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reserveCells crashes mint mesh inside Umpire #1271

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merged 21 commits into from
Oct 10, 2024
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f25bdc4
Add reproducers for bug crashing UnstructuredMesh::reserveCells().
gunney1 Feb 6, 2024
ba90110
Add missing include guard.
gunney1 Feb 7, 2024
10972e8
Merge remote-tracking branch 'gh/develop' into bugfix/gunney/ug-immed…
gunney1 Mar 26, 2024
0e0d51a
Merge remote-tracking branch 'gh/develop' into bugfix/gunney/ug-immed…
gunney1 Jun 10, 2024
2076165
Merge remote-tracking branch 'gh/develop' into bugfix/gunney/ug-immed…
gunney1 Oct 4, 2024
c96baed
Work-around for the crash: Use allocate + copy + deallocate.
gunney1 Oct 4, 2024
c36ec8c
Disable the work-around and add tests that bypass mint.
gunney1 Oct 9, 2024
cdf6ffb
Fix an un-related compile fail in the new test code.
gunney1 Oct 9, 2024
681d035
Add test to allocate and reallocate in sidre package.
gunney1 Oct 9, 2024
276c37d
Add test that use only Buffer interface, eliminating Views code as
gunney1 Oct 9, 2024
cc83e71
Add tests to verify allocate/deallocate works without sidre::Buffer.
gunney1 Oct 9, 2024
49abe98
Merge remote-tracking branch 'gh/develop' into bugfix/gunney/ug-immed…
gunney1 Oct 9, 2024
b8cf67d
Fix a bug in new test.
gunney1 Oct 10, 2024
ccced65
Build Umpire TPL shared in docker.
gunney1 Oct 10, 2024
7a449f9
Rebuild docker images with shared Umpire library.
gunney1 Oct 10, 2024
5202846
Use new docker images with shared Umpire libs.
gunney1 Oct 10, 2024
3aae97a
Backout work-around and remove a redundant test.
gunney1 Oct 10, 2024
7c2bcc2
Merge remote-tracking branch 'gh/develop' into bugfix/gunney/ug-immed…
gunney1 Oct 10, 2024
6c50977
Guard code for non-Sidre builds.
gunney1 Oct 10, 2024
cf9f910
Add comment explaining why new tests are in quest instead of sidre or…
gunney1 Oct 10, 2024
e9844ea
Autoformat.
gunney1 Oct 10, 2024
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4 changes: 2 additions & 2 deletions azure-pipelines.yml
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@ variables:
DO_BUILD: 'yes'
DO_TEST: 'yes'
DO_CLEAN: 'no'
CLANG14_IMAGENAME: 'axom/tpls:clang-14_09-23-24_17h-07m'
GCC13_IMAGENAME: 'axom/tpls:gcc-13_09-23-24_17h-07m'
CLANG14_IMAGENAME: 'axom/tpls:clang-14_10-10-24_01h-31m'
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Is this change required?

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@gunney1 gunney1 Oct 10, 2024

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Yes. The new images have Umpire shared libs. That's the key to the bug fix.

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@white238 @kennyweiss are you OK with switching to Umpire shared libs for azure testing?

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We (@kennyweiss , @gunney1 , @davidbeckingsale ) met about this last night. Basically a static umpire with a shared axom creates multiple singletons in Umpire. We need to not allow this to happen in our Spack recipe as well but this seems to be the only way around this.

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Do you mean add a constraint in the Axom Spack package that static Umpire conflicts with shared Axom?

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yes and/or a conflict

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@kennyweiss kennyweiss Oct 10, 2024

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Yes -- the three of us had a meeting yesterday w/ @davidbeckingsale and concluded that the static umpire combined w/ a shared axom in the docker configuration was leading to more than one umpire instance.

There might be a solution to this w/ improved linking orders and/or linker flags, but it will be difficult to track down in the short term, and is not necessary for @gunney1's actual deliverable (i.e. the CI is testing a different configuration than the one we actually need). @gunney1 is planning to create an issue summarizing that discussion so we can look into it in the future.

It's also worth noting that we've encountered similar issues in the past when mixing libraries w/ singletons with upstream shared or Fortran libraries (e.g. #865 and #270).

