Merge branch 'develop' into feature/chai-submodule

LLNL · Jul 15, 2024 · 6f1d305 · 6f1d305
2 parents 1f50e9c + a5dde1d
commit 6f1d305
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diff --git a/.gitlab/scripts.yml b/.gitlab/scripts.yml
@@ -98,38 +98,12 @@
   script:
     - INSTALL_DIR=/usr/gapps/Spheral/$SYS_TYPE/spheral-$SPHERAL_REV_STR
     - DEV_PKG_NAME=$SYS_TYPE-spheral-dev-pkg-$SPHERAL_REV_STR
-    - DEV_PKG_PATH=$INSTALL_DIR/$DEV_PKG_NAME
+
+    - env SPHERAL_REV_STR=$SPHERAL_REV_STR INSTALL_DIR=$INSTALL_DIR SPEC=$SPEC SPACK_PKG_NAME=$SPACK_PKG_NAME BUILD_ALLOC="$BUILD_ALLOC" SCRIPT_DIR=$SCRIPT_DIR
+      bash ./$SCRIPT_DIR/lc/generate-buildcache.sh
+
     - echo $INSTALL_DIR &> install-dir.txt
     - echo $DEV_PKG_NAME &> dev-pkg-name.txt
-
-    # *** Copy spheral src and all submodules. ***
-    - mkdir -p $DEV_PKG_PATH/resources && cp -a $CI_PROJECT_DIR/. $DEV_PKG_PATH
-
-    ### Initialize the upstream spack instance for this platform.
-    ###   - We do this to load system configs / externals for this machine.
-    - ./$SCRIPT_DIR/devtools/tpl-manager.py --init-only --spheral-spack-dir=$UPSTREAM_DIR --spec=none
-    - source $UPSTREAM_DIR/spack/share/spack/setup-env.sh
-
-    ### Installation Directory w/ Spheral rev numbers.
-
-    ### Create a temporary spack environement with only the TPL specs for this specific commit of Spheral
-    - spack env create -d $INSTALL_DIR
-    - spack env activate $INSTALL_DIR
-    - spack add $SPACK_PKG_NAME@develop%$SPEC
-    - spack concretize --fresh -f
-
-    # *** Pre-built binaries for $SYS_TYPE. ***
-    - spack buildcache create -auf -d $DEV_PKG_PATH/resources $(spack find --format /{hash})
-    # *** All TPL tar files. ***
-    - spack mirror create -a -d $DEV_PKG_PATH/resources/mirror --exclude-specs "llnlspheral spheral"
-    # *** Spack bootstrapping resources. ***
-    - spack bootstrap mirror --binary-packages $DEV_PKG_PATH/resources
-
-    ### Wrap it all up. 
-    - tar -czvf "$DEV_PKG_PATH".tar.gz -C $INSTALL_DIR $DEV_PKG_NAME
-
-    ### Cleanup
-    - rm -rf $DEV_PKG_PATH
 
   artifacts:
     paths:

diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
@@ -1,12 +1,23 @@
-Version vYYYY.MM.p -- Release date YYYY-MM-DD
+Version v2024.06.1 -- Release date 2024-07-09
+==============================================
+
+  * Important Notes:
+    * This is a patch release for v2024.06.0.
+
+  * Bug Fixes / improvements:
+    * CD pipeline hotfix for installing release builds on LC machines.
+    * Fixes an issue with the use of the axom::quest::SignedDistance interface. 
+
+Version v2024.06.0 -- Release date 2024-06-27
 ==============================================
   * Important Notes:
     * External users of the code will need to supply config files for tpl-manager to find system libraries correctly. Steps to do this are detailed in the external user build guide. 
 
 Notable changes include:
 
-  * New features/ API changes:
-    * added MFV hydro from Hopkins 2015 with extension for ALE options
+  * New features / API changes:
+    * Added MFV hydro from Hopkins 2015 with extension for ALE options.
+    * Adding optional user specified smoothing scale method for SPH, FSISPH, and CRKSPH.
 
