I have a Julia project on my machine, and I then run the project on a different machine (cluster). To do that I copy the relevant files including the Project.toml, manifest.toml files.
I included the package JLD2, and ran instantiate on the cluster machine. This did not work well.
I got tome errors that the registry is dirty. Looking on the discourse I removed it, and downloaded again, but now I see this error Error: Tree Hash Mismatch! when I try to update the environment packages.
How can this be solved?
I am running Julia 1.5.3.
What filesystem are you using on the cluster? Any chance of upgrading to Julia v1.6?
2 Likes
Hey, it’s a cluster machine (linux). So I think there are many filesystems there… But I am not sure. When I am running df, I see many filesystems.
To upgrade to julia 1.6 I need to ask someone else to do that (and I will), but that can happen only in a few days.
Are Julia packages installed in your home directory? You can run
df "${HOME}"
to see the filesystem where your home directory is mounted.
Or without waiting for your sysadmins you can download it from Download Julia and that’s it 
1 Like
Sure, it gives:
$ df "${HOME}"
Filesystem 1K-blocks Used Available Use% Mounted on
gpfs_home_labs 104857600 61083648 43773952 59% /home/labs
But isn’t there something special someone needs to do on the cluster? I know that everytime I log in to the cluster I need to load a module of julia to be able to run it. I am not sure how to configure these things…
Ugh, sorry, I forgot you need the -T flag to see the type:
df -T "${HOME}"
Not really, you can follow the instructions about how to use Julia on Linux
1 Like
the type is gpfs.
It is tempting to try to install it myself, but I am afraid to do something wrong… I might just wait for someone to do it…
That’s very likely the issue. Julia v1.6 should be able to deal with it (well, it should still show some warning messages, but it won’t be a fatal error, I believe).
It’d be a good occasion for you to learn how to fiddle a bit with programs in Linux systems You may ask for help to install Julia in a different thread if you have problems. But I also understand if you don’t really feel comfortable doing it yourself.
2 Likes
Thanks! I already addressed the cluster people asking them teach me how to install julia myself:)
I hope that will solve the issue!
I will update here as soon as I figure it out.
I have julia 1.6.1 installed on the cluster!
I instantiated my project on the cluster and got errors (only attached those that failed):
Precompiling project...
✗ Xorg_libxcb_jll
✗ Xorg_xcb_util_jll
✗ Xorg_libX11_jll
✗ Xorg_libXfixes_jll
✗ Xorg_libxkbfile_jll
✗ Xorg_libXrender_jll
✗ Xorg_libXext_jll
✗ Xorg_xcb_util_wm_jll
✗ Xorg_xcb_util_keysyms_jll
✗ Xorg_xcb_util_image_jll
✗ Xorg_xcb_util_renderutil_jll
✗ Xorg_libXcursor_jll
✗ Xorg_libXi_jll
✗ Libglvnd_jll
✗ Xorg_libXinerama_jll
✗ Xorg_libXrandr_jll
✗ Cairo_jll
✗ Xorg_xkbcomp_jll
✗ Xorg_xkeyboard_config_jll
✗ GLFW_jll
✗ xkbcommon_jll
✗ Qt5Base_jll
✗ GR_jll
119 dependencies successfully precompiled in 618 seconds (7 already precompiled)
23 dependencies errored. To see a full report either run `import Pkg; Pkg.precompile()` or load the packages
do you know what is the problem?
I’d start from doing what the message suggests 
1 Like
I tried, but I don’t get anything…
julia> import Pkg; Pkg.precompile()
Precompiling project...
✗ Xorg_libxcb_jll
✗ Xorg_xcb_util_jll
✗ Xorg_libX11_jll
✗ Xorg_libXfixes_jll
✗ Xorg_libxkbfile_jll
✗ Xorg_libXrender_jll
✗ Xorg_libXext_jll
✗ Xorg_xcb_util_image_jll
✗ Xorg_xcb_util_renderutil_jll
✗ Xorg_xcb_util_wm_jll
✗ Xorg_xcb_util_keysyms_jll
✗ Xorg_xkbcomp_jll
✗ Libglvnd_jll
✗ Xorg_libXinerama_jll
✗ Xorg_libXi_jll
✗ Cairo_jll
✗ Xorg_libXcursor_jll
✗ Xorg_libXrandr_jll
✗ Xorg_xkeyboard_config_jll
✗ GLFW_jll
✗ xkbcommon_jll
✗ Qt5Base_jll
✗ GR_jll
0 dependencies successfully precompiled in 197 seconds (126 already precompiled)
Try to load one of those packages, as suggested by the error message I quoted before already note that in order to load a package it must be in the environment, so you may have to ]add it
1 Like
It also does not give much information…
(Ising2d) pkg> add Cairo_jll
Updating registry at `~/.julia/registries/General`
┌ Warning: Some registries failed to update:
│ — `~/.julia/registries/General` — registry dirty
└ @ Pkg.Types /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:1229
Resolving package versions...
