add carpenter cray modules

[hyeoksu-lee]

User description

Description

This PR introduces DoD Carpenter Cray modules.

Type of change

Please delete options that are not relevant.

• Something else

Scope

• This PR comprises a set of related changes with a common goal

If you cannot check the above box, please split your PR into multiple PRs that each have a common goal.

How Has This Been Tested?

MFC compiles ok on Carpenter with Cray modules and test suite passes.

Test Configuration:

• What computers and compilers did you use to test this: Carpenter Cray

Checklist

• I have added comments for the new code
• I added Doxygen docstrings to the new code
• I have made corresponding changes to the documentation (docs/)
• I have added regression tests to the test suite so that people can verify in the future that the feature is behaving as expected
• I have added example cases in examples/ that demonstrate my new feature performing as expected.
  They run to completion and demonstrate "interesting physics"
• I ran ./mfc.sh format before committing my code
• New and existing tests pass locally with my changes, including with GPU capability enabled (both NVIDIA hardware with NVHPC compilers and AMD hardware with CRAY compilers) and disabled
• This PR does not introduce any repeated code (it follows the DRY principle)
• I cannot think of a way to condense this code and reduce any introduced additional line count

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PR Type

Enhancement

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Description

• Add Carpenter Cray module configuration for DoD system

• Update module selection interface to distinguish Cray/GNU compilers

• Create new batch template for Carpenter Cray environment

• Modify module loading logic to handle Cray-specific paths

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Changes walkthrough 📝

	Relevant files
Configuration changes	modules.sh Update module selection for Carpenter Cray support              toolchain/bootstrap/modules.sh Update system selection menu to include Carpenter Cray (cc) option Modify module reset logic to exclude both Carpenter variants Update Cray library path handling for GNU Carpenter only +4/-4      modules Define Carpenter Cray module configuration                              toolchain/modules Add new cc configuration for Carpenter Cray modules Include Cray-specific modules like PrgEnv-cray and cray-fftw Rename existing Carpenter entry to specify GNU compiler +5/-1
Enhancement	carpenter-cray.mako Add Carpenter Cray batch execution template                            toolchain/templates/carpenter-cray.mako Create new PBS batch template for Carpenter Cray system Configure MPI execution with proper node/task allocation Set up module loading with Cray-specific parameters +48/-0

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[qodo-merge-pro]

PR Reviewer Guide 🔍

(Review updated until commit 7801bbe)

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Inconsistent Syntax Mixed use of '!=' and '!=' operators in conditional statements. Line 71 uses '!=' while line 100 uses '!=' which may cause shell compatibility issues or unexpected behavior. if [ "$u_c" '!=' 'cc' ] && [ "$u_c" '!=' 'c' ]; then module reset > /dev/null 2>&1 code="$?" # Purge if reset is not available if [ "$code" -ne '0' ]; then module purge > /dev/null 2>&1 fi else module purge > /dev/null 2>&1 fi ELEMENTS="$(__extract "$u_c-all") $(__extract "$u_c-$cg")" MODULES=`echo "$ELEMENTS" | tr ' ' '\n' | grep -v = | xargs` VARIABLES=`echo "$ELEMENTS" | tr ' ' '\n' | grep = | xargs` log " $ module load $MODULES" if ! module load $MODULES; then error "Failed to load modules." return fi if [ $(echo "$VARIABLES" | grep = | wc -c) -gt 0 ]; then log " $ export $(eval "echo $VARIABLES")" export $(eval "echo $VARIABLES") > /dev/null fi # Don't check for Cray paths on Carpenter, otherwise do check if they exist if [ ! -z ${CRAY_LD_LIBRARY_PATH+x} ] && [ "$u_c" '!=' 'c' ]; then Missing Tests New batch template for Carpenter Cray system lacks corresponding test cases to verify proper functionality, module loading, and job submission behavior. #!/usr/bin/env bash <%namespace name="helpers" file="helpers.mako"/> % if engine == 'batch': #PBS -l select=${nodes}:ncpus=192:mpiprocs=${tasks_per_node} #PBS -N "${name}" #PBS -l walltime=${walltime} % if partition: #PBS -q ${partition} % endif % if account: #PBS -A ${account} % endif % if email: #PBS -M ${email} #PBS -m abe % endif #PBS -o "${name}.out" #PBS -e "${name}.err" #PBS -V % endif ${helpers.template_prologue()} ok ":) Loading modules:\n" cd "${MFC_ROOT_DIR}" . ./mfc.sh load -c cc -m ${'g' if gpu else 'c'} cd - > /dev/null echo % for target in targets: ${helpers.run_prologue(target)} % if not mpi: (set -x; ${profiler} "${target.get_install_binpath(case)}") % else: (set -x; ${profiler} \ mpirun -np ${nodes*tasks_per_node} \ "${target.get_install_binpath(case)}") % endif ${helpers.run_epilogue(target)} echo % endfor ${helpers.template_epilogue()}

