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Recent Releases of hpc_submit_scripts

hpc_submit_scripts - v0.5.0

What's Changed

New Features

  • New Slurm job scripts densmap-z_Li.sh, densmap-z_NBT.sh, densmap-z_OBT.sh, densmap-z_OE.sh, densmap-z_NTf2.sh, densmap-z_ether.sh that run the MDTools script scripts/structure/densmap.py for different compounds by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/144
  • Slurm job scripts discrete-z_Li_back_jump_prob_discrete.sh, renewal_events_Li-ether_back_jump_prob_discrete.sh and renewal_events_Li-NTf2_back_jump_prob_discrete.sh: Use the new command-line option of the MDTools script back_jump_prob_discrete.py, --norm-out, to receive an output file with the normalization factors used to calculate the back-jump probabilities (see https://github.com/andthum/mdtools/pull/201) by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/142

Bug Fixes

  • Python submit scripts submit_gmx_analyses_lintf2_ether.py and submit_mdt_analyses_lintf2_ether.py: Use absolute path to Slurm job scripts by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/144 and https://github.com/andthum/hpcsubmitscripts/pull/145
  • Python submit scripts submit_gmx_analyses_lintf2_ether.py and submit_mdt_analyses_lintf2_ether.py: Fix the function _submit_discretized: Reset the submit command after each loop instead of appending it by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/143 and https://github.com/andthum/hpcsubmitscripts/pull/145
  • Python submit script submit_mdt_analyses_lintf2_ether.py: Convert the box length that is read from the .gro file from nanometers to Angstrom by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/143

Code Refactoring

  • Slurm job scripts discrete-hex_*.sh: Increase time limit by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/149
  • Slurm job scripts analysis/lintf2_ether/mdt/lifetime_autocorr_Li-*.sh: Decrease time limit and increase memory limit by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/148 and https://github.com/andthum/hpcsubmitscripts/pull/150
  • Bash script .cleanup_mdt_analyses.sh: Change how specific analyses are gathered/ordered into sub-directories. This affects axial_hex_dist, discrete-hex, contact_hist_at_pos_change and lig_change_at_pos_change* by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/147 and https://github.com/andthum/hpcsubmitscripts/pull/153
  • Slurm job scripts lig_change_at_pos_change_blocks_*.sh: Increase memory limit by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/144

Full Changelog: https://github.com/andthum/hpcsubmitscripts/compare/v0.4.0...v0.5.0

- Shell
Published by andthum about 2 years ago

hpc_submit_scripts - v0.4.0

What's Changed

Bug fixes

  • Slurm job script axial_hex_dist_1nn_OBT.sh: Fix typo in analysis name by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/137
  • Bash script .cleanup_mdt_analyses.sh: Fix typo in cleanup of discrete-hex by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/136
  • Slurm job scripts discrete_hex_*.sh: Fix cleanup and the path to the MDTools script discrete_hex.py by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/136 and https://github.com/andthum/hpcsubmitscripts/pull/137
  • Slurm job scripts axial_hex_dist_*nn_*.sh: Fix cleanup by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/136 and https://github.com/andthum/hpcsubmitscripts/pull/137
  • Slurm job scripts contact_hist_slab-z_Li-*.sh: Fix cleanup by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/136 and https://github.com/andthum/hpcsubmitscripts/pull/137
  • Slurm job scripts densmap-z_*.sh: Fix cleanup by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/136 and https://github.com/andthum/hpcsubmitscripts/pull/137
  • Slurm job scripts *rdf_slab-z_*.sh: Fix cleanup by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/136 and https://github.com/andthum/hpcsubmitscripts/pull/137

Code refactoring

  • Change time and memory limits of various scripts by @andthum in various pull requests

Full Changelog: https://github.com/andthum/hpcsubmitscripts/compare/v0.3.0...v0.4.0

