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Bug fix in parallel-netcdf to avoid linking to libirc.so AND cherry-pick spack develop PR 48251 (conflict Intel Classic with [email protected])#495

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climbfuji merged 6 commits intoJCSDA:spack-stack-devfrom
climbfuji:feature/libirc_parallel_netcdf_and_scipy
Jan 28, 2025
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@climbfuji climbfuji commented Dec 24, 2024 •
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Description

Bug fix in parallel-netcdf: avoid linking to legacy and incomplete libirc.so due to parallel-netcdf's bad configure script - see JCSDA/spack-stack#1436 for details.

Testing

  1. Built unified environment manually on Ubuntu CI runner and verified that libirc.so is not linked in libpnetcdf.so or any library that links against pnetcdf.so (PIO, ESMF). Example:
$ ldd /work/noaa/gmtb/dheinzel/spst-libirc/envs/ue-intel-2021.9.0/install/intel/2021.9.0/parallel-netcdf-1.12.3-5fkm2ji/bin/ncmpidump
        linux-vdso.so.1 (0x00007ffdf0ffd000)
        libpnetcdf.so.4 => /work/noaa/gmtb/dheinzel/spst-libirc/envs/ue-intel-2021.9.0/install/intel/2021.9.0/parallel-netcdf-1.12.3-5fkm2ji/lib/libpnetcdf.so.4 (0x00007f9742dea000)
        libifport.so.5 => /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2023.1.0-sb753366rvywq75zeg4ml5k5c72xgj72/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libifport.so.5 (0x00007f9742dbb000)
        libmpifort.so.12 => /apps/spack-managed/oneapi-2023.1.0/intel-oneapi-mpi-2021.9.0-a66eaipzsnyrdgaqzxmqmqz64qzvhkse/mpi/2021.9.0/lib/libmpifort.so.12 (0x00007f9742a07000)
        libmpi.so.12 => /apps/spack-managed/oneapi-2023.1.0/intel-oneapi-mpi-2021.9.0-a66eaipzsnyrdgaqzxmqmqz64qzvhkse/mpi/2021.9.0/lib/release/libmpi.so.12 (0x00007f97410bc000)
        libm.so.6 => /usr/lib64/libm.so.6 (0x00007f9740fe1000)
        libgcc_s.so.1 => /usr/lib64/libgcc_s.so.1 (0x00007f9740fc4000)
        libc.so.6 => /usr/lib64/libc.so.6 (0x00007f9740dbb000)
        libmpicxx.so.12 => /apps/spack-managed/oneapi-2023.1.0/intel-oneapi-mpi-2021.9.0-a66eaipzsnyrdgaqzxmqmqz64qzvhkse/mpi/2021.9.0/lib/libmpicxx.so.12 (0x00007f9740b9b000)
        libimf.so => /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2023.1.0-sb753366rvywq75zeg4ml5k5c72xgj72/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libimf.so (0x00007f97407a4000)
        libirng.so => /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2023.1.0-sb753366rvywq75zeg4ml5k5c72xgj72/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libirng.so (0x00007f9740489000)
        libcilkrts.so.5 => /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2023.1.0-sb753366rvywq75zeg4ml5k5c72xgj72/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libcilkrts.so.5 (0x00007f9740248000)
        libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f9740021000)
        libintlc.so.5 => /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2023.1.0-sb753366rvywq75zeg4ml5k5c72xgj72/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libintlc.so.5 (0x00007f973ffa5000)
        libsvml.so => /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2023.1.0-sb753366rvywq75zeg4ml5k5c72xgj72/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libsvml.so (0x00007f973e8d1000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f9743724000)
        librt.so.1 => /usr/lib64/librt.so.1 (0x00007f973e8ca000)
        libdl.so.2 => /usr/lib64/libdl.so.2 (0x00007f973e8c5000)
        libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00007f973e8c0000)
orion-login-4[49] dheinzel$ ldd /work/noaa/gmtb/dheinzel/spst-libirc/envs/ue-intel-2021.9.0/install/intel/2021.9.0/parallel-netcdf-1.12.3-5fkm2ji/lib/libpnetcdf.so
