Update atlas-bash-util to set time for SLURM job if specified (#35)

* Update atlas-slurm adds time from command

* Update slurm.sh

* Update atlas-slurm

* Update README.md

* Update VERSION

---------

Co-authored-by: Pedro Madrigal <[email protected]>

README.md

@@ -163,10 +163,11 @@ Usage:
 
 ```
 ./slurm/atlas-slurm -h
-Usage: ./slurm/atlas-slurm [ -c <command string, mandatory field> ] \
+Usage: ./atlas-slurm [ -c <command string, mandatory field> ] \
            [ -w <working directory, mandatory field> ] \
            [ -m <memory in MB or in the format <size>[units], defaults to cluster default. Different units can be specified using the suffix [K|M|G|T]> ] \
            [ -p <number of cores, defaults to cluster default> ] \
+           [ -t <allocated maxtime, defaults to max allowed time for queue/partition. SLURM accepted format> ]
            [ -j <job name, defaults to cluster default> ] \
            [ -g <job group name, defaults to cluster default> ] \
            [ -l <log prefix, no logs written by default> ] \
@@ -175,12 +176,12 @@ Usage: ./slurm/atlas-slurm [ -c <command string, mandatory field> ] \
            [ -o <with -l, print standard output content? Defaults to no> ] \
            [ -s <monitor style: 'status' for job status updates on polling, 'std_out_err' to report ongoing content of logs (where used). Defaults to std_out_err> ] \
            [ -f <poll frequency in seconds if job is monitored. Defaults to 10.> ] \
-           [ -q <slurm queue, defaults to cluster default> ] \
+           [ -q <slurm queue/partition, defaults to cluster default> ] \
            [ -u <suppress logging output? Default: no> ] \
            [ -v <name of the conda environment in which to run the job> ]
 
 ```
-Here, command (`-c`) and working directory (`-w`) are mandatory field for `atlas-slurm`. Specifying memory (`-m`) is advised, if memory is not specified with `-m` flag (e.g. `-m 1G`), it will use 4000Mb by default. If queue/partition is not specified it will use production by default. 
+Here, command (`-c`) and working directory (`-w`) are mandatory field for `atlas-slurm`. Specifying memory (`-m`) is advised, if memory is not specified with `-m` flag (e.g. `-m 1G`), it will use 4000Mb by default. Specifying time (`-t`) is advised, if time is not specified with `-t` flag (e.g. `-t 1:00:00`), it will use max allowed time for the queue/partition by default. If queue/partition is not specified it will use production by default. 
 
 Here, CPU-time is a mandatory field for SLURM submission. It will allocate maximum allowed time for the partition/queue by default.
 

VERSION

@@ -1 +1 @@
-0.2.7
+0.2.8

atlas-slurm

@@ -8,6 +8,7 @@ usageOpts="[ -c <command string, mandatory field> ] \
            [ -w <working directory, mandatory field> ] \
            [ -m <memory in MB or in the format <size>[units], defaults to cluster default. Different units can be specified using the suffix [K|M|G|T]> ] \
            [ -p <number of cores, defaults to cluster default> ] \
+           [ -t <allocated maxtime, defaults to max allowed time for partition. SLURM accepted format > ] \
            [ -j <job name, defaults to cluster default> ] \
            [ -l <log prefix, no logs written by default> ] \
            [ -e <clean up log files after monitored run? Defaults to no> ] \
@@ -28,6 +29,7 @@ commandString=
 workingDir=
 memory=
 cores=
+maxTime=
 jobName=
 queue=
 logPrefix=
@@ -39,7 +41,7 @@ monitorStyle=std_out_err
 prioritise=no
 quiet=no
 
-while getopts ":c:w:m:p:j:g:l:o:e:n:f:q:s:r:v:u:" o; do
+while getopts ":c:w:m:p:t:j:g:l:o:e:n:f:q:s:r:v:u:" o; do
     case "${o}" in
         c)
             commandString=${OPTARG}
@@ -53,6 +55,9 @@ while getopts ":c:w:m:p:j:g:l:o:e:n:f:q:s:r:v:u:" o; do
         p)
             cores=${OPTARG}
             ;;
+        t)
+            maxTime=${OPTARG}
+            ;;
         j)
             jobName=${OPTARG}
             ;;
@@ -103,13 +108,21 @@ if [[ ! -d "${workingDir}" ]]; then
     mkdir -p "$workingDir" || die "Failed to create directory: $workingDir"
 fi
 
+if [ -z "$queue" ]; then
+    queue="production"
+fi
+
+if [ -z "$maxTime" ]; then
+    maxTime=$(slurm_maxtime_for_partition "$queue")
+fi
+
 # Submit the jobs
 # if [ -n "${workingDir}/${logPrefix}.out" ]; then
 #         jobStdout="${workingDir}/${logPrefix}.out"
 #         jobStderr="${workingDir}/${logPrefix}.err"
 #         rm -rf $jobStdout $jobStderr
 #     fi
-slurmJobId=$(slurm_submit "$commandString" "$queue" "$jobName" "$memory" "$cores" "$workingDir" "$logPrefix" "$prioritise" "$condaEnv" "$quiet")
+slurmJobId=$(slurm_submit "$commandString" "$queue" "$jobName" "$memory" "$cores" "$maxTime" "$workingDir" "$logPrefix" "$prioritise" "$condaEnv" "$quiet")
 submitStatus=$?
 
 if [ "$submitStatus" -ne "0" ] && [ -n "$slurmJobId" ]; then

slurm.sh

@@ -2,18 +2,16 @@
 
 slurm_submit(){
     local commandString="$1"
-    local jobQueue="${2:-production}"
+    local jobQueue="${2}"
     local jobName="$3"
     local slurmMem="${4:-4000}"
     local nThreads="$5"     
-    local workingDir="$6"
-    local logPrefix="$7"
-    local prioritise="$8"
-    local condaEnv="${9}"
-    local quiet="${10:-'no'}"
-
-
-    maxTime=$(slurm_maxtime_for_partition "$jobQueue")
+    local maxTime="$6"     
+    local workingDir="$7"
+    local logPrefix="$8"
+    local prioritise="$9"
+    local condaEnv="${10}"
+    local quiet="${11:-'no'}"
 
     if [ -n "$jobQueue" ]; then jobQueue=" -p ${jobQueue}"; fi
     if [ -n "$jobName" ]; then jobName=" -J ${jobName}"; fi