Edit: My response took too long and @white238 beat me to the punch

GCC13_IMAGENAME: 'axom/tpls:gcc-13_10-10-24_01h-31m'
system.debug: false

jobs:
Expand Down
8 changes: 4 additions & 4 deletions host-configs/docker/[email protected]
Original file line number Diff line number Diff line change
Expand Up @@ -4,13 +4,13 @@
# CMake executable path: /usr/local/bin/cmake
#------------------------------------------------------------------------------

set(CMAKE_PREFIX_PATH "/home/axom/axom_tpls/clang-14.0.0/umpire-2024.07.0-sm47io5l4xfgy3enimczrmiijsw4pdol;/home/axom/axom_tpls/clang-14.0.0/fmt-11.0.2-zxzr5ejl2icv2wkxrmytysohcwa56dym;/home/axom/axom_tpls/clang-14.0.0/raja-2024.07.0-wvpmv7ubnzad5frbffxkco37c4zwdh66;/home/axom/axom_tpls/clang-14.0.0/camp-2024.07.0-drhul62p64d42qwqnc6sbazwxudcgtzo;/home/axom/axom_tpls/clang-14.0.0/mfem-4.6.0-4khgoizhebqald4wsjiriiep2nsuqrj2;/home/axom/axom_tpls/clang-14.0.0/hypre-2.24.0-gmgla43c3i2sasbyvrzvvynfheah5dki;/home/axom/axom_tpls/clang-14.0.0/gmake-4.4.1-z6rav4bbtoxhlimk3lo3zuhcobg2p5l6;/home/axom/axom_tpls/clang-14.0.0/conduit-0.9.2-am5eywgjadrfdslkbm2iiukrgony25jx;/home/axom/axom_tpls/clang-14.0.0/parmetis-4.0.3-totaqsyyaqqne76f3h3utf6he5hnfj3i;/home/axom/axom_tpls/clang-14.0.0/metis-5.1.0-vstqxoisaqzmauseelggw2ipkjxpxyb2;/home/axom/axom_tpls/clang-14.0.0/hdf5-1.8.23-pd77dfbbqmoujqh64homnougp5stx4mr;/home/axom/axom_tpls/clang-14.0.0/caliper-2.10.0-oirvdfkyevzclrrtc4d4fkoiccw7oshp;/home/axom/axom_tpls/clang-14.0.0/libunwind-1.6.2-yovgajxilzs4khvufv73arjcgya5tr25;/home/axom/axom_tpls/clang-14.0.0/elfutils-0.191-jzxk7dbbigew6uulryjbu3p3zmjobpa7;/home/axom/axom_tpls/clang-14.0.0/zstd-1.5.6-jdvede5e5ftsojui6ghblyl7u2znbnu3;/home/axom/axom_tpls/clang-14.0.0/zlib-ng-2.2.1-oevfc4jn574mzjvfakgsrsso5g7vc3uj;/home/axom/axom_tpls/clang-14.0.0/xz-5.4.6-zovyngtilewkrzialvu453oy3usgahmu;/home/axom/axom_tpls/clang-14.0.0/pkgconf-2.2.0-fs63yvwfbbvxaxmqdhh5jhtn6ch6slbg;/home/axom/axom_tpls/clang-14.0.0/libiconv-1.17-ejpqqyvgaa3bcjowgoxdtknuwbtja3bz;/home/axom/axom_tpls/clang-14.0.0/blt-0.6.2-i23yaxmyycvounaz4wfduk5vvaurliye;/home/axom/axom_tpls/clang-14.0.0/adiak-0.4.0-axvlay3g64yralqxz6tet3dg2ilxsd2z" CACHE STRING "")
