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ERROR: LoadError: UndefVarError: ismmappable not defined

Hi,
Just trying to use the sampler on the Palu setup with only seafloor displacement.

(base) ulrich@ulrich-ThinkPad-T490s:~/trash/julia_test/SAMPLER$ julia sampler.jl -m 4G -o ~/sampler-output.nc --seafloor-only ~/trash/julia_test/outputSeisSol/Sul8e6_straight_short-surface.xdmf 
["-m", "4G", "-o", "/home/ulrich/sampler-output.nc", "--seafloor-only", "/home/ulrich/trash/julia_test/outputSeisSol/Sul8e6_straight_short-surface.xdmf"]
Using 4 threads.
Precompiling project...
Done.
ERROR: LoadError: UndefVarError: ismmappable not defined
Stacktrace:
 [1] mmap_data_item(::XMLDict.XMLDictElement, ::String) at /home/ulrich/trash/julia_test/SAMPLER/io/xdmf.jl:151
 [2] grid_of(::String) at /home/ulrich/trash/julia_test/SAMPLER/io/xdmf.jl:24
 [3] main() at /home/ulrich/trash/julia_test/SAMPLER/sampler.jl:79
 [4] top-level scope at /home/ulrich/trash/julia_test/SAMPLER/sampler.jl:142
 [5] include(::Module, ::String) at ./Base.jl:377
 [6] exec_options(::Base.JLOptions) at ./client.jl:288
 [7] _start() at ./client.jl:484
in expression starting at /home/ulrich/trash/julia_test/SAMPLER/sampler.jl:141

Here is an overview of my xdmf file (tested in paraview, not broken):

(base) ulrich@ulrich-ThinkPad-T490s:~/trash/julia_test/SAMPLER$ head  ~/trash/julia_test/outputSeisSol/Sul8e6_straight_short-surface.xdmf -n 50
<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="2.0">
 <Domain>
  <Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">
   <Grid Name="step_000000000000" GridType="Uniform"><!-- mesh id: 0, mesh step: 0 -->
    <Topology TopologyType="Triangle" NumberOfElements="296120">
     <DataItem NumberType="Int" Precision="8" Format="HDF" Dimensions="296120 3">Sul8e6_straight_short-surface_cell.h5:/mesh0/connect</DataItem>
    </Topology>
    <Geometry name="geo" GeometryType="XYZ" NumberOfElements="148580">
     <DataItem NumberType="Float" Precision="8" Format="HDF" Dimensions="148580 3">Sul8e6_straight_short-surface_vertex.h5:/mesh0/geometry</DataItem>
    </Geometry>
    <Time Value="0"/>
    <Attribute Name="partition" Center="Cell">
     <DataItem  NumberType="Int" Precision="4" Format="HDF" Dimensions="296120">Sul8e6_straight_short-surface_cell.h5:/mesh0/partition</DataItem>
    </Attribute>
    <Attribute Name="u" Center="Cell">
     <DataItem ItemType="HyperSlab" Dimensions="296120">
      <DataItem NumberType="UInt" Precision="4" Format="XML" Dimensions="3 2">0 0 1 1 1 296120</DataItem>
      <DataItem NumberType="Float" Precision="8" Format="HDF" Dimensions="1 296120">Sul8e6_straight_short-surface_cell.h5:/mesh0/u</DataItem>
     </DataItem>
    </Attribute>
    <Attribute Name="v" Center="Cell">
     <DataItem ItemType="HyperSlab" Dimensions="296120">
      <DataItem NumberType="UInt" Precision="4" Format="XML" Dimensions="3 2">0 0 1 1 1 296120</DataItem>
      <DataItem NumberType="Float" Precision="8" Format="HDF" Dimensions="1 296120">Sul8e6_straight_short-surface_cell.h5:/mesh0/v</DataItem>
     </DataItem>
    </Attribute>
    <Attribute Name="w" Center="Cell">
     <DataItem ItemType="HyperSlab" Dimensions="296120">
      <DataItem NumberType="UInt" Precision="4" Format="XML" Dimensions="3 2">0 0 1 1 1 296120</DataItem>
      <DataItem NumberType="Float" Precision="8" Format="HDF" Dimensions="1 296120">Sul8e6_straight_short-surface_cell.h5:/mesh0/w</DataItem>
     </DataItem>
    </Attribute>
    <Attribute Name="U" Center="Cell">
     <DataItem ItemType="HyperSlab" Dimensions="296120">
      <DataItem NumberType="UInt" Precision="4" Format="XML" Dimensions="3 2">0 0 1 1 1 296120</DataItem>
      <DataItem NumberType="Float" Precision="8" Format="HDF" Dimensions="1 296120">Sul8e6_straight_short-surface_cell.h5:/mesh0/U</DataItem>
     </DataItem>
    </Attribute>
    <Attribute Name="V" Center="Cell">
     <DataItem ItemType="HyperSlab" Dimensions="296120">
      <DataItem NumberType="UInt" Precision="4" Format="XML" Dimensions="3 2">0 0 1 1 1 296120</DataItem>
      <DataItem NumberType="Float" Precision="8" Format="HDF" Dimensions="1 296120">Sul8e6_straight_short-surface_cell.h5:/mesh0/V</DataItem>
     </DataItem>
    </Attribute>
    <Attribute Name="W" Center="Cell">
     <DataItem ItemType="HyperSlab" Dimensions="296120">
      <DataItem NumberType="UInt" Precision="4" Format="XML" Dimensions="3 2">0 0 1 1 1 296120</DataItem>
      <DataItem NumberType="Float" Precision="8" Format="HDF" Dimensions="1 296120">Sul8e6_straight_short-surface_cell.h5:/mesh0/W</DataItem>

