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Bring in -check all and -ftrapuv to DEBUG intelllvm builds#1256

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WenMeng-NOAA merged 23 commits into
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BrianCurtis-NOAA:nco_debug_changes
Aug 6, 2025
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Bring in -check all and -ftrapuv to DEBUG intelllvm builds#1256
WenMeng-NOAA merged 23 commits into
NOAA-EMC:developfrom
BrianCurtis-NOAA:nco_debug_changes

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@BrianCurtis-NOAA
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Bring in NCO DEBUG flag change for ops implement in intelllvm as well

The following flags will be added for DEBUG builds: -check all -check noarg_temp_created -ftrapuv

Two are required by NCO: -check all -ftrapuv
One will drastically reduce build output file size: -check noarg_temp_created

I've tested the build on the UFSWM. I will run the full UFSWM RT suite soon to ensure the build change does not impact results. I do not anticipate any changes.

@BrianCurtis-NOAA
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@WenMeng-NOAA Does any of the UPP testing check the debug builds for success? Is there UPP tests that run all debug builds to completion? If so, I wouldn't object to adding these changes however you see necessary.

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@WenMeng-NOAA Does any of the UPP testing check the debug builds for success? Is there UPP tests that run all debug builds to completion? If so, I wouldn't object to adding these changes however you see necessary.

I will run the build test in debug mode on Ursa.

@WenMeng-NOAA
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@BrianCurtis-NOAA My build test failed on Ursa with the intelllvm compiler and debug mode enabled. Here are my procedure:

> cd UPP/tests
> ./compile_upp.sh -c intelllvm -v -d

Here are the error message:

ld: cannot find -lm
ld: attempted static link of dynamic object `/contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/netcdf-fortran-4.6.1-5fzfhfs/lib/libnetcdff.so'
make[2]: *** [sorc/ncep_post.fd/CMakeFiles/upp.x.dir/build.make:327: sorc/ncep_post.fd/upp.x] Error 1
make[2]: Leaving directory '/scratch4/NCEPDEV/stmp/Wen.Meng/Brian/UPP/tests/build'
make[1]: *** [CMakeFiles/Makefile2:141: sorc/ncep_post.fd/CMakeFiles/upp.x.dir/all] Error 2
make[1]: Leaving directory '/scratch4/NCEPDEV/stmp/Wen.Meng/Brian/UPP/tests/build'
make: *** [Makefile:136: all] Error 2

Can you take a look at that?

@BrianCurtis-NOAA
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I've been successful on Hera with intel with that command, i'll try Ursa intelllvm next.

@BrianCurtis-NOAA
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@jkbk2004 it looks like the spack build might have an issue for intelllvm 1.9.2 on Ursa?