   * Build changes / improvements:
     * PYBind11 libraries no longer depend on the structure of the PYB11 source directory.
@@ -24,6 +35,9 @@ Notable changes include:
       * Versions for python dependencies in the Spheral spack recipe are fixed and updated (in some cases).
 
   * Bug Fixes / improvements:
+    * Corrected an erroneous VERIFY in the P-alpha porosity constructor (with Fields of porosity and sound speed) that forced runs to stop even with correct input parameters
+    * Fixed a bug in the standard ASPH hydros (ASPH, SolidASPH, and RZ varieties) that gave incorrect results.  FSI ad CRK models with ASPH smoothing scales were OK, but standard
+      SPH using ASPH smoothing scales were simply incorrect for non-unit aspect ratio H's.  Also added ATS tests to help catch such errors going forward.
 
 Version v2024.01.1 -- Release date 2024-02-17
 ==============================================

diff --git a/cmake/FindSphinx.cmake b/cmake/FindSphinx.cmake
diff --git a/cmake/SetupSpheral.cmake b/cmake/SetupSpheral.cmake
@@ -26,6 +26,7 @@ set(Python3_EXECUTABLE ${python_DIR}/bin/python3)
 
 set(ENABLE_MPI ON CACHE BOOL "")
 set(ENABLE_OPENMP ON CACHE BOOL "")
+set(BLT_DOCS_TARGET_NAME "blt_docs" CACHE STRING "")
 
 if(NOT SPHERAL_BLT_DIR) 
   set (SPHERAL_BLT_REL_DIR "${SPHERAL_ROOT_DIR}/cmake/blt" CACHE PATH "")

diff --git a/cmake/SpheralVersion.cmake b/cmake/SpheralVersion.cmake
@@ -1 +1 @@
-set(SPHERAL_VERSION 2024.01.1)
+set(SPHERAL_VERSION 2024.06.1)
diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
@@ -1,11 +1,4 @@
-#find_package(Sphinx)
-set(SPHINX_FOUND true)
-if (NOT DEFINED SPHINX_EXEC)
-  set(SPHINX_EXEC "${sphinx_DIR}/bin/sphinx-build" CACHE STRING "Path to sphinx documentation generator")
-endif()
-message("-- Sphinx ${SPHINX_EXEC}")
-
-if(ENABLE_DOCS AND NOT SPHINX_EXEC STREQUAL "SPHINX_EXEC-NOTFOUND")
+if(ENABLE_DOCS)
   if(NOT DEFINED SPHINX_THEME)
     set(SPHINX_THEME sphinx_rtd_theme)
   endif()
@@ -28,8 +21,8 @@ if(ENABLE_DOCS AND NOT SPHINX_EXEC STREQUAL "SPHINX_EXEC-NOTFOUND")
     "${BINARY_BUILD_DIR}/conf.py"
     @ONLY)
 
-  add_custom_target(Spheral_docs ALL
-    ${CMAKE_COMMAND} -E env PYTHONPATH=${SPACK_PYTHONPATH} ${PYTHON_EXE} -m sphinx
+  add_custom_target(docs ALL
+    env PYTHONPATH=${SPACK_PYTHONPATH} ${PYTHON_EXE} -m sphinx
     -q -b html
     -c "${BINARY_BUILD_DIR}"
     -d "${SPHINX_CACHE_DIR}"

diff --git a/docs/conf.py b/docs/conf.py
@@ -26,9 +26,9 @@
 author = 'J. Michael Owen'
 
 # The short X.Y version
-version = '2024.01.1'
+version = '2024.06.1'
 # The full version, including alpha/beta/rc tags
-release = '2024.01.1'
+release = '2024.06.1'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/conf.py.in b/docs/conf.py.in
@@ -26,9 +26,9 @@ copyright = '2012, LLNS'
 author = 'J. Michael Owen'
 
 # The short X.Y version
-version = '2024.01.1'
+version = '2024.06.1'
 # The full version, including alpha/beta/rc tags
-release = '2024.01.1'
+release = '2024.06.1'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/developer/dev/continuous_deployment.rst b/docs/developer/dev/continuous_deployment.rst
@@ -9,11 +9,10 @@ to their environment.
 