[qodo-merge-pro]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
Possible issue	Fix inequality operator syntax The inequality operator should be != instead of '!='. The quotes around the operator make it a literal string comparison rather than a proper inequality test. toolchain/bootstrap/modules.sh [71] -if [ "$u_c" '!=' 'cc' ] && [ "$u_c" '!=' 'c' ]; then +if [ "$u_c" != 'cc' ] && [ "$u_c" != 'c' ]; then Suggestion importance[1-10]: 9 __ Why: The suggestion correctly identifies a critical bug. In bash's test ([) command, quoting the inequality operator '!=' causes it to be treated as a literal string instead of an operator, which breaks the conditional logic. This fix is essential for the script to function as intended.	High
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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 45.77%. Comparing base (a34f0ca) to head (7801bbe).
Report is 4 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #903   +/-   ##
=======================================
  Coverage   45.77%   45.77%           
=======================================
  Files          68       68           
  Lines       18664    18664           
  Branches     2251     2251           
=======================================
  Hits         8543     8543           
  Misses       8763     8763           
  Partials     1358     1358           

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[sbryngelson]

does it work? when it compiles cmake prints the compilers it finds (it's one of the first things it does), can you put the output here so I can see?

[hyeoksu-lee]

@sbryngelson It works. Here's the outputs:

Not searching for unused variables given on the command line.
-- The C compiler identification is Clang 18.1.6
-- The CXX compiler identification is Clang 18.1.6
-- The Fortran compiler identification is Cray 18.0.0
-- Cray Programming Environment 2.7.32 C
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /opt/cray/pe/craype/2.7.32/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Cray Programming Environment 2.7.32 CXX
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /opt/cray/pe/craype/2.7.32/bin/CC - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Cray Programming Environment 2.7.32 Fortran
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /opt/cray/pe/craype/2.7.32/bin/ftn - skipped
-- Checking whether /opt/cray/pe/craype/2.7.32/bin/ftn supports Fortran 90
-- Checking whether /opt/cray/pe/craype/2.7.32/bin/ftn supports Fortran 90 - yes
-- Performing Test SUPPORTS_MARCH_NATIVE
-- Performing Test SUPPORTS_MARCH_NATIVE - Failed
-- Performing Test SUPPORTS_MCPU_NATIVE
-- Performing Test SUPPORTS_MCPU_NATIVE - Failed
-- IPO / LTO is NOT available
-- Found MPI_Fortran: /opt/cray/pe/craype/2.7.32/bin/ftn (found version "3.1")
-- Found MPI: TRUE (found version "3.1") found components: Fortran
-- Found SILO: /p/global/hyeoksu/MFC/carpenter-cray/build/install/silo/lib/libsiloh5.a
-- Found HDF5: /opt/cray/pe/hdf5/1.14.3.1/CRAY/18.0/lib/libhdf5.so
-- Found FFTW: /opt/cray/pe/fftw/3.3.10.8/x86_rome/lib/libfftw3.so
-- Configuring done
-- Generating done
-- Build files have been written to: /p/global/hyeoksu/MFC/carpenter-cray/build/staging/dd3ec89703

[qodo-merge-pro]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
Possible issue	Fix inequality operator syntax The inequality operator should be != instead of '!='. The quotes around the operator make it a literal string comparison rather than a proper inequality test. toolchain/bootstrap/modules.sh [71] -if [ "$u_c" '!=' 'cc' ] && [ "$u_c" '!=' 'c' ]; then +if [ "$u_c" != 'cc' ] && [ "$u_c" != 'c' ]; then Suggestion importance[1-10]: 9 __ Why: The suggestion correctly identifies a critical bug. In bash's test ([) command, quoting the inequality operator '!=' causes it to be treated as a literal string instead of an operator, which breaks the conditional logic. This fix is essential for the script to function as intended.	High
More

[sbryngelson]

fantastic, merging