Am I doing something wrong?

dimension are swapped

Example:

with this file:
image

and this command:


julia --project src/main.jl -m 2G --water-height=2000 -o ~/trash/scA.nc ~/trash/output_AscSimple_dip16_withCoh_PfLith_mu4_scenario_A2-surface.xdmf --sampling-rate 1e3

I get:

Using 1 threads.
Will write output to "/home/ulrich/trash/scA.nc".
locationFlag not found, assuming locationFlag=2...
Domain is (-325000.0, 425000.0) × (-375000.0, 375000.0) × (0.0, 0.0).

but then y ranges between -324000 and 425000.0...

error during instantiate

I tried the instruction in the read me and got:

(base) ulrich@ulrich-ThinkPad-T490s:~/SeisSol/Sampler$ export JULIA_NUM_THREADS=4
(base) ulrich@ulrich-ThinkPad-T490s:~/SeisSol/Sampler$ julia
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.4.1
 _/ |\__'_|_|_|\__'_|  |  Ubuntu ⛬  julia/1.4.1+dfsg-1
|__/                   |

(@v1.4) pkg> 

(@v1.4) pkg> activate .
 Activating environment at `~/SeisSol/Sampler/Project.toml`

(SAMPLER) pkg> instantiate
   Updating registry at `~/.julia/registries/General`
   Updating git-repo `https://github.com/JuliaRegistries/General.git`
ERROR: TypeError: in typeassert, expected VersionNumber, got Pkg.Types.VersionSpec
Stacktrace:
 [1] load_urls(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/Operations.jl:456
 [2] #download_source#39 at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/Operations.jl:632 [inlined]
 [3] download_source at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/Operations.jl:631 [inlined]
 [4] instantiate(::Pkg.Types.Context; manifest::Nothing, update_registry::Bool, verbose::Bool, platform::Pkg.BinaryPlatforms.Linux, kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:820
 [5] instantiate(::Pkg.Types.Context) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:748
 [6] #instantiate#116 at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:744 [inlined]
 [7] instantiate() at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:744
 [8] do_cmd!(::Pkg.REPLMode.Command, ::REPL.LineEditREPL) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/REPLMode/REPLMode.jl:400
 [9] do_cmd(::REPL.LineEditREPL, ::String; do_rethrow::Bool) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/REPLMode/REPLMode.jl:381
 [10] do_cmd at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/REPLMode/REPLMode.jl:376 [inlined]
 [11] (::Pkg.REPLMode.var"#24#27"{REPL.LineEditREPL,REPL.LineEdit.Prompt})(::REPL.LineEdit.MIState, ::Base.GenericIOBuffer{Array{UInt8,1}}, ::Bool) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/REPLMode/REPLMode.jl:542
 [12] #invokelatest#1 at ./essentials.jl:712 [inlined]
 [13] invokelatest at ./essentials.jl:711 [inlined]
 [14] run_interface(::REPL.Terminals.TextTerminal, ::REPL.LineEdit.ModalInterface, ::REPL.LineEdit.MIState) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/REPL/src/LineEdit.jl:2354
 [15] run_frontend(::REPL.LineEditREPL, ::REPL.REPLBackendRef) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/REPL/src/REPL.jl:1055
 [16] run_repl(::REPL.AbstractREPL, ::Any) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/REPL/src/REPL.jl:206
 [17] (::Base.var"#764#766"{Bool,Bool,Bool,Bool})(::Module) at ./client.jl:383
 [18] #invokelatest#1 at ./essentials.jl:712 [inlined]
 [19] invokelatest at ./essentials.jl:711 [inlined]
 [20] run_main_repl(::Bool, ::Bool, ::Bool, ::Bool, ::Bool) at ./client.jl:367
 [21] exec_options(::Base.JLOptions) at ./client.jl:305
 [22] _start() at ./client.jl:484

Tanioka filter : high resolution bathymetry required

When applying Tanioka, the bathymetry should be read from a highly resolved bathymetry file (e.g. NetCDF file), not from SeisSol geometry, which incorporates most of the time coarser bathymetry data (else the SeisSol mesh would be huge).
This is not the case currently, as the bathymetry file is not given as an argument.
https://github.com/SeisSol/SAMPLER#rasterize-seafloor-using-taniokas-method

see https://gitlab.lrz.de/samoa/displacement-converter/-/tree/thomas/tanioka_reconstruction for an example of implementation.

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