From f25bdc45e81e96eeebc029a241072aad8f83d1c9 Mon Sep 17 00:00:00 2001 From: "Brian T.N. Gunney" Date: Tue, 6 Feb 2024 14:05:57 -0800 Subject: [PATCH 01/16] Add reproducers for bug crashing UnstructuredMesh::reserveCells(). --- src/axom/mint/tests/mint_mesh.cpp | 12 ++++++++++++ src/axom/quest/tests/quest_initialize.cpp | 13 +++++++++++++ 2 files changed, 25 insertions(+) diff --git a/src/axom/mint/tests/mint_mesh.cpp b/src/axom/mint/tests/mint_mesh.cpp index cc707aed21..36adb1080d 100644 --- a/src/axom/mint/tests/mint_mesh.cpp +++ b/src/axom/mint/tests/mint_mesh.cpp @@ -725,6 +725,18 @@ TEST(mint_mesh, get_mixed_topology_unstructured_from_sidre) delete m; } +//------------------------------------------------------------------------------ +TEST(mint_mesh, immediate_ug_reserve) +{ + axom::sidre::DataStore objectDS; + axom::sidre::Group* meshGroup = objectDS.getRoot()->createGroup("myGroup"); + axom::mint::UnstructuredMesh contourMesh( + 2, + axom::mint::CellType::SEGMENT, + meshGroup); + contourMesh.reserveCells(10); // This may crash. +} + #endif /* AXOM_MINT_USE_SIDRE */ } /* namespace mint */ diff --git a/src/axom/quest/tests/quest_initialize.cpp b/src/axom/quest/tests/quest_initialize.cpp index f8f2f6c67f..fb1423e26d 100644 --- a/src/axom/quest/tests/quest_initialize.cpp +++ b/src/axom/quest/tests/quest_initialize.cpp @@ -5,6 +5,7 @@ // Axom includes #include "axom/mint.hpp" +#include "axom/sidre.hpp" #include "quest_test_utilities.hpp" #include "axom/quest/interface/inout.hpp" @@ -72,6 +73,18 @@ TEST(quest_initialize, signed_distance_pointer_initialize) delete input_mesh; } +// Test immediately reserving space in UnstructuredMesh. +TEST(quest_initialize, immediate_ug_reserve) +{ + axom::sidre::DataStore objectDS; + axom::sidre::Group* meshGroup = objectDS.getRoot()->createGroup("myGroup"); + axom::mint::UnstructuredMesh contourMesh( + 2, + axom::mint::CellType::SEGMENT, + meshGroup); + contourMesh.reserveCells(10); // This may unexpectedly crash. +} + int main(int argc, char** argv) { #ifdef AXOM_USE_MPI From ba90110f7782ab9dd545ab47b52c2c9ef3718102 Mon Sep 17 00:00:00 2001 From: "Brian T.N. Gunney" Date: Wed, 7 Feb 2024 07:35:07 -0800 Subject: [PATCH 02/16] Add missing include guard. --- src/axom/quest/tests/quest_initialize.cpp | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/axom/quest/tests/quest_initialize.cpp b/src/axom/quest/tests/quest_initialize.cpp index fb1423e26d..8e5194ba21 100644 --- a/src/axom/quest/tests/quest_initialize.cpp +++ b/src/axom/quest/tests/quest_initialize.cpp @@ -5,8 +5,10 @@ // Axom includes #include "axom/mint.hpp" -#include "axom/sidre.hpp" #include "quest_test_utilities.hpp" +#if defined AXOM_USE_SIDRE + #include "axom/sidre.hpp" +#endif #include "axom/quest/interface/inout.hpp" #include "axom/quest/interface/signed_distance.hpp" @@ -73,6 +75,7 @@ TEST(quest_initialize, signed_distance_pointer_initialize) delete input_mesh; } +#if defined AXOM_USE_SIDRE // Test immediately reserving space in UnstructuredMesh. TEST(quest_initialize, immediate_ug_reserve) { @@ -84,6 +87,7 @@ TEST(quest_initialize, immediate_ug_reserve) meshGroup); contourMesh.reserveCells(10); // This may unexpectedly crash. } +#endif int main(int argc, char** argv) { From c96baed342db4d9dbdb5c8c6311d5054b39ae36a Mon Sep 17 00:00:00 2001 From: "Brian T.N. Gunney" Date: Fri, 4 Oct 2024 16:58:40 -0700 