set(CMAKE_PREFIX_PATH "/home/axom/axom_tpls/clang-14.0.0/umpire-2024.07.0-x3qc35tst2zhry545rgvowwbgomgc2ql;/home/axom/axom_tpls/clang-14.0.0/fmt-11.0.2-zxzr5ejl2icv2wkxrmytysohcwa56dym;/home/axom/axom_tpls/clang-14.0.0/raja-2024.07.0-wvpmv7ubnzad5frbffxkco37c4zwdh66;/home/axom/axom_tpls/clang-14.0.0/camp-2024.07.0-drhul62p64d42qwqnc6sbazwxudcgtzo;/home/axom/axom_tpls/clang-14.0.0/mfem-4.6.0-4khgoizhebqald4wsjiriiep2nsuqrj2;/home/axom/axom_tpls/clang-14.0.0/hypre-2.24.0-gmgla43c3i2sasbyvrzvvynfheah5dki;/home/axom/axom_tpls/clang-14.0.0/gmake-4.4.1-z6rav4bbtoxhlimk3lo3zuhcobg2p5l6;/home/axom/axom_tpls/clang-14.0.0/conduit-0.9.2-am5eywgjadrfdslkbm2iiukrgony25jx;/home/axom/axom_tpls/clang-14.0.0/parmetis-4.0.3-totaqsyyaqqne76f3h3utf6he5hnfj3i;/home/axom/axom_tpls/clang-14.0.0/metis-5.1.0-vstqxoisaqzmauseelggw2ipkjxpxyb2;/home/axom/axom_tpls/clang-14.0.0/hdf5-1.8.23-pd77dfbbqmoujqh64homnougp5stx4mr;/home/axom/axom_tpls/clang-14.0.0/caliper-2.10.0-oirvdfkyevzclrrtc4d4fkoiccw7oshp;/home/axom/axom_tpls/clang-14.0.0/libunwind-1.6.2-yovgajxilzs4khvufv73arjcgya5tr25;/home/axom/axom_tpls/clang-14.0.0/elfutils-0.191-jzxk7dbbigew6uulryjbu3p3zmjobpa7;/home/axom/axom_tpls/clang-14.0.0/zstd-1.5.6-jdvede5e5ftsojui6ghblyl7u2znbnu3;/home/axom/axom_tpls/clang-14.0.0/zlib-ng-2.2.1-oevfc4jn574mzjvfakgsrsso5g7vc3uj;/home/axom/axom_tpls/clang-14.0.0/xz-5.4.6-zovyngtilewkrzialvu453oy3usgahmu;/home/axom/axom_tpls/clang-14.0.0/pkgconf-2.2.0-fs63yvwfbbvxaxmqdhh5jhtn6ch6slbg;/home/axom/axom_tpls/clang-14.0.0/libiconv-1.17-ejpqqyvgaa3bcjowgoxdtknuwbtja3bz;/home/axom/axom_tpls/clang-14.0.0/blt-0.6.2-i23yaxmyycvounaz4wfduk5vvaurliye;/home/axom/axom_tpls/clang-14.0.0/adiak-0.4.0-axvlay3g64yralqxz6tet3dg2ilxsd2z" CACHE STRING "")

