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Status Functionality already exists
Workspace Spectrum LSF
Components Reporting/Explorer
Created by Guest
Created on Mar 29, 2024

Be able to send stdout/stderr to both file and email

See ticket TS015786331; currently cannot have stderr & stdout go to both a file and email.  We would like the option to do both.

Needed By Quarter
  • Admin
    Bill McMillan
    Apr 2, 2024

    You can achieve this by forcing an email to be sent upon completion, and defining a custom $LSB_MAILPROG (set in lsf.conf) which will be called instead of sendmail.

    Specifying -N in addition to -o/-e will force an email to be generated when the job completes.

    $bsub -N -o out.txt -e out.err echo hello

    Create a custom LSB_MAILPROG, for example:

    #The standard email message is buffered on stdin, so save that to the file first.
    cat >$tmpfile

    echo "Stdout from $LSB_OUTPUTFILE" >> $tmpfile
    cat $LSB_OUTPUTFILE >> $tmpfile

    echo "stderr from $LSB_ERRORFILE" >> $tmpfile
    cat $LSB_ERRORFILE >> $tmpfile

    /usr/lib/sendmail $1 $2 $3 $4 < $tmpfile
    rm $tmpfile

    The custom mailprog ultimately needs to call sendmail if you want the mail sent. Note, if the output or error are huge, you may clobber your mail system. So it it prudent to do some size checks, or maybe just head/tail the output.

    The generated $tmpfile would be something like:

    To: billmc
    From: LSF <billmc>
    Auto-submitted: auto-generated
    X-Auto-Response-Suppress: OOF, AutoReply
    Sender: LSF System <billmc@pf3>
    Subject: Job 1454: <echo hello> in cluster <wsl> Done

    Job <echo hello> was submitted from host <pf3> by user <billmc> in cluster <wsl> at Tue Apr 2 10:07:48 2024
    Job was executed on host(s) <pf3>, in queue <normal>, as user <billmc> in cluster <wsl> at Tue Apr 2 10:07:48 2024
    </home/billmc> was used as the home directory.
    </home/billmc> was used as the working directory.
    Started at Tue Apr 2 10:07:48 2024
    Terminated at Tue Apr 2 10:07:52 2024
    Results reported at Tue Apr 2 10:07:52 2024

    Your job looked like:

    # LSBATCH: User input
    echo hello

    Successfully completed.

    Resource usage summary:

    CPU time : 0.02 sec.
    Max Memory : -
    Average Memory : -
    Total Requested Memory : -
    Delta Memory : -
    Max Swap : -
    Max Processes : -
    Max Threads : -
    Run time : 4 sec.
    Turnaround time : 4 sec.

    Read file <out.txt> for stdout output of this job.
    Read file <out.err> for stderr output of this job.

    Stdout from out.txt
    stderr from out.err