Subject: [PATCH 03/16] Work-around for the crash: Use allocate + copy + deallocate. I don't know the true cause of the crash or why it only exhibits on our docker environments. An ideal fix based on an understanding of the bug should be pursued. This commit also backs out work-arounds for avoiding trigging the crash. --- src/axom/core/memory_management.hpp | 23 ++++++++++++++++++- .../examples/quest_marching_cubes_example.cpp | 5 ++-- 2 files changed, 24 insertions(+), 4 deletions(-) diff --git a/src/axom/core/memory_management.hpp b/src/axom/core/memory_management.hpp index 3475694e6a..92f046c990 100644 --- a/src/axom/core/memory_management.hpp +++ b/src/axom/core/memory_management.hpp @@ -235,7 +235,28 @@ inline T* reallocate(T* pointer, std::size_t n, int allocID) noexcept } else { - pointer = static_cast(rm.reallocate(pointer, numbytes)); + constexpr bool workAround = true; + if(workAround) + { + /* + This work-around addresses issue #1287 and PR #1271. + The reproducer is the immediate_ug_reserve test in file + axom/src/axom/quest/test/quest_initialize.cpp. This + work-around doesn't address the actual cause of the problem, + something we should try to identify and fix. + */ + auto oldPointer = pointer; + auto foundAllocator = rm.getAllocator(pointer); + auto oldSize = foundAllocator.getSize(pointer); + pointer = static_cast(foundAllocator.allocate(numbytes)); + auto copysize = std::min(oldSize, numbytes); + axom::copy(pointer, oldPointer, copysize); + axom::deallocate(oldPointer); + } + else + { + pointer = static_cast(rm.reallocate(pointer, numbytes)); + } } #else diff --git a/src/axom/quest/examples/quest_marching_cubes_example.cpp b/src/axom/quest/examples/quest_marching_cubes_example.cpp index f324660ecb..3e17fedfab 100644 --- a/src/axom/quest/examples/quest_marching_cubes_example.cpp +++ b/src/axom/quest/examples/quest_marching_cubes_example.cpp @@ -916,13 +916,12 @@ struct ContourTestBase AXOM_ANNOTATE_BEGIN("convert to mint mesh"); std::string sidreGroupName = "contour_mesh"; sidre::DataStore objectDS; - // While awaiting fix for PR #1271, don't use Sidre storage in contourMesh. auto* meshGroup = objectDS.getRoot()->createGroup(sidreGroupName); - AXOM_UNUSED_VAR(meshGroup); // variable is only referenced in debug configs axom::mint::UnstructuredMesh contourMesh( DIM, - DIM == 2 ? mint::CellType::SEGMENT : mint::CellType::TRIANGLE); + DIM == 2 ? mint::CellType::SEGMENT : mint::CellType::TRIANGLE, + meshGroup); axom::utilities::Timer extractTimer(false); extractTimer.start(); mc.populateContourMesh(contourMesh, m_parentCellIdField, m_domainIdField); From c36ec8c43cff78116921fe303a962dd70329fad0 Mon Sep 17 00:00:00 2001 From: "Brian T.N. Gunney" Date: Wed, 9 Oct 2024 03:48:14 +0000 Subject: [PATCH 04/16] Disable the work-around and add tests that bypass mint. New tests reproduces the crash without involving mint and seems to implicate sidre::View memory management. --- src/axom/core/memory_management.hpp | 2 +- src/axom/quest/tests/quest_initialize.cpp | 22 ++++++++++++++++++++++ 2 files changed, 23 insertions(+), 1 deletion(-) diff --git a/src/axom/core/memory_management.hpp b/src/axom/core/memory_management.hpp index 92f046c990..60b553f487 100644 --- a/src/axom/core/memory_management.hpp +++ b/src/axom/core/memory_management.hpp @@ -235,7 +235,7 @@ inline T* reallocate(T* pointer, std::size_t n, int