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Use non-login shell for
launch_FV3LAM_wflow.sh; remove support for …
…`WCOSS_CRAY`; fix cron capability for `tcsh` users on Cheyenne (ufs-community#675) * Remove unneeded sourcing of source_util_funcs.sh; add "%s" to printf calls since that's the proper calling method; edit comments. * Generalize machine files. Details: * Add a wrapper (source_machine_file.sh) for sourcing the machine file that allows other commands common to all machines to be called. * Change the scalar variable MODULE_INIT_PATH in the machine files to the array variable ENV_INIT_SCRIPTS_FPS that specifies the list of system scripts that need to be sourced (e.g. to make the "module" command available in a given script). This is needed because on Cheyenne, at least two system scripts need to be sourced (to enable "module" and "qsub"). * Move the "ulimit" commands at the ends of the machine files into the new variable PRE_TASK_CMDS so that they are not called every time the machine file is sourced. They will be called only if a given script issues an "eval ${PRE_TASK_CMDS}" (which all the ex-scripts will do). * In the relevant ex-scripts: (1) Change sourcing of machine files to use the wrapper source_machine_file.sh; (2) Use "eval" to evaluate the contents of PRE_TASK_CMDS. * In the WE2E script, change sourcing of the machine file to use the wrapper source_machine_file.sh. * Add new variable valid_vals_BOOLEAN to constants.sh so that this file can be sourced and the valid values for a boolean can be made available to any other script. * Bug fix. * Remove file that was accidentally added in previous commit. * Change the way crontab is called so that it also works on Cheyenne (for tcsh users). Details: * Introduce new function get_crontab_contents() that takes as input whether or not the calling script is itself being called from a cron job and returns (1) the path to the appropriate crontab command and (2) the contents of the user's cron table. * Such a function is needed because on Cheyenne, the location of the crontab command is different depending on whether or not the script that's calling crontab is itself called from a cron job (because on Cheyenne, "crontab" is containerized, and that complicates things). * Use get_crontab_contents() in generate_FV3LAM_wflow.sh and launch_FV3LAM_wflow.sh (instead of simply calling "crontab" because the latter approach doesn't work on Cheyenne, at least not with users whose login shell is tcsh). * Add "called_from_cron" as an optional argument to launch_FV3LAM_wflow.sh [so that it can then be passed on to get_crontab_contents()]. This argument is only used in the cron job that relaunches the workflow (which is created only if USE_CRON_TO_RELAUNCH is set to "TRUE"). * Having an optional argument like this seems to be the best way to tell launch_FV3LAM_wflow.sh whether or not it is running from a cron job. * launch_FV3LAM_wflow.sh can still be called from the command line without any arguments (since the default value of "called_from_cron" is "FALSE"). * Generalize the way commands are initialized so that any number of system scripts can be sourced in a given script (currently, only "module" is initialized). Details: * Introduce the new function init_env() that initializes the envrionment of a script by sourcing necessary system scripts. The full paths to these system scripts are specified in the array ENV_INIT_SCRIPTS_FPS in the machine files. * This function is needed because (1) this sourcing needs to be done in a couple of different scripts in the SRW App and (2) on some machines (e.g. Cheyenne), more than one system script may need to be sourced. * Use the new init_env() function in launch_FV3LAM_wflow.sh and load_modules_run_task.sh. * In load_modules_run_task.sh, init_env() replaces sourcing of only the system script that defines the "module" command. That is because on Cheyenne, in addition to the "module" command, the "qsub" command needs to be defined/initialized (by sourcing a second system script named pbs.sh). * Replace calls to "crontab -l" by echoing of already obtained contents. Fix comments and informational messages. * For Cheyenne, don't need to source two separate system scripts. Just sourcing "/etc/profile" is enough to make both the "module" and "qsub" commands (and probably all other system-supported commands) available in non-login scripts. * Make script exit with an error message if rocoto commands fail. * Fix the system script that needs to be sourced on Hera to get "module" (and other commands) to work. * In init_env.sh, declare "local" variables and change the index of the for-loop so it's different than the variable i used (and unset) by the system script on Hera. * Fix the system script that needs to be sourced on Orion to enable the "module" and other commands in a non-login bash shell. * Fix the system script on Jet that needs to be sourced to enable the "module" and other commands in a non-login bash shell. * Update comments. * Bug fix: Make sure the variable __crontab_cmd__ is defined for WCOSS_DELL_P3. * Try changing the system script to source on WCOSS_DELL_P3 to "/etc/profile" (since it works on the other machines to enable the "module" and other commands). This needs to be tested by someone who has access to WCOSS_DELL_P3. * Changes to try to make the machine file work for WCOSS_DELL_P3. Not yet tested. * Fix modulepath issue on wcoss * Fix issues on wcoss cray * Fix crontab issue on wcoss cray * Remove support for WCOSS_CRAY. * Place double qoutes around ${RUN_CMD_...} in if-statements that check whether the RUN_CMD_... variable is empty, i.e. -z "${RUN_CMD_...}". This is needed because on Cheyenne, not having the double quotes generates an error when RUN_CMD_... consists of a command that contains spaces (e.g. "mpirun -np ..."). Co-authored-by: chan-hoo <[email protected]>
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