["size"]

Dict{Any, Any} with 4 entries:
  "folder"   => Any[6101105264, "Bytes"]
  "selected" => Any[4.29676e9, "Bytes"]
  "ondisc"   => Any[1402573523, "Bytes"]
  "used"     => Any[2.53259e9, "Bytes"]

<div class="alert alert-block alert-info"> <b>NOTE</b> The compressed JLD2 file takes a significantly smaller disk space than the original RAMSES folder.</div>

factor = cvd["size"]["folder"][1] / cvd["size"]["ondisc"][1]
println("==============================================================================")
println("In this example, the disk space is reduced by a factor of $factor !!")
println("==============================================================================")

==============================================================================
In this example, the disk space is reduced by a factor of 4.349936145201281 !!
==============================================================================

Selected Datatypes

cvd = convertdata(300, [:hydro, :particles], 
                  path="../../testing/simulations/mw_L10",
                  fpath="../../testing/simulations/JLD2_files/");

[Mera]: 2023-04-10T18:17:17.373

Requested datatypes: [:hydro, :particles]

domain:
xmin::xmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
ymin::ymax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
zmin::zmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]


reading/writing lmax: 10 of 10
-----------------------------------
Compression: CodecLz4.LZ4FrameCompressor(Base.RefValue{Ptr{CodecLz4.LZ4F_cctx}}(Ptr{CodecLz4.LZ4F_cctx} @0x0000000000000000), Base.RefValue{CodecLz4.LZ4F_preferences_t}(CodecLz4.LZ4F_preferences_t(CodecLz4.LZ4F_frameInfo_t(0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x0000000000000000, 0x00000000, 0x00000000), 0, 0x00000000, (0x00000000, 0x00000000, 0x00000000, 0x00000000))), TranscodingStreams.Memory(Ptr{UInt8} @0x000000011dbea7b0, 0x0000000000000013), false)
-----------------------------------
- hydro
Reading data...


Progress: 100%|█████████████████████████████████████████| Time: 0:00:24


- particles

Total datasize:
- total folder: 5.682 GB
- selected: 4.002 GB
- used: 2.359 GB
- new on disc: 1.306 GB

By default, the data is compressed by a standard compressor. Therefore, if you want to use a different compression algorithm better suited to your needs, you can also directly pass a compressor. https://juliaio.github.io/JLD2.jl/stable/compression/

Library	Compressor
CodecZlib.jl	ZlibCompressor	The default as it is very widely used.
CodecBzip2.jl	Bzip2Compressor	Can often times be faster
CodecLz4.jl	LZ4FrameCompressor	Fast, but not compatible to the LZ4 shipped by HDF5

To use any of these, replace the compress = true argument with an instance of the compressor, e.g.

using CodecZlib
cvd = convertdata(300, [:hydro, :particles], compress=ZlibCompressor(),
                  path="../../testing/simulations/mw_L10",
                  fpath="../../testing/simulations/JLD2_files/");

[Mera]: 2023-04-10T18:25:31.061

Requested datatypes: [:hydro, :particles]

domain:
xmin::xmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
ymin::ymax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
zmin::zmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]


reading/writing lmax: 10 of 10
-----------------------------------
Compression: ZlibCompressor(level=-1, windowbits=15)
-----------------------------------
- hydro
Reading data...


Progress: 100%|█████████████████████████████████████████| Time: 0:00:23


- particles

Total datasize:
- total folder: 5.682 GB
- selected: 4.002 GB
- used: 2.359 GB
- new on disc: 1.24 GB

savedata(gas, "../../testing/simulations/JLD2_files/", 
            fmode=:write, compress=ZlibCompressor());

[Mera]: 2023-04-10T19:38:12.259


Create file: output_00300.jld2
Directory: /Users/mabe/Documents/codes/github/Mera.jl/tutorials/version_1/../../testing/simulations/mw_L10
-----------------------------------
merafile_version: 1.0  -  Simulation code: RAMSES
-----------------------------------
DataType: hydro  -  Data variables: (:level, :cx, :cy, :cz, :rho, :vx, :vy, :vz, :p, :var6, :var7)
-----------------------------------
I/O mode: write  -  Compression: ZlibCompressor(level=-1, windowbits=15)
-----------------------------------
CodecZlib  0.6.0
Mera  1.2.0   https://github.com/ManuelBehrendt/Mera.jl
CodecBzip2  0.7.2
JLD2  0.4.31
CodecLz4  0.4.0
-----------------------------------
Memory size: 2.321 GB (uncompressed)
Total file size: 1.213 GB
-----------------------------------