allocID) noexcept } else { - constexpr bool workAround = true; + constexpr bool workAround = false; if(workAround) { /* diff --git a/src/axom/quest/tests/quest_initialize.cpp b/src/axom/quest/tests/quest_initialize.cpp index 8e5194ba21..470506591b 100644 --- a/src/axom/quest/tests/quest_initialize.cpp +++ b/src/axom/quest/tests/quest_initialize.cpp @@ -75,6 +75,28 @@ TEST(quest_initialize, signed_distance_pointer_initialize) delete input_mesh; } +TEST(quest_initialize, direct_reallocations) +{ + int* b3 = axom::allocate(0); + EXPECT_NE(b3, nullptr); + + int* b4 = axom::reallocate(b3, 20); + EXPECT_NE(b4, nullptr); +} + +TEST(quest_initialize, sidre_reallocations) +{ + axom::sidre::DataStore objectDS; + axom::sidre::Group* group = objectDS.getRoot()->createGroup("myGroup"); + + axom::sidre::View* v3 = group->createView("v3", conduit::DataType::int32(10)); + v3->allocate(); + EXPECT_NE(v3->getVoidPtr(), nullptr); + + v3->reallocate(20); + EXPECT_NE(v3->getVoidPtr(), nullptr); +} + #if defined AXOM_USE_SIDRE // Test immediately reserving space in UnstructuredMesh. TEST(quest_initialize, immediate_ug_reserve) From cdf6ffb3615e539a2093e5982a052a46cf39405a Mon Sep 17 00:00:00 2001 From: "Brian T.N. Gunney" Date: Wed, 9 Oct 2024 04:45:00 +0000 Subject: [PATCH 05/16] Fix an un-related compile fail in the new test code. --- src/axom/quest/tests/quest_initialize.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/axom/quest/tests/quest_initialize.cpp b/src/axom/quest/tests/quest_initialize.cpp index 470506591b..88c8fcc237 100644 --- a/src/axom/quest/tests/quest_initialize.cpp +++ b/src/axom/quest/tests/quest_initialize.cpp @@ -84,10 +84,12 @@ TEST(quest_initialize, direct_reallocations) EXPECT_NE(b4, nullptr); } +#if defined AXOM_USE_SIDRE +// Test allocation/reallocation using sidre::View. TEST(quest_initialize, sidre_reallocations) { axom::sidre::DataStore objectDS; - axom::sidre::Group* group = objectDS.getRoot()->createGroup("myGroup"); + axom::sidre::Group* group = objectDS.getRoot(); axom::sidre::View* v3 = group->createView("v3", conduit::DataType::int32(10)); v3->allocate(); @@ -97,7 +99,6 @@ TEST(quest_initialize, sidre_reallocations) EXPECT_NE(v3->getVoidPtr(), nullptr); } -#if defined AXOM_USE_SIDRE // Test immediately reserving space in UnstructuredMesh. TEST(quest_initialize, immediate_ug_reserve) { From 681d03532659c685ffa3d85cab781e64fbcfbd8f Mon Sep 17 00:00:00 2001 From: "Brian T.N. Gunney" Date: Wed, 9 Oct 2024 04:45:43 +0000 Subject: [PATCH 06/16] Add test to allocate and reallocate in sidre package. --- src/axom/sidre/tests/sidre_view.cpp | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/src/axom/sidre/tests/sidre_view.cpp b/src/axom/sidre/tests/sidre_view.cpp index a210a72f99..1775a1d157 100644 --- a/src/axom/sidre/tests/sidre_view.cpp +++ b/src/axom/sidre/tests/sidre_view.cpp @@ -402,6 +402,23 @@ TEST(sidre_view, dealloc) //------------------------------------------------------------------------------ +// allocate/reallocate. + +TEST(sidre_view, allocate_reallocate) +{ + axom::sidre::DataStore objectDS; + axom::sidre::Group* group = objectDS.getRoot(); + + axom::sidre::View* v1 = group->createView("v1", conduit::DataType::int32(10)); + v1->allocate(); + EXPECT_NE(v1->getVoidPtr(), nullptr); + + v1->reallocate(20); + EXPECT_NE(v1->getVoidPtr(), nullptr); +} + +//------------------------------------------------------------------------------ + // allocate/reallocate with zero items results in allocated (yet zero). TEST(sidre_view, alloc_zero_items) From 276c37d887fbd679b876017a25f1aa2a941280c0 Mon Sep 17 00:00:00 2001 From: "Brian T.N. Gunney" Date: Wed, 9 Oct 2024 03:43:53 -0700 Subject: [PATCH 07/16] Add test that use only Buffer interface, eliminating Views code as source of error. --- src/axom/quest/tests/quest_initialize.cpp | 23 ++++++++++++++++++----- 1 file changed, 18 insertions(+), 5 deletions(-) diff --git a/src/axom/quest/tests/quest_initialize.cpp b/src/axom/quest/tests/quest_initialize.cpp index 88c8fcc237..5898582475 100644 --- a/src/axom/quest/tests/quest_initialize.cpp +++ b/src/axom/quest/tests/quest_initialize.cpp @@ -86,10 +86,23 @@ TEST(quest_initialize, direct_reallocations) #if defined AXOM_USE_SIDRE // Test allocation/reallocation using sidre::View. -TEST(quest_initialize, sidre_reallocations) +TEST(quest_initialize, buffer_reallocations) { - axom::sidre::DataStore objectDS; - axom::sidre::Group* group = objectDS.getRoot(); + axom::sidre::DataStore dataStore; + + axom::sidre::Buffer* b1 = dataStore.createBuffer(axom::sidre::DataTypeId::INT32_ID, 10); + b1->allocate(); + EXPECT_NE(b1->getVoidPtr(), nullptr); + + b1->reallocate(20); + EXPECT_NE(b1->getVoidPtr(), nullptr); +} + +// Test allocation/reallocation using sidre::View. +TEST(quest_initialize, view_reallocations) +{ + axom::sidre::DataStore dataStore; + axom::sidre::Group* group = dataStore.getRoot(); axom::sidre::View* v3 = group->createView("v3", conduit::DataType::int32(10)); v3->allocate(); @@ -102,8 +115,8 @@ TEST(quest_initialize, sidre_reallocations) // Test immediately reserving space in UnstructuredMesh. TEST(quest_initialize, immediate_ug_reserve) { - axom::sidre::DataStore objectDS; - axom::sidre::Group* meshGroup = objectDS.getRoot()->createGroup("myGroup"); + axom::sidre::DataStore dataStore; + axom::sidre::Group* meshGroup = dataStore.getRoot()->createGroup("myGroup"); axom::mint::UnstructuredMesh contourMesh( 2, axom::mint::CellType::SEGMENT, From cc83e71ef4cc459a75f4c2453af16d10dc8de8c8 Mon Sep 17 00:00:00 2001 From: "Brian T.N. Gunney" Date: Wed, 9 Oct 2024 04:33:02 -0700 Subject: [PATCH 08/16] Add tests to verify allocate/deallocate works without sidre::Buffer. --- src/axom/quest/tests/quest_initialize.cpp | 32 ++++++++++++++++++----- 1 file changed, 26 insertions(+), 6 deletions(-) diff --git a/src/axom/quest/tests/quest_initialize.cpp b/src/axom/quest/tests/quest_initialize.cpp index 5898582475..238f4aa1f0 100644 --- a/src/axom/quest/tests/quest_initialize.cpp +++ b/src/axom/quest/tests/quest_initialize.cpp @@ -75,27 +75,45 @@ TEST(quest_initialize, signed_distance_pointer_initialize) delete input_mesh; } -TEST(quest_initialize, direct_reallocations) +// Test allocation/reallocation using axom::allocate and axom::reallocate bytes +TEST(quest_initialize, byte_reallocations) { - int* b3 = axom::allocate(0); + std::int8_t* b1 = axom::allocate(40); + EXPECT_NE(b1, nullptr); + + b1 = axom::reallocate(b1, 80); + EXPECT_NE(b1, nullptr); + + axom::deallocate(b1); +} + +// Test allocation/reallocation using axom::allocate and axom::reallocate ints +TEST(quest_initialize, int_reallocations) +{ + int* b3 = axom::allocate(10); EXPECT_NE(b3, nullptr); - int* b4 = axom::reallocate(b3, 20); - EXPECT_NE(b4, nullptr); + b3 = axom::reallocate(b3, 20); + EXPECT_NE(b3, nullptr); + + axom::deallocate(b3); } #if defined AXOM_USE_SIDRE -// Test allocation/reallocation using sidre::View. +// Test allocation/reallocation using sidre::Buffer. TEST(quest_initialize, buffer_reallocations) { axom::sidre::DataStore dataStore; - axom::sidre::Buffer* b1 = dataStore.createBuffer(axom::sidre::DataTypeId::INT32_ID, 10); + axom::sidre::Buffer* b1 = + dataStore.createBuffer(axom::sidre::DataTypeId::INT32_ID, 10); b1->allocate(); EXPECT_NE(b1->getVoidPtr(), nullptr); b1->reallocate(20); EXPECT_NE(b1->getVoidPtr(), nullptr); + + axom::deallocate(b1); } // Test allocation/reallocation using sidre::View. @@ -110,6 +128,8 @@ TEST(quest_initialize, view_reallocations) v3->reallocate(20); EXPECT_NE(v3->getVoidPtr(), nullptr); + + v3->deallocate(); } // Test immediately reserving space in UnstructuredMesh. From b8cf67dd6e1e4f2af96f8dbe3b3b5cee5bfb3f06 Mon Sep 17 00:00:00 2001 From: "Brian T.N. Gunney" Date: Wed, 9 Oct 2024 18:08:31 -0700 Subject: [PATCH 09/16] Fix a bug in new test. --- src/axom/quest/tests/quest_initialize.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/axom/quest/tests/quest_initialize.cpp b/src/axom/quest/tests/quest_initialize.cpp index 238f4aa1f0..7dd6af95c4 100644 --- a/src/axom/quest/tests/quest_initialize.cpp +++ b/src/axom/quest/tests/quest_initialize.cpp @@ -113,7 +113,7 @@ TEST(quest_initialize, buffer_reallocations) b1->reallocate(20); EXPECT_NE(b1->getVoidPtr(), nullptr); - axom::deallocate(b1); + b1->deallocate(); } // Test allocation/reallocation using sidre::View. From ccced65222842b2b11f63adb4da8b895dd7f6063 Mon Sep 17 00:00:00 2001 From: "Brian T.N. Gunney" Date: Wed, 9 Oct 2024 18:11:33 -0700 Subject: [PATCH 10/16] Build Umpire TPL shared in docker. See if that fixes the crash. Our hypothesis is that static Umpire and shared Axom somehow leads to two ResourceManager singletons. --- scripts/spack/configs/docker/ubuntu22/spack.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/spack/configs/docker/ubuntu22/spack.yaml b/scripts/spack/configs/docker/ubuntu22/spack.yaml index 78908269a6..0ab4d7f192 100644 --- a/scripts/spack/configs/docker/ubuntu22/spack.yaml +++ b/scripts/spack/configs/docker/ubuntu22/spack.yaml @@ -165,7 +165,7 @@ spack: scr: require: "@3.0.1~shared~tests~examples" umpire: - require: "@2024.07.0~shared~examples~werror" + require: "@2024.07.0+shared~examples~werror" # Globally lock in version of devtools cmake: From 7a449f92f9ffad70a8c0961e9383335370cef264 Mon Sep 17 00:00:00 2001 From: "Brian T.N. Gunney" Date: Thu, 10 Oct 2024 08:34:13 -0700 Subject: [PATCH 11/16] Rebuild docker images with shared Umpire library. --- host-configs/docker/clang@14.0.0.cmake | 8 ++++---- host-configs/docker/gcc@13.1.0.cmake | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/host-configs/docker/clang@14.0.0.cmake b/host-configs/docker/clang@14.0.0.cmake index b10bf5239b..2d0ebf438f 100644 --- a/host-configs/docker/clang@14.0.0.cmake +++ b/host-configs/docker/clang@14.0.0.cmake @@ -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" 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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 "") @@ -91,7 +91,7 @@ set(LUA_DIR "/usr" CACHE PATH "") 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 "") diff --git a/host-configs/docker/gcc@13.1.0.cmake