julia 1.8.2-5, 1.9 compile error

[benibilme]

Hello,

I am new to GMT as well as julia.

I have installed julia 1.8.2 in an arch linux environment. I have installed GMT without issues but it gives error during precompilation while using the module.

Following is the error:

julia> using GMT
[ Info: Precompiling GMT [5752ebe1-31b9-557e-87aa-f909b540aa54]
ERROR: LoadError: could not load library "/usr/lib/libgmt.so"
/home/user/opt/julia-1.8.2/bin/../lib/julia/libcurl.so: version `CURL_OPENSSL_4' not found (required by /usr/lib/libgmt.so)
Stacktrace:
 [1] GMT_Create_Session (repeats 2 times)
   @ ~/.julia/packages/GMT/mzT4h/src/libgmt.jl:2 [inlined]
 [2] top-level scope
   @ ~/.julia/packages/GMT/mzT4h/src/get_enums.jl:9
 [3] include(mod::Module, _path::String)
   @ Base ./Base.jl:419
 [4] include(x::String)
   @ GMT ~/.julia/packages/GMT/mzT4h/src/GMT.jl:1
 [5] top-level scope
   @ ~/.julia/packages/GMT/mzT4h/src/GMT.jl:287
 [6] include
   @ ./Base.jl:419 [inlined]
 [7] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
   @ Base ./loading.jl:1554
 [8] top-level scope
   @ stdin:1
in expression starting at /home/user/.julia/packages/GMT/mzT4h/src/get_enums.jl:9
in expression starting at /home/user/.julia/packages/GMT/mzT4h/src/GMT.jl:1
in expression starting at stdin:1
ERROR: Failed to precompile GMT [5752ebe1-31b9-557e-87aa-f909b540aa54] to /home/user/.julia/compiled/v1.8/GMT/jl_WsZzh7.
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:35
 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
   @ Base ./loading.jl:1707
 [3] compilecache
   @ ./loading.jl:1651 [inlined]
 [4] _require(pkg::Base.PkgId)
   @ Base ./loading.jl:1337
 [5] _require_prelocked(uuidkey::Base.PkgId)
   @ Base ./loading.jl:1200
 [6] macro expansion
   @ ./loading.jl:1180 [inlined]
 [7] macro expansion
   @ ./lock.jl:223 [inlined]
 [8] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1144

Any help insight much appreciated.

[joa-quim]

Oh dear, Linux is soooo painful. So it looks like booth Julia and GMT were linked against incompatible libcurl versions.

See if this is of any help https://askubuntu.com/questions/1211782/curl-openssl-4-not-found-required-by-curl

[benibilme]

Hello,

Arch wiki states following:

`Note: The julia package is compiled against system libraries and is therefore unsupported by the upstream. While it may be suitable for basic usage it is incompatible with external packages (e.g. MKL, LLVM, LLVMExtra, or packages that depend on these, like CUDA or Flux) which rely on Julia's bundled versions of its dependencies. Bugs reported against this binary will be closed.

Install julia-binAUR. The package provides official builds compiled against patched LLVM libs.`

Because of that, I have downloaded the official julia package from the julia web site which gave above error. I have also tried julia binary which is not officially supported Arch user repository, it gave the same error as well.

I have not understood the solution, should I delete the system libcurl library...

[benibilme]

I installed 1.8.3 from julia web site, deleted internal softlink in the installation and linked the system library instead. In this case, julia did not start .

[joa-quim]

I'm sorry you are suffering this and I'm also sorry of being of little help here (I'm a Windows guy). Post this in the Julia forum. There are Arch Linux users there.

How did you install GMT? Via a package manager?

[benibilme]

I installed in both ways. By using julia binary tarball from https://julialang-s3.julialang.org/bin/linux/x64/1.8/julia-1.8.3-linux-x86_64.tar.gz and later by downloading and building from Arch Linux User repository. As stated above, Arch advises not to use official repositories because of julia environment depends on the bundled version of LLVM.

[joa-quim]

I meant, how did you install GMT (not GMT.jl). Was it the automatic way, which is done via Conda or from the Arch Linux package manager, or even built by yourself?

[benibilme]

I installed gmt via arc linux package manager from official repositories via pacman. However after your post, I removed it and tried using GMT. Julia tried to install it via conda. However I received following error.

