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SeisSol / SAMPLER

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ERROR: LoadError: UndefVarError: ismmappable not defined #3

Closed Thomas-Ulrich closed 3 years ago

Thomas-Ulrich commented 3 years ago

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?

mojomex commented 3 years ago

Hi,

thank you for pointing out the issue. As you already mentioned in your PR (#2), the problem was a missing dependency. In the latest pull request (#5), this has been fixed and the dependencies can now be automatically installed.