set(CMAKE_INSTALL_RPATH_USE_LINK_PATH "ON" CACHE STRING "")

set(CMAKE_BUILD_RPATH "/home/axom/axom_tpls/clang-14.0.0/axom-develop-77bsfofkeh2hi2ff7fstp2qsg2fzimak/lib;/home/axom/axom_tpls/clang-14.0.0/axom-develop-77bsfofkeh2hi2ff7fstp2qsg2fzimak/lib64;/home/axom/axom_tpls/clang-14.0.0/adiak-0.4.0-axvlay3g64yralqxz6tet3dg2ilxsd2z/lib;/home/axom/axom_tpls/clang-14.0.0/caliper-2.10.0-oirvdfkyevzclrrtc4d4fkoiccw7oshp/lib;/home/axom/axom_tpls/clang-14.0.0/elfutils-0.191-jzxk7dbbigew6uulryjbu3p3zmjobpa7/lib;/home/axom/axom_tpls/clang-14.0.0/libiconv-1.17-ejpqqyvgaa3bcjowgoxdtknuwbtja3bz/lib;/home/axom/axom_tpls/clang-14.0.0/pkgconf-2.2.0-fs63yvwfbbvxaxmqdhh5jhtn6ch6slbg/lib;/home/axom/axom_tpls/clang-14.0.0/xz-5.4.6-zovyngtilewkrzialvu453oy3usgahmu/lib;/home/axom/axom_tpls/clang-14.0.0/zlib-ng-2.2.1-oevfc4jn574mzjvfakgsrsso5g7vc3uj/lib;/home/axom/axom_tpls/clang-14.0.0/zstd-1.5.6-jdvede5e5ftsojui6ghblyl7u2znbnu3/lib;/home/axom/axom_tpls/clang-14.0.0/libunwind-1.6.2-yovgajxilzs4khvufv73arjcgya5tr25/lib;/home/axom/axom_tpls/clang-14.0.0/conduit-0.9.2-am5eywgjadrfdslkbm2iiukrgony25jx/lib;/home/axom/axom_tpls/clang-14.0.0/hdf5-1.8.23-pd77dfbbqmoujqh64homnougp5stx4mr/lib;/home/axom/axom_tpls/clang-14.0.0/metis-5.1.0-vstqxoisaqzmauseelggw2ipkjxpxyb2/lib;/home/axom/axom_tpls/clang-14.0.0/parmetis-4.0.3-totaqsyyaqqne76f3h3utf6he5hnfj3i/lib;/home/axom/axom_tpls/clang-14.0.0/mfem-4.6.0-4khgoizhebqald4wsjiriiep2nsuqrj2/lib;/home/axom/axom_tpls/clang-14.0.0/hypre-2.24.0-gmgla43c3i2sasbyvrzvvynfheah5dki/lib;/home/axom/axom_tpls/clang-14.0.0/raja-2024.07.0-wvpmv7ubnzad5frbffxkco37c4zwdh66/lib;/home/axom/axom_tpls/clang-14.0.0/camp-2024.07.0-drhul62p64d42qwqnc6sbazwxudcgtzo/lib;/home/axom/axom_tpls/clang-14.0.0/umpire-2024.07.0-sm47io5l4xfgy3enimczrmiijsw4pdol/lib;/home/axom/axom_tpls/clang-14.0.0/fmt-11.0.2-zxzr5ejl2icv2wkxrmytysohcwa56dym/lib" CACHE STRING "")
set(CMAKE_BUILD_RPATH "/home/axom/axom_tpls/clang-14.0.0/axom-develop-emwf5bt2abor2soesihp7f66mf2lhw4z/lib;/home/axom/axom_tpls/clang-14.0.0/axom-develop-emwf5bt2abor2soesihp7f66mf2lhw4z/lib64;/home/axom/axom_tpls/clang-14.0.0/adiak-0.4.0-axvlay3g64yralqxz6tet3dg2ilxsd2z/lib;/home/axom/axom_tpls/clang-14.0.0/caliper-2.10.0-oirvdfkyevzclrrtc4d4fkoiccw7oshp/lib;/home/axom/axom_tpls/clang-14.0.0/elfutils-0.191-jzxk7dbbigew6uulryjbu3p3zmjobpa7/lib;/home/axom/axom_tpls/clang-14.0.0/libiconv-1.17-ejpqqyvgaa3bcjowgoxdtknuwbtja3bz/lib;/home/axom/axom_tpls/clang-14.0.0/pkgconf-2.2.0-fs63yvwfbbvxaxmqdhh5jhtn6ch6slbg/lib;/home/axom/axom_tpls/clang-14.0.0/xz-5.4.6-zovyngtilewkrzialvu453oy3usgahmu/lib;/home/axom/axom_tpls/clang-14.0.0/zlib-ng-2.2.1-oevfc4jn574mzjvfakgsrsso5g7vc3uj/lib;/home/axom/axom_tpls/clang-14.0.0/zstd-1.5.6-jdvede5e5ftsojui6ghblyl7u2znbnu3/lib;/home/axom/axom_tpls/clang-14.0.0/libunwind-1.6.2-yovgajxilzs4khvufv73arjcgya5tr25/lib;/home/axom/axom_tpls/clang-14.0.0/conduit-0.9.2-am5eywgjadrfdslkbm2iiukrgony25jx/lib;/home/axom/axom_tpls/clang-14.0.0/hdf5-1.8.23-pd77dfbbqmoujqh64homnougp5stx4mr/lib;/home/axom/axom_tpls/clang-14.0.0/metis-5.1.0-vstqxoisaqzmauseelggw2ipkjxpxyb2/lib;/home/axom/axom_tpls/clang-14.0.0/parmetis-4.0.3-totaqsyyaqqne76f3h3utf6he5hnfj3i/lib;/home/axom/axom_tpls/clang-14.0.0/mfem-4.6.0-4khgoizhebqald4wsjiriiep2nsuqrj2/lib;/home/axom/axom_tpls/clang-14.0.0/hypre-2.24.0-gmgla43c3i2sasbyvrzvvynfheah5dki/lib;/home/axom/axom_tpls/clang-14.0.0/raja-2024.07.0-wvpmv7ubnzad5frbffxkco37c4zwdh66/lib;/home/axom/axom_tpls/clang-14.0.0/camp-2024.07.0-drhul62p64d42qwqnc6sbazwxudcgtzo/lib;/home/axom/axom_tpls/clang-14.0.0/umpire-2024.07.0-x3qc35tst2zhry545rgvowwbgomgc2ql/lib;/home/axom/axom_tpls/clang-14.0.0/fmt-11.0.2-zxzr5ejl2icv2wkxrmytysohcwa56dym/lib" CACHE STRING "")