By the way, I also changed the julia installation location to /opt from home directory.

julia> using GMT
[ Info: Precompiling GMT [5752ebe1-31b9-557e-87aa-f909b540aa54]
Base.IOError("could not spawn `gmt --version`: no such file or directory (ENOENT)", -2)
ERROR: LoadError: could not load library "/home/user/.julia/conda/3/lib/libgmt.so"
/opt/dev/julia-1.8.3/bin/../lib/julia/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/user/.julia/conda/3/lib/./libgdal.so.31)
Stacktrace:
 [1] GMT_Create_Session (repeats 2 times)
   @ ~/.julia/packages/GMT/mzT4h/src/libgmt.jl:2 [inlined]
 [2] top-level scope
   @ ~/.julia/packages/GMT/mzT4h/src/get_enums.jl:9
 [3] include(mod::Module, _path::String)
   @ Base ./Base.jl:419
 [4] include(x::String)
   @ GMT ~/.julia/packages/GMT/mzT4h/src/GMT.jl:1
 [5] top-level scope
   @ ~/.julia/packages/GMT/mzT4h/src/GMT.jl:287
 [6] include
   @ ./Base.jl:419 [inlined]
 [7] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
   @ Base ./loading.jl:1554
 [8] top-level scope
   @ stdin:1
in expression starting at /home/user/.julia/packages/GMT/mzT4h/src/get_enums.jl:9
in expression starting at /home/user/.julia/packages/GMT/mzT4h/src/GMT.jl:1
in expression starting at stdin:1
ERROR: Failed to precompile GMT [5752ebe1-31b9-557e-87aa-f909b540aa54] to /home/toktay/.julia/compiled/v1.8/GMT/jl_3zBdJr.
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:35
 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
   @ Base ./loading.jl:1707
 [3] compilecache
   @ ./loading.jl:1651 [inlined]
 [4] _require(pkg::Base.PkgId)
   @ Base ./loading.jl:1337
 [5] _require_prelocked(uuidkey::Base.PkgId)
   @ Base ./loading.jl:1200
 [6] macro expansion
   @ ./loading.jl:1180 [inlined]
 [7] macro expansion
   @ ./lock.jl:223 [inlined]
 [8] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1144

[t-bltg]

/opt/dev/julia-1.8.3/bin/../lib/julia/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/user/.julia/conda/3/lib/./libgdal.so.31)

@benibilme, this issue is know (see JuliaLang/julia#34276), use:

$ LD_PRELOAD=$(g++ --print-file-name=libstdc++.so) julia
# or if you know the path to your `libstdc++.so`:
$ LD_PRELOAD=/usr/lib/gcc/x86_64-linux-gnu/11/libstdc++.so julia  # this is on `ubuntu 22.04`

Can you also try:

julia> ENV["FORCE_INSTALL_GMT"] = 1
julia> using GMT
[ Info: Precompiling GMT [5752ebe1-31b9-557e-87aa-f909b540aa54]
ErrorException("Forcing an automatic GMT install")
Building GMT ──→ [...]
[...]
julia> GMT.get_GMTver()
Base.IOError("could not spawn `gmt --version`: no such file or directory (ENOENT)", -2)
(v"6.4.0", true, "[...]/conda/lib/libgmt.so", "[...]/conda/lib/./libgdal.so.31", "[...]/conda/lib/././libproj.so.25", "[...]/conda/bin")

[joa-quim]

Yes, as @t-bltg said that is a known issue (it lasts since July (!!)) and although it finally was fixed recently it still not in 1.8.3 (really don't understand this, as if this was a minor issue). But it is fixed in 1.9 dev so I think the easiest is to install that Julia version that just got into the alpha stage.

Edit: But I suspect the libcurl problem can still persist even with the GMT Conda build. The problem seams really be tied to the Julia shipped libcurl.

[benibilme]

julia> ENV["FORCE_INSTALL_GMT"] = 1
1

julia> using GMT
[ Info: Precompiling GMT [5752ebe1-31b9-557e-87aa-f909b540aa54]
ErrorException("Forcing an automatic GMT install")
ERROR: LoadError: could not load library "/home/user/.julia/conda/3/lib/libgmt.so"
/opt/dev/julia-1.8.3/bin/../lib/julia/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/user/.julia/conda/3/lib/./libgdal.so.31)

[t-bltg]

You are not using LD_PRELOAD as explained in #1052 (comment), are you ?