        linux-vdso.so.1 (0x00007fff8d9f3000)
        libifport.so.5 => /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2023.1.0-sb753366rvywq75zeg4ml5k5c72xgj72/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libifport.so.5 (0x00007fad2b37a000)
        libmpicxx.so.12 => /apps/spack-managed/oneapi-2023.1.0/intel-oneapi-mpi-2021.9.0-a66eaipzsnyrdgaqzxmqmqz64qzvhkse/mpi/2021.9.0/lib/libmpicxx.so.12 (0x00007fad2b15a000)
        libmpifort.so.12 => /apps/spack-managed/oneapi-2023.1.0/intel-oneapi-mpi-2021.9.0-a66eaipzsnyrdgaqzxmqmqz64qzvhkse/mpi/2021.9.0/lib/libmpifort.so.12 (0x00007fad2ada6000)
        libmpi.so.12 => /apps/spack-managed/oneapi-2023.1.0/intel-oneapi-mpi-2021.9.0-a66eaipzsnyrdgaqzxmqmqz64qzvhkse/mpi/2021.9.0/lib/release/libmpi.so.12 (0x00007fad2945b000)
        libimf.so => /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2023.1.0-sb753366rvywq75zeg4ml5k5c72xgj72/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libimf.so (0x00007fad29064000)
        libirng.so => /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2023.1.0-sb753366rvywq75zeg4ml5k5c72xgj72/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libirng.so (0x00007fad28d49000)
        libm.so.6 => /usr/lib64/libm.so.6 (0x00007fad28c6e000)
        libcilkrts.so.5 => /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2023.1.0-sb753366rvywq75zeg4ml5k5c72xgj72/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libcilkrts.so.5 (0x00007fad28a2d000)
        libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fad28806000)
        libintlc.so.5 => /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2023.1.0-sb753366rvywq75zeg4ml5k5c72xgj72/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libintlc.so.5 (0x00007fad2878a000)
        libsvml.so => /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2023.1.0-sb753366rvywq75zeg4ml5k5c72xgj72/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libsvml.so (0x00007fad270b4000)
        libgcc_s.so.1 => /usr/lib64/libgcc_s.so.1 (0x00007fad27099000)
        libc.so.6 => /usr/lib64/libc.so.6 (0x00007fad26e90000)
        /lib64/ld-linux-x86-64.so.2 (0x00007fad2bce3000)
        librt.so.1 => /usr/lib64/librt.so.1 (0x00007fad26e8b000)
        libdl.so.2 => /usr/lib64/libdl.so.2 (0x00007fad26e86000)
        libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00007fad26e7f000)
  1. Ran ncmpidump (from parallel-netcdf) on netCDF files on Orion (srun -n 2 ncmpidump ...).
  2. See Avoid linking to libirc.so in spack (parallel-netcdf), turn off crypt variant for Python, and update Orion site config to fix tar issue spack-stack#1435

@climbfuji climbfuji force-pushed the feature/libirc_parallel_netcdf_and_scipy branch from 2ef57a4 to 1ab4656 Compare December 24, 2024 02:40
@climbfuji climbfuji mentioned this pull request Dec 26, 2024
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@rickgrubin-noaa rickgrubin-noaa mentioned this pull request Jan 27, 2025
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@climbfuji climbfuji marked this pull request as ready for review January 28, 2025 13:59
@climbfuji climbfuji self-assigned this Jan 28, 2025
climbfuji
climbfuji commented Jan 28, 2025
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srherbener
srherbener approved these changes Jan 28, 2025
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Thanks for this update!

@climbfuji climbfuji merged commit 5ca934f into JCSDA:spack-stack-dev Jan 28, 2025
@climbfuji climbfuji deleted the feature/libirc_parallel_netcdf_and_scipy branch January 28, 2025 20:22
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@srherbener srherbener srherbener approved these changes

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