Nsoblath/issue 226: FETK update (#227)

* Address missing linkages

* Cleanup FETK import

* Multithreaded build in docker now controlled by a build argument

* Install superlu as a dependency in the Ubuntu docker build

* Update the FETK version in use by the automatic builds (still on a development branch)

* Add in debugging tmate session for mac

* Manually build arpack to get the static lib (which seems to have disappeared?)

* Remove -j flags

* Set fortran compiler for arpack build

* Engaging brain, fixing mac-build commands

* Comment out tmate session

* Update the FETK commit to be the main branch, pre-release

* Update the changelog

* Updated default FETK build to commit v1.9.3 (57195e)

Co-authored-by: Noah Oblath <noah.oblath@pnnl.gov>

.build.sh

@@ -51,7 +51,7 @@ echo "Install dir: ${INSTALL_DIR}"
 : ${ENABLE_PYGBE:=ON}
 : ${ENABLE_BEM:=ON}
 : ${ENABLE_GEOFLOW:=ON}
-: ${FETK_VERSION:="857a0cf6ae40410471ea10f0e67e370cbd8ed6a3"}
+: ${FETK_VERSION:="57195e55351e04ce6ee0ef56a143c996a9aee7e2"}
 : ${ENABLE_iAPBS:=ON}
 : ${ENABLE_OPENMP:=OFF}
 : ${ENABLE_PBAM:=OFF}

.github/workflows/build-alt-config.yaml

@@ -22,7 +22,7 @@ env:
   ENABLE_BEM: ON
   ENABLE_GEOFLOW: ON
 #  FETK_VERSION: "1.9.2"
-  FETK_VERSION: 857a0cf6ae40410471ea10f0e67e370cbd8ed6a3
+  FETK_VERSION: 57195e55351e04ce6ee0ef56a143c996a9aee7e2
   ENABLE_iAPBS: ON
   ENABLE_OPENMP: OFF
   ENABLE_PBAM: OFF

.github/workflows/build.yaml

@@ -20,7 +20,7 @@ env:
   ENABLE_BEM: ON
   ENABLE_GEOFLOW: ON
 #  FETK_VERSION: "1.9.2"
-  FETK_VERSION: 857a0cf6ae40410471ea10f0e67e370cbd8ed6a3
+  FETK_VERSION: 57195e55351e04ce6ee0ef56a143c996a9aee7e2
   ENABLE_iAPBS: ON
   ENABLE_PBAM: OFF
   ENABLE_PBSAM: OFF
@@ -117,7 +117,6 @@ jobs:
             swig \
             boost \
             eigen \
-            arpack \
             lapack \
             suite-sparse
           wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz
@@ -126,6 +125,14 @@ jobs:
           cd metis-5.1.0
           make config prefix=/usr/local
           make install
+          cd ..
+          git clone https://github.com/opencollab/arpack-ng.git
+          cd arpack-ng
+          git fetch --all --tags
+          git checkout tags/3.8.0 -b latest
+          mkdir build && cd build
+          cmake -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release -DCMAKE_Fortran_COMPILER=$(which gfortran-11) -DEXAMPLES=OFF -DMPI=OFF -DBUILD_SHARED_LIBS=OFF  ..
+          make install
 #          brew upgrade gcc@9
 
       - name: Linux Prereqs and Remove broken apt repos [Ubuntu]
@@ -259,6 +266,7 @@ jobs:
 
 # For debugging
 #      - name: Setup tmate session
+#        if: startsWith(matrix.os, 'macos') || ! success()
 #        if: startsWith(matrix.os, 'windows') || ! success()
 #        if: ${{ ! success() }}
 #        uses: mxschmitt/action-tmate@v3

CMakeLists.txt

@@ -164,7 +164,7 @@ message(STATUS "")
 # FETK is currently required, and therefore this option is disabled
 #option(ENABLE_FETK "Enable the finite element solver" ON)
 
-set(FETK_VERSION "857a0cf6ae40410471ea10f0e67e370cbd8ed6a3" CACHE STRING "Version of FETK to use")
+set(FETK_VERSION "57195e55351e04ce6ee0ef56a143c996a9aee7e2" CACHE STRING "Version of FETK to use")
 include(ImportFETK)
 import_fetk(${FETK_VERSION})
 
@@ -443,8 +443,6 @@ if(ENABLE_BEM)
     )
     FetchContent_MakeAvailable( tabi )
 