[100%] Linking Fortran executable upp.x
cd /scratch4/NCEPDEV/nems/Brian.Curtis/git/BrianCurtis-NOAA/ufs-weather-model/nco_debug_changes/FV3/upp/tests/build/sorc/ncep_post.fd && /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/cmake-3.27.9-ggd7nbu/bin/cmake -E cmake_link_script CMakeFiles/upp.x.dir/link.txt --verbose=1
/apps/spack-2024-12/linux-rocky9-x86_64/oneapi-2024.2.1/intel-oneapi-mpi-2021.13.1-ss72gbndvat3oz22sa6lhmlbjkeabrn4/mpi/2021.13/bin/mpiifx -fiopenmp -g -traceback -fp-model precise -free -convert big_endian -O0 -check all -check noarg_temp_created -ftrapuv CMakeFiles/upp.x.dir/INITPOST.F.o CMakeFiles/upp.x.dir/INITPOST_MPAS.F.o CMakeFiles/upp.x.dir/INITPOST_NETCDF.f.o CMakeFiles/upp.x.dir/WRFPOST.F.o CMakeFiles/upp.x.dir/getIVariableN.f.o CMakeFiles/upp.x.dir/getVariable.f.o CMakeFiles/upp.x.dir/getlvls.f.o CMakeFiles/upp.x.dir/intio_tags.f.o CMakeFiles/upp.x.dir/retrieve_index.f.o CMakeFiles/upp.x.dir/wrf_io_flags.f.o CMakeFiles/upp.x.dir/ASSIGNNEMSIOVAR.f.o CMakeFiles/upp.x.dir/GETNEMSNDSCATTER.f.o CMakeFiles/upp.x.dir/GFSPOSTSIG.F.o CMakeFiles/upp.x.dir/INITPOST_GFS_NEMS_MPIIO.f.o CMakeFiles/upp.x.dir/INITPOST_NEMS.f.o -o upp.x   -L/apps/spack-2024-12/linux-rocky9-x86_64/gcc-11.4.1/intel-oneapi-compilers-2024.2.1-oqhstbmawnrsdw472p4pjsopj547o6xs/compiler/2024.2/opt/compiler/lib  -Wl,-rpath,/contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/libpng-1.6.37-ghg5tyw/lib64:/contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/zlib-1.2.13-mkqknv7/lib:/contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/jasper-2.0.32-6xwcnqt/lib64:/contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/libjpeg-turbo-2.1.0-qxbwasr/lib64:/contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/netcdf-fortran-4.6.1-5fzfhfs/lib:/contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/netcdf-c-4.9.2-idnwcbr/lib: libupp.a /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/w3emc-2.10.0-o27swxn/lib64/libw3emc_4.a /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/ip-5.1.0-wbal3sn/lib64/libip_4.a /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/nemsio-2.5.4-usa45yy/lib64/libnemsio.a /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/sigio-2.3.3-ijtj4go/lib64/libsigio.a /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/wrf-io-1.2.0-vayxo2a/lib/libwrf_io.a /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/crtm-2.4.0.1-6cyxlcc/lib/libcrtm.a /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/g2-3.5.1-6onncjm/lib64/libg2_4.a /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/libpng-1.6.37-ghg5tyw/lib64/libpng.so /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/zlib-1.2.13-mkqknv7/lib/libz.so /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/jasper-2.0.32-6xwcnqt/lib64/libjasper.so /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/libjpeg-turbo-2.1.0-qxbwasr/lib64/libjpeg.so /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/g2tmpl-1.13.0-5mqi7bs/lib64/libg2tmpl.a /apps/spack-2024-12/linux-rocky9-x86_64/oneapi-2024.2.1/intel-oneapi-mkl-2024.2.1-xnoyobr3t3tov375bqiwzuue5fbtjixa/mkl/2024.2/lib/libmkl_intel_lp64.so /apps/spack-2024-12/linux-rocky9-x86_64/oneapi-2024.2.1/intel-oneapi-mkl-2024.2.1-xnoyobr3t3tov375bqiwzuue5fbtjixa/mkl/2024.2/lib/libmkl_intel_thread.so /apps/spack-2024-12/linux-rocky9-x86_64/oneapi-2024.2.1/intel-oneapi-mkl-2024.2.1-xnoyobr3t3tov375bqiwzuue5fbtjixa/mkl/2024.2/lib/libmkl_core.so /apps/spack-2024-12/linux-rocky9-x86_64/gcc-11.4.1/intel-oneapi-compilers-2024.2.1-oqhstbmawnrsdw472p4pjsopj547o6xs/compiler/2024.2/lib/libiomp5.so -lm -ldl /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/w3emc-2.10.0-o27swxn/lib64/libw3emc_4.a /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/bacio-2.4.1-ah7c33v/lib/libbacio_4.a /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/netcdf-fortran-4.6.1-5fzfhfs/lib/libnetcdff.so -L/contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/netcdf-fortran-4.6.1-5fzfhfs/lib -lnetcdff -lnetcdf -lnetcdf -lm /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/netcdf-c-4.9.2-idnwcbr/lib/libnetcdf.so -L/contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/netcdf-c-4.9.2-idnwcbr/lib -lnetcdf -lirng 
ld: cannot find -lm
ld: attempted static link of dynamic object `/contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/netcdf-fortran-4.6.1-5fzfhfs/lib/libnetcdff.so'

@BrianCurtis-NOAA
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@WenMeng-NOAA this is also a problem in the current hash used in FV3 develop branch, FYI.

