From 27c5a2825642eafe75e26e1cf6e555a7b05027ce Mon Sep 17 00:00:00 2001
From: Aaron Donahue <donahue.aaron@gmail.com>
Date: Fri, 21 Aug 2026 11:58:43 -0700
Subject: [PATCH 1/2] Fix Flux batch system command-line arguments

Update Flux batch configuration to use correct command-line flags:
- Change --time to --time-limit for time specification
- Change --queue to -q for queue selection
- Change --bank to -B for bank/account specification
- Replace hardcoded 60m with $JOB_WALLCLOCK_TIME variable

These changes align with Flux batch system syntax and allow proper
walltime configuration from case XML variables.

Co-Authored-By: Claude <noreply@anthropic.com>
---
 cime_config/machines/config_batch.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/cime_config/machines/config_batch.xml b/cime_config/machines/config_batch.xml
index f884ca88450a..cd1923668765 100644
--- a/cime_config/machines/config_batch.xml
+++ b/cime_config/machines/config_batch.xml
@@ -239,9 +239,9 @@
     <depend_separator>:</depend_separator>
     <walltime_format>%Mm</walltime_format>
     <submit_args>
-      <arg flag="--time" name="60m"/>
-      <arg flag="--queue" name="$JOB_QUEUE"/>
-      <arg flag="--bank" name="$PROJECT"/>
+      <arg flag="--time-limit" name="$JOB_WALLCLOCK_TIME"/>
+      <arg flag="-q" name="$JOB_QUEUE"/>
+      <arg flag="-B" name="$PROJECT"/>
     </submit_args>
     <directives>
       <directive> --job-name={{ job_id }}</directive>

From 1bec203f43aa28b505ed4c49354632fcb92ff440 Mon Sep 17 00:00:00 2001
From: Aaron Donahue <donahue.aaron@gmail.com>
Date: Fri, 21 Aug 2026 11:59:05 -0700
Subject: [PATCH 2/2] Fix tuo_crayamd-mphipcc cmake configuration for threading
 and linking

Add missing compiler flags for tuo machine with crayamd-mphipcc compiler:
- Add OpenMP threading support via -fopenmp flags for C, C++, Fortran,
  and linker when compile_threaded is enabled
- Add -DFORTRANUNDERSCORE and -DNO_R16 to CPPDEFS for proper Fortran/C
  interoperability and to match standard Cray compiler configurations

These flags resolve linking errors:
- Undefined references to OpenMP functions (omp_get_thread_num, etc.)
  in GPTL library when building threaded executables
- Undefined references to shr_reprosumx86_fix_start/end functions due
  to Fortran/C name mangling mismatch

The configuration now aligns with other Cray machine configs like
craycray-mphipcc.cmake and frontier_craycray-mphipcc.cmake.

Co-Authored-By: Claude <noreply@anthropic.com>
---
 .../machines/cmake_macros/tuo_crayamd-mphipcc.cmake      | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/cime_config/machines/cmake_macros/tuo_crayamd-mphipcc.cmake b/cime_config/machines/cmake_macros/tuo_crayamd-mphipcc.cmake
index 0fe97c35cefc..77d1be0648d1 100644
--- a/cime_config/machines/cmake_macros/tuo_crayamd-mphipcc.cmake
+++ b/cime_config/machines/cmake_macros/tuo_crayamd-mphipcc.cmake
@@ -10,12 +10,19 @@ set(SCC  "${MPICC}")
 set(SCXX "${MPICXX}")
 set(SFC  "${MPIFC}")
 
+if (compile_threaded)
+  string(APPEND CMAKE_C_FLAGS " -fopenmp")
+  string(APPEND CMAKE_Fortran_FLAGS " -fopenmp")
+  string(APPEND CMAKE_CXX_FLAGS " -fopenmp")
+  string(APPEND CMAKE_EXE_LINKER_FLAGS " -fopenmp")
+endif()
+
 if (COMP_NAME STREQUAL gptl)
 	string(APPEND CPPDEFS " -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY")
 endif()
 
 # required to resolve bshr_infnan_mod.F90 compile issue
-string(APPEND CPPDEFS " -DCPRCRAY")
+string(APPEND CPPDEFS " -DFORTRANUNDERSCORE -DNO_R16 -DCPRCRAY")
 
 set(USE_HIP "TRUE")