@sigmafelix @mitchellmanware

We need to try to test out being as careful as possible with environment variables to ensure all aspects of the timeline communicate appropriately. I know @mitchellmanware has built environment variables in the bash scripts and with beethoven code like beethoven::sys_beethoven

So for documentation purposes, I am putting in environment variables from the different systems. Feel free to edit as needed:

Linux HPC system

• BASH_FUNC_ml%%
• BASH_FUNC_module%%
• BASH_FUNC_scl%%
• BASH_FUNC_switchml%%
• BASH_FUNC_which%%
• BOWTIE2_INDEXES
• BROWSER
• COLORTERM
• COLUMNS
• DBUS_SESSION_BUS_ADDRESS
• DEBUGINFOD_URLS
• EDITOR
• GIT_ASKPASS
• HISTCONTROL
• HISTSIZE
• HOME
• HOSTNAME
• LANG
• LD_LIBRARY_PATH
• LESSOPEN
• LINES
• LN_S
• LOADEDMODULES
• LOGNAME
• MAIL
• MAKE
• MANPATH
• MODULEPATH
• MODULEPATH_modshare
• MODULES_CMD
• MODULES_RUN_QUARANTINE
• MODULESHOME
• OMP_NUM_THREADS
• OPENBLAS_NUM_THREADS
• ORA_REF_PATH
• PAGER
• PATH
• PICARD
• PWD
• PYTHON_BASIC_REPL
• PYTHONSTARTUP
• R_ARCH
• R_BROWSER
• R_BZIPCMD
• R_DOC_DIR
• R_GZIPCMD
• R_HOME
• R_INCLUDE_DIR
• R_LIBS_SITE
• R_LIBS_USER
• R_PAPERSIZE
• R_PDFVIEWER
• R_PLATFORM
• R_PRINTCMD
• R_PROFILE_USER
• R_PROFILE_USER_OLD
• R_RD4PDF
• R_SESSION_TMPDIR
• R_SHARE_DIR
• R_STRIP_SHARED_LIB
• R_STRIP_STATIC_LIB
• R_SYSTEM_ABI
• R_TEXI2DVICMD
• R_UNZIPCMD
• R_ZIPCMD
• RENV_CONFIG_SANDBOX_ENABLED
• RENV_CONFIG_SYNCHRONIZED_CHECK
• S_COLORS
• SED
• SHELL
• SHLVL
• SSH_ASKPASS
• SSH_CLIENT
• SSH_CONNECTION
• SSL_CERT_DIR
• SSL_CERT_FILE
• TAR
• TERM
• TERM_PROGRAM
• TERM_PROGRAM_VERSION
• USER
• VSCODE_GIT_ASKPASS_EXTRA_ARGS
• VSCODE_GIT_ASKPASS_MAIN
• VSCODE_GIT_ASKPASS_NODE
• VSCODE_GIT_IPC_HANDLE
• VSCODE_INIT_R
• VSCODE_IPC_HOOK_CLI
• VSCODE_NONCE
• VSCODE_WATCHER_DIR
• which_declare
• XDG_DATA_DIRS
• XDG_RUNTIME_DIR
• XDG_SESSION_ID

Apptainer

https://apptainer.org/docs/user/1.4/appendix.html#apptainer-s-environment-variables

Additional Software

• CUDA_HOME