@BrianCurtis-NOAA BrianCurtis-NOAA marked this pull request as ready for review July 29, 2025 13:46
@gspetro-NOAA
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@RatkoVasic-NOAA @ulmononian Any chance you could look into these stack issues?

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I am seeing the same issues with Ursa intelllvm on both Brian's branch and in the UPP develop branch with spack-stack 1.9.1 and 1.9.2. The problem has existed since UPP was ported to Ursa LLVM via PR #1231 (commit 274b886). With that PR, it used spack-stack 1.9.1. The intel build on Ursa with HEAD of develop worked for me. No errors.

For the failed LLVM build, I ran:

git clone https://github.com/NOAA-EMC/UPP.git
cd UPP/tests
./compile_upp.sh -d -c intelllvm

which produced:

ld: cannot find -lm
ld: attempted static link of dynamic object `/contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/netcdf-fortran-4.6.1-5fzfhfs/lib/libnetcdff.so'
make[2]: *** [sorc/ncep_post.fd/CMakeFiles/upp.x.dir/build.make:327: sorc/ncep_post.fd/upp.x] Error 1
make[1]: *** [CMakeFiles/Makefile2:141: sorc/ncep_post.fd/CMakeFiles/upp.x.dir/all] Error 2
make: *** [Makefile:136: all] Error 2

@gspetro-NOAA
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In this PR, the -check all flag seems to be the source of the problem. When I change line 189 of CMakeLists.txt to say: set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check all") and run ./compile_upp.sh -d -c intelllvm, it produces the following error:

ld: cannot find -lm
ld: attempted static link of dynamic object `/contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/netcdf-fortran-4.6.1-5fzfhfs/lib/libnetcdff.so'
make[2]: *** [sorc/ncep_post.fd/CMakeFiles/upp.x.dir/build.make:327: sorc/ncep_post.fd/upp.x] Error 1
make[1]: *** [CMakeFiles/Makefile2:141: sorc/ncep_post.fd/CMakeFiles/upp.x.dir/all] Error 2
make: *** [Makefile:136: all] Error 2

When I run with only -check noarg_temp_created or only -ftrapuv, the UPP builds successfully on Ursa LLVM without issues. The ending output looks like this:

-- Installing: /scratch3/NAGAPE/epic/Gillian.Petro/ursa/RTs/upp-rts/1256-bc/sorc/ncep_post.fd/install/lib/cmake/upp/upp-targets-debug.cmake
+ [[ YES == YES ]]
+ rm -rf /scratch3/NAGAPE/epic/Gillian.Petro/ursa/RTs/upp-rts/1256-bc/exec
+ test -d /scratch3/NAGAPE/epic/Gillian.Petro/ursa/RTs/upp-rts/1256-bc/exec
+ mkdir -p /scratch3/NAGAPE/epic/Gillian.Petro/ursa/RTs/upp-rts/1256-bc/exec
+ cp ../install/bin/upp.x /scratch3/NAGAPE/epic/Gillian.Petro/ursa/RTs/upp-rts/1256-bc/exec/upp.x
+ [[ NO == YES ]]

@TaylorRoper-NOAA
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I am seeing the same issues with Ursa intelllvm on both Brian's branch and in the UPP develop branch with spack-stack 1.9.1 and 1.9.2. The problem has existed since UPP was ported to Ursa LLVM via PR #1231 (commit 274b886). With that PR, it used spack-stack 1.9.1. The intel build on Ursa with HEAD of develop worked for me. No errors.

For the failed LLVM build, I ran:

git clone https://github.com/NOAA-EMC/UPP.git
cd UPP/tests
./compile_upp.sh -d -c intelllvm

which produced:

ld: cannot find -lm
ld: attempted static link of dynamic object `/contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/netcdf-fortran-4.6.1-5fzfhfs/lib/libnetcdff.so'
make[2]: *** [sorc/ncep_post.fd/CMakeFiles/upp.x.dir/build.make:327: sorc/ncep_post.fd/upp.x] Error 1
make[1]: *** [CMakeFiles/Makefile2:141: sorc/ncep_post.fd/CMakeFiles/upp.x.dir/all] Error 2
make: *** [Makefile:136: all] Error 2

