Using Julia packages on Bianca¶
UPPMAX Central library¶
Info
The Julia application at UPPMAX comes with several preinstalled packages. A selection of the Julia packages and libraries installed on UPPMAX are:
- BenchmarkTools
- CSV
- CUDA
- MPI (needs gcc and openmpi loaded)
- Distributed
- IJulia (needs python loaded)
- Plots
- PyPlot (needs python loaded)
- Gadfly
- DataFrames
- DistributedArrays
- PlotlyJS
- In Julia you can check if the packages are their by:
using <package-name>
- The first time Julia will precompile the package for you!
- You may control the present "central library" by typing
ml help julia/<version>
in the BASH shell.- There you will also find which python, gcc and openmpi version that are compatible.
- Or see the Julia user guide at UPPMAX
- A possibly more up-to-date status can be found from the Julia shell:
using Pkg
Pkg.activate(DEPOT_PATH[2]*"/environments/v1.8"); #change version (1.8) accordingly if you have another main version of Julia
Pkg.status()
Pkg.activate(DEPOT_PATH[1]*"/environments/v1.8"); #to return to user library
First time run on Bianca¶
You may have to build some package the first time with Pkg.build(“<package>”)
. Since “
Install yourself¶
If you have started Julia once you will get the folders like this in the ~/.julia
folder.
$ tree .julia/ -d -L 1
.
├── artifacts
├── bin
├── compiled
├── conda
├── environments
├── logs
├── packages
├── prefs
├── registries
└── scratchspaces
The plan is that what you install on Rackham should be moved here in the same manner
- Make an installation of the package on Rackham in the Julia package manager
- Use a transfer method to move the package files to the
wharf
- To be certain to include all files, you may transfer the whole
.julia
dir. However, that can grow rather big with time.
- To be certain to include all files, you may transfer the whole
Transfer to the wharf
wharf
, this will be empty. It might have a few things in it.
- Alt1: If you would like all your locally installed packages:
put
command.
-
Alt 2: Just transfer the latest installed julia package(s)
The following part still needs some update
-
Check what was installed. It may have been several dependency packages as well. Look at the times!
sftp> put -r ~/.julia/packages/<package name 1>
# and if several packages
sftp> put -r ~/.julia/packages/<package name 2>
# and so on...
Move to site-packages folder On Bianca
If many files or packages
you may want to tar before copying to include all possible symbolic links:
and in target directory (wharf_mnt) on Bianca:More info
- Julia course: isolated environments