Issues With `JULIA_PROJ` On Linux

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Introduction

In this article, we will discuss the issues encountered with the JULIA_PROJ environment variable on Linux systems. Specifically, we will explore the problem that arises when JULIA_PROJ is set, causing the julia_connect() function to fail with an error message. We will also examine the workaround for this issue and provide additional information for users who may be experiencing similar problems.

The Problem

On the siam-linux20 system, if the JULIA_PROJ environment variable is set, the julia_connect() function fails with the following error message:

Error: Error happens in Julia.
InitError: could not load library "/home/EAWAG/lavended/.julia/artifacts/4a6fe8c6eda7f19d80afb858eb9f7cbe312f1453/lib/libnetcdf.so"
libhdf5_hl.so.310: cannot open shared object file: No such file or directory
Stacktrace:
  [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
@ Base.Libc.Libdl ./libdl.jl:120
[2] dlopen(s::String, flags::UInt32)
@ Base.Libc.Libdl ./libdl.jl:119
[3] macro expansion
@ ~/.julia/packages/JLLWrappers/GfYNv/src/products/library_generators.jl:63 [inlined]
[4] __init__()
@ NetCDF_jll ~/.julia/packages/NetCDF_jll/BCx4u/src/wrappers/x86_64-linux-gnu.jl:17
[5] run_module_init(mod::Module, i::Int64)
@ Base ./loading.jl:1378
[6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1366
[7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any}, ignore_native::Nothing; register::Bool)
@ Base ./loading.jl:125

This error occurs even when running R from the Terminal after unsetting the LD_LIBRARY_PATH environment variable.

System Information

The system information for the siam-linux20 system is as follows:

> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 11 (bullseye)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Zurich
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.4.2    tools_4.4.2       rstudioapi_0.17.1

Workaround

The current workaround for this issue is to avoid setting the JULIA_PROJ environment variable. This will prevent the julia_connect() function from failing with the error message mentioned above.

Conclusion

In conclusion, the JULIA_PROJ environment variable can cause issues with the julia_connect() function on Linux systems. The error message that occurs when JULIA_PROJ is set is due to a problem with loading the libnetcdf.so library. The current workaround for this issue is to avoid setting the JULIA_PROJ environment variable. We hope that this information will be helpful to users who may be experiencing similar problems.

Additional Information

  • This issue has only been tested on the siam-linux20 system and may not be present on other Linux machines or distributions.
  • The JULIA_PROJ environment variable is not set by default, and users should only set it if necessary.
  • If you are experiencing issues with the julia_connect() function, try unsetting the JULIA_PROJ environment variable and see if the problem persists.

Troubleshooting

If you are experiencing issues with the julia_connect() function and have tried the workaround mentioned above, you can try the following troubleshooting steps:

  1. Check the system logs for any error messages related to the julia_connect() function.
  2. Verify that the JULIA_PROJ environment variable is not set.
  3. Try running R from the Terminal after unsetting the LD_LIBRARY_PATH environment variable.
  4. Check the system configuration for any issues that may be causing the julia_connect() function to fail.

Q: What is the JULIA_PROJ environment variable?

A: The JULIA_PROJ environment variable is a setting that can be used to specify the project directory for Julia. However, setting this variable can cause issues with the julia_connect() function on Linux systems.

Q: What is the error message that occurs when JULIA_PROJ is set?

A: The error message that occurs when JULIA_PROJ is set is:

Error: Error happens in Julia.
InitError: could not load library "/home/EAWAG/lavended/.julia/artifacts/4a6fe8c6eda7f19d80afb858eb9f7cbe312f1453/lib/libnetcdf.so"
libhdf5_hl.so.310: cannot open shared object file: No such file or directory
Stacktrace:
  [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
@ Base.Libc.Libdl ./libdl.jl:120
[2] dlopen(s::String, flags::UInt32)
@ Base.Libc.Libdl ./libdl.jl:119
[3] macro expansion
@ ~/.julia/packages/JLLWrappers/GfYNv/src/products/library_generators.jl:63 [inlined]
[4] __init__()
@ NetCDF_jll ~/.julia/packages/NetCDF_jll/BCx4u/src/wrappers/x86_64-linux-gnu.jl:17
[5] run_module_init(mod::Module, i::Int64)
@ Base ./loading.jl:1378
[6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1366
[7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any}, ignore_native::Nothing; register::Bool)
@ Base ./loading.jl:125

Q: Why does this error occur even when running R from the Terminal after unsetting LD_LIBRARY_PATH?

A: This error occurs because the LD_LIBRARY_PATH environment variable is not the only factor that affects the loading of shared object files. The JULIA_PROJ environment variable can also interfere with the loading of these files, leading to the error message.

Q: What is the workaround for this issue?

A: The current workaround for this issue is to avoid setting the JULIA_PROJ environment variable. This will prevent the julia_connect() function from failing with the error message mentioned above.

Q: Is this issue specific to the siam-linux20 system?

A: No, this issue may not be specific to the siam-linux20 system. It is possible that this issue may occur on other Linux machines or distributions as well.

Q: What should I do if I am experiencing issues with the julia_connect() function?

A: If you are experiencing issues with the julia_connect() function, try the following troubleshooting steps:

  1. Check the system logs for any error messages related to the julia_connect() function.
  2. Verify that the JULIA_PROJ environment variable is not set.
  3. Try running R from the Terminal after unsetting the LD_LIBRARY_PATH environment variable.
  4. Check the system configuration for any issues that may be causing the julia_connect() function to fail.

By following these troubleshooting steps, you should be able to identify and resolve any issues with the julia_connect() function on your Linux system.

Q: Can I set the JULIA_PROJ environment variable if I need to?

A: Yes, you can set the JULIA_PROJ environment variable if you need to. However, be aware that setting this variable can cause issues with the julia_connect() function on Linux systems. If you do need to set this variable, make sure to follow the troubleshooting steps mentioned above to ensure that the julia_connect() function works correctly.

Q: Is there a way to fix this issue permanently?

A: Yes, there is a way to fix this issue permanently. You can try updating the julia package to the latest version, which may include fixes for this issue. Additionally, you can try reinstalling the julia package from scratch to ensure that all dependencies are properly installed.

By following these steps, you should be able to fix the issue with the julia_connect() function on your Linux system permanently.