Include deprecation notices for bsub #42

Author: polyluxus

README.md

@@ -102,7 +102,7 @@ The following script options are available:
 | `-o <ARG>`  | Trap the output (without errors) of `xtb` into a file called `<ARG>`. (Default: `auto`)
 | `-s`        | Write a submit script instead of interactive execution (default: PBS). Resulting file needs to be submitted.
 | `-S`        | Write submit script and directly submit it to the queue, requires setting a queueing system with `-Q`.
-| `-Q <ARG>`  | Set a queueing system for which the submit script should be prepared, supported `pbs-gen`, `slurm-gen`, `bsub-gen`.
+| `-Q <ARG>`  | Set a queueing system for which the submit script should be prepared, supported `pbs-gen`, `slurm-gen`, (`bsub-gen`).
 | `-P <ARG>`  | Account to project or account `<ARG>`, only slurm, LSF (bsub).
 | `-M`        | Use pre-installed modules instead of path settings, also needs specified module(s). 
 | `-l <ARG>`  | Specify a module to be used, will also invoke `-M`, may be specified multiple times to create a list, `<ARG>=purge` unloads all modules and `<ARG>=0` clears the list.
@@ -114,6 +114,8 @@ The following script options are available:
 | `-H`        | Retrieve the man page of xtb of the original xtb distribution.
 | `-X`        | Retrieve the man page of xcontrol of the original xtb distribution.
 
+Please note that support for LSF (bsub) is now deprecated and will be removed in a future update.
+
 ## Included files and directories
 
 The following files and/or directories come with this script:

configure/configure.sh

@@ -533,6 +533,7 @@ ask_qsys_details ()
 {
   ask "What queueing system would you like to use?"
   message "Currently supported: pbs-gen, bsub-gen, slurm-gen, bsub-rwth, slurm-rwth"
+  message "Please note that support for LSF (bsub) is now deprecated and will be removed in a future update."
   local test_queue
   test_queue=$(read_human_input)
   debug "test_queue=$test_queue"
@@ -756,6 +757,7 @@ print_settings ()
 
   echo     "## Set default queueing system for which the script should be written"
   echo     "## (pbs-gen, bsub-gen, slurm-gen, or *-rwth [special cases, see source])"
+  echo     "## Please note that support for LSF (bsub) is now deprecated and will be removed in a future update."
   echo     "#  "
   if [[ -z $use_queue ]] ; then
     echo   "#  request_qsys=\"pbs-gen\""

guides/usage-opts.md

@@ -74,9 +74,10 @@ Command line: `-Q <ARG>`
 Configuration: `request_qsys=<ARG>`
 
 In order for the `-s` and `-S` switches to work, a queueing system for which the submit script should be prepared must be set.
-Currently supported are `pbs-gen` (the default), `slurm-gen`, `slurm-rwth`, `bsub-gen`, and `bsub-rwth`
-The `*rwth` suffix will test a few more options and will set some constraints according to the recommendations of the RWTH IT centre
-(this is currently v0.4.0 maintained only as backwards compatibility and will be removed from future versions).
+Currently supported are `pbs-gen` (the default), `slurm-gen` and `slurm-rwth`.
+The support for `bsub-gen` and `bsub-rwth` is now discontinued and will be removed in a future version.
+The `*rwth` suffix will test a few more options and will set some constraints according to the recommendations of the RWTH IT centre.
+This is currently (as of v0.4.0) only included as backwards compatibility and will also be removed in future versions.
 
 ### Accounting
 

runxtb.rc

@@ -63,7 +63,8 @@
 
 ## Set default queueing system for which the script should be written.
 ## Format <queue>-<special>
-## Recognised values for <queue>: pbs, bsub, slurm
+## Recognised values for <queue>: pbs, slurm, (bsub)
+## Please note that LSF (bsub) is now deprecated and will be removed in a future version.
 ## Recognised values for <special>: gen, rwth (no effect for pbs) [special cases, see source code]
 #
    request_qsys="slurm-gen"

runxtb.sh

@@ -532,6 +532,9 @@ write_submit_script ()
     local queue="$1" queue_short
     local output_file_local="$2" submitscript_filename
     [[ -z $queue ]] && fatal "No queueing systen selected. Abort."
+    if [[ "$queue" =~ [Bb][Ss][Uu][Bb] ]] ; then
+      message "Please note that support for LSF (bsub) is now deprecated and will be removed in a future update."
+    fi
     queue_short="${queue%-*}"
     submitscript_filename="${output_file_local%.*}.${queue_short}.bash"
     debug "Selected queue: $queue; short: $queue_short"
@@ -812,7 +815,8 @@ while getopts :p:m:w:o:sSQ:P:Ml:iB:C:qhHX options ; do
       ;;
     #hlp   -Q <ARG> Select queueing system (Default: pbs-gen)
     #hlp            Format: <queue>-<special>
-    #hlp            Recognised values for <queue>: pbs, bsub, slurm
+    #hlp            Recognised values for <queue>: pbs, slurm, (bsub)
+    #hlp            Please note that LSF (bsub) is now deprecated and will be removed in a future version.
     #hlp            Recognised values for <special>: gen, rwth (no effect for pbs)
     Q)
       request_qsys="$OPTARG"
@@ -988,6 +992,7 @@ if [[ $run_interactive =~ ([Nn][Oo]|[Ss][Uu][Bb]) ]] ; then
       qsub_bin=$(command -v qusb 2>&1) || fatal "Command qsub was not found."
       submit_id="Submitted as $("$qsub_bin" "$submitscript" 2>&1)" || exit_status="$?"
     elif [[ $request_qsys =~ [Bb][Ss][Uu][Bb] ]] ; then
+      message "Please note that support for LSF (bsub) is now deprecated and will be removed in a future update."
       bsub_bin=$(command -v busb 2>&1) || fatal "Command bsub was not found."
       submit_id="$("$bsub_bin" < "$submitscript" 2>&1 )" || exit_status="$?"
       submit_id="${submit_id#Info: }"