Someone else had this error in 2018 and opened a GMT issue for it: https://github.com/GenericMappingTools/GMT.jl/issues/59 (I’m not sure if it proper precedure to ask for the error to be reopened or to post here.)
Things that are the same:
- the error message
Things that are different:
- I installed GMT late last year, so a 2018 installation issue feels unrelated. That being said, I am open to completely uninstalling GMT from my computer and reinstalling it if you can tell me how to make sure I do this correctly.
- I’m using Julia 1.10.4, but I don’t know how to tell if I am using GMT5 or GMT6. I doubt those are even the relevant numbers anymore. (The error first occurred when I was using Julia 1.8.5 and I was hoping that updating to 1.10.4 would solve it, but it persisted in the same manner as before.) If it matters, I use VS code as my environment and made sure to update both the kernel and environment to 1.10.4. I have also restarted my computer multiple times.
- The code I am using is running a for loop that seems to successfully run over 10,900 times before it stops and I get the error message. Thus, I don’t know how to share a simple code that will output this same error. When I restart the kernel the code will again run successfully before stopping after several thousand iterations.
Here is the error message in its entirety:
GMT: Failure to open virtual file
Stacktrace:
[1] error(s::String)
@ Base .\error.jl:35
[2] GMTJL_Set_Object(API::Ptr{Nothing}, X::GMT.GMT_RESOURCE, ptr::GMTdataset{Float64, 2}, pad::Int64)
@ GMT C:\Users\johns\.julia\packages\GMT\bf7CV\src\gmt_main.jl:744
[3] gmt(::String, ::Matrix{Float64}, ::Vararg{Any})
@ GMT C:\Users\johns\.julia\packages\GMT\bf7CV\src\gmt_main.jl:160
[4] common_grd(::Dict{Symbol, Any}, ::String, ::Matrix{Float64}, ::GMTdataset{Float64, 2})
@ GMT C:\Users\johns\.julia\packages\GMT\bf7CV\src\common_options.jl:3965
[5] common_grd(::Dict{Symbol, Any}, ::String, ::String, ::String, ::Matrix{Float64}, ::Vararg{Any})
@ GMT C:\Users\johns\.julia\packages\GMT\bf7CV\src\common_options.jl:3955
[6] gmtselect(cmd0::String, arg1::Matrix{Float64}, arg2::Nothing, arg3::Nothing, arg4::Nothing; kwargs::@Kwargs{polygon::GMTdataset{Float64, 2}})
@ GMT C:\Users\johns\.julia\packages\GMT\bf7CV\src\gmtselect.jl:88
[7] gmtselect (repeats 2 times)
@ C:\Users\johns\.julia\packages\GMT\bf7CV\src\gmtselect.jl:63 [inlined]
[8] gmtselect
@ C:\Users\johns\.julia\packages\GMT\bf7CV\src\gmtselect.jl:92 [inlined]
[9] inwhichpolygon(D::Vector{GMTdataset{Float64, 2}}, point::Vector{Float64})
@ GMT C:\Users\johns\.julia\packages\GMT\bf7CV\src\spatial_funs.jl:282
[10] top-level scope
@ c:\Users\johns\Documents\GitHub\TC-cell-research\Basins of Attraction.ipynb:73
