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License: BSD 3-Clause "New" or "Revised" License
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?
Example:
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...
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
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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