From 80eca356c2f26ec3593f1b85b8784b4353baa1bf Mon Sep 17 00:00:00 2001
From: Elynn Wu <elynn510@gmail.com>
Date: Wed, 20 Dec 2023 14:00:43 -0800
Subject: [PATCH] enable ruby to execucte ML corrected run

---
 cime_config/machines/config_machines.xml              | 11 +++++++----
 components/eamxx/cmake/machine-files/ruby-intel.cmake |  5 +++++
 components/eamxx/scripts/machines_specs.py            |  2 +-
 3 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/cime_config/machines/config_machines.xml b/cime_config/machines/config_machines.xml
index 05d535e3be8..2770be42069 100644
--- a/cime_config/machines/config_machines.xml
+++ b/cime_config/machines/config_machines.xml
@@ -2690,16 +2690,19 @@
         <command name="load">intel-classic/2021.6.0-magic</command>
         <command name="load">mvapich2/2.3.7</command>
         <command name="load">cmake/3.19.2</command>
-        <command name="load">netcdf-fortran-parallel/4.6.0</command>
-        <command name="load">netcdf-c-parallel/4.9.0</command>
+        <command name="use --append">/usr/gdata/climdat/install/quartz/modulefiles</command>
+        <command name="load">hdf5/1.12.2</command>
+        <command name="load">netcdf-c/4.9.0</command>
+        <command name="load">netcdf-fortran/4.6.0</command>
         <command name="load">parallel-netcdf/1.12.3</command>
+        <command name="load">screamML-venv/0.0.1</command>
       </modules>
     </module_system>
     <RUNDIR>$CIME_OUTPUT_ROOT/$CASE/run</RUNDIR>
     <EXEROOT>$CIME_OUTPUT_ROOT/$CASE/bld</EXEROOT>
     <environment_variables compiler="intel">
-      <env name="NETCDF_PATH">/usr/tce/packages/netcdf-fortran/netcdf-fortran-4.6.0-mvapich2-2.3.7-intel-classic-2021.6.0/</env>
-      <env name="PNETCDF_PATH">/usr/tce/packages/parallel-netcdf/parallel-netcdf-1.12.3-mvapich2-2.3.7-intel-classic-2021.6.0/</env>
+      <env name="NETCDF_PATH">/usr/gdata/climdat/install/quartz/netcdf-fortran/</env>
+      <env name="PNETCDF_PATH">/usr/tce/packages/parallel-netcdf/parallel-netcdf-1.12.3-mvapich2-2.3.7-intel-classic-2021.6.0</env>
     </environment_variables>
   </machine>
 
diff --git a/components/eamxx/cmake/machine-files/ruby-intel.cmake b/components/eamxx/cmake/machine-files/ruby-intel.cmake
index dea1354ca07..63fff478fda 100644
--- a/components/eamxx/cmake/machine-files/ruby-intel.cmake
+++ b/components/eamxx/cmake/machine-files/ruby-intel.cmake
@@ -1,2 +1,7 @@
 include(${CMAKE_CURRENT_LIST_DIR}/ruby.cmake)
 set(CMAKE_EXE_LINKER_FLAGS "-L/usr/tce/packages/mkl/mkl-2022.1.0/lib/intel64/ -qmkl" CACHE STRING "" FORCE)
+set(PYTHON_EXECUTABLE "/usr/tce/packages/python/python-3.9.12/bin/python3" CACHE STRING "" FORCE)
+set(PYTHON_LIBRARIES "/usr/lib64/libpython3.9.so.1.0" CACHE STRING "" FORCE)
+option (SCREAM_ENABLE_ML_CORRECTION "Whether to enable ML correction parametrization" ON)
+set(HDF5_DISABLE_VERSION_CHECK 1 CACHE STRING "" FORCE)
+execute_process(COMMAND source /usr/WS1/climdat/python_venv/3.9.2/screamML/bin/activate)
diff --git a/components/eamxx/scripts/machines_specs.py b/components/eamxx/scripts/machines_specs.py
index 373a13c5aa3..cd717cba6b9 100644
--- a/components/eamxx/scripts/machines_specs.py
+++ b/components/eamxx/scripts/machines_specs.py
@@ -37,7 +37,7 @@
                 ["mpicxx","mpifort","mpicc"],
                  "bsub -Ip -qpdebug",
                  ""),
-    "ruby-intel" : (["module --force purge", "module load StdEnv cmake/3.19.2 mkl/2022.1.0 intel-classic/2021.6.0-magic netcdf-c-parallel/4.9.0 netcdf-fortran-parallel/4.6.0 mvapich2/2.3.7 parallel-netcdf/1.12.3 python/3.9.12"],
+    "ruby-intel" : (["module --force purge", "module use --append /usr/gdata/climdat/install/quartz/modulefiles", "module load StdEnv cmake/3.19.2 mkl/2022.1.0 intel-classic/2021.6.0-magic mvapich2/2.3.7 hdf5/1.12.2 netcdf-c/4.9.0 netcdf-fortran/4.6.0 parallel-netcdf/1.12.3 python/3.9.12 screamML-venv/0.0.1"],
                  ["mpicxx","mpifort","mpicc"],
                   "salloc --partition=pdebug",
                   ""),