fmihpc/vlasiator: v5.3.1

This release brings various minor quality-of-life improvements and security updates.

• dynamic AMR criteria updated to match Kotipalo et al 2024: vg_amr_alpha -> vg_amr_alpha1, vg_amr_jperb -> vg_amr_alpha2, scaling fixes
• Ionospheric parameters written to vlsv files
• Added option to deactivate refinement by Cartesian coordinate thresholds
• Fixes to timers
• New testpackage and CI structure
• Cleaned up sample configuration files
• Fix to 3D dipole field in solar wind inflow cells

Auto-generated release notes follow:

What's Changed

• Use newer docker image in CI runs. by @ursg in https://github.com/fmihpc/vlasiator/pull/899
• Github actions workflow to automatically sync branches to HLRS gitlab by @ursg in https://github.com/fmihpc/vlasiator/pull/901
• static dipole copysphere.zeroPerB = 1 in testpackage Magnetopshere_small by @ykempf in https://github.com/fmihpc/vlasiator/pull/905
• Fix gitlab sync action yaml syntax by @ursg in https://github.com/fmihpc/vlasiator/pull/910
• Fix git remote syntax in gitlab sync action. by @ursg in https://github.com/fmihpc/vlasiator/pull/911
• vlsvExtract std containers dis-ambiguation by @alhom in https://github.com/fmihpc/vlasiator/pull/913
• refine_radius for dAMR version support, a QoL improvements: output b … by @alhom in https://github.com/fmihpc/vlasiator/pull/912
• updated dccrg and fsgrid submodule commits by @markusbattarbee in https://github.com/fmihpc/vlasiator/pull/907
• updated dccrg and fsgrid submodule commits by @markusbattarbee in https://github.com/fmihpc/vlasiator/pull/908
• Use Github "Retry Step" Action to wait for vlasiator binary on lustre. by @ursg in https://github.com/fmihpc/vlasiator/pull/921
• Mpi in block adjustment by @markusbattarbee in https://github.com/fmihpc/vlasiator/pull/919
• Refinement param renames by @lkotipal in https://github.com/fmihpc/vlasiator/pull/920
• Some explanations of config option groups in sample cfg by @ykempf in https://github.com/fmihpc/vlasiator/pull/917
• Output time difference in vlsvdiff by @lkotipal in https://github.com/fmihpc/vlasiator/pull/925
• Fix CI runs on RISCV failing, probably due to old libraries still lingering in the work directory. by @ursg in https://github.com/fmihpc/vlasiator/pull/931
• Makefile and github actions steps to build on apple M1 by @ursg in https://github.com/fmihpc/vlasiator/pull/930
• Use mpirun instead of srun for tool runs on carrington for CI by @ursg in https://github.com/fmihpc/vlasiator/pull/934
• Update appleM1 CI build boost version. by @ursg in https://github.com/fmihpc/vlasiator/pull/935
• Cross-compile on BSC RiscV cluster for much faster CI builds by @ursg in https://github.com/fmihpc/vlasiator/pull/941
• Squelch a big bunch of unused variable warnings. by @ursg in https://github.com/fmihpc/vlasiator/pull/942
• Reverting submodule urls to https instead of ssh, for easier accessib… by @alhom in https://github.com/fmihpc/vlasiator/pull/932
• Fix Warnings by @lkotipal in https://github.com/fmihpc/vlasiator/pull/900
• Face neighbor caching by @lkotipal in https://github.com/fmihpc/vlasiator/pull/933
• Refinement hotfix by @lkotipal in https://github.com/fmihpc/vlasiator/pull/914
• Amr translation cleanup by @markusbattarbee in https://github.com/fmihpc/vlasiator/pull/767
• Minor moments fixes by @markusbattarbee in https://github.com/fmihpc/vlasiator/pull/947
• Amr translation cleanup addon by @alhom in https://github.com/fmihpc/vlasiator/pull/948
• Bug fix (Add parameters into the VLSV file) by @ArnaudLalague in https://github.com/fmihpc/vlasiator/pull/950
• Add support for DCCRG/FSgrid split feature (requires support from DCCRG and FSgrid) by @hokkanen in https://github.com/fmihpc/vlasiator/pull/926
• Push to GitLab only from fmihpc by @alhom in https://github.com/fmihpc/vlasiator/pull/954
• Reworked testpackage in a major fashion. by @markusbattarbee in https://github.com/fmihpc/vlasiator/pull/927
• Added Eigen as a submodule by @alhom in https://github.com/fmihpc/vlasiator/pull/890
• Move spatial cell to cpu-specific file by @markusbattarbee in https://github.com/fmihpc/vlasiator/pull/955
• Concurrency check and trap to scancel testpackage_run if caught cancel signal by @alhom in https://github.com/fmihpc/vlasiator/pull/961