Can you show:

$ LD_PRELOAD=$(g++ --print-file-name=libstdc++.so) julia  # from your arch terminal
julia> using Libdl
julia> foreach(println, Libdl.dllist())
linux-vdso.so.1
/usr/lib/gcc/x86_64-linux-gnu/11/libstdc++.so  # uses the system `libstdc++.so`, forced by `LD_PRELOAD`
/lib/x86_64-linux-gnu/libdl.so.2
/lib/x86_64-linux-gnu/libpthread.so.0
/lib/x86_64-linux-gnu/libc.so.6
[...]/bin/../lib/libjulia.so.1  # [...] denotes the directory where downloaded `julia` is extracted
/lib/x86_64-linux-gnu/libm.so.6
/lib64/ld-linux-x86-64.so.2
[...]/bin/../lib/julia/libgcc_s.so.1
[...]/bin/../lib/julia/libopenlibm.so
[...]/bin/../lib/julia/libjulia-internal.so.1
[...]/bin/../lib/julia/libunwind.so.8
/lib/x86_64-linux-gnu/librt.so.1
[...]/bin/../lib/julia/libz.so.1
[...]/bin/../lib/julia/libatomic.so.1
[...]/bin/../lib/julia/libjulia-codegen.so.1
[...]/bin/../lib/julia/libLLVM-13jl.so
[...]/lib/julia/sys.so
[...]/bin/../lib/julia/libpcre2-8.so
[...]/bin/../lib/julia/libgmp.so
[...]/bin/../lib/julia/libmpfr.so
[...]/bin/../lib/julia/libopenblas64_.so
[...]/bin/../lib/julia/libgfortran.so.5
[...]/bin/../lib/julia/libquadmath.so.0
[...]/bin/../lib/julia/libblastrampoline.so
[...]/bin/../lib/julia/libcholmod.so
[...]/bin/../lib/julia/libamd.so.2
[...]/bin/../lib/julia/libcolamd.so.2
[...]/bin/../lib/julia/libsuitesparseconfig.so.5
[...]/bin/../lib/julia/libccolamd.so.2
[...]/bin/../lib/julia/libcamd.so.2
[...]/bin/../lib/julia/libnghttp2.so.14
[...]/bin/../lib/julia/libcurl.so  # this is `libcurl` shipped by julia
[...]/bin/../lib/julia/libssh2.so.1
[...]/bin/../lib/julia/libmbedtls.so.14
[...]/bin/../lib/julia/libmbedx509.so.1
[...]/bin/../lib/julia/libmbedcrypto.so.7
julia> using GMT
julia> GMT.get_GMTver()

[benibilme]

Sorry about missing what you pointed out. Following sequence, which you suggested, solved the problem. However, I need to preload libstd for each invokation to do using GMT even though ENV["FORCE_INSTALL_GMT"] = 1 is not needed. Yes, while I tried this, gmt from OS package manager was not installed. To be sure, I just cleaned ~/.julia directory where environments, packages are kept before doing below. Of course, after cleaning .julia, I have added GMT via Pkg.add

$  LD_PRELOAD=$(g++ --print-file-name=libstdc++.so)  julia
 julia> ENV["FORCE_INSTALL_GMT"] = 1
1
julia> using GMT
[ Info: Precompiling GMT [5752ebe1-31b9-557e-87aa-f909b540aa54]
ErrorException("Forcing an automatic GMT install")

Below is the additional things that you requested at the above comment.

