Am 17.10.2018 um 19:50 schrieb Nelson Kick:
> Is there any way to add variables to the standard “beas” mail? Would like to
> add
> additional info to this list… if possible, like SGE_O_PATH or other env
> variables.
Please find below the complete mail-wrapper script. Be default, we are
interested in the context variables set by our script generator:
#$ -ac COMMAND=
#$ -ac OUTPUT=
#$ -ac MAIL_ATTACHMENT=
#$ -ac MAIL_RECIPIENTS_LIST=
The content of OUTPUT= and MAIL_ATTACHMENT= are most likely the same, but the
users wanted a way to get the name of the output file without it being attached
to the email all the time. Hence these two context variable, which have a
similar purpose. A flag could have done the same. The mail-wrapper script also
tries to mangle the suffix of the file from *.log or *.out file to read (only
in the attachment) *.txt instead. This way even mail applications on a
smartphone should be able to display the attachment without complaining.
The MAIL_RECIPIENTS_LIST= are alternate or additional receivers of the email.
If the list starts with a "+", these will be added to the original receiver
(bug/feature alert: if the list in SGE has several receivers already (added by
-M in `qsub`), the mail-wrapper script will be called for each of them once –
hence the additional receivers will get duplicate emails). Without the "+" the
list will replace the original receiver. The list entries must be delimited by
";", as the "," will already be used to separate all the fields in SGE's output
of the context variables.
(The context script I posted already will convert the ";" in ",", as in the
context file it creates the entries are already on separates lines. The mail
wrapper in turn will replace the "," with a " ", as this is what our mail
application expects if several receivers are specified as delimiter.)
One variable is created by the prolog itself with the line:
qconf -ac NODES=…
to get a list of used nodes for this particular job.
Please let me know, if something is unclear. I hope it will work in a general
case too.
-- Reuti
================ mail-wrapper script follows ================
#!/bin/sh
#
# Assemble an email and attach an output file.
# Note: SGE will call this routine for each and every recipient specified
# with the -M option. It won't use the feature of the mail application
# to honor a list of recipients. This wrapper will do.
#
export PATH=/usr/local/bin:/bin:/usr/bin
. /usr/sge/default/common/settings.sh
line() {
if [ -f /var/spool/sge/context/$JOB_ID -a -r /var/spool/sge/context/$JOB_ID
]; then
echo $(sed -n -e "/^${1}=/s///p" /var/spool/sge/context/$JOB_ID)
fi
}
entry() {
RESULT=$(line ${1})
if [ -n "${RESULT}" ]; then
echo "${1}: ${RESULT}"
else
echo "${1}: [none recorded]"
fi
}
command_line() {
COMMAND_LINE=$(qstat -j ${JOB_ID} | sed -n -e "/^context/{s/^context:
*//;s/,/\n/g;s/;/,/g;p}" | sed -n -e "/^COMMAND=/s///p")
echo
if [ -n "${COMMAND_LINE}" ]; then
echo "COMMAND: ${COMMAND_LINE}"
else
echo "COMMAND: [none recorded]"
fi
}
context() {
echo
entry COMMAND
entry OUTPUT
entry NODES
}
assemble_recipients_list() {
if [ -n "${MAIL_RECIPIENTS_LIST}" ]; then
if [ "${MAIL_RECIPIENTS_LIST:0:1}" = "+" ]; then
MAIL_RECIPIENTS_LIST="$1,${MAIL_RECIPIENTS_LIST:1}"
fi
else
MAIL_RECIPIENTS_LIST="${1}"
fi
MAIL_RECIPIENTS_LIST="${MAIL_RECIPIENTS_LIST//,/ }"
}
check_and_prepare_attachment() {
tmpdir="/tmp"
if [ -n "${MAIL_ATTACHMENT}" ]; then
if [ ! -f "${MAIL_ATTACHMENT}" ]; then
ATTACHMENT_ERROR="The requested attachment file
\`${MAIL_ATTACHMENT}' does not exist."
return 1
elif [ ! -r "${MAIL_ATTACHMENT}" ]; then
ATTACHMENT_ERROR="The requested attachment file
\`${MAIL_ATTACHMENT}' couldn't be read."
return 1
fi
filename=$(basename "${MAIL_ATTACHMENT}")
suffix=${filename##*.}
if [ "${suffix}" = "${filename}" ]; then
suffix=""
fi
filename="${filename%.*}"
if [ $(stat --printf="%s" "${MAIL_ATTACHMENT}") -gt 1048576 ]; then
ATTACHMENT_WARNING1="The requested attachment file
\`${MAIL_ATTACHMENT}' has a size > 1 MiB. The attachment in this email was
truncated and contains the last MiB only."