• Remove . /etc/profile from generate_version.sh by @astatide in https://github.com/fmihpc/vlasiator/pull/963
• Updates to the Kelvin-Helmholtz instability project by @vetarvus in https://github.com/fmihpc/vlasiator/pull/960
• Fix ig_rhon units incorrectly being a mass density by @ursg in https://github.com/fmihpc/vlasiator/pull/971
• Update github artefact actions to v4. by @ursg in https://github.com/fmihpc/vlasiator/pull/968
• Add Makefile for MareNostrum 5's general partition by @astatide in https://github.com/fmihpc/vlasiator/pull/964
• Ci carrington fs ops to srun by @ykempf in https://github.com/fmihpc/vlasiator/pull/974
• Fix crash if OMPI_MCA_io is not set in environment. by @ursg in https://github.com/fmihpc/vlasiator/pull/984
• Dev up-to-speed by @alhom in https://github.com/fmihpc/vlasiator/pull/967
• Don't checkout submodules in testpackage CI run. by @ursg in https://github.com/fmihpc/vlasiator/pull/975
• Write out vg_f_saved if any VDFs are coming as well. by @ykempf in https://github.com/fmihpc/vlasiator/pull/976
• Add LFM (Merkin et al 2010) ionosphere solver test. by @ursg in https://github.com/fmihpc/vlasiator/pull/957
• Pass scancel --full to cancel jobs by @ykempf in https://github.com/fmihpc/vlasiator/pull/989
• Check script default local by @ykempf in https://github.com/fmihpc/vlasiator/pull/987
• Patch tracing to spheres at shallow angles. by @ykempf in https://github.com/fmihpc/vlasiator/pull/970
• Refinement exclusion halfspaces by @ykempf in https://github.com/fmihpc/vlasiator/pull/985
• Harris update, after #967 by @alhom in https://github.com/fmihpc/vlasiator/pull/986
• Update ci reference data runner by @markusbattarbee in https://github.com/fmihpc/vlasiator/pull/991
• Added trap output by @alhom in https://github.com/fmihpc/vlasiator/pull/977
• Purge dead projects projects/unsupported/* and projects/VelocityBox by @ykempf in https://github.com/fmihpc/vlasiator/pull/992
• change CI reference data generation job name by @markusbattarbee in https://github.com/fmihpc/vlasiator/pull/993
• Parallel timer fixes by @lkotipal in https://github.com/fmihpc/vlasiator/pull/966
• Add a "check cfg files" CI step. by @ursg in https://github.com/fmihpc/vlasiator/pull/990
• Try to use a cancel job step to scancel by @ykempf in https://github.com/fmihpc/vlasiator/pull/995
• Add rescaleDensity to Flowthrough to stabilize testing. by @alhom in https://github.com/fmihpc/vlasiator/pull/994
• Ensure dtIsChanged is false on static timestep by @lkotipal in https://github.com/fmihpc/vlasiator/pull/997
• Squelch two compiler warnings. by @ursg in https://github.com/fmihpc/vlasiator/pull/996
• Document refinement region limits behaviour by @ykempf in https://github.com/fmihpc/vlasiator/pull/998
• Makefile for MPCDF's Viper system by @ursg in https://github.com/fmihpc/vlasiator/pull/1010
• AMR Testpackage by @lkotipal in https://github.com/fmihpc/vlasiator/pull/902
• Long overdue fix to the glueChunksTogether.sh script that usually doe… by @ykempf in https://github.com/fmihpc/vlasiator/pull/1011
• Removed block adjustment in initialization of donotcompute cells. by @ykempf in https://github.com/fmihpc/vlasiator/pull/1009
• Adding omp simd-pragmas to moment filtering by @veetihaaja in https://github.com/fmihpc/vlasiator/pull/1002
• No noDipoleInSW by @ykempf in https://github.com/fmihpc/vlasiator/pull/1005
• Only proc boundary cells in one trans loop by @ykempf in https://github.com/fmihpc/vlasiator/pull/1008
• Simplify division by kernelSum. by @ykempf in https://github.com/fmihpc/vlasiator/pull/1018
• Reinstate shrink_to_fit in SpatialCell. by @ykempf in https://github.com/fmihpc/vlasiator/pull/1016
• Move submodule include paths by @lkotipal in https://github.com/fmihpc/vlasiator/pull/895
• Vlasiator 5.3.1 dev into master merge by @ykempf in https://github.com/fmihpc/vlasiator/pull/1025

New Contributors

• @ArnaudLalague made their first contribution in https://github.com/fmihpc/vlasiator/pull/950
• @astatide made their first contribution in https://github.com/fmihpc/vlasiator/pull/963
• @veetihaaja made their first contribution in https://github.com/fmihpc/vlasiator/pull/1002

Full Changelog: https://github.com/fmihpc/vlasiator/compare/v5.3...v5.3.1