-    list(APPEND APBS_LIB_DIRS "${tabi_BINARY_DIR}/lib")
-    list(APPEND APBS_LIBS TABIPBlib)
     include_directories(${tabi_SOURCE_DIR}/src)
     include_directories(${tabi_SOURCE_DIR}/src/tabipb_wrap)
     add_definitions(-DTABIPB_APBS)
@@ -483,14 +481,18 @@ if(ENABLE_BEM)
 
     set(TABIPB_LIBNAME TABIPBlib)
     add_library(${TABIPB_LIBNAME} ${TABIPB_LIBFILES})
+    target_link_libraries(${TABIPB_LIBNAME} ${APBS_LIBS})
     target_compile_features(${TABIPB_LIBNAME} PRIVATE cxx_std_11)
     target_compile_options(${TABIPB_LIBNAME} PRIVATE 
                            $<$<CONFIG:RELEASE>:-O3>
                            $<$<CONFIG:RELWITHDEBINFO>:-O3>
                            $<$<CONFIG:DEBUG>:-O0 -Wall>)
     install(FILES ${TABIPB_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/tabi COMPONENT headers)
     install(TARGETS ${TABIPB_LIBNAME} DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
-
+
+    list(APPEND APBS_LIB_DIRS "${tabi_BINARY_DIR}/lib")
+    list(APPEND APBS_LIBS TABIPBlib)
+
 endif() # ENABLE_BEM
 
 

Dockerfile.centos

@@ -70,7 +70,7 @@ ARG ENABLE_PYGBE=ON
 ARG ENABLE_BEM=ON
 ARG ENABLE_GEOFLOW=ON
 #ARG FETK_VERSION="1.9.1"
-ARG FETK_VERSION=857a0cf6ae40410471ea10f0e67e370cbd8ed6a3
+ARG FETK_VERSION=57195e55351e04ce6ee0ef56a143c996a9aee7e2
 ARG ENABLE_iAPBS=ON
 ARG ENABLE_OPENMP=OFF
 ARG ENABLE_PBAM=OFF
@@ -82,6 +82,7 @@ ARG PYTHON_MIN_VERSION="3.6"
 ARG PYTHON_MAX_VERSION="3.7"
 ARG PYTHON3_INCLUDE_DIR="/usr/include/python3.6m"
 ARG PYTHON3_LIBRARY="/usr/lib64/libpython3.6m.so"
+ARG MAKEJOBS="-j"
 
 RUN source scl_source enable devtoolset-11 && \
     cd /tmp_source && \
@@ -109,5 +110,5 @@ RUN source scl_source enable devtoolset-11 && \
       -DPython3_INCLUDE_DIR=${PYTHON3_INCLUDE_DIR} \
       -DPython3_LIBRARY=${PYTHON3_LIBRARY} \
       .. && \
-    make -j install && \
+    make ${MAKEJOBS} install && \
     /bin/true

Dockerfile.ubuntu

@@ -28,6 +28,7 @@ RUN apt-get update && \
         libopenblas-serial-dev \
         liblapack-dev \
         libsuitesparse-dev \
+        libsuperlu-dev \
         && \
     wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz && \
     gunzip metis-5.1.0.tar.gz && \
@@ -54,7 +55,7 @@ ARG ENABLE_PYGBE=ON
 ARG ENABLE_BEM=ON
 ARG ENABLE_GEOFLOW=ON
 #ARG FETK_VERSION="1.9.1"
-ARG FETK_VERSION=857a0cf6ae40410471ea10f0e67e370cbd8ed6a3
+ARG FETK_VERSION=57195e55351e04ce6ee0ef56a143c996a9aee7e2
 ARG ENABLE_iAPBS=ON
 ARG ENABLE_OPENMP=OFF
 ARG ENABLE_PBAM=OFF
@@ -64,6 +65,7 @@ ARG ENABLE_TESTS=ON
 ARG GET_NanoShaper=ON
 ARG PYTHON_MIN_VERSION="3.9"
 ARG PYTHON_MAX_VERSION="3.10"
+ARG MAKEJOBS="-j"
 
 RUN cd /tmp_source && \
     mkdir build && cd build && \
@@ -88,5 +90,5 @@ RUN cd /tmp_source && \
       -DPYTHON_MIN_VERSION="${PYTHON_MIN_VERSION}" \
       -DPYTHON_MAX_VERSION="${PYTHON_MAX_VERSION}" \
       .. && \
-    make -j install && \
+    make ${MAKEJOBS} install && \
     /bin/true

cmake/ImportFETK.cmake

@@ -37,6 +37,9 @@ macro(import_fetk FETK_IMPORT_VERSION)
 
         else()
 