The only part that is from my code (as far as I can tell) is line 73 in Basins of Attraction.ipynb which is
WhichTri = inwhichpolygon(tri_point,[nPtθ,nPtζ])
[nPtθ,nPtζ]is a point in or close to my domain, I doubt this is causing the errorinwhichpolygonis a GMT function. If this is causing the error, hopefully you have an idea on how I can change my implementation.tri_pointwas saved in a different .ipynb file and is created usingtriplot(data, noplot=true). It is then saved and loaded into Basins of Attraction.ipynb using JLD2 as a .jld2 file. My gut is telling me that my method of savingtri_pointis causing the error. If you agree, please tell me how I should be saving it. (Note: the .jld2 file is saved in the same windows folder as both .ipynb files)
Finally, I did test GMT in the command prompt (as suggested in the GMT issue that I linked above) and I did get an error, but I don’t understand what it means. So here is the print out:
Testing GMT
Status `C:\Users\johns\AppData\Local\Temp\jl_84WQcX\Project.toml`
[5752ebe1] GMT v1.15.0
[aea7be01] PrecompileTools v1.2.1
[08abe8d2] PrettyTables v2.3.2
[bd369af6] Tables v1.11.1
⌃ [a7073274] GDAL_jll v301.900.0+0
[b68b8c3f] GMT_jll v6.5.2+0
[61579ee1] Ghostscript_jll v9.55.0+4
[58948b4f] PROJ_jll v901.300.0+1
[ade2ca70] Dates
[f43a241f] Downloads v1.6.0
[37e2e46d] LinearAlgebra
[de0858da] Printf
[10745b16] Statistics v1.10.0
[8dfed614] Test
Status `C:\Users\johns\AppData\Local\Temp\jl_84WQcX\Manifest.toml`
[a8cc5b0e] Crayons v4.1.1
[9a962f9c] DataAPI v1.16.0
[e2d170a0] DataValueInterfaces v1.0.0
[5752ebe1] GMT v1.15.0
[82899510] IteratorInterfaceExtensions v1.0.0
[692b3bcd] JLLWrappers v1.5.0
[b964fa9f] LaTeXStrings v1.3.1
[3da0fdf6] MPIPreferences v0.1.11
[bac558e1] OrderedCollections v1.6.3
[aea7be01] PrecompileTools v1.2.1
[21216c6a] Preferences v1.4.3
[08abe8d2] PrettyTables v2.3.2
[189a3867] Reexport v1.2.2
[892a3eda] StringManipulation v0.3.4
[3783bdb8] TableTraits v1.0.1
[bd369af6] Tables v1.11.1
[8ce61222] Arrow_jll v10.0.0+1
[0b7ba130] Blosc_jll v1.21.5+0
[6e34b625] Bzip2_jll v1.0.8+1
[2e619515] Expat_jll v2.6.2+0
[f5851436] FFTW_jll v3.3.10+0
⌃ [a7073274] GDAL_jll v301.900.0+0
[d604d12d] GEOS_jll v3.12.2+0
[b68b8c3f] GMT_jll v6.5.2+0
[78b55507] Gettext_jll v0.21.0+0
[61579ee1] Ghostscript_jll v9.55.0+4
[7746bdde] Glib_jll v2.80.2+0
[0951126a] GnuTLS_jll v3.8.4+0
[0234f1f7] HDF5_jll v1.14.3+3
[e33a78d0] Hwloc_jll v2.11.0+0
⌅ [a51ab1cf] ICU_jll v69.1.0+0
[aacddb02] JpegTurbo_jll v3.0.3+0
[b39eb1a6] Kerberos_krb5_jll v1.19.3+0
[17f450c3] LAPACK32_jll v3.12.0+0
⌅ [88015f11] LERC_jll v3.0.0+1
[1d63c593] LLVMOpenMP_jll v15.0.7+0
[dd4b983a] LZO_jll v2.10.2+0
[08be9ffa] LibPQ_jll v16.0.0+0
⌅ [e9f186c6] Libffi_jll v3.2.2+1
[94ce4f54] Libiconv_jll v1.17.0+0
[4b2f31a3] Libmount_jll v2.40.1+0
