Link gsi diag.* directories instead of moving them and enable Gaea emails in v17

dev/scripts/exglobal_atmos_analysis.sh

@@ -418,6 +418,8 @@ if [[ "${GENDIAG}" == "YES" ]]; then
     fi
     # Make the gsidiags directory to house the GSI diagnostic data
     GSIDIAGDIR=${GSIDIAGDIR:-"${pCOMOUT_ATMOS_ANALYSIS}/gsidiags"}
+    rm -rf "${GSIDIAGDIR}"
+    mkdir -p "${GSIDIAGDIR}"
 fi
 
 ##############################################################
@@ -670,6 +672,18 @@ if [[ "${USE_SELECT}" == "YES" ]]; then
     fi
 fi
 
+# If diags are to be generated, create the gsi.* directories in GSIDIAGDIR and link them here.
+# This will allow the GSI to write directly to the GSIDIAGDIR.
+if [[ "${GENDIAG}" == "YES" ]]; then
+    # The number of directories is controlled by the number of tasks
+    # (one each + 1, though the last will contain no data)
+    for task in $(seq 0 "${ntasks}"); do
+        dir="dir.$(printf %04d "${task}")"
+        mkdir -p "${GSIDIAGDIR}/${dir}"
+        ${NLN} "${GSIDIAGDIR}/${dir}" "./${dir}"
+    done
+fi
+
 ##############################################################
 # If requested, copy and de-tar guess radstat file
 if [[ "${USE_RADSTAT}" == "YES" ]]; then
@@ -909,33 +923,6 @@ fi
 # shellcheck disable=SC2312
 echo "${rCDUMP} ${PDY}${cyc} atminc done at $(date)" > "${COMOUT_ATMOS_ANALYSIS}/${APREFIX}increment.done.txt"
 
-# Diagnostic files
-# if requested, GSI diagnostic file directories for use later
-if [[ "${GENDIAG}" == "YES" ]]; then
-    # Move the gsidiags dir.* directories to pCOMOUT_ATMOS_ANALYSIS for diagnostic jobs
-    # First, check that the directories exist (we need at least one, so stop after the first match)
-    # shellcheck disable=SC2312
-    count_dirs=$(find . -maxdepth 1 -type d -name 'dir.????' -printf "." -quit | wc -c)
-    if [[ ${count_dirs:-0} -gt 0 ]]; then
-        mkdir -p "${GSIDIAGDIR}"
-        err=$?
-
-        if [[ ! -d "${GSIDIAGDIR}" || ${err} -ne 0 ]]; then
-            err_exit "Failed to create gsidiags directory at ${GSIDIAGDIR}"
-        fi
-
-        for dir in dir.????; do
-            mv "${dir}" "${GSIDIAGDIR}/"
-            export err=$?
-            if [[ ${err} -ne 0 ]]; then
-                err_exit "Failed to move ${dir} to ${GSIDIAGDIR}/"
-            fi
-        done
-    else
-        echo "WARNING: No gsidiags dir.* directories found to move."
-    fi
-fi
-
 ################################################################################
 
 exit "${err}"

dev/workflow/generate_workflows.sh

@@ -182,6 +182,18 @@ function send_email() {
     echo "${_body}" | mail -s "${_subject}" "${_email}"
 }
 
+# Function to notify user about REPLYTO for scrontab workflows
+function mail_warning() {
+    if [[ "${_use_scron}" == true && "${_set_email}" == false && -z "${REPLYTO:-}" ]]; then
+        echo -e "\033[0;33mWARNING:\033[0m Set \033[0;32mexport REPLYTO=\"your_email\"\033[0m in your .bashrc or use generate_workflows.sh with \033[0;32m-e \"your_email\"\033[0m to receive job failure notifications."
+    fi
+}
+
+# Export REPLYTO if email was provided via -e flag and is not empty
+if [[ "${_set_email}" == "true" && -n "${_email}" ]]; then
+    export REPLYTO="${_email}"
+fi
+
 function delete_dir() {
     local dir_to_rm="${1:-}"
     if [[ -z "${dir_to_rm}" ]]; then
@@ -577,20 +589,35 @@ for _case in "${_yaml_list[@]}"; do
 
