From 94a43fe965c174725420b7b148b20bb1e6b0e7ff Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Mon, 9 Feb 2026 12:56:18 -0500
Subject: [PATCH 1/4] Create dir.* directories and link instead of moving

---
 dev/scripts/exglobal_atmos_analysis.sh | 35 ++++++++------------------
 1 file changed, 11 insertions(+), 24 deletions(-)

diff --git a/dev/scripts/exglobal_atmos_analysis.sh b/dev/scripts/exglobal_atmos_analysis.sh
index eb2d0e557ab..5a4634ccf39 100755
--- a/dev/scripts/exglobal_atmos_analysis.sh
+++ b/dev/scripts/exglobal_atmos_analysis.sh
@@ -670,6 +670,17 @@ 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)
+    for task in $(seq 1 "${NTASKS_GSI}"); 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
@@ -907,30 +918,6 @@ fi
 
 echo "${rCDUMP} ${PDY}${cyc} atminc done at $(date)" > "${COMOUT_ATMOS_ANALYSIS}/${APREFIX}increment.done.txt"
 
-if [[ "${GENDIAG}" == "YES" ]]; then
-    # Move the gsidiags dir.* directories to pCOMOUT_ATMOS_ANALYSIS for diagnostic jobs
-    # First, check that the directories exist (we need at least one, so stop after the first match)
-    count_dirs=$(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}"

From 865aa51603974d1d8afaede7dc580b59f16d55fd Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Thu, 12 Feb 2026 10:34:04 -0500
Subject: [PATCH 2/4] Remove GSIDIAGDIR before re-populating it; correct
 dir.XXXX numbering

---
 dev/scripts/exglobal_atmos_analysis.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/dev/scripts/exglobal_atmos_analysis.sh b/dev/scripts/exglobal_atmos_analysis.sh
index 5a4634ccf39..1668a5dfbdc 100755
--- a/dev/scripts/exglobal_atmos_analysis.sh
+++ b/dev/scripts/exglobal_atmos_analysis.sh
@@ -421,6 +421,8 @@ 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
 
 ##############################################################
@@ -674,7 +676,7 @@ fi
 # 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)
-    for task in $(seq 1 "${NTASKS_GSI}"); do
+    for task in $(seq 0 $((ntasks - 1))); do
         dir="dir.$(printf %04d "${task}")"
         mkdir -p "${GSIDIAGDIR}/${dir}"
         ${NLN} "${GSIDIAGDIR}/${dir}" "./${dir}"

From 663dfded700bd21a4978c0d3cd6163b731dab1c6 Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Thu, 12 Feb 2026 11:16:58 -0500
Subject: [PATCH 3/4] Add one more mkdir

---
 dev/scripts/exglobal_atmos_analysis.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/dev/scripts/exglobal_atmos_analysis.sh b/dev/scripts/exglobal_atmos_analysis.sh
index 1668a5dfbdc..72f0319b1b0 100755
--- a/dev/scripts/exglobal_atmos_analysis.sh
+++ b/dev/scripts/exglobal_atmos_analysis.sh
@@ -675,8 +675,9 @@ 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)
-    for task in $(seq 0 $((ntasks - 1))); do
+    # 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}"

From 5f8c4a2572ed81f004502929b1f168de64469961 Mon Sep 17 00:00:00 2001
From: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Thu, 12 Feb 2026 11:39:44 -0500
Subject: [PATCH 4/4] Double-quote ntasks

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 dev/scripts/exglobal_atmos_analysis.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev/scripts/exglobal_atmos_analysis.sh b/dev/scripts/exglobal_atmos_analysis.sh
index 72f0319b1b0..94314be9e95 100755
--- a/dev/scripts/exglobal_atmos_analysis.sh
+++ b/dev/scripts/exglobal_atmos_analysis.sh
@@ -677,7 +677,7 @@ fi
 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
+    for task in $(seq 0 "${ntasks}"); do
         dir="dir.$(printf %04d "${task}")"
         mkdir -p "${GSIDIAGDIR}/${dir}"
         ${NLN} "${GSIDIAGDIR}/${dir}" "./${dir}"