 On LC systems we maintain:
   * ``Spheral/risky``
+  * ``Spheral/2024.06.1``
   * ``Spheral/2024.01.1``
   * ``Spheral/2023.06.0``
   * ``Spheral/2023.03.1``
-  * ``Spheral/2023.03.0`` (deprecated as of TOSS4 upgrade)
-  * ``Spheral/2022.06.0`` (deprecated as of TOSS4 upgrade)
 
 Spheral/risky
 =============

diff --git a/scripts/lc/generate-buildcache.sh b/scripts/lc/generate-buildcache.sh
@@ -0,0 +1,46 @@
+trap 'echo "# $BASH_COMMAND"' DEBUG
+
+SPEC=${SPEC:-gcc@10.3.1}
+SPACK_PKG_NAME=${SPACK_PKG_NAME:-spheral}
+SPHERAL_SPEC=$SPACK_PKG_NAME@develop%$SPEC
+echo $SPHERAL_SPEC
+
+INSTALL_DIR=${INSTALL_DIR:-$PWD/../$SYS_TYPE/spheral-cache}
+SPHERAL_REV_STR=${SPHERAL_REV_STR:-undefined}
+
+
+UPSTREAM_DIR=${UPSTREAM_DIR:-/usr/WS2/sduser/Spheral/spack_upstream/0.22}
+SCRIPT_DIR=${SCRIPT_DIR:-'scripts'}
+DEV_PKG_NAME=$SYS_TYPE-spheral-dev-pkg-$SPHERAL_REV_STR
+DEV_PKG_DIR=$INSTALL_DIR/$DEV_PKG_NAME
+
+CI_PROJECT_DIR=${CI_PROJECT_DIR:-$PWD}
+
+RESOURCE_DIR=$DEV_PKG_DIR/resources
+echo $RESOURCE_DIR
+
+echo $INSTALL_DIR
+#echo $INSTALL_DIR &> install-dir.txt
+
+echo $DEV_PKG_DIR
+#echo $DEV_PKG_NAME &> dev-pkg-name.txt
+
+rm -rf $INSTALL_DIR
+mkdir -p $RESOURCE_DIR && cp -a $CI_PROJECT_DIR/. $DEV_PKG_DIR
+
+./$SCRIPT_DIR/devtools/tpl-manager.py --init-only --spheral-spack-dir=$UPSTREAM_DIR --spec=none
+source $UPSTREAM_DIR/spack/share/spack/setup-env.sh
+
+spack env rm -y -f $INSTALL_DIR
+spack env create -d $INSTALL_DIR
+spack env activate $INSTALL_DIR
+spack add $SPHERAL_SPEC
+spack concretize -f --fresh --deprecated
+
+spack mirror create -a -d $RESOURCE_DIR/mirror --exclude-specs "llnlspheral spheral"
+spack buildcache push -auf $RESOURCE_DIR/mirror $(spack find --format /{hash})
+
+spack bootstrap mirror --binary-packages $RESOURCE_DIR
+
+tar -czf $DEV_PKG_DIR.tar.gz -C $INSTALL_DIR $DEV_PKG_NAME
+
diff --git a/scripts/lc/install-from-dev-pkg.sh b/scripts/lc/install-from-dev-pkg.sh
@@ -22,16 +22,19 @@ echo $INSTALL_DIR
 echo $SCRIPT_DIR
 echo $BUILD_ALLOC
 
+rm -rf $INSTALL_DIR
 mkdir -p $INSTALL_DIR
 
 ./$SCRIPT_DIR/devtools/tpl-manager.py --spack-url $SPACK_URL --init-only --spec=none --no-upstream --spheral-spack-dir $INSTALL_DIR/spheral-spack-tpls
 
 source $INSTALL_DIR/spheral-spack-tpls/spack/share/spack/setup-env.sh
 spack bootstrap add --trust local-sources $PWD/resources/metadata/sources
 spack bootstrap add --trust local-binaries $PWD/resources/metadata/binaries
-spack mirror add spheral-mirror $PWD/resources/mirror
-spack mirror add spheral-cache $PWD/resources
-spack buildcache update-index -d $PWD/resources
+spack mirror rm spheral-mirror
+spack mirror rm spheral-cache
+spack mirror add --unsigned spheral-mirror $PWD/resources/mirror
+spack mirror add --unsigned spheral-cache $PWD/resources
+spack buildcache update-index $PWD/resources/mirror
 