     if [[ "${_use_scron}" == true ]]; then
         {
-            grep "^#.*${_pslot}" "${_runtests}/EXPDIR/${_pslot}/${_pslot}.crontab"
+            grep "^####" "${cron_file}"
             grep "^#SCRON" "${cron_file}"
-            grep "${scron_sh_file}" "${_runtests}/EXPDIR/${_pslot}/${_pslot}.crontab"
+            grep "${scron_sh_file}" "${cron_file}"
         } >> tests.cron
     else
         grep "${_pslot}" "${_runtests}/EXPDIR/${_pslot}/${_pslot}.crontab" >> tests.cron
     fi
 done
 echo
 
+# Add MAILTO to tests.cron for regular crontab
+if [[ "${_use_scron}" == false ]]; then
+    if [[ "${_set_email}" == "true" ]]; then
+        # Use email from -e flag
+        sed -i "1i MAILTO=\"${_email}\"" tests.cron
+    elif [[ -n "${REPLYTO:-}" ]]; then
+        # Use REPLYTO environment variable
+        sed -i "1i MAILTO=\"${REPLYTO}\"" tests.cron
+    else
+        # Use empty MAILTO
+        sed -i "1i MAILTO=\"\"" tests.cron
+    fi
+fi
+
 # Update the cron
 if [[ "${_update_cron}" == "true" ]]; then
     printf "Updating the existing crontab\n\n"
     echo
+    mail_warning
     rm -f existing.cron final.cron "${_verbose_flag}"
     touch existing.cron final.cron
 
@@ -603,16 +630,43 @@ if [[ "${_update_cron}" == "true" ]]; then
         echo "#######################"
     fi
 
+    # Save existing MAILTO before removing it
+    # shellcheck disable=SC2312
+    existing_mailto=$(grep "^MAILTO=" existing.cron 2> /dev/null | head -1 || echo "")
+
+    # Remove ALL MAILTO lines from existing.cron and tests.cron to prevent duplicates
+    sed -i '/^MAILTO=/d' existing.cron 2> /dev/null || true
+    sed -i '/^MAILTO=/d' tests.cron 2> /dev/null || true
+
     if [[ "${_set_email}" == "true" ]]; then
-        # Replace the existing email in the crontab
+        # For scrontab, REPLYTO is already exported earlier; for crontab, set MAILTO
         if [[ "${_verbose}" == "true" ]]; then
             printf "Updating crontab/scrontab email to %s\n\n" "${_email}"
         fi
 
-        if [[ "${_use_scron}" == true ]]; then
-            sed -i "s/.*--mail-user.*/#SCRON --mail-user=\"${_email}\"/" tests.cron
-        else
-            sed -i "s/^MAILTO.*/MAILTO=\"${_email}\"/" existing.cron
+        if [[ "${_use_scron}" == false ]]; then
+            # For regular crontab, set MAILTO at the top of final.cron
+            echo "MAILTO=\"${_email}\"" > final.cron
+        fi
+    else
+        # Preserve existing MAILTO if present with non-empty value (only for regular crontab)
+        if [[ "${_use_scron}" == false ]]; then
+            # Check if there was a MAILTO with a non-empty value in the original crontab
+            # Extract the email value from MAILTO="email" or MAILTO=email
+            if [[ -n "${existing_mailto}" ]]; then
+                # Extract email value between quotes or after =
+                existing_email=$(echo "${existing_mailto}" | sed -n 's/^MAILTO=["'\'']*\([^"'\'']*\)["'\'']*$/\1/p')
+            else
+                existing_email=""
+            fi
+
+            if [[ -n "${existing_email}" ]]; then
+                echo "${existing_mailto}" > final.cron
+            elif [[ -n "${REPLYTO:-}" ]]; then
+                echo "MAILTO=\"${REPLYTO}\"" > final.cron
+            else
+                echo "MAILTO=\"\"" > final.cron
+            fi
         fi
     fi
 
