From 0baef72b56ff364de7e328864cb5243a7d26ebfa Mon Sep 17 00:00:00 2001
From: dougiesquire <dougiesquire@gmail.com>
Date: Fri, 2 Aug 2024 20:39:25 +1000
Subject: [PATCH] Use Payu userscripts from om3-scripts
 (https://github.com/COSIMA/access-om3/issues/182) to: - work-around symlink
 restart bug in CICE - concatenate CICE daily output - auto-generate an
 intake-esm datastore

---
 archive_cice_restarts.sh | 12 ------------
 config.yaml              | 12 ++++++++++--
 setup_cice_restarts.sh   | 13 -------------
 3 files changed, 10 insertions(+), 27 deletions(-)
 delete mode 100755 archive_cice_restarts.sh
 delete mode 100755 setup_cice_restarts.sh

diff --git a/archive_cice_restarts.sh b/archive_cice_restarts.sh
deleted file mode 100755
index 10acde4..0000000
--- a/archive_cice_restarts.sh
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/bin/bash
-# clean up cice_restarts.sh
-
-if [ -f archive/output*/access-om3.cice.r.* ]
-then
-rm archive/output*/access-om3.cice.r.*
-fi
-
-if [ -f archive/output*/input/iced.1900-01-01-10800.nc ] 
-then
-rm archive/output*/input/iced.1900-01-01-10800.nc
-fi
diff --git a/config.yaml b/config.yaml
index e640514..77dac1e 100644
--- a/config.yaml
+++ b/config.yaml
@@ -48,5 +48,13 @@ metadata:
     enable: false
 
 userscripts:
-    setup: ./setup_cice_restarts.sh
-    archive: ./archive_cice_restarts.sh
+    setup: /usr/bin/bash /g/data/vk83/apps/om3-scripts/payu_config/setup.sh
+    archive: /usr/bin/bash /g/data/vk83/apps/om3-scripts/payu_config/archive.sh
+
+modules:
+    use:
+        - /g/data/ik11/spack/0.21.2/modules/access-om3/0.x.0/linux-rocky8-cascadelake
+        - /g/data/hh5/public/modules
+    load:
+        - access-om3/63ed4a4777aeac0c62720ddbe7f85e4ed16f82eb_main
+        - conda/analysis3-24.01
diff --git a/setup_cice_restarts.sh b/setup_cice_restarts.sh
deleted file mode 100755
index e800e07..0000000
--- a/setup_cice_restarts.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/bin/bash
-# patch for https://github.com/open-mpi/ompi/issues/12141
-if ! [ -f work/access-om3.cice.r.* ]
-then 
-# no restart files yet, use initial conditions
-IC=$(readlink work/input/iced.1900-01-01-10800.nc)
-rm work/input/iced.1900-01-01-10800.nc
-cp $IC work/input/iced.1900-01-01-10800.nc
-else
-# change restart symlink to hardlink
-RESTART=$(echo work/access-om3.cice.r.*)
-ln -f $(readlink $RESTART) $RESTART
-fi