Get more information about the parameters of the compressor:

?ZlibCompressor

search: ZlibCompressor ZlibCompressorStream ZlibDecompressor

ZlibCompressor(;level=-1, windowbits=15)

Create a zlib compression codec.

Arguments

level: compression level (-1..9)
windowbits: size of history buffer (8..15)

Comments

Add a description to the files:

comment = "The simulation is...."
cvd = convertdata(300, [:hydro, :particles], comments=comment,
                  path="../../testing/simulations/mw_L10",
                  fpath="../../testing/simulations/JLD2_files/");

[Mera]: 2023-04-10T19:40:13.068

Requested datatypes: [:hydro, :particles]

domain:
xmin::xmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
ymin::ymax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
zmin::zmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]


reading/writing lmax: 10 of 10
-----------------------------------
Compression: CodecLz4.LZ4FrameCompressor(Base.RefValue{Ptr{CodecLz4.LZ4F_cctx}}(Ptr{CodecLz4.LZ4F_cctx} @0x0000000000000000), Base.RefValue{CodecLz4.LZ4F_preferences_t}(CodecLz4.LZ4F_preferences_t(CodecLz4.LZ4F_frameInfo_t(0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x0000000000000000, 0x00000000, 0x00000000), 0, 0x00000000, (0x00000000, 0x00000000, 0x00000000, 0x00000000))), TranscodingStreams.Memory(Ptr{UInt8} @0x000000011d36bcb0, 0x0000000000000013), false)
-----------------------------------
- hydro
Reading data...


Progress: 100%|█████████████████████████████████████████| Time: 0:00:29


- particles


Progress: 100%|█████████████████████████████████████████| Time: 0:00:02



Total datasize:
- total folder: 5.682 GB
- selected: 4.002 GB
- used: 2.359 GB
- new on disc: 1.306 GB

comment = "The simulation is...."
savedata(gas, "../../testing/simulations/JLD2_files/", comments=comment, fmode=:write);

[Mera]: 2023-04-10T19:42:11.007


Create file: output_00300.jld2
Directory: /Users/mabe/Documents/codes/github/Mera.jl/tutorials/version_1/../../testing/simulations/mw_L10
-----------------------------------
merafile_version: 1.0  -  Simulation code: RAMSES
-----------------------------------
DataType: hydro  -  Data variables: (:level, :cx, :cy, :cz, :rho, :vx, :vy, :vz, :p, :var6, :var7)
-----------------------------------
I/O mode: write  -  Compression: CodecLz4.LZ4FrameCompressor(Base.RefValue{Ptr{CodecLz4.LZ4F_cctx}}(Ptr{CodecLz4.LZ4F_cctx} @0x0000000000000000), Base.RefValue{CodecLz4.LZ4F_preferences_t}(CodecLz4.LZ4F_preferences_t(CodecLz4.LZ4F_frameInfo_t(0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x0000000000000000, 0x00000000, 0x00000000), 0, 0x00000000, (0x00000000, 0x00000000, 0x00000000, 0x00000000))), TranscodingStreams.Memory(Ptr{UInt8} @0x000000011a279cc0, 0x0000000000000013), false)
-----------------------------------
CodecZlib  0.6.0
Mera  1.2.0   https://github.com/ManuelBehrendt/Mera.jl
CodecBzip2  0.7.2
JLD2  0.4.31
CodecLz4  0.4.0
-----------------------------------
Memory size: 2.321 GB (uncompressed)
Total file size: 1.276 GB
-----------------------------------

Load the comment (hydro) from JLD2 file:

vd = viewdata(300, "../../testing/simulations/JLD2_files/", verbose=false);

vd["hydro"]["comments"]

"The simulation is...."