Code

Generic HPC Install Script#329

Code

Merged

TimothyWillard merged 71 commits intomainHopkinsIDD/flepiMoP:mainfrom GH-191/longleaf-batch-submissionHopkinsIDD/flepiMoP:GH-191/longleaf-batch-submissionCopy head branch name to clipboardOct 23, 2024

+393-5

Commits

Commits on Sep 13, 2024

• Copy slurm_init.sh to slurm_init_longleaf.sh

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  committed
  aa0c077

• Restore slurm_init.sh

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• Merge branch 'copy-file' into GH-191/longleaf-batch-submission

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• Added UNC Longleaf Specific Init/Prerun Scripts

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  TimothyWillard

  committed
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Commits on Sep 16, 2024

• Draft implementation of HPC install script

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  TimothyWillard

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• Minor changes to hpc_install.sh

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  TimothyWillard

  committed
  2436640

• Added slurm --partition flag to inference script

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  TimothyWillard

  committed
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Commits on Oct 2, 2024

• Initial pass at HPC install on rockfish

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• Remove longleaf specific slurm scripts

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  TimothyWillard

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• Remove --partion flag

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Commits on Oct 3, 2024

• Minor updates to hpc_install.sh

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  TimothyWillard

  committed
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Commits on Oct 9, 2024

• initial tweaks to make flepimop-inference-* runnable

  

  pearsonca

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• further install scripts fixes

  

  pearsonca

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• fix reinvocation of inference-slot

  

  pearsonca

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• initial installation for ubuntu re-org

  

  pearsonca

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• updates addressing use of installed r scripts

  

  pearsonca

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• README revs

  

  pearsonca

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• add arrow installation

  

  pearsonca

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• Switch R pkg install to use build/setup.R

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  TimothyWillard

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• Add $WORKDIR to hpc_install.R

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  TimothyWillard

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• Add missing flepi path arg to setup.R

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• Force pin arrow version between python and R

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• Change rockfish default directories

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  9ca12ed

• Split hpc_install.sh into init and install

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  TimothyWillard

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  f78ee75

• Use devtools::install in setup.R

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  committed
  6d69186

• Unset error exit around R pkg install

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• Add set +e an exit to flepi_init.sh

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• install_cli installs to conda bin

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  TimothyWillard

  and

  pearsonca

  committed
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• Remove init call from install script

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  TimothyWillard

  committed
  e443626

• Remove old version restrictions, add optparse

  TimothyWillard

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• Move R deps install into conda environment

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  TimothyWillard

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  385eeb5

• Readd inference CLI install

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  committed
  f0571ae

• Update example command to use installed CLI

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• Manually install covidcast package

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  TimothyWillard

  committed
  ec7978d

• Downgrade r-base dependency to 4.3

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• Remove symlinks if exists on reinstall

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Commits on Oct 10, 2024

• Script to generate environment.yml

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  committed
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• Add dnachun to channels, add r-sf dependency

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  a4631db

• GitHub action to generate environment.yml

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• Remove unneeded comment

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• Merge main into GH-191/auto-generate-environment.yml

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• GitHub action checkout with attached head

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• Update environment.yml

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  6ad753d

• Make clear source of environment.yml commit

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  committed
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• Use premade environment.yml in hpc_install.sh

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  committed
  bacf6f4

• Remove setup.R and install_ubuntu.sh

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• Restore README.md

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• Bug fix to only remove files present

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  committed
  cbcdfbd

• Add spaces for style in build/hpc_install.sh

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Commits on Oct 14, 2024

• Merge main into GH-191/longleaf-batch-submission

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Commits on Oct 18, 2024

• Merge main into GH-191/longleaf-batch-submission

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• Move everything on longleaf into /work

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• Rename install script to clarify uses

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• Change exec of hpc install script

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• Change longleaf dirs in init script

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• Move rockfish userdir

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• Change default python to 3.11

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  committed
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• Merge main into GH-191/longleaf-batch-submission

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• Make flepi path/conda configurable

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  committed
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• Update environment.yml via GitHub action

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• Formatting of flepi path/conda inputs

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• Use realpath to make format file paths

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• Remove python/R name check

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  8ba4474

• Remove whitespace from README.md

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Commits on Oct 21, 2024

• Add missing slurm module for rockfish

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  committed
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• Add --editable to gempyor install

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• Cleanup error handling

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Commits on Oct 22, 2024

• Update conda env to use ~/.conda

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  70ced08

• Remove --force-reinstall from pip install

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  TimothyWillard

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• Minor typo

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• Merge main into GH-191/longleaf-batch-submission

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  TimothyWillard

  committed
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