Installed XML2_jll ─────────── v2.9.11+0
Installed MutableArithmetics ─ v0.2.18
Installed FFTW ─────────────── v1.4.0
Installed Polynomials ──────── v2.0.9
Downloaded artifact: Glib
Downloaded artifact: Gettext
Downloaded artifact: Expat
Downloaded artifact: GLFW
Downloaded artifact: Libiconv
Downloaded artifact: XML2
Downloaded artifact: Libffi
Downloaded artifact: Libmount
Downloaded artifact: Zstd
Downloaded artifact: Libuuid
Downloaded artifact: PCRE
Updating `~/Mpemba/Ising2d/Project.toml`
[6e4b80f9] ↓ BenchmarkTools v1.0.0 ⇒ v0.7.0
[a93c6f00] ↓ DataFrames v1.1.1 ⇒ v1.0.1
[7a1cc6ca] ↑ FFTW v1.3.2 ⇒ v1.4.0
[033835bb] ↓ JLD2 v0.4.5 ⇒ v0.4.4
[91a5bcdd] ↓ Plots v1.14.0 ⇒ v1.13.1
[295af30f] ↓ Revise v3.1.16 ⇒ v3.1.15
[2913bbd2] ↓ StatsBase v0.33.8 ⇒ v0.33.6
[83423d85] + Cairo_jll v1.16.0+6
Updating `~/Mpemba/Ising2d/Manifest.toml`
[6e4b80f9] ↓ BenchmarkTools v1.0.0 ⇒ v0.7.0
[35d6a980] ↓ ColorSchemes v3.12.1 ⇒ v3.12.0
[3da002f7] ↓ ColorTypes v0.11.0 ⇒ v0.10.12
[34da2185] ↓ Compat v3.30.0 ⇒ v3.27.0
[a93c6f00] ↓ DataFrames v1.1.1 ⇒ v1.0.1
[7a1cc6ca] ↑ FFTW v1.3.2 ⇒ v1.4.0
[5789e2e9] ↓ FileIO v1.9.0 ⇒ v1.8.0
[42e2da0e] ↓ Grisu v1.0.2 ⇒ v1.0.0
[cd3eb016] ↓ HTTP v0.9.8 ⇒ v0.9.6
[033835bb] ↓ JLD2 v0.4.5 ⇒ v0.4.4
[aa1ae85d] ↓ JuliaInterpreter v0.8.16 ⇒ v0.8.14
[6f1432cf] ↓ LoweredCodeUtils v2.1.0 ⇒ v2.0.0
[d8a4904e] ↓ MutableArithmetics v0.2.19 ⇒ v0.2.18
[bac558e1] ↓ OrderedCollections v1.4.1 ⇒ v1.4.0
[91a5bcdd] ↓ Plots v1.14.0 ⇒ v1.13.1
[f27b6e38] ↓ Polynomials v2.0.10 ⇒ v2.0.9
[21216c6a] ↓ Preferences v1.2.2 ⇒ v1.2.1
[08abe8d2] ↓ PrettyTables v1.0.1 ⇒ v1.0.0
[295af30f] ↓ Revise v3.1.16 ⇒ v3.1.15
[992d4aef] ↓ Showoff v1.0.3 ⇒ v1.0.2
[a2af1166] ↓ SortingAlgorithms v1.0.0 ⇒ v0.3.1
[90137ffa] ↓ StaticArrays v1.2.0 ⇒ v1.1.2
[82ae8749] - StatsAPI v1.0.0
[2913bbd2] ↓ StatsBase v0.33.8 ⇒ v0.33.6
[f269a46b] ↓ TimeZones v1.5.5 ⇒ v1.5.3
[5c2747f8] ↓ URIs v1.3.0 ⇒ v1.2.0
[2e619515] ↓ Expat_jll v2.2.10+0 ⇒ v2.2.7+6
[0656b61e] ↓ GLFW_jll v3.3.4+0 ⇒ v3.3.3+0
[78b55507] ↓ Gettext_jll v0.21.0+0 ⇒ v0.20.1+7
[7746bdde] ↓ Glib_jll v2.68.1+0 ⇒ v2.59.0+4
[e9f186c6] ↓ Libffi_jll v3.2.2+0 ⇒ v3.2.1+4
[94ce4f54] ↓ Libiconv_jll v1.16.1+0 ⇒ v1.16.0+7
[4b2f31a3] ↓ Libmount_jll v2.35.0+0 ⇒ v2.34.0+3
[38a345b3] ↓ Libuuid_jll v2.36.0+0 ⇒ v2.34.0+7
[2f80f16e] ↓ PCRE_jll v8.44.0+0 ⇒ v8.42.0+4
[02c8fc9c] ↓ XML2_jll v2.9.12+0 ⇒ v2.9.11+0
[3161d3a3] ↓ Zstd_jll v1.5.0+0 ⇒ v1.4.8+0
Precompiling project...