- Shell
Published by andthum over 2 years ago

hpc_submit_scripts - v0.3.0

What's Changed

Breaking changes

  • Python submit script submit_gmx_analyses_lintf2_ether.py: Replace the --every option ("read every n-th frame from the trajectory") by a --skip and --dt option. The new options mirror the -skip and -dt options of Gromacs analysis tools and therefore should by less confusing by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/126
  • Slurm job scripts gmx/trjconv_*.sh: Replace the -dt option with -skip, which should be more robust (see https://www.mail-archive.com/gmx-users@gromacs.org/msg35903.html and https://www.mail-archive.com/gmx-users@gromacs.org/msg06868.html) by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/119
  • Compress all created text output files with gzip by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/119

New features

  • New Slurm job scripts renewal_events_Li-*_kaplan_meier*.sh by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/132
  • New Slurm job scripts renewal_events_Li-*_back_jump_prob*.sh by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/132
  • New Slurm job script discrete-z_Li_kaplan_meier_discrete.sh by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/132
  • New Slurm job script discrete-z_Li_back_jump_prob_discrete.sh by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/132
  • Slurm job script discrete-hex_*.sh: Additionally run the MDTools scripts scripts/discretization/back_jump_prob and scripts/discretization/kaplan_meier by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/132
  • Python submit script submit_mdt_analyses_lintf2_ether.py: Submit the msd_layer* scripts together with all other bulk scripts (command-line option --scritps 1), because the issue that has prevented the msd_layer* scripts to work on bulk simulations has been fixed (see https://github.com/andthum/mdtools/pull/181) by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/132
  • Slurm job script gmx/energy.sh: Add -skip option by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/126

Bug fixes

  • Adjust memory and time limits of various Slurm job scripts by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/123
  • Increase robustness of the Bash cleanup scripts .cleanup_gmx_analyses.sh and .cleanup_mdt_analyses.sh by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/123
  • Increase memory limits of some Slurm job scripts by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/122

Documentation updates

  • Python submit script submit_gmx_analyses_lintf2_ether.py: Format docstring and fix error in the argparse help text that led to an error when calling the script with the -h option by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/127
  • Python submit script submit_mdt_analyses_lintf2_ether.py: Fix wrong length unit: --binwidth must be given in Angstrom not nanometers by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/122

Project maintenance

  • Fix Development Tools by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/122
  • Include Sphinx linkcheck in CI workflow by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/118

Full Changelog: https://github.com/andthum/hpcsubmitscripts/compare/v0.2.0...v0.3.0

- Shell
Published by andthum over 2 years ago

hpc_submit_scripts - v0.2.0

There have been quite some of changes since version 0.1.0. From now on, I will try to publish new releases already when there have been only small changes, so that the change log will not become overwhelming. And I will try to make the changelog more human-friendly.

What's Changed

Breaking changes

  • [submitgmxmdrun.py]: Change Default Backup Behavior by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/61
  • [Feat]: Support Compressed Files by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/64
  • Change Default of --every Option of submit_gmx_analyses_lintf2_ether.py by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/74
  • [energy_dist.py]: Adopt to Changed CLI of plot_energy_dist.py by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/116

New features

  • Create Bash Scripts to Load Compression Tools on Palma2 by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/59
  • [gmx energy]: Also Calculate Conserved Energy by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/60
  • [submitmdtanalyseslintf2ether.py]: Additional --scripts Options by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/84
  • [submitmdtanalyseslintf2ether.py]: Support .npz Archives by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/85
  • New Slurm Job Script subvolume charg.sh by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/87
  • [Feat]: New Job Script energy_dist.sh by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/92
  • Create Source Script vmd1-9-4_foss_cuda.sh by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/98
  • New Slurm Job Scripts: attribute hist* by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/104
  • [create_mda_universe.sh]: Create Universe for .trr Trajectory by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/115