 $BUILD_ALLOC spack install --fresh --deprecated --no-check-signature --only dependencies $SPACK_PKG_NAME@develop%$SPEC
 

diff --git a/scripts/spack/configs/toss_4_x86_64_ib/packages.yaml b/scripts/spack/configs/toss_4_x86_64_ib/packages.yaml
@@ -10,6 +10,7 @@ packages:
       mpi: [mvapich2]
       pkgconfig: [pkg-config]
       pil: [py-pillow]
+      jpeg: [libjpeg]
       zlib-api: [zlib]
   cmake:
     version: [3.23.1]

diff --git a/src/CRKSPH/CRKSPHHydros.py b/src/CRKSPH/CRKSPHHydros.py
@@ -22,7 +22,8 @@ def CRKSPH(dataBase,
            damageRelieveRubble = False,
            ASPH = False,
            etaMinAxis = 0.1,
-           crktype = "default"):
+           crktype = "default",
+           smoothingScaleMethod = None):
 
     # We use the provided DataBase to sniff out what sort of NodeLists are being
     # used, and based on this determine which SPH object to build.
@@ -62,10 +63,11 @@ def CRKSPH(dataBase,
         Q = eval("LimitedMonaghanGingoldViscosity%id(Clinear=%g, Cquadratic=%g)" % (ndim, Cl, Cq))
 
     # Smoothing scale update
-    if ASPH:
-        smoothingScaleMethod = eval("ASPHSmoothingScale%id()" % ndim)
-    else:
-        smoothingScaleMethod = eval("SPHSmoothingScale%id()" % ndim)
+    if smoothingScaleMethod is None:
+        if ASPH:
+            smoothingScaleMethod = eval("ASPHSmoothingScale%id()" % ndim)
+        else:
+            smoothingScaleMethod = eval("SPHSmoothingScale%id()" % ndim)
 
     # Build the constructor arguments
     kwargs = {"smoothingScaleMethod" : smoothingScaleMethod,

diff --git a/src/FSISPH/FSISPHHydros.py b/src/FSISPH/FSISPHHydros.py
@@ -4,32 +4,34 @@
 dims = spheralDimensions()
 
 def FSISPH(dataBase,
-        W,
-        Q = None,
-        slides=None,
-        cfl = 0.35,
-        surfaceForceCoefficient=0.0,
-        densityStabilizationCoefficient=0.1, 
-        specificThermalEnergyDiffusionCoefficient=0.1, 
-        xsphCoefficient=0.0,
-        interfaceMethod=HLLCInterface, 
-        kernelAveragingMethod = NeverAverageKernels,      
-        sumDensityNodeLists=[],
-        useVelocityMagnitudeForDt = False,
-        compatibleEnergyEvolution = True,
-        evolveTotalEnergy = False,
-        linearCorrectGradients = True,
-        planeStrain = False,
-        interfacePmin = 0.0,
-        interfaceNeighborAngleThreshold=0.707,
-        HUpdate = IdealH,
-        densityUpdate = FSISumMassDensity,
-        epsTensile = 0.0,
-        nTensile = 4.0,
-        xmin = (-1e100, -1e100, -1e100),
-        xmax = ( 1e100,  1e100,  1e100),
-        ASPH = False,
-        RZ = False):
+           W,
+           Q = None,
+           slides=None,
+           cfl = 0.35,
+           surfaceForceCoefficient=0.0,
+           densityStabilizationCoefficient=0.1, 
+           specificThermalEnergyDiffusionCoefficient=0.1, 
+           xsphCoefficient=0.0,
+           interfaceMethod=HLLCInterface, 
+           kernelAveragingMethod = NeverAverageKernels,      
+           sumDensityNodeLists=[],
+           useVelocityMagnitudeForDt = False,
+           compatibleEnergyEvolution = True,
+           evolveTotalEnergy = False,
+           linearCorrectGradients = True,
+           planeStrain = False,
+           interfacePmin = 0.0,
+           interfaceNeighborAngleThreshold=0.707,
+           HUpdate = IdealH,
+           densityUpdate = FSISumMassDensity,
+           epsTensile = 0.0,
+           nTensile = 4.0,
+           xmin = (-1e100, -1e100, -1e100),
+           xmax = ( 1e100,  1e100,  1e100),
+           ASPH = False,
+           RZ = False,
+           smoothingScaleMethod = None):
+
     ######################################################################
     # some of these parameters are inactive and possible on there was out.
     # strengthInDamage and damageRelieveRubble are old switches and are not
@@ -86,10 +88,11 @@ def FSISPH(dataBase,
         slides = eval("SlideSurface%id(dataBase,contactTypes)" % ndim)
 
