Stokesian Dynamics (#3790)

Add a Stokesian Dynamics integrator with thermalization.
espressomd · Jul 17, 2020 · 95a9464 · 95a9464
2 parents 10f9a04 + b582e31
commit 95a9464
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Showing 41 changed files with 1,818 additions and 72 deletions.
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -77,7 +77,8 @@ default:
      CC: 'gcc-9'
      CXX: 'g++-9'
   script:
-    - export with_cuda=false myconfig=default with_coverage=true with_scafacos=true
+    - export with_cuda=false myconfig=default with_coverage=true
+    - export with_scafacos=true with_stokesian_dynamics=true
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
@@ -90,7 +91,8 @@ maxset:
      CC: 'gcc-9'
      CXX: 'g++-9'
   script:
-    - export with_cuda=false myconfig=maxset with_coverage=true with_scafacos=true
+    - export with_cuda=false myconfig=maxset with_coverage=true
+    - export with_scafacos=true with_stokesian_dynamics=true
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
@@ -125,20 +127,20 @@ ubuntu:wo-dependencies:
 debian:10:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/debian:446ff604bbfa63f30ddb462697fa0d0dc2630460
+  image: docker.pkg.github.com/espressomd/docker/debian:d496478230db4e5c286680e3bdc1621af1fccffc
   script:
-    - export with_cuda=false myconfig=maxset make_check_python=false
+    - export with_cuda=false myconfig=maxset make_check_python=false with_stokesian_dynamics=true
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
     - linux
 
-opensuse:15.1:
+opensuse:15.2:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/opensuse:446ff604bbfa63f30ddb462697fa0d0dc2630460
+  image: docker.pkg.github.com/espressomd/docker/opensuse:d496478230db4e5c286680e3bdc1621af1fccffc
   script:
-    - export with_cuda=false myconfig=maxset make_check_python=false
+    - export with_cuda=false myconfig=maxset make_check_python=false with_stokesian_dynamics=true
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
@@ -149,7 +151,7 @@ centos:7:
   stage: build
   image: docker.pkg.github.com/espressomd/docker/centos:446ff604bbfa63f30ddb462697fa0d0dc2630460
   script:
-    - export with_cuda=false myconfig=maxset make_check_python=true
+    - export with_cuda=false myconfig=maxset make_check_python=true with_stokesian_dynamics=true
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
@@ -160,7 +162,7 @@ fedora:32:
   stage: build
   image: docker.pkg.github.com/espressomd/docker/fedora:fc7628d32de0fce605976ba9edebe7eff186e618
   script:
-    - export with_cuda=false myconfig=maxset make_check_python=false
+    - export with_cuda=false myconfig=maxset make_check_python=false with_stokesian_dynamics=true
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
@@ -187,8 +189,9 @@ clang-sanitizer:
      CC: 'clang-9'
      CXX: 'clang++-9'
   script:
-    - export myconfig=maxset with_cuda=true with_cuda_compiler=clang with_coverage=false with_scafacos=true
+    - export myconfig=maxset with_cuda=true with_cuda_compiler=clang with_coverage=false
     - export with_static_analysis=true test_timeout=900 with_asan=true with_ubsan=true
+    - export with_scafacos=true with_stokesian_dynamics=true
     - bash maintainer/CI/build_cmake.sh
   timeout: 2h
   tags:
@@ -203,7 +206,8 @@ cuda10-maxset:
      CC: 'gcc-8'
      CXX: 'g++-8'
   script:
-    - export myconfig=maxset with_cuda=true with_coverage=false with_scafacos=true test_timeout=900 srcdir=${CI_PROJECT_DIR}
+    - export myconfig=maxset with_cuda=true with_coverage=false test_timeout=900 srcdir=${CI_PROJECT_DIR}
+    - export with_scafacos=true with_stokesian_dynamics=true
     - bash maintainer/CI/build_cmake.sh
   artifacts:
     paths:
@@ -217,13 +221,14 @@ cuda10-maxset:
 cuda9-maxset:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-18.04:06b6216c7aa3555bcf28c90734dbb84e7285c96f
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-18.04:d496478230db4e5c286680e3bdc1621af1fccffc
   variables:
      CC: 'gcc-6'
      CXX: 'g++-6'
      GCOV: 'gcov-6'
   script:
-    - export myconfig=maxset with_cuda=true with_coverage=true with_scafacos=true test_timeout=900 srcdir=${CI_PROJECT_DIR}
+    - export myconfig=maxset with_cuda=true with_coverage=true test_timeout=900 srcdir=${CI_PROJECT_DIR}
+    - export with_scafacos=true with_stokesian_dynamics=true
     - bash maintainer/CI/build_cmake.sh
   artifacts:
     paths:
@@ -307,7 +312,8 @@ installation:
      CC: 'gcc-8'
      CXX: 'g++-8'
   script:
-    - export myconfig=maxset with_cuda=true with_coverage=false with_scafacos=true make_check_unit_tests=false make_check_python=false
+    - export myconfig=maxset with_cuda=true with_coverage=false make_check_unit_tests=false make_check_python=false
+    - export with_scafacos=true with_stokesian_dynamics=true
     - export srcdir=${CI_PROJECT_DIR} build_type=Release
     - bash maintainer/CI/build_cmake.sh
     - cd build
@@ -335,7 +341,8 @@ empty:
      CC: 'clang-9'
      CXX: 'clang++-9'
   script:
-    - export myconfig=empty with_cuda=true with_cuda_compiler=clang with_static_analysis=true with_scafacos=false
+    - export myconfig=empty with_cuda=true with_cuda_compiler=clang with_static_analysis=true
+    - export with_scafacos=false with_stokesian_dynamics=false
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
@@ -347,9 +354,10 @@ empty:
 rocm-maxset:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/rocm:06b6216c7aa3555bcf28c90734dbb84e7285c96f
+  image: docker.pkg.github.com/espressomd/docker/rocm:d496478230db4e5c286680e3bdc1621af1fccffc
   script:
     - export myconfig=maxset with_cuda=true with_cuda_compiler=hip
+    - export with_stokesian_dynamics=false
     - bash maintainer/CI/build_cmake.sh
   tags:
     - amdgpu
@@ -360,6 +368,7 @@ rocm:latest:
   image: docker.pkg.github.com/espressomd/docker/rocm:latest_base
   script:
     - export myconfig=maxset with_cuda=true with_cuda_compiler=hip
+    - export with_stokesian_dynamics=false
     - bash maintainer/CI/build_cmake.sh
   tags:
     - amdgpu