set(CMAKE_INSTALL_RPATH "/home/axom/axom_tpls/clang-14.0.0/axom-develop-77bsfofkeh2hi2ff7fstp2qsg2fzimak/lib;/home/axom/axom_tpls/clang-14.0.0/axom-develop-77bsfofkeh2hi2ff7fstp2qsg2fzimak/lib64;/home/axom/axom_tpls/clang-14.0.0/adiak-0.4.0-axvlay3g64yralqxz6tet3dg2ilxsd2z/lib;/home/axom/axom_tpls/clang-14.0.0/caliper-2.10.0-oirvdfkyevzclrrtc4d4fkoiccw7oshp/lib;/home/axom/axom_tpls/clang-14.0.0/elfutils-0.191-jzxk7dbbigew6uulryjbu3p3zmjobpa7/lib;/home/axom/axom_tpls/clang-14.0.0/libiconv-1.17-ejpqqyvgaa3bcjowgoxdtknuwbtja3bz/lib;/home/axom/axom_tpls/clang-14.0.0/pkgconf-2.2.0-fs63yvwfbbvxaxmqdhh5jhtn6ch6slbg/lib;/home/axom/axom_tpls/clang-14.0.0/xz-5.4.6-zovyngtilewkrzialvu453oy3usgahmu/lib;/home/axom/axom_tpls/clang-14.0.0/zlib-ng-2.2.1-oevfc4jn574mzjvfakgsrsso5g7vc3uj/lib;/home/axom/axom_tpls/clang-14.0.0/zstd-1.5.6-jdvede5e5ftsojui6ghblyl7u2znbnu3/lib;/home/axom/axom_tpls/clang-14.0.0/libunwind-1.6.2-yovgajxilzs4khvufv73arjcgya5tr25/lib;/home/axom/axom_tpls/clang-14.0.0/conduit-0.9.2-am5eywgjadrfdslkbm2iiukrgony25jx/lib;/home/axom/axom_tpls/clang-14.0.0/hdf5-1.8.23-pd77dfbbqmoujqh64homnougp5stx4mr/lib;/home/axom/axom_tpls/clang-14.0.0/metis-5.1.0-vstqxoisaqzmauseelggw2ipkjxpxyb2/lib;/home/axom/axom_tpls/clang-14.0.0/parmetis-4.0.3-totaqsyyaqqne76f3h3utf6he5hnfj3i/lib;/home/axom/axom_tpls/clang-14.0.0/mfem-4.6.0-4khgoizhebqald4wsjiriiep2nsuqrj2/lib;/home/axom/axom_tpls/clang-14.0.0/hypre-2.24.0-gmgla43c3i2sasbyvrzvvynfheah5dki/lib;/home/axom/axom_tpls/clang-14.0.0/raja-2024.07.0-wvpmv7ubnzad5frbffxkco37c4zwdh66/lib;/home/axom/axom_tpls/clang-14.0.0/camp-2024.07.0-drhul62p64d42qwqnc6sbazwxudcgtzo/lib;/home/axom/axom_tpls/clang-14.0.0/umpire-2024.07.0-sm47io5l4xfgy3enimczrmiijsw4pdol/lib;/home/axom/axom_tpls/clang-14.0.0/fmt-11.0.2-zxzr5ejl2icv2wkxrmytysohcwa56dym/lib" CACHE STRING "")