@@ -627,10 +681,12 @@ if [[ "${_update_cron}" == "true" ]]; then
 
     ${_crontab_cmd} final.cron
 else
+    mail_warning
     _message="Add the following to your crontab or scrontab to start running:"
     _cron_tests=$(cat tests.cron)
     _message="${_message}"$'\n'"${_cron_tests}"
     echo "${_message}"
+    echo
     if [[ "${_set_email}" == true ]]; then
         final_message="${final_message:-}"$'\n'"${_message}"
     fi

dev/workflow/rocoto/rocoto_scron.sh.j2

@@ -0,0 +1,74 @@
+#! /usr/bin/env bash
+source "{{ HOMEgfs }}/dev/ush/gw_setup.sh"
+
+# Run rocotorun
+bash -c "{{ rocotorunstr }}"
+
+# Monitor for failed jobs using rocotostat
+LOCKFILE="{{ expdir }}/.failed_jobs.lock"
+ROCOTOSTAT=$(command -v rocotostat)
+
+if [[ -n "${ROCOTOSTAT}" ]]; then
+    # shellcheck disable=SC2312
+    FAILED_JOBS=$(${ROCOTOSTAT} -d "{{ expdir }}/{{ pslot }}.db" -w "{{ expdir }}/{{ pslot }}.xml" -c all 2> /dev/null | grep -E 'DEAD')
+
+    if [[ -n "${FAILED_JOBS}" ]]; then
+        # Read previously reported failures
+        PREV_FAILED=""
+        if [[ -f "${LOCKFILE}" ]]; then
+            PREV_FAILED=$(cat "${LOCKFILE}")
+        fi
+
+        # Check for NEW failures only (not just changes)
+        NEW_FAILURES=""
+        while IFS= read -r job; do
+            if [[ -n "${job}" ]] && ! echo "${PREV_FAILED}" | grep -qF "${job}"; then
+                NEW_FAILURES="${NEW_FAILURES}${job}"$'\n'
+            fi
+        done <<< "${FAILED_JOBS}"
+
+        # Send email only if there are NEW failures
+        if [[ -n "${NEW_FAILURES}" ]]; then
+            MSGFILE="/tmp/rocoto_fail_msg_$$.txt"
+            {
+                echo "The following jobs have failed in experiment {{ pslot }} on ${MACHINE_ID}:"
+                echo ""
+
+                # Format each failed job with detailed information
+                while IFS= read -r line; do
+                    if [[ -n "${line}" ]]; then
+                        # Parse rocotostat output: Cycle Task JobID State Try MaxTries Duration
+                        read -r cycle task jobid state try maxtries duration <<< "${line}"
+                        # Extract YYYYMMDDHH from cycle (first 10 characters)
+                        cycle_short=${cycle:0:10}
+                        # Get current timestamp
+                        timestamp=$(date -u '+%m/%d/%y %H:%M:%S UTC')
+
+                        # Format similar to user's example
+                        echo "${timestamp} :: {{ pslot }}.xml :: Cycle ${cycle}, Task ${task}, jobid=${jobid}, in state ${state}, ran for ${duration} seconds, try=${try} (of ${maxtries})"
+                        echo "Check log: {{ comroot }}/{{ pslot }}/logs/${cycle_short}/${task}.log"
+                        echo ""
+                    fi
+                done <<< "${NEW_FAILURES}"
+            } > "${MSGFILE}"
+
+            # Try to send email
+            EMAIL="{{ replyto }}"
+            hostname_domain=$(hostname -d)
+            FROM_EMAIL="no-reply@${hostname_domain}"
+            if [[ "${EMAIL}" != "None" ]] && command -v mail &> /dev/null; then
+                # On Gaea, the mail utility requires the -v (verbose) flag to ensure delivery.
+                # To avoid receiving verbose output as an actual email, a spoofed 'from' address is used for notifications.
+                mail -r "${FROM_EMAIL}" -v -s "[{{ pslot }}] Workflow Job Failures Detected" "${EMAIL}" < "${MSGFILE}" 2>&1
+            fi
+
+            rm -f "${MSGFILE}"
+        fi
+
+        # Always update lockfile to reflect current failures
+        echo "${FAILED_JOBS}" > "${LOCKFILE}"
+    else
+        # No failures, remove lockfile if it exists
+        [[ -f "${LOCKFILE}" ]] && rm -f "${LOCKFILE}"
+    fi
+fi