diff --git a/AUTHORS b/AUTHORS
@@ -39,6 +39,7 @@ Ashreya Jayaram
 Ben Reynwar (formerly: Reynolds)
 Bogdan Tanygin
 Cameron Stewart
+Carl Georg Biermann
 Christian Haege
 Christoph Lohrmann
 Christoph Schneider

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -74,6 +74,7 @@ option(WITH_CUDA "Build with GPU support" OFF)
 option_if_available(WITH_HDF5 "Build with HDF5 support" ON)
 option(WITH_TESTS "Enable tests" ON)
 option_if_available(WITH_SCAFACOS "Build with ScaFaCoS support" OFF)
+option_if_available(WITH_STOKESIAN_DYNAMICS "Build with Stokesian Dynamics" ON)
 option(WITH_BENCHMARKS "Enable benchmarks" OFF)
 option(WITH_VALGRIND_INSTRUMENTATION
        "Build with valgrind instrumentation markers" OFF)
@@ -253,6 +254,62 @@ if(WITH_GSL)
   endif(GSL_FOUND)
 endif(WITH_GSL)
 
+find_package(BLAS)
+if(BLAS_FOUND)
+  set(BLAS 1)
+endif()
+find_package(LAPACK)
+if(LAPACK_FOUND)
+  set(LAPACK 1)
+endif()
+
+if(WITH_STOKESIAN_DYNAMICS)
+  if(BLAS AND LAPACK)
+    set(STOKESIAN_DYNAMICS 1)
+  endif()
+  if(CUDA)
+    set(STOKESIAN_DYNAMICS_GPU 1)
+    if(HIP)
+      find_gpu_library(VARNAME CUDA_CUBLAS_LIBRARIES NAMES rocblas)
+      find_gpu_library(VARNAME CUDA_cusolver_LIBRARY NAMES rocsolver)
+    else()
+      if(CMAKE_CUDA_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)
+        # when importing package cublas, CMake versions older than 3.12.2 will
+        # look for a library cublas_device that no longer exists in CUDA 10
+        cmake_minimum_required(VERSION 3.12.2)
+      endif()
+      find_gpu_library(VARNAME CUDA_CUBLAS_LIBRARIES NAMES cublas)
+      find_gpu_library(VARNAME CUDA_cusolver_LIBRARY NAMES cusolver)
+    endif()
+  endif(CUDA)
+  if(NOT (STOKESIAN_DYNAMICS
+          OR (STOKESIAN_DYNAMICS_GPU AND CUDA_CUBLAS_LIBRARIES
+              AND CUDA_cusolver_LIBRARY))
+     AND NOT WITH_STOKESIAN_DYNAMICS_IS_DEFAULT_VALUE)
+    message(
+      FATAL_ERROR
+        "Optional feature Stokesian Dynamics explicitly requested, but dependencies not found."
+    )
+  endif()
+endif(WITH_STOKESIAN_DYNAMICS)
+
+if(WITH_STOKESIAN_DYNAMICS)
+  set(CMAKE_INSTALL_LIBDIR
+      "${CMAKE_INSTALL_PREFIX}/${PYTHON_INSTDIR}/espressomd")
+  cmake_minimum_required(VERSION 3.11)
+  include(FetchContent)
+  FetchContent_Declare(
+    stokesian_dynamics
+    GIT_REPOSITORY https://github.com/hmenke/espresso-stokesian-dynamics.git
+    GIT_TAG 860ceac208175)
+  FetchContent_GetProperties(stokesian_dynamics)
+  if(NOT stokesian_dynamics_POPULATED)
+    FetchContent_Populate(stokesian_dynamics)
+    add_subdirectory(${stokesian_dynamics_SOURCE_DIR}
+                     ${stokesian_dynamics_BINARY_DIR})
+  endif()
+endif(WITH_STOKESIAN_DYNAMICS)
+
 if(WITH_VALGRIND_INSTRUMENTATION)
   find_package(PkgConfig)
   pkg_check_modules(VALGRIND valgrind)

diff --git a/cmake/cmake_config.cmakein b/cmake/cmake_config.cmakein
@@ -13,6 +13,14 @@
 
 #cmakedefine GSL
 
+#cmakedefine BLAS
+
+#cmakedefine LAPACK
+
+#cmakedefine STOKESIAN_DYNAMICS
+
+#cmakedefine STOKESIAN_DYNAMICS_GPU
+
 #cmakedefine VALGRIND_INSTRUMENTATION
 
 #define PACKAGE_NAME "${PROJECT_NAME}"