filename="${filename}_last_MiB"
mangle_attachment="1"
fi
if [ -z "${suffix}" -o "${suffix}" = "log" -o "${suffix}" = "out" -o
"${suffix}" = "last" ]; then
ATTACHMENT_WARNING2="The suffix of the requested attachment file
\`${MAIL_ATTACHMENT}' was mangled to \`.txt' for this email only."
suffix="txt"
mangle_attachment="1"
fi
if [ -n "${mangle_attachment}" ]; then
if [ ! -d "${tmpdir}" -o ! -w "${tmpdir}" -o ! -r "${tmpdir}" ]; then
ATTACHMENT_ERROR="The temporary scratch space can't be accessed
to create a directory for the mangled attachment."
return 1
fi
if ! directory=$(mktemp -d); then
ATTACHMENT_ERROR="The directory in the temporary scratch space
can't be created to store a mangled mangled."
return 1
fi
target_filename="${directory}/${filename}${suffix:+.${suffix}}"
if ! tail -c 1048576 "${MAIL_ATTACHMENT}" > "${target_filename}";
then
ATTACHMENT_ERROR="A mangled attachment couldn't be saved."
MAIL_ATTACHMENT=""
return 1
else
MAIL_ATTACHMENT="${target_filename}"
fi
fi
fi
}
clean_attachment() {
if [ -n "${directory}" -a "${directory:0:${#tmpdir}}" = "${tmpdir}" ]; then
if [ -w "${tmpdir}" -a -r "${tmpdir}" ]; then
rm -rf "${directory}"
fi
fi
}
processing_error() {
if [ -n "${ATTACHMENT_ERROR}" -o -n "${APPENDIX}" -o \
-n "${ATTACHMENT_WARNING1}" -o -n "${ATTACHMENT_WARNING2}" ]; then
echo
fi
if [ -n "${APPENDIX}" ]; then
echo "Reason for job abort:"
echo "${APPENDIX}"
if [ -n "${ATTACHMENT_ERROR}" ]; then
echo
fi
fi
if [ -n "${ATTACHMENT_WARNING1}" ]; then
echo "${ATTACHMENT_WARNING1}"
fi
if [ -n "${ATTACHMENT_WARNING2}" ]; then
echo "${ATTACHMENT_WARNING2}"
fi
if [ -n "${ATTACHMENT_ERROR}" ]; then
echo "${ATTACHMENT_ERROR}"
fi
}
#
# Distinguish between normal jobs and an array job.
#
case `echo "$2" | cut -d " " -f 1` in
Job) JOB_ID=`echo "$2" | cut -d " " -f 2`
CONDITION=`echo "$2" | cut -d " " -f 4` ;;
Job-array) JOB_ID=`echo "$2" | cut -d " " -f 3`
CONDITION=`echo "$2" | cut -d " " -f 5` ;;
*) ;;
esac
#
# Get the entries for the context of the job and the
# reason in case of an abortion of the job.
#
if [ "$CONDITION" = "Started" ]; then
#
# Now construct and send the email for started jobs.
#
MAIL_RECIPIENTS_LIST=$(qstat -j ${JOB_ID} | sed -n -e
"/^context/{s/^context: *//;s/,/\n/gp}" | sed -n -e
"/^MAIL_RECIPIENTS_LIST=/s///p")
assemble_recipients_list "${3}"
(cat; command_line) | mail -s "$2" ${MAIL_RECIPIENTS_LIST}
elif [ "$CONDITION" = "Complete" -o "$CONDITION" = "Aborted" ]; then
#
# Now construct and send the email for completed or aborted jobs.
#
if [ "$CONDITION" = "Aborted" ]; then
if [ -f /var/spool/sge/$HOSTNAME/messages -a -r
/var/spool/sge/$HOSTNAME/messages ]; then
APPENDIX=`egrep "[|]job $JOB_ID([.][[:digit:]]+)? exceed"
/var/spool/sge/$HOSTNAME/messages | head -n 1`
fi
if [ -z "$APPENDIX" ]; then
APPENDIX="Unknown, no entry found in messages file on the master
node of the job."
fi
fi
#
# Extra Processing for attachments.
#
MAIL_RECIPIENTS_LIST=$(line MAIL_RECIPIENTS_LIST)
assemble_recipients_list "${3}"
MAIL_ATTACHMENT=$(line MAIL_ATTACHMENT)
check_and_prepare_attachment
if [ -z "${ATTACHMENT_ERROR}" -a -n "${MAIL_ATTACHMENT}" ]; then
(cat; context; processing_error) | mail -a "${MAIL_ATTACHMENT}" -s "$2"
${MAIL_RECIPIENTS_LIST}
else
(cat; context; processing_error) | mail -s "$2" ${MAIL_RECIPIENTS_LIST}
fi
if [ -f /var/spool/sge/context/$JOB_ID -a -w /var/spool/sge/context/$JOB_ID
]; then
rm -f /var/spool/sge/context/$JOB_ID
fi
clean_attachment
else
mail -s "$2" "$3"
fi
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