julia> using Libdl

julia> foreach(println, Libdl.dllist())
linux-vdso.so.1
/usr/lib/gcc/x86_64-pc-linux-gnu/12.2.0/../../../../lib/libstdc++.so
/usr/lib/libdl.so.2
/usr/lib/libpthread.so.0
/usr/lib/libc.so.6
/opt/dev/julia-1.8.3/bin/../lib/libjulia.so.1
/usr/lib/libm.so.6
/lib64/ld-linux-x86-64.so.2
/opt/dev/julia-1.8.3/bin/../lib/julia/libgcc_s.so.1
/opt/dev/julia-1.8.3/bin/../lib/julia/libopenlibm.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libjulia-internal.so.1
/opt/dev/julia-1.8.3/bin/../lib/julia/libunwind.so.8
/usr/lib/librt.so.1
/opt/dev/julia-1.8.3/bin/../lib/julia/libz.so.1
/opt/dev/julia-1.8.3/bin/../lib/julia/libatomic.so.1
/opt/dev/julia-1.8.3/bin/../lib/julia/libjulia-codegen.so.1
/opt/dev/julia-1.8.3/bin/../lib/julia/libLLVM-13jl.so
/opt/dev/julia-1.8.3/lib/julia/sys.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libpcre2-8.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libgmp.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libmpfr.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libopenblas64_.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libgfortran.so.5
/opt/dev/julia-1.8.3/bin/../lib/julia/libquadmath.so.0
/opt/dev/julia-1.8.3/bin/../lib/julia/libblastrampoline.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libcholmod.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libamd.so.2
/opt/dev/julia-1.8.3/bin/../lib/julia/libcolamd.so.2
/opt/dev/julia-1.8.3/bin/../lib/julia/libsuitesparseconfig.so.5
/opt/dev/julia-1.8.3/bin/../lib/julia/libccolamd.so.2
/opt/dev/julia-1.8.3/bin/../lib/julia/libcamd.so.2
/opt/dev/julia-1.8.3/bin/../lib/julia/libnghttp2.so.14
/opt/dev/julia-1.8.3/bin/../lib/julia/libcurl.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libssh2.so.1
/opt/dev/julia-1.8.3/bin/../lib/julia/libmbedtls.so.14
/opt/dev/julia-1.8.3/bin/../lib/julia/libmbedx509.so.1
/opt/dev/julia-1.8.3/bin/../lib/julia/libmbedcrypto.so.7

julia> using GMT

julia> GMT.get_GMTver()
Base.IOError("could not spawn `gmt --version`: no such file or directory (ENOENT)", -2)
(v"6.4.0", true, "/home/user/.julia/conda/3/lib/libgmt.so", "/home/user/.julia/conda/3/lib/./libgdal.so.31", "/home/user/.julia/conda/3/lib/././libproj.so.25", "/home/user/.julia/conda/3/bin")

I would like to be able to use gmt from console or bash as well. Can't OS gmt and julia install gmt live together?

[t-bltg]

I would like to be able to use gmt from console or bash as well. Can't OS gmt and julia install gmt live together?

Can you run:

$ /home/user/.julia/conda/3/bin/gmt --version

Maybe the path exists at that location, and GMT.jl needs to adjust to the conda one ?

Good news, now that you know libstdc++ is incriminated, you can make the changes a bit more permanent (but still reversible):

$ cd /opt/dev/julia-1.8.3/bin
$ mv julia Julia  # if this fails, you need to prepend commands with `sudo`
$ echo -e '#!/usr/bin/env bash\nLD_PRELOAD='$(g++ --print-file-name=libstdc++.so)' exec '$(pwd)/'Julia "$@"' >julia
$ chmod +x julia
$ ./julia --version
julia version 1.8.3  # <-- should show this if correct

, so now that you run julia it always preloads libstdc++.

You need to use ENV["FORCE_INSTALL_GMT"] = 1 only once if the system gmt is uninstalled.

But now, you can maybe re-install gmt from arch repos an try with the modified julia (which uses libstdc++), it might work and fix the original libcurl issue !

$ ... # reinstall gmt using `pacman` (I guess) on `arch`
$ julia
julia> using Libdl
julia> foreach(println, Libdl.dllist())
/usr/lib/gcc/x86_64-pc-linux-gnu/12.2.0/../../../../lib/libstdc++.so  # this is the path you want, please confirm
[...]  # rest truncated
julia> using GMT
julia> GMT.get_GMTver()
# <-- should use system paths, not paths with `conda` in it ...

[benibilme]

Hello,

Thank you for the detailed instructions. Before reading your comment, I had done a similar thing to preload the libstdc++ when ever I started julia. I have local ~/sbin directory in my home, which comes before any path in my $PATH. I often use it replace or enhance some system commands for similar cases like this.

I again installed system provided gmt via package manager. Here are the versions.