⌅ [89763e89] Libtiff_jll v4.5.1+1
[d3a379c0] LittleCMS_jll v2.16.0+0
[5ced341a] Lz4_jll v1.9.4+0
[7cb0a576] MPICH_jll v4.2.1+1
[f1f71cc9] MPItrampoline_jll v5.4.0+0
[9237b28f] MicrosoftMPI_jll v10.1.4+2
[7243133f] NetCDF_jll v400.902.211+1
⌅ [4c82536e] Nettle_jll v3.7.2+0
⌅ [656ef2d0] OpenBLAS32_jll v0.3.24+0
[643b3616] OpenJpeg_jll v2.5.2+0
⌅ [fe0851c0] OpenMPI_jll v4.1.6+0
[458c3c95] OpenSSL_jll v3.0.14+0
[c2071276] P11Kit_jll v0.24.1+0
[2f80f16e] PCRE_jll v8.45.0+0
[58948b4f] PROJ_jll v901.300.0+1
[76ed43ae] SQLite_jll v3.45.3+0
⌅ [e0b8ae26] Thrift_jll v0.16.0+0
[02c8fc9c] XML2_jll v2.13.1+0
[ffd25f8a] XZ_jll v5.4.6+0
[3161d3a3] Zstd_jll v1.5.6+0
⌅ [28df3c45] boost_jll v1.76.0+1
[477f73a3] libaec_jll v1.1.2+0
[06c338fa] libgeotiff_jll v100.701.300+0
[b53b4c65] libpng_jll v1.6.43+1
[337d8026] libzip_jll v1.10.1+0
⌅ [fe1e1685] snappy_jll v1.1.10+0
[0dad84c5] ArgTools v1.1.1
[56f22d72] Artifacts
[2a0f44e3] Base64
[ade2ca70] Dates
[f43a241f] Downloads v1.6.0
[7b1f6079] FileWatching
[b77e0a4c] InteractiveUtils
[4af54fe1] LazyArtifacts
[b27032c2] LibCURL v0.6.4
[76f85450] LibGit2
[8f399da3] Libdl
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[d6f4376e] Markdown
[ca575930] NetworkOptions v1.2.0
[44cfe95a] Pkg v1.10.0
[de0858da] Printf
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA v0.7.0
[9e88b42a] Serialization
[6462fe0b] Sockets
[2f01184e] SparseArrays v1.10.0
[10745b16] Statistics v1.10.0
[fa267f1f] TOML v1.0.3
[a4e569a6] Tar v1.10.0
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
[e66e0078] CompilerSupportLibraries_jll v1.1.1+0
[781609d7] GMP_jll v6.2.1+6
[deac9b47] LibCURL_jll v8.4.0+0
[e37daf67] LibGit2_jll v1.6.4+0
[29816b5a] LibSSH2_jll v1.11.0+1
[c8ffd9c3] MbedTLS_jll v2.28.2+1
[14a3606d] MozillaCACerts_jll v2023.1.10
[4536629a] OpenBLAS_jll v0.3.23+4
[efcefdf7] PCRE2_jll v10.42.0+1
[bea87d4a] SuiteSparse_jll v7.2.1+1
[83775a58] Zlib_jll v1.2.13+1
[8e850b90] libblastrampoline_jll v5.8.0+1
[8e850ede] nghttp2_jll v1.52.0+1
[3f19e933] p7zip_jll v17.4.0+2
Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading.
Precompiling project...
69 dependencies successfully precompiled in 54 seconds. 7 already precompiled.
Testing Running tests...
Entering: test_proj4.jl
Rel. 9.3.0, September 1st, 2023
Located at: C:\Users\johns\AppData\Local/proj;C:\Users\johns\.julia\artifacts\1a92056bb5245200776914024d9a9ec6e44ccd4e/share/proj;/workspace/destdir/share/proj
GMT [WARNING]: GMT_COMPATIBILITY: Expects values from 6 to 6; reset to 6.
Entering: test_gd_ext.jl
Entering: test_gdal.jl
┌ Info: GDAL 3.9.0, released 2024/05/07
│ 207 GDAL drivers found
└ 75 OGR drivers found
ERROR 1: Zero positional arguments expected
ERROR 1: Zero positional arguments expected
[ Info: 1...
[ Info: 2...