+            # PMG is turned off because of some missing symbols: dc_vec__, dc_scal__, rand_, c_vec__, tsecnd_, and c_scal__
+            set(BUILD_PMG OFF)
+
             message(STATUS "Building FETK from commit ${FETK_IMPORT_VERSION}")
             FetchContent_Declare( fetk
                 GIT_REPOSITORY https://github.com/Electrostatics/FETK.git
@@ -45,52 +48,14 @@ macro(import_fetk FETK_IMPORT_VERSION)
             FetchContent_MakeAvailable( fetk )
 
             list(APPEND CMAKE_MODULE_PATH ${fetk_SOURCE_DIR}/cmake)
-            include_directories(
-                ${fetk_SOURCE_DIR}/maloc/src/base
-                ${fetk_SOURCE_DIR}/maloc/src/psh
-                ${fetk_SOURCE_DIR}/maloc/src/vsh
-                ${fetk_SOURCE_DIR}/maloc/src/vsys
-                ${fetk_SOURCE_DIR}/mc/src/aprx
-                ${fetk_SOURCE_DIR}/mc/src/bam
-                ${fetk_SOURCE_DIR}/mc/src/base
-                ${fetk_SOURCE_DIR}/mc/src/dyn
-                ${fetk_SOURCE_DIR}/mc/src/gem
-                ${fetk_SOURCE_DIR}/mc/src/mcsh
-                ${fetk_SOURCE_DIR}/mc/src/nam
-                ${fetk_SOURCE_DIR}/mc/src/pde
-                ${fetk_SOURCE_DIR}/mc/src/whb
-                ${fetk_SOURCE_DIR}/punc/src/base
-            )
 
         endif()
 
+        # Only need to link to mc because mc depends on the others
         list(APPEND APBS_LIBS
-            maloc
-            punc
             mc
-            gamer
-            superlu
-            vf2c
         )
 
-    #    find_package( BLAS REQUIRED )
-    #    find_package( UMFPACK REQUIRED )
-    #    list(APPEND APBS_LIBS
-    #        ${UMFPACK_LIBRARIES}
-    #        ${BLAS_LIBRARIES}
-    #    )
-
-    #    find_package( SuperLU )
-    #    if(SuperLU_FOUND)
-    #        # include from find_package variables
-    #        list(APPEND APBS_LIBS
-    #            ${SUPERLU_LIBRARIES}
-    #        )
-    #    else()
-    #        # library built with FETK
-    #        list(APPEND APBS_LIBS superlu)
-    #    endif()
-
         SET(HAVE_MC 1)
         SET(HAVE_PUNC 1)
         SET(HAVE_GAMER 1)

contrib/iapbs/src/CMakeLists.txt

@@ -7,7 +7,8 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR} ${APBS_ROOT}/src)
 LINK_DIRECTORIES(${APBS_ROOT_PATH}/lib)
 
 #ADD_LIBRARY(iapbs SHARED apbs_driver.c apbs_driver.h)
-ADD_LIBRARY(iapbs STATIC apbs_driver.c apbs_driver.h)
+ADD_LIBRARY(iapbs apbs_driver.c apbs_driver.h)
+target_link_libraries(iapbs ${APBS_LIBS} ${APBS_INTERNAL_LIBS})
 
 option(BUILD_iAPBS_FORTRAN_WRAPPER "Optionally build iAPBS Fortran wrapper" OFF)
 if(BUILD_iAPBS_FORTRAN_WRAPPER)

docs/releases.rst

@@ -31,6 +31,8 @@ Minor Updates
 * Specified Ubuntu build (20.04) and Mac build (11)
 * Fixed CMake syntax error around Python detection
 * Statically link Python in the Mac and Ubuntu builds
+* Build arpack manually in the Mac build to get the static library
+* Updated FETK to v1.9.3
 
 ^^^^^
 Notes

src/CMakeLists.txt

@@ -55,7 +55,7 @@ if(ENABLE_GEOFLOW)
 endif(ENABLE_GEOFLOW)
 
 add_items(SOURCES routines.c)
-add_sublibrary(routines ${APBS_INTERNAL_LIBS})
+add_sublibrary(routines ${APBS_LIBS} ${APBS_INTERNAL_LIBS})
 
 message(STATUS "External Headers: ${EXTERNAL_HEADERS}")
 

tools/manip/CMakeLists.txt

@@ -1,10 +1,12 @@
 message(STATUS "Building manip")
 
-set(LIBS "")
-list(APPEND LIBS "apbs_generic")
-list(APPEND LIBS "apbs_mg")
-list(APPEND LIBS "apbs_pmgc")
-list(APPEND LIBS "apbs_fem")
+set( LIBS 
+    apbs_generic
+    apbs_mg
+    apbs_pmgc
+    apbs_fem
+    apbs_routines
+)
 
 message(STATUS "libraries: ${LIBS}")
 

tools/mesh/CMakeLists.txt

@@ -1,10 +1,12 @@
 message(STATUS "Building mesh")
 
-set(LIBS "")
-list(APPEND LIBS "apbs_generic")
-list(APPEND LIBS "apbs_mg")
-list(APPEND LIBS "apbs_pmgc")
-list(APPEND LIBS "apbs_fem")
+set( LIBS 
+    apbs_generic
+    apbs_mg
+    apbs_pmgc
+    apbs_fem
+    apbs_routines
+)
 
 message(STATUS "libraries: ${LIBS}")