$ /home/user/.julia/conda/3/bin/gmt --version
6.4.0
$ which gmt
/usr/bin/gmt
$  gmt --version
6.4.0

The list of linked libraries

julia> foreach(println, Libdl.dllist())
linux-vdso.so.1
/usr/lib/gcc/x86_64-pc-linux-gnu/12.2.0/../../../../lib/libstdc++.so
/usr/lib/libdl.so.2
/usr/lib/libpthread.so.0
/usr/lib/libc.so.6
/opt/dev/julia-1.8.3/bin/../lib/libjulia.so.1
/usr/lib/libm.so.6
/lib64/ld-linux-x86-64.so.2
/opt/dev/julia-1.8.3/bin/../lib/julia/libgcc_s.so.1
/opt/dev/julia-1.8.3/bin/../lib/julia/libopenlibm.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libjulia-internal.so.1
/opt/dev/julia-1.8.3/bin/../lib/julia/libunwind.so.8
/usr/lib/librt.so.1
/opt/dev/julia-1.8.3/bin/../lib/julia/libz.so.1
/opt/dev/julia-1.8.3/bin/../lib/julia/libatomic.so.1
/opt/dev/julia-1.8.3/bin/../lib/julia/libjulia-codegen.so.1
/opt/dev/julia-1.8.3/bin/../lib/julia/libLLVM-13jl.so
/opt/dev/julia-1.8.3/lib/julia/sys.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libpcre2-8.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libgmp.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libmpfr.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libopenblas64_.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libgfortran.so.5
/opt/dev/julia-1.8.3/bin/../lib/julia/libquadmath.so.0
/opt/dev/julia-1.8.3/bin/../lib/julia/libblastrampoline.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libcholmod.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libamd.so.2
/opt/dev/julia-1.8.3/bin/../lib/julia/libcolamd.so.2
/opt/dev/julia-1.8.3/bin/../lib/julia/libsuitesparseconfig.so.5
/opt/dev/julia-1.8.3/bin/../lib/julia/libccolamd.so.2
/opt/dev/julia-1.8.3/bin/../lib/julia/libcamd.so.2
/opt/dev/julia-1.8.3/bin/../lib/julia/libnghttp2.so.14
/opt/dev/julia-1.8.3/bin/../lib/julia/libcurl.so
/opt/dev/julia-1.8.3/bin/../lib/julia/libssh2.so.1
/opt/dev/julia-1.8.3/bin/../lib/julia/libmbedtls.so.14
/opt/dev/julia-1.8.3/bin/../lib/julia/libmbedx509.so.1
/opt/dev/julia-1.8.3/bin/../lib/julia/libmbedcrypto.so.7
/home/user/.julia/conda/3/lib/./libgdal.so.31
/home/user/.julia/conda/3/lib/././libcrypto.so.3
/home/user/.julia/conda/3/lib/././libtiledb.so.2.11
/home/user/.julia/conda/3/lib/././libpoppler.so.125
/home/user/.julia/conda/3/lib/././libjson-c.so.5
/home/user/.julia/conda/3/lib/././libfreexl.so.1
/home/user/.julia/conda/3/lib/././libgeos_c.so.1
/home/user/.julia/conda/3/lib/././libwebp.so.7
/home/user/.julia/conda/3/lib/././libkmlbase.so.1
/home/user/.julia/conda/3/lib/././libkmldom.so.1
/home/user/.julia/conda/3/lib/././libkmlengine.so.1
/home/user/.julia/conda/3/lib/././libkmlxsd.so.1
/home/user/.julia/conda/3/lib/././libkmlregionator.so.1
/home/user/.julia/conda/3/lib/././libexpat.so.1
/home/user/.julia/conda/3/lib/././libxerces-c-3.2.so
/home/user/.julia/conda/3/lib/././libopenjp2.so.7
/home/user/.julia/conda/3/lib/././libnetcdf.so.19
/home/user/.julia/conda/3/lib/././libmfhdf.so.0
/home/user/.julia/conda/3/lib/././libdf.so.0
/home/user/.julia/conda/3/lib/././libgif.so.7
/home/user/.julia/conda/3/lib/././libgeotiff.so.5
/home/user/.julia/conda/3/lib/././libpng16.so.16
/home/user/.julia/conda/3/lib/././libcfitsio.so.9
/home/user/.julia/conda/3/lib/././libpq.so.5
/home/user/.julia/conda/3/lib/././liblz4.so.1
/home/user/.julia/conda/3/lib/././libblosc.so.1
/home/user/.julia/conda/3/lib/././libzstd.so.1
/home/user/.julia/conda/3/lib/././liblzma.so.5