Bug fixes

  • Fix Cleanup Step in msd_layer*.py Analysis Scripts by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/57
  • [gmxmdrun.sh]: Add --ntasks 1 to the srun Call of gzip by @andthum in https://github.com/andthum/hpcsubmit_scripts/pull/68
  • [gmxmdrun.sh]: Exit When gmx mdrun Fails by @andthum in https://github.com/andthum/hpcsubmit_scripts/pull/69
  • [gmxmdrun.sh]: Exit Slurm Script with Gromacs Exit Code by @andthum in https://github.com/andthum/hpcsubmit_scripts/pull/70
  • Fix Log-File Search in submit_gmx_analyses_lintf2_ether.py by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/71
  • Fix Search for Compressed Files in submit_gmx_analyses_lintf2_ether.py by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/72
  • [energy.sh]: Fix Call of decompres.sh by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/82
  • [submitmdtanalyseslintf2ether.py]: Fix Submit Option 11.3 / 11.4 by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/86
  • [subvolumecharge.sh]: Fix Argument Parsing by @andthum in https://github.com/andthum/hpcsubmit_scripts/pull/89
  • Update pre-commit Config and pyproject.toml by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/99
  • Fix Typo in submit_mdt_analyses_lintf2_ether.py by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/105

Dependency updates

  • Update flake8 by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/77
  • Update Config Files by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/108

Documentation updates

  • Fix Typos in the Developer's Guide by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/67
  • Add Badge "Doc Style NumPy" by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/103
  • Update Documentation by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/113
  • [submit_mdt_analyses.py]: Correct Documentation of the --mdt-path Option by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/114

Code refactoring

  • Refactor Analysis Scripts in analysis/lintf2_ether/* by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/62
  • [subvolumecharge.sh]: Change sbatch Options by @andthum in https://github.com/andthum/hpcsubmit_scripts/pull/88
  • [hpcssrc.ini]: Remove Unused Section by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/90
  • energy_dist.sh: Increase Memory Limit from 2G to 4G by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/93

Project maintenance

  • Grant the PR-Labeler Write Access to Pull Requests by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/58
  • [pullrequesttemplate.md]: Link PR to Issue Correctly by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/63
  • PR Template: Change Mark for Unrelated Checkboxes by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/76
  • Rename shellcheckrc to .shellcheckrc by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/78
  • Create Config Files for VSCode by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/83
  • Update Project-Specific VSCode Settings by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/100
  • Update pre-commit-config.yaml by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/102
  • Fix Wrong Glob Patterns in .gitignore and settings.json by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/109
  • Update Configuration of Development Tools by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/110
  • Update GitHub Actions by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/112
  • Prepare Release 0.2.0 by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/117

Other changes

  • Unskip All pre-commit Hooks for the CI Workflow by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/52
  • [dependabot.yml]: Add Search Directories for pip by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/53
  • [dependabot.yml]: Fix directory Key by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/54
  • Clarify Docs about the Config File by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/55
  • Automatically label pull requests using issue-labler by @andthum in https://github.com/andthum/hpcsubmitscripts/pull/56
  • Update flake8-isort requirement from <5.0,>=4.0 to >=4.0,<6.0 by @dependabot in https://github.com/andthum/hpcsubmitscripts/pull/80
  • Update flake8-builtins requirement from <2.0,>=1.0 to >=1.0,<3.0 by @dependabot in https://github.com/andthum/hpcsubmitscripts/pull/81
  • Update flake8-isort requirement from <6.0,>=4.2 to >=4.2,<7.0 by @dependabot in https://github.com/andthum/hpcsubmitscripts/pull/94
  • Update sphinx requirement from <6.0,>=3.0 to >=3.0,<7.0 in /docs by @dependabot in https://github.com/andthum/hpcsubmitscripts/pull/96
  • Bump github/issue-labeler from 2.5 to 2.6 by @dependabot in https://github.com/andthum/hpcsubmitscripts/pull/106

Full Changelog: https://github.com/andthum/hpcsubmitscripts/compare/v0.1.0...v0.2.0

- Shell
Published by andthum about 3 years ago