Hi all, I believe I saw a similar error when I was working on updating the cloud environments to work with both RDHPCS /apps stacks: #1211. I had to add paths to the LLVM linker, archiver, and ranlib for CMake:

set(CMAKE_AR "${LLVM_BIN}/llvm-ar" CACHE FILEPATH "")
set(CMAKE_RANLIB "${LLVM_BIN}/llvm-ranlib" CACHE FILEPATH "")
set(CMAKE_LINKER "${INTEL_COMPILER_BIN}/xild" CACHE FILEPATH "")

I'm not sure if this approach will help here, but wanted to mention in case it proves helpful.

@gspetro-NOAA
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@TaylorRoper-NOAA Thanks for this suggestion! I noticed that you ultimately removed that code block and file from the repo in PR #1260 . What prompted that? Did hard-coding the paths in the modulefiles solve the problem? Or is that an unrelated change?

Comment thread sorc/ncep_post.fd/CMakeLists.txt Outdated
@WenMeng-NOAA
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The following UPP build tests have been successfully completed on WCOSS2 with intel compiler:

  • compiling general UPP code in debug mode
  • compiling general UPP code along with ifi code in debug mode
  • compiling general UPP code along with gtg and ifi code in debug mode

@WenMeng-NOAA
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The UPP RTs have been completed on WCOSS2 without baseline changes.
@gspetro-NOAA This PR is ready for the UPP RTs on R&D machines. There should be no baseline changes.

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@WenMeng-NOAA I'll test once @BrianCurtis-NOAA makes Alex's requested change. Otherwise it won't pass when Ursa (LLVM) becomes available. ;)

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There is no need to rerun the UPP RTs on WCOSS2 since the UPP executable in the RTs is not build in debug mode.

gspetro-NOAA
gspetro-NOAA previously approved these changes Aug 6, 2025
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RTs pass without baseline changes without debug mode. Testing now with debug.

@gspetro-NOAA gspetro-NOAA dismissed their stale review August 6, 2025 03:37

Oops! Forgot to run tests WITH debug. Doing that now!

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gspetro-NOAA commented Aug 6, 2025

When I run the RTs on Ursa LLVM in debug mode, the tests are all exiting early with MemorySanitizer errors such as these from out.post.rrfs:

==46435==WARNING: MemorySanitizer: use-of-uninitialized-value
==46461==WARNING: MemorySanitizer: use-of-uninitialized-value
srun: error: u11c12: tasks 0-47: Exited with exit code 1
srun: Terminating StepId=1942938.0
forrtl: error (78): process killed (SIGTERM)

forrtl: error (78): process killed (SIGTERM)
Image              PC                Routine            Line        Source
upp_no_ifi.x       0000000000471B43  Unknown               Unknown  Unknown
libc.so.6          00007F7E5C2E9730  Unknown               Unknown  Unknown
upp_no_ifi.x       0000000000487232  Unknown               Unknown  Unknown
upp_no_ifi.x       00000000004895A4  Unknown               Unknown  Unknown
...
upp_no_ifi.x       0000000000491927  Unknown               Unknown  Unknown
upp_no_ifi.x       0000000000491CA9  Unknown               Unknown  Unknown
MemorySanitizer: nested bug in the same thread, aborting.
forrtl: error (78): process killed (SIGTERM)
Image              PC                Routine            Line        Source
upp_no_ifi.x       0000000000471B43  Unknown               Unknown  Unknown
libc.so.6          00007F5CD9E29730  Unknown               Unknown  Unknown
upp_no_ifi.x       0000000000487232  Unknown               Unknown  Unknown
upp_no_ifi.x       00000000004895A4  Unknown               Unknown  Unknown
...
upp_no_ifi.x       000000000040FC1A  Unknown               Unknown  Unknown
upp_no_ifi.x       0000000000424AB8  Unknown               Unknown  Unknown
libmpi.so.12.0.0   00007F7E5DFDF1A4  Unknown               Unknown  Unknown
libmpi.so.12.0.0   00007F7E5E1FFDCA  Unknown               Unknown  Unknown
libmpi.so.12.0.0   00007F7E5E1FFA7D  MPI_Init              Unknown  Unknown
libmpifort.so.12.  00007F7E67C2BECF  MPI_INIT              Unknown  Unknown
upp_no_ifi.x       0000000001EA2C28  mpi_init_.t164p             0  SETUP_SERVERS.f
upp_no_ifi.x       0000000001E9B35A  setup_servers              46  SETUP_SERVERS.f
upp_no_ifi.x       0000000000FE273E  setup_servers_.t3           0  WRFPOST.F