/home/user/.julia/conda/3/lib/././libproj.so.25
/home/user/.julia/conda/3/lib/././libsqlite3.so.0
/home/user/.julia/conda/3/lib/././libtiff.so.5
/home/user/.julia/conda/3/lib/././libjpeg.so.9
/home/user/.julia/conda/3/lib/././libdeflate.so.0
/home/user/.julia/conda/3/lib/././libspatialite.so.7
/home/user/.julia/conda/3/lib/././libLerc.so.4
/home/user/.julia/conda/3/lib/././libiconv.so.2
/home/user/.julia/conda/3/lib/././libxml2.so.2
/home/user/.julia/conda/3/lib/././libkea.so.1.4
/home/user/.julia/conda/3/lib/././libhdf5_cpp.so.200
/home/user/.julia/conda/3/lib/././libhdf5.so.200
/home/user/.julia/conda/3/lib/./././libbz2.so.1.0
/home/user/.julia/conda/3/lib/./././libssl.so.3
/home/user/.julia/conda/3/lib/./././libfreetype.so.6
/home/user/.julia/conda/3/lib/./././libfontconfig.so.1
/home/user/.julia/conda/3/lib/./././liblcms2.so.2
/home/user/.julia/conda/3/lib/./././libnss3.so
/home/user/.julia/conda/3/lib/./././libsmime3.so
/home/user/.julia/conda/3/lib/./././libplc4.so
/home/user/.julia/conda/3/lib/./././libnspr4.so
/home/user/.julia/conda/3/lib/./././libgeos.so.3.11.0
/home/user/.julia/conda/3/lib/./././libminizip.so
/home/user/.julia/conda/3/lib/./././liburiparser.so
/home/user/.julia/conda/3/lib/./././libkmlconvenience.so.1
/home/user/.julia/conda/3/lib/./././libnsl.so.3
/home/user/.julia/conda/3/lib/./././libicui18n.so.70
/home/user/.julia/conda/3/lib/./././libicuuc.so.70
/home/user/.julia/conda/3/lib/./././libicudata.so.70
/home/user/.julia/conda/3/lib/./././libhdf5_hl.so.200
/home/user/.julia/conda/3/lib/./././libzip.so.5
/home/user/.julia/conda/3/lib/./././libgssapi_krb5.so.2
/home/user/.julia/conda/3/lib/./././libsnappy.so.1
/home/user/.julia/conda/3/lib/./././librttopo.so.1
/home/user/.julia/conda/3/lib/./././libcharset.so.1
/home/user/.julia/conda/3/lib/././././libnssutil3.so
/home/user/.julia/conda/3/lib/././././libplds4.so
/home/user/.julia/conda/3/lib/././././libkrb5.so.3
/home/user/.julia/conda/3/lib/././././libk5crypto.so.3
/home/user/.julia/conda/3/lib/././././libcom_err.so.3
/home/user/.julia/conda/3/lib/././././libkrb5support.so.0
/home/user/.julia/conda/3/lib/././././libkeyutils.so.1
/usr/lib/libresolv.so.2
/home/user/.julia/conda/3/lib/libgmt.so
/home/user/.julia/conda/3/lib/./libpcre.so.1
/home/user/.julia/conda/3/lib/./libfftw3f.so.3
/home/user/.julia/conda/3/lib/./libfftw3f_threads.so.3
/home/user/.julia/conda/3/lib/./liblapack.so.3
/home/user/.julia/conda/3/lib/./libpostscriptlight.so.6

GMT version

julia> using GMT
julia> GMT.get_GMTver()
(v"6.4.0", false, "", "", "", "")

As far as I understand, GMT.jl do not install conda version if the system has available GMT installation. Since I preload the system libstdc++, I presume I should be able to use system gmt even if I remove gmt that comes with conda, I suppose.

[t-bltg]

So everything works now ?

As far as I understand, GMT.jl do not install conda version if the system has available GMT installation.

Exactly, it tries first to use a system gmt, and if it fails, try to use a conda based one.

A note to @joa-quim, you might want to set up a Preferences.jl mechanism and maybe drop deps/build.jl. This is the way to go nowadays.

It's strange though that no path is listed in (v"6.4.0", false, "", "", "", "").
==> this is hardcoded, maybe GMT.jl should do something about it.
The false indicates that GMT.jl uses a system gmt.

It this works, you can remove the conda based gmt.