b/host-configs/docker/gcc@13.1.0.cmake index 9903e02b9e..69821f301b 100644 --- a/host-configs/docker/gcc@13.1.0.cmake +++ b/host-configs/docker/gcc@13.1.0.cmake @@ -4,13 +4,13 @@ # CMake executable path: /usr/local/bin/cmake #------------------------------------------------------------------------------ -set(CMAKE_PREFIX_PATH 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"/home/axom/axom_tpls/gcc-13.1.0/axom-develop-luxg4gk3kz7dz5varsclvghbav6m7jh4/lib;/home/axom/axom_tpls/gcc-13.1.0/axom-develop-luxg4gk3kz7dz5varsclvghbav6m7jh4/lib64;/home/axom/axom_tpls/gcc-13.1.0/adiak-0.4.0-a5snac3dmnvrdevxvs6g3fgswpl6rwk3/lib;/home/axom/axom_tpls/gcc-13.1.0/gcc-runtime-13.1.0-hxyekq6c3ihrn66ro3b6ypzq6kg5awrm/lib;/home/axom/axom_tpls/gcc-13.1.0/caliper-2.10.0-tdr37n7gay6uoqmdw2oj4wwaxdghgtn5/lib;/home/axom/axom_tpls/gcc-13.1.0/elfutils-0.191-kptewlijpd6x3ft3hroikmkc6qjfncpu/lib;/home/axom/axom_tpls/gcc-13.1.0/libiconv-1.17-g5wxbxpkhhpcimbmmstmwv4qg366swp4/lib;/home/axom/axom_tpls/gcc-13.1.0/pkgconf-2.2.0-po553barjadpcxi66bmnkzhpornl7ei2/lib;/home/axom/axom_tpls/gcc-13.1.0/xz-5.4.6-rosh6ypotokoprccdmjiemlg7ne5bmyq/lib;/home/axom/axom_tpls/gcc-13.1.0/zlib-ng-2.2.1-adq5uevpd2ikujgb33j7beigfmchh25t/lib;/home/axom/axom_tpls/gcc-13.1.0/zstd-1.5.6-7csff4jw5wtgljbl4y5j7hvjghuqrni2/lib;/home/axom/axom_tpls/gcc-13.1.0/libunwind-1.6.2-uirmjkjmcnqqt6xth2bptu5eoeqzu4nn/lib;/home/axom/axom_tpls/gcc-13.1.0/conduit-0.9.2-lcdtevgkh5bbpklklnvsowc3vdditqpo/lib;/home/axom/axom_tpls/gcc-13.1.0/hdf5-1.8.23-oi5ufdr27irz6rnjdj656eou2od3zfrc/lib;/home/axom/axom_tpls/gcc-13.1.0/metis-5.1.0-rjlnybcmutwgdsb27z42ijaoe7wds5o5/lib;/home/axom/axom_tpls/gcc-13.1.0/parmetis-4.0.3-utygb5gonzx3cgj4woxncetbsw2zi2tm/lib;/home/axom/axom_tpls/gcc-13.1.0/mfem-4.6.0-5fjoim3uxggiliuc44wui67rbjmgh7hq/lib;/home/axom/axom_tpls/gcc-13.1.0/hypre-2.24.0-7pacjj7ewndpjzazjwbp6qghas4ws3ip/lib;/home/axom/axom_tpls/gcc-13.1.0/raja-2024.07.0-rymjdaxurpykwax25lwylyiv772poffj/lib;/home/axom/axom_tpls/gcc-13.1.0/camp-2024.07.0-wneowcxzurhqrmg42ogjv63gyfhr2lnd/lib;/home/axom/axom_tpls/gcc-13.1.0/umpire-2024.07.0-dhvhgdddiby4qvci3xvlvtw2dbzrglje/lib;/home/axom/axom_tpls/gcc-13.1.0/fmt-11.0.2-hsbwcggb37md6wtz4tjbh3z2paokho4y/lib" CACHE STRING "") set(CMAKE_BUILD_TYPE "Release" CACHE STRING "") @@ -89,7 +89,7 @@ set(LUA_DIR "/usr" CACHE PATH "") set(RAJA_DIR "${TPL_ROOT}/raja-2024.07.0-rymjdaxurpykwax25lwylyiv772poffj" CACHE PATH "") -set(UMPIRE_DIR "${TPL_ROOT}/umpire-2024.07.0-k3g2kkrgg3xm7gd4wk77muqugnot6fft" CACHE PATH "") +set(UMPIRE_DIR "${TPL_ROOT}/umpire-2024.07.0-dhvhgdddiby4qvci3xvlvtw2dbzrglje" CACHE PATH "") set(ADIAK_DIR "${TPL_ROOT}/adiak-0.4.0-a5snac3dmnvrdevxvs6g3fgswpl6rwk3" CACHE PATH "") From 5202846b61940de73f16740aa0e0480101d39d49 Mon Sep 17 00:00:00 2001 From: "Brian T.N. Gunney" Date: Thu, 10 Oct 2024 09:04:51 -0700 Subject: [PATCH 12/16] Use new docker images with shared Umpire libs. --- azure-pipelines.