set(CMAKE_INSTALL_RPATH "/home/axom/axom_tpls/clang-14.0.0/axom-develop-emwf5bt2abor2soesihp7f66mf2lhw4z/lib;/home/axom/axom_tpls/clang-14.0.0/axom-develop-emwf5bt2abor2soesihp7f66mf2lhw4z/lib64;/home/axom/axom_tpls/clang-14.0.0/adiak-0.4.0-axvlay3g64yralqxz6tet3dg2ilxsd2z/lib;/home/axom/axom_tpls/clang-14.0.0/caliper-2.10.0-oirvdfkyevzclrrtc4d4fkoiccw7oshp/lib;/home/axom/axom_tpls/clang-14.0.0/elfutils-0.191-jzxk7dbbigew6uulryjbu3p3zmjobpa7/lib;/home/axom/axom_tpls/clang-14.0.0/libiconv-1.17-ejpqqyvgaa3bcjowgoxdtknuwbtja3bz/lib;/home/axom/axom_tpls/clang-14.0.0/pkgconf-2.2.0-fs63yvwfbbvxaxmqdhh5jhtn6ch6slbg/lib;/home/axom/axom_tpls/clang-14.0.0/xz-5.4.6-zovyngtilewkrzialvu453oy3usgahmu/lib;/home/axom/axom_tpls/clang-14.0.0/zlib-ng-2.2.1-oevfc4jn574mzjvfakgsrsso5g7vc3uj/lib;/home/axom/axom_tpls/clang-14.0.0/zstd-1.5.6-jdvede5e5ftsojui6ghblyl7u2znbnu3/lib;/home/axom/axom_tpls/clang-14.0.0/libunwind-1.6.2-yovgajxilzs4khvufv73arjcgya5tr25/lib;/home/axom/axom_tpls/clang-14.0.0/conduit-0.9.2-am5eywgjadrfdslkbm2iiukrgony25jx/lib;/home/axom/axom_tpls/clang-14.0.0/hdf5-1.8.23-pd77dfbbqmoujqh64homnougp5stx4mr/lib;/home/axom/axom_tpls/clang-14.0.0/metis-5.1.0-vstqxoisaqzmauseelggw2ipkjxpxyb2/lib;/home/axom/axom_tpls/clang-14.0.0/parmetis-4.0.3-totaqsyyaqqne76f3h3utf6he5hnfj3i/lib;/home/axom/axom_tpls/clang-14.0.0/mfem-4.6.0-4khgoizhebqald4wsjiriiep2nsuqrj2/lib;/home/axom/axom_tpls/clang-14.0.0/hypre-2.24.0-gmgla43c3i2sasbyvrzvvynfheah5dki/lib;/home/axom/axom_tpls/clang-14.0.0/raja-2024.07.0-wvpmv7ubnzad5frbffxkco37c4zwdh66/lib;/home/axom/axom_tpls/clang-14.0.0/camp-2024.07.0-drhul62p64d42qwqnc6sbazwxudcgtzo/lib;/home/axom/axom_tpls/clang-14.0.0/umpire-2024.07.0-x3qc35tst2zhry545rgvowwbgomgc2ql/lib;/home/axom/axom_tpls/clang-14.0.0/fmt-11.0.2-zxzr5ejl2icv2wkxrmytysohcwa56dym/lib" CACHE STRING "")

set(CMAKE_BUILD_TYPE "Release" CACHE STRING "")

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set(RAJA_DIR "${TPL_ROOT}/raja-2024.07.0-wvpmv7ubnzad5frbffxkco37c4zwdh66" CACHE PATH "")

set(UMPIRE_DIR "${TPL_ROOT}/umpire-2024.07.0-sm47io5l4xfgy3enimczrmiijsw4pdol" CACHE PATH "")
set(UMPIRE_DIR "${TPL_ROOT}/umpire-2024.07.0-x3qc35tst2zhry545rgvowwbgomgc2ql" CACHE PATH "")

set(ADIAK_DIR "${TPL_ROOT}/adiak-0.4.0-axvlay3g64yralqxz6tet3dg2ilxsd2z" CACHE PATH "")

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