ERROR 1: Zero positional arguments expected
Warning 1: OGR_G_Area() called against non-surface geometry type.
┌ Warning: Format not supported. Only TIF, PNG or netCDF are allowed. Resorting to TIF
└ @ GMT.Gdal C:\Users\johns\.julia\packages\GMT\bf7CV\src\gdal_tools.jl:502
[ Info: 3...
ERROR 10: Pointer 'hBand' is NULL in 'GDALGetRasterDataType'.
[ Info: 4...
[ Info: 5...
Warning 1: Non closed ring detected. To avoid accepting it, set the OGR_GEOMETRY_ACCEPT_UNCLOSED_RING configuration option to NO
[ Info: 6...
[ Info: 7...
ERROR 6: Incompatible geometry for operation
ERROR 6: Incompatible geometry for operation
[ Info: 8...
Geometry: POLYGON ((1198554.34 648493.09,1198553.65476738 64 ... .09))[ Info: 9...
[ Info: 10...
Layer: SELECT (100)
Field 0 (HEX(GeomFromText('POINT(10 20)'))): [String], ...
[ Info: 11...
CUBES
grdblend [NOTICE]: Remote data courtesy of GMT data server oceania [http://oceania.generic-mapping-tools.org]
grdblend [NOTICE]: SRTM15 Earth Relief v2.6 at 05x05 arc minutes reduced by Gaussian Cartesian filtering (26.2 km fullwidth) [Tozer et al., 2019].
grdblend [NOTICE]: -> Download 180x180 degree grid tile (earth_relief_05m_g): S90E000
WMS
serverURL: http://tiles.maps.eox.at/wms?
OnlineResource: http://tiles.maps.eox.at/?
version: 1.1.1
request: GetMap
layernames: ["s2cloudless-2018_3857", "coastline", "s2cloudless-2020", "osm_3857", "s2cloudless_3857", "terrain_3857", "overlay_base_bright_3857", "hydrography", "graticules", "overlay_3857", "bluemarble", "coastline_black", "s2cloudless-2017_3857", "streets_3857", "overlay_bright", "s2cloudless-2019_3857", "overlay", "blackmarble_3857", "hydrography_3857", "s2cloudless-2017", "streets", "s2cloudless-2018", "s2cloudless-2019", "osm", "blackmarble", "terrain-light_3857", "s2cloudless-2020_3857_512", "bluemarble_3857", "overlay_base_3857", "s2cloudless", "terrain", "overlay_bright_3857", "coastline_3857", "s2cloudless-2020_3857", "magnetic_graticules", "terrain-light", "overlay_base_bright", "overlay_base"]
layer: 38 Layers. Use layer[k] to see the contents of layer k
name: s2cloudless-2018_3857
title: Sentinel-2 cloudless layer for 2018 by EOX - 3857
srs: EPSG:900913
crs:
bbox: (-2.0037508342789e7, 2.0037508342789e7, -2.0037508342789e7, 2.0037508342789e7)
imgformat: image/jpeg
tilesize: 256
overviewcount: 18
resolution: 0.5971642834779395
tiled: true
transparent: false
WMS:http://tiles.maps.eox.at/?SERVICE=WMS&VERSION=1.1.1&REQUEST=GetMap&LAYERS=coastline&SRS=EPSG:4326&BBOX=-180,-90,180,90&FORMAT=image/png&TILESIZE=256&OVERVIEWCOUNT=17&MINRESOLUTION=0.00000536441803&TILED=true
Entering: test_imgfuns.jl
IMGFUNS
Entering: test_imgtiles.jl
TILES MOSAIC
Entering: test_makecpts.jl
MAKECPT
MAKECPT - 0
MAKECPT - 1
MAKECPT - 2
Entering: test_avatars.jl
PLOT
┌ Warning: option *ms* is ignored when either 'S' or 'symbol' options are used
└ @ GMT C:\Users\johns\.julia\packages\GMT\bf7CV\src\psxy.jl:690
┌ Warning: markerline overrides markeredgecolor