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index b5cdc6bfb8..d19f52ba60 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -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' + GCC13_IMAGENAME: 'axom/tpls:gcc-13_10-10-24_01h-31m' system.debug: false jobs: From 3aae97af368bd5b8c3bb776fd190ccc86292ff0d Mon Sep 17 00:00:00 2001 From: "Brian T.N. Gunney" Date: Thu, 10 Oct 2024 09:19:36 -0700 Subject: [PATCH 13/16] Backout work-around and remove a redundant test. --- src/axom/core/memory_management.hpp | 23 +---------------------- src/axom/sidre/tests/sidre_view.cpp | 17 ----------------- 2 files changed, 1 insertion(+), 39 deletions(-) diff --git a/src/axom/core/memory_management.hpp b/src/axom/core/memory_management.hpp index 60b553f487..3475694e6a 100644 --- a/src/axom/core/memory_management.hpp +++ b/src/axom/core/memory_management.hpp @@ -235,28 +235,7 @@ inline T* reallocate(T* pointer, std::size_t n, int allocID) noexcept } else { - constexpr bool workAround = false; - if(workAround) - { - /* - This work-around addresses issue #1287 and PR #1271. - The reproducer is the immediate_ug_reserve test in file - axom/src/axom/quest/test/quest_initialize.cpp. This - work-around doesn't address the actual cause of the problem, - something we should try to identify and fix. - */ - auto oldPointer = pointer; - auto foundAllocator = rm.getAllocator(pointer); - auto oldSize = foundAllocator.getSize(pointer); - pointer = static_cast(foundAllocator.allocate(numbytes)); - auto copysize = std::min(oldSize, numbytes); - axom::copy(pointer, oldPointer, copysize); - axom::deallocate(oldPointer); - } - else - { - pointer = static_cast(rm.reallocate(pointer, numbytes)); - } + pointer = static_cast(rm.reallocate(pointer, numbytes)); } #else diff --git a/src/axom/sidre/tests/sidre_view.cpp b/src/axom/sidre/tests/sidre_view.cpp index 1775a1d157..a210a72f99 100644 --- a/src/axom/sidre/tests/sidre_view.cpp +++ b/src/axom/sidre/tests/sidre_view.cpp @@ -402,23 +402,6 @@ TEST(sidre_view, dealloc) //------------------------------------------------------------------------------ -// allocate/reallocate. - -TEST(sidre_view, allocate_reallocate) -{ - axom::sidre::DataStore objectDS; - axom::sidre::Group* group = objectDS.getRoot(); - - axom::sidre::View* v1 = group->createView("v1", conduit::DataType::int32(10)); - v1->allocate(); - EXPECT_NE(v1->getVoidPtr(), nullptr); - - v1->reallocate(20); - EXPECT_NE(v1->getVoidPtr(), nullptr); -} - -//------------------------------------------------------------------------------ - // allocate/reallocate with zero items results in allocated (yet zero). TEST(sidre_view, alloc_zero_items) From 6c509777fcf80f2984ec2950411b87d70029398c Mon Sep 17 00:00:00 2001 From: "Brian T.N. Gunney" Date: Thu, 10 Oct 2024 12:58:05 -0700 Subject: [PATCH 14/16] Guard code for non-Sidre builds. --- src/axom/quest/examples/quest_marching_cubes_example.cpp | 8 +++++++- src/axom/quest/tests/quest_initialize.cpp | 4 +++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/src/axom/quest/examples/quest_marching_cubes_example.cpp b/src/axom/quest/examples/quest_marching_cubes_example.cpp index 3e17fedfab..3c1223533e 100644 --- a/src/axom/quest/examples/quest_marching_cubes_example.cpp +++ b/src/axom/quest/examples/quest_marching_cubes_example.cpp @@ -916,12 +916,18 @@ struct ContourTestBase AXOM_ANNOTATE_BEGIN("convert to mint mesh"); std::string sidreGroupName = "contour_mesh"; sidre::DataStore objectDS; - auto* meshGroup = objectDS.getRoot()->createGroup(sidreGroupName); +#ifdef AXOM_MINT_USE_SIDRE + auto* meshGroup = objectDS.getRoot()->createGroup(sidreGroupName); axom::mint::UnstructuredMesh contourMesh( DIM, DIM == 2 ? mint::CellType::SEGMENT : mint::CellType::TRIANGLE, meshGroup); +#else + axom::mint::UnstructuredMesh contourMesh( + DIM, + DIM == 2 ? mint::CellType::SEGMENT : mint::CellType::TRIANGLE); +#endif axom::utilities::Timer extractTimer(false); extractTimer.start(); mc.populateContourMesh(contourMesh, m_parentCellIdField, m_domainIdField); diff --git a/src/axom/quest/tests/quest_initialize.cpp b/src/axom/quest/tests/quest_initialize.cpp index 7dd6af95c4..6edcf8706b 100644 --- a/src/axom/quest/tests/quest_initialize.cpp +++ b/src/axom/quest/tests/quest_initialize.cpp @@ -99,7 +99,7 @@ TEST(quest_initialize, int_reallocations) axom::deallocate(b3); } -#if defined AXOM_USE_SIDRE +#if defined(AXOM_USE_SIDRE) // Test allocation/reallocation using sidre::Buffer. TEST(quest_initialize, buffer_reallocations) { @@ -132,6 +132,7 @@ TEST(quest_initialize, view_reallocations) v3->deallocate(); } +#ifdef AXOM_MINT_USE_SIDRE // Test immediately reserving space in UnstructuredMesh. TEST(quest_initialize, immediate_ug_reserve) { @@ -144,6 +145,7 @@ TEST(quest_initialize, immediate_ug_reserve) contourMesh.reserveCells(10); // This may unexpectedly crash. } #endif +#endif int main(int argc, char** argv) { From cf9f91036e3a8a04253c5968cbf61f47bbbdf76b Mon Sep 17 00:00:00 2001 From: "Brian T.N. Gunney" Date: Thu, 10 Oct 2024 13:16:06 -0700 Subject: [PATCH 15/16] Add comment explaining why new tests are in quest instead of sidre or mint. --- src/axom/quest/tests/quest_initialize.cpp | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/axom/quest/tests/quest_initialize.cpp b/src/axom/quest/tests/quest_initialize.cpp index 6edcf8706b..2c49c8f2f0 100644 --- a/src/axom/quest/tests/quest_initialize.cpp +++ b/src/axom/quest/tests/quest_initialize.cpp @@ -4,6 +4,7 @@ // SPDX-License-Identifier: (BSD-3-Clause) // Axom includes +#include "axom/config.hpp" #include "axom/mint.hpp" #include "quest_test_utilities.hpp" #if defined AXOM_USE_SIDRE @@ -75,6 +76,15 @@ TEST(quest_initialize, signed_distance_pointer_initialize) delete input_mesh; } +/* + The *_reallocations tests and the immediate_ug_reserve are + reproducers for the case of multiple Umpire instances that happens + when Umpire is built with static lib and Axom with shared libs. + The failures only appear when there are several shared libs that + include the static Umpire, e.g. axom::core, axom::sidre, axom::mint + and axom::quest. This issue is specific to the linker commands in + quest. +*/ // Test allocation/reallocation using axom::allocate and axom::reallocate bytes TEST(quest_initialize, byte_reallocations) { From e9844eaeb5049c0b6c6dfb2a901b9df257455e4f Mon Sep 17 00:00:00 2001 From: "Brian T.N. Gunney" Date: Thu, 10 Oct 2024 13:33:46 -0700 Subject: [PATCH 16/16] Autoformat. --- src/axom/quest/tests/quest_initialize.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/axom/quest/tests/quest_initialize.cpp b/src/axom/quest/tests/quest_initialize.cpp index 2c49c8f2f0..cc78cff609 100644 --- a/src/axom/quest/tests/quest_initialize.cpp +++ b/src/axom/quest/tests/quest_initialize.cpp @@ -142,7 +142,7 @@ TEST(quest_initialize, view_reallocations) v3->deallocate(); } -#ifdef AXOM_MINT_USE_SIDRE + #ifdef AXOM_MINT_USE_SIDRE // Test immediately reserving space in UnstructuredMesh. TEST(quest_initialize, immediate_ug_reserve) { @@ -154,7 +154,7 @@ TEST(quest_initialize, immediate_ug_reserve) meshGroup); contourMesh.reserveCells(10); // This may unexpectedly crash. } -#endif + #endif #endif int main(int argc, char** argv)