On Ursa Intel, there are also several errors, both ones similar to those above and others. For example, from out.post.sfs:

forrtl: error (65): floating invalid
Image              PC                Routine            Line        Source
libc.so.6          000014978EFEF730  Unknown               Unknown  Unknown
upp_no_ifi.x       000000000140D8EB  mdl2agl_                 1263  MDL2AGL.f
upp_no_ifi.x       0000000000B507A8  process_                   92  PROCESS.f
upp_no_ifi.x       0000000000734D74  MAIN__                    725  WRFPOST.F
upp_no_ifi.x       0000000000414DAD  Unknown               Unknown  Unknown
libc.so.6          000014978EFDA5D0  Unknown               Unknown  Unknown
libc.so.6          000014978EFDA680  __libc_start_main     Unknown  Unknown
upp_no_ifi.x       0000000000414CC5  Unknown               Unknown  Unknown
...
srun: error: u02c01: tasks 24-32,34-47: Aborted (core dumped)
srun: Terminating StepId=1942643.0
slurmstepd: error: *** STEP 1942643.0 ON u01c32 CANCELLED AT 2025-08-06T03:35:00 ***
srun: error: u01c32: tasks 0-15,17-23: Aborted (core dumped)
srun: error: u02c01: task 33: Aborted (core dumped)
srun: error: u01c32: task 16: Aborted (core dumped)

I'm seeing similar errors on Orion & Hercules in debug.
Because of these errors, the RTs can't run in debug mode. However, I tested the debug build on Ursa LLVM, Ursa Intel, Hercules, and Orion, and they all build without issue. It seems like the PR itself is not a problem, but rather the UPP code.

My tests on Ursa are at:

/scratch3/NAGAPE/epic/Gillian.Petro/ursa/RTs/upp-rts/1256-intel/ci
/scratch3/NAGAPE/epic/Gillian.Petro/ursa/RTs/upp-rts/1256-llvm/ci

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@gspetro-NOAA @WenMeng-NOAA I was able to build the UPP code successfully on Ursa in debug mode using intelllvm. I am not surprised that the RTs do not run in debug mode; I agree those issues are unrelated to this PR. If desired they can be fixed in a future PR.

@BrianCurtis-NOAA (and others) thanks for your work on this!

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@gspetro-NOAA @WenMeng-NOAA I was able to build the UPP code successfully on Ursa in debug mode using intelllvm. I am not surprised that the RTs do not run in debug mode; I agree those issues are unrelated to this PR. If desired they can be fixed in a future PR.

@BrianCurtis-NOAA (and others) thanks for your work on this!

I agree with @BenjaminBlake-NOAA that the UPP code might have hidden issues that could bypass the whole sanity checks. We will address them case by case in the future.

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@BenjaminBlake-NOAA @WenMeng-NOAA Agreed. I don't think this PR is the problem, since RTs pass without baseline changes on all supported machine/compiler combinations when running normally (non-debug), and in debug mode, the UPP executable builds properly on all supported systems. I'll approve the PR.

I think what shows up with the RTs in debug is likely a snapshot of what Ed Hartnett was talking about. If I have time (ha!), I will try to look into the errors case by case to see what we can potentially clean up over the long term.

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This PR is ready for merging.

@WenMeng-NOAA WenMeng-NOAA added the No Baseline Change No baseline of the UPP regression tests are made. label Aug 6, 2025
@WenMeng-NOAA WenMeng-NOAA merged commit bdd52a7 into NOAA-EMC:develop Aug 6, 2025
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Update compile options for building UPP in debug mode with intelllvm complier

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