Julia SLURM script erropr

Question

I have installed Julia on a remote High Performance Computing centre and am in the process of calling .jl-files via SLURM batch script. However, it seems like the "Pkg" command is not available because the following message pops up:

ERROR: LoadError: UndefVarError: Pkg not defined
Stacktrace:
 [1] top-level scope at /users/pa19/lanast/taskp/LAfem.jl:1
 [2] include at ./boot.jl:328 [inlined]
 [3] include_relative(::Module, ::String) at ./loading.jl:1105
 [4] include(::Module, ::String) at ./Base.jl:31
 [5] exec_options(::Base.JLOptions) at ./client.jl:287
 [6] _start() at ./client.jl:460
in expression starting at /users/pa19/lanast/taskp/LAfem.jl:1

Could it be an issue with the installation of Julia? Does one have to provide the exact links for Julia to know where to fetch them from?

Thanks Lysandros

Can you share what code resulted in the error? In particular, what is on line 1 of /users/pa19/lanast/taskp/LAfem.jl from where the error is thrown? Maybe you just didnt load the Pkg module (using Pkg)? — fredrikekre
The first (and only line) is:Pkg.installed(). Now I tried to add before this line the using Pkgcommand but a different error appears, namely 'ERROR: LoadError: IOError: stat: permission denied (EACCES) for file "/users/apps/compilers/julia/1.3.1/share/julia/stdlib/v1.3/Pkg/src/Pkg.jl" ' Thank you — LysandrosAn
For the first case, it is: ERROR: LoadError: UndefVarError: Pkg not defined Stacktrace: [1] top-level scope at /users/pa19/lanast/taskp/LAfem.jl:2 [2] include at ./boot.jl:328 [inlined] [3] include_relative(::Module, ::String) at ./loading.jl:1105 [4] include(::Module, ::String) at ./Base.jl:31 [5] exec_options(::Base.JLOptions) at ./client.jl:287 [6] _start() at ./client.jl:460 in expression starting at /users/pa19/lanast/taskp/LAfem.jl:2 — LysandrosAn
But we already solved that issue; you didn't load Pkg. What is it in the second case (the file permission one). — fredrikekre

LysandrosAn LysandrosAn · Accepted Answer · 2020-01-20T13:54:09

Thank you fredrikekre and Przemyslaw. If instead I write the two lines

using Pkg
Pkg.installed()

then the following appears:

ERROR: LoadError: IOError: stat: permission denied (EACCES) for file "/users/apps/compilers/julia/1.3.1/share/julia/stdlib/v1.3/Pkg/src/Pkg.jl"
Stacktrace:
 [1] stat(::String) at ./stat.jl:69
 [2] isfile at ./stat.jl:311 [inlined]
 [3] isfile_casesensitive at ./loading.jl:9 [inlined]
 [4] entry_point_and_project_file_inside at ./loading.jl:438 [inlined]
 [5] entry_point_and_project_file(::String, ::String) at ./loading.jl:453
 [6] implicit_project_deps_get at ./loading.jl:605 [inlined]
 [7] project_deps_get(::String, ::String) at ./loading.jl:308
 [8] identify_package(::String) at ./loading.jl:220
 [9] identify_package(::Base.PkgId, ::String) at ./loading.jl:206
 [10] identify_package at ./loading.jl:200 [inlined]
 [11] require(::Module, ::Symbol) at ./loading.jl:882
 [12] include at ./boot.jl:328 [inlined]
 [13] include_relative(::Module, ::String) at ./loading.jl:1105
 [14] include(::Module, ::String) at ./Base.jl:31
 [15] exec_options(::Base.JLOptions) at ./client.jl:287
 [16] _start() at ./client.jl:460
in expression starting at /users/pa19/lanast/taskp/LAfem.jl:1

In order to build julia I use the script:

## LOAD MODULES ##
module purge            # clean up loaded modules 

# load necessary modules
module load intel/18.0.5
module load gnu/4.9.2
module load java/9.0
module load julia


## RUN CODE ##
date
julia LAfem.jl 
date

I will check whether the master node has different hardware than the worker node. But generally, only one node is used for this job. Kind regards

Julia SLURM script erropr

1 Answers