     # Smoothing scale update
-    if ASPH:
-        smoothingScaleMethod = eval("ASPHSmoothingScale%id()" % ndim)
-    else:
-        smoothingScaleMethod = eval("SPHSmoothingScale%id()" % ndim)
+    if smoothingScaleMethod is None:
+        if ASPH:
+            smoothingScaleMethod = eval("ASPHSmoothingScale%id()" % ndim)
+        else:
+            smoothingScaleMethod = eval("SPHSmoothingScale%id()" % ndim)
 
     # Build the constructor arguments
     xmin = (ndim,) + xmin

diff --git a/src/Porosity/PalphaPorosity.cc b/src/Porosity/PalphaPorosity.cc
@@ -109,9 +109,6 @@ PalphaPorosity(const SolidNodeList<Dimension>& nodeList,
     for (auto i = 0u; i < n; ++i) {
       mc0[i] = c0[i];
     }
-    const auto alpha0_min = mAlpha0.min();
-    VERIFY2((1.0 <= mAlphae) and (mAlphae <= mAlphat) and (mAlphat <= alpha0_min),
-            "PalphaPorosity input ERROR : require 1.0 <= alphae <= alphat <= alpha0, (alphae, alphat, alpha0) = " << mAlphae << ", " << mAlphat << ", " << alpha0_min);
   }
 }
 

diff --git a/src/SPH/SPHHydroBase.cc b/src/SPH/SPHHydroBase.cc
@@ -843,15 +843,16 @@ evaluateDerivatives(const typename Dimension::Scalar time,
       const auto etaj = Hj*rij;
       const auto etaMagi = etai.magnitude();
       const auto etaMagj = etaj.magnitude();
-      const auto etaUnit = etai*safeInvVar(etaMagi);
+      const auto etaiUnit = etai*safeInvVar(etaMagi);
+      const auto etajUnit = etaj*safeInvVar(etaMagj);
       CHECK(etaMagi >= 0.0);
       CHECK(etaMagj >= 0.0);
 
       // Symmetrized kernel weight and gradient.
       W.kernelAndGradValue(etaMagi, Hdeti, Wi, gWi);
       W.kernelAndGradValue(etaMagj, Hdetj, Wj, gWj);
-      gradWi = gWi*Hi*etaUnit;
-      gradWj = gWj*Hj*etaUnit;
+      gradWi = gWi*Hi*etaiUnit;
+      gradWj = gWj*Hj*etajUnit;
       if (oneKernel) {
         WQi = Wi;
         WQj = Wj;
@@ -860,8 +861,8 @@ evaluateDerivatives(const typename Dimension::Scalar time,
       } else {
         WQ.kernelAndGradValue(etaMagi, Hdeti, WQi, gWQi);
         WQ.kernelAndGradValue(etaMagj, Hdetj, WQj, gWQj);
-        gradWQi = gWQi*Hi*etaUnit;
-        gradWQj = gWQj*Hj*etaUnit;
+        gradWQi = gWQi*Hi*etaiUnit;
+        gradWQj = gWQj*Hj*etajUnit;
       }
 
       // Zero'th and second moment of the node distribution -- used for the