└ @ GMT C:\Users\johns\.julia\packages\GMT\bf7CV\src\psxy.jl:706
┌ Warning: option *ms* is ignored when either 'S' or 'symbol' options are used
└ @ GMT C:\Users\johns\.julia\packages\GMT\bf7CV\src\psxy.jl:690
┌ Warning: option *marker* is ignored when either 'S' or 'symbol' options are used
└ @ GMT C:\Users\johns\.julia\packages\GMT\bf7CV\src\psxy.jl:692
arg1 = GMTdataset{Float64, 2}
arg2 = GMTcpt
makecpt [ERROR]: Option -G: Unable to parse 0.25
GMT: Error During Test at C:\Users\johns\.julia\packages\GMT\bf7CV\test\runtests.jl:5
Got exception outside of a @test
LoadError: Something went wrong when calling the module. GMT error number = 72
Stacktrace:
[1] error(s::String)
@ Base .\error.jl:35
[2] gmt(::String)
@ GMT C:\Users\johns\.julia\packages\GMT\bf7CV\src\gmt_main.jl:169
[3] fish_bg(d::Dict{Symbol, Any}, cmd::Vector{String})
@ GMT C:\Users\johns\.julia\packages\GMT\bf7CV\src\psxy.jl:528
[4] common_plot_xyz(cmd0::String, arg1::GMTdataset{Float64, 2}, caller::String, first::Bool, is3D::Bool, kwargs::Pair{Symbol, String})
@ GMT C:\Users\johns\.julia\packages\GMT\bf7CV\src\psxy.jl:308
[5] plot(arg1::Matrix{Float64}; first::Bool, kw::@Kwargs{bg::String})
@ GMT C:\Users\johns\.julia\packages\GMT\bf7CV\src\plot.jl:122
[6] top-level scope
@ C:\Users\johns\.julia\packages\GMT\bf7CV\test\test_avatars.jl:61
[7] include(fname::String)
@ Base.MainInclude .\client.jl:489
[8] macro expansion
@ C:\Users\johns\.julia\packages\GMT\bf7CV\test\runtests.jl:51 [inlined]
[9] macro expansion
@ C:\Users\johns\AppData\Local\Programs\julia-1.10.4\share\julia\stdlib\v1.10\Test\src\Test.jl:1577 [inlined]
[10] top-level scope
@ C:\Users\johns\.julia\packages\GMT\bf7CV\test\runtests.jl:9
[11] include(fname::String)
@ Base.MainInclude .\client.jl:489
[12] top-level scope
@ none:6
[13] eval
@ .\boot.jl:385 [inlined]
[14] exec_options(opts::Base.JLOptions)
@ Base .\client.jl:291
[15] _start()
@ Base .\client.jl:552
in expression starting at C:\Users\johns\.julia\packages\GMT\bf7CV\test\test_avatars.jl:61
Test Summary: | Pass Error Total Time
GMT | 94 1 95 55.1s
PROJ4 | 3 3 6.6s
GDALext | 44 44 2.6s
GDAL | 30 30 8.1s
IMGFUNS | None 1.3s
MOSAIC | None 5.0s
MAKECPT | 3 3 0.6s
ERROR: LoadError: Some tests did not pass: 94 passed, 0 failed, 1 errored, 0 broken.
in expression starting at C:\Users\johns\.julia\packages\GMT\bf7CV\test\runtests.jl:5
ERROR: Package GMT errored during testing
If it matters, my larger code is trying to find the basins of attraction of a dynamical system that has been simplified to a mix between mesh points and an analytic process. To acheive this, I need to find points within the triangularization a lot. (I’m basically coloring the triangles based on their attraction.) I am working towards simplifying the process so that I don’t need to do as many iterations, but I will still have to do several thousand iterations, so I would really love to know why this error is happenning without needing to work around it.
Thank you for your willingness to help me work though this issue.