dev/workflow/rocoto/rocoto_xml.py

@@ -8,7 +8,7 @@
 from applications.applications import AppConfig
 from workflow_suite import WorkflowSuite
 from rocoto.workflow_tasks import get_wf_tasks
-from wxflow import which, mkdir
+from wxflow import which, mkdir, parse_j2tmpl
 import rocoto.rocoto as rocoto
 from abc import ABC, abstractmethod
 from logging import getLogger
@@ -123,6 +123,36 @@ def write(self, xml_file: str = None, crontab_file: str = None):
         if self._base["DO_ARCHCOM"] and self._base["ARCHCOM_TO"] == "globus_hpss":
             self._write_server_crontab()
 
+    def _get_scron_script_content(self, rocotorunstr: str, replyto: str) -> str:
+        """
+        Load and format the cron script template with experiment-specific values.
+
+        Parameters
+        ----------
+        rocotorunstr : str
+            The rocotorun command string
+        replyto : str
+            Email address for notifications
+
+        Returns
+        -------
+        str
+            Formatted bash script content
+        """
+        template_path = os.path.join(os.path.dirname(__file__), 'rocoto_scron.sh.j2')
+
+        # Format the template with experiment-specific values
+        context = {
+            'HOMEgfs': self.HOMEgfs,
+            'rocotorunstr': rocotorunstr,
+            'expdir': self.expdir,
+            'pslot': self.pslot,
+            'replyto': replyto,
+            'comroot': self._base.get('COMROOT')
+        }
+        template_content = parse_j2tmpl(template_path, context)
+        return template_content
+
     def _write_xml(self, xml_file: str = None) -> None:
 
         if xml_file is None:
@@ -147,8 +177,7 @@ def _write_crontab(self, crontab_file: str = None, cronint: int = 5) -> None:
         rocotorunstr = f'{rocotoruncmd} -d {self.expdir}/{self.pslot}.db -w {self.expdir}/{self.pslot}.xml'
         cronintstr = f'*/{cronint} * * * *'
 
-        replyto = os.environ.get('REPLYTO', "")
-
+        replyto = os.environ.get('REPLYTO', None)
         crontab_strings = [
             '',
             f'#################### {self.pslot} ####################'
@@ -169,27 +198,22 @@ def _write_crontab(self, crontab_file: str = None, cronint: int = 5) -> None:
             crontab_strings.extend([
                 f'#SCRON --partition={partition}',
                 f'#SCRON --account={account}',
-                f'#SCRON --mail-user={replyto}',
                 f'#SCRON --job-name={self.pslot}_scron',
                 f'#SCRON --output={self.expdir}/logs/scron.log',
-                '#SCRON --time=00:10:00',
-                '#SCRON --dependency=singleton'
+                f'#SCRON --time=00:10:00',
+                f'#SCRON --dependency=singleton'
             ])
 
-            # Now write the script that actually runs rocotorun
+            # Now write the script that actually runs rocotorun and monitors for failures
             cron_cmd = f"{self.expdir}/{self.pslot}.scron.sh"
             with open(cron_cmd, "w") as script_fh:
-                script_fh.write(
-                    "#!/usr/bin/env bash\n" +
-                    "set -x\n" +
-                    f"source {self.HOMEgfs}/dev/ush/gw_setup.sh" + "\n" +
-                    rocotorunstr + "\n"
-                )
+                script_fh.write(self._get_scron_script_content(rocotorunstr, replyto))
 
             # Make the script executable
             mode = os.stat(cron_cmd)
             os.chmod(cron_cmd, mode.st_mode | stat.S_IEXEC)
         else:
+            # For regular crontab, create a wrapper script with monitoring
             cron_cmd = rocotorunstr
             crontab_strings.extend([
                 'SHELL="/bin/bash"',