✗ Xorg_libxcb_jll
✗ Xorg_xcb_util_jll
✗ Xorg_libX11_jll
✗ Xorg_xcb_util_wm_jll
✗ Xorg_xcb_util_keysyms_jll
✗ Xorg_xcb_util_image_jll
✗ Xorg_xcb_util_renderutil_jll
✗ Xorg_libXfixes_jll
✗ Xorg_libxkbfile_jll
✗ Xorg_libXrender_jll
✗ Xorg_libXext_jll
✗ Libglvnd_jll
✗ Xorg_libXinerama_jll
✗ Cairo_jll
✗ Xorg_libXrandr_jll
✗ Xorg_libXcursor_jll
✗ Xorg_libXi_jll
✗ Xorg_xkbcomp_jll
✗ Xorg_xkeyboard_config_jll
✗ GLFW_jll
✗ xkbcommon_jll
✗ Qt5Base_jll
✗ GR_jll
78 dependencies successfully precompiled in 561 seconds (47 already precompiled)
23 dependencies errored. To see a full report either run `import Pkg; Pkg.precompile()` or load the packages
Because you aren’t loading the package as I asked, you only installed it. You now need to do
using Cairo_jll
to load the package
1 Like
I actually now did precompile again, and I get
(Ising2d) pkg> precompile
Precompiling project...
✗ Xorg_libxcb_jll
✗ Xorg_xcb_util_jll
✗ Xorg_libX11_jll
✗ Xorg_libXfixes_jll
✗ Xorg_libxkbfile_jll
✗ Xorg_libXrender_jll
✗ Xorg_libXext_jll
✗ Xorg_xcb_util_image_jll
✗ Xorg_xcb_util_renderutil_jll
✗ Xorg_xcb_util_wm_jll
✗ Xorg_xcb_util_keysyms_jll
✗ Xorg_libXcursor_jll
✗ Xorg_xkbcomp_jll
✗ Libglvnd_jll
✗ Xorg_libXinerama_jll
✗ Xorg_libXrandr_jll
✗ Xorg_libXi_jll
✗ Cairo_jll
✗ Xorg_xkeyboard_config_jll
✗ GLFW_jll
✗ xkbcommon_jll
✗ Qt5Base_jll
✗ GR_jll
0 dependencies successfully precompiled in 227 seconds (125 already precompiled)
ERROR: The following 1 direct dependency failed to precompile:
Cairo_jll [83423d85-b0ee-5818-9007-b63ccbeb887a]
ERROR: LoadError: LoadError: InitError: could not load library "/home/labs/orenraz/roiho/.julia/artifacts/323b2adff3bbf2980e9f1f62990860b61470af16/lib/libgobject-2.0.so"
/home/labs/orenraz/roiho/.julia/artifacts/323b2adff3bbf2980e9f1f62990860b61470af16/lib/libgobject-2.0.so: undefined symbol: g_date_copy
Stacktrace:
[1] dlopen(s::String, flags::UInt32; throw_error::Bool)
@ Base.Libc.Libdl ./libdl.jl:114
[2] dlopen(s::String, flags::UInt32)
@ Base.Libc.Libdl ./libdl.jl:114
[3] macro expansion
@ ~/.julia/packages/JLLWrappers/bkwIo/src/products/library_generators.jl:54 [inlined]
[4] __init__()
@ Glib_jll ~/.julia/packages/Glib_jll/nZezQ/src/wrappers/x86_64-linux-gnu.jl:36
[5] _include_from_serialized(path::String, depmods::Vector{Any})
@ Base ./loading.jl:674
[6] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
@ Base ./loading.jl:760
[7] _require(pkg::Base.PkgId)
@ Base ./loading.jl:998
[8] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:914
[9] require(into::Module, mod::Symbol)
@ Base ./loading.jl:901
[10] include(mod::Module, _path::String)
@ Base ./Base.jl:386
[11] top-level scope
@ ~/.julia/packages/JLLWrappers/bkwIo/src/toplevel_generators.jl:170
[12] include
@ ./Base.jl:386 [inlined]
[13] 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:1213
[14] top-level scope
@ none:1
[15] eval
@ ./boot.jl:360 [inlined]
[16] eval(x::Expr)
@ Base.MainInclude ./client.jl:446
[17] top-level scope
@ none:1
during initialization of module Glib_jll
in expression starting at /home/labs/orenraz/roiho/.julia/packages/Cairo_jll/OlXYv/src/wrappers/x86_64-linux-gnu.jl:4
in expression starting at /home/labs/orenraz/roiho/.julia/packages/Cairo_jll/OlXYv/src/Cairo_jll.jl:2
Before going on with other guesses, can you please show the value of the LD_LIBRARY_PATH environment variable inside Julia, for example with
ENV["LD_LIBRARY_PATH"]
?
1 Like
sure:
julia> ENV["LD_LIBRARY_PATH"]
"/apps/RH7U2/gnu/julia/1.6.1/lib:/apps/RH7U2/gnu/python/3.6.3/lib:/usr/share/lsf/10.1/linux3.10-glibc2.17-x86_64/lib:/apps/RH7U2/general/IMOD/4.10.8/IMOD/lib:"
What happens if you start Julia with
LD_LIBRARY_PATH="" julia
so that this environment variable is cleared before starting Julia?
4 Likes
seems to be working fine! no errors!
julia> using Cairo_jll
[ Info: Precompiling Cairo_jll [83423d85-b0ee-5818-9007-b63ccbeb887a]
does this mean I should always start julia like that?
is there a way to configure this environment variable?