Merge pull request #2609 from akohlmey/collected-small-changes

Python MPI compatibility improvements

cmake/CMakeLists.txt

@@ -156,8 +156,7 @@ if(BUILD_MPI)
     endif()
   endif()
 else()
-  enable_language(C)
-  file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
+  file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.cpp)
   add_library(mpi_stubs STATIC ${MPI_SOURCES})
   set_target_properties(mpi_stubs PROPERTIES OUTPUT_NAME lammps_mpi_stubs${LAMMPS_MACHINE})
   target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)

cmake/Modules/Packages/MESSAGE.cmake

@@ -2,9 +2,8 @@ if(LAMMPS_SIZES STREQUAL BIGBIG)
   message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
 endif()
 option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
-file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
-    ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
-    ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
+file(GLOB_RECURSE cslib_SOURCES
+        ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
 
 add_library(cslib STATIC ${cslib_SOURCES})
 target_compile_definitions(cslib PRIVATE -DLAMMPS_${LAMMPS_SIZES})

doc/src/Build_basics.rst

@@ -95,7 +95,7 @@ standard. A more detailed discussion of that is below.
 
       .. note::
 
-         The file ``src/STUBS/mpi.c`` provides a CPU timer function
+         The file ``src/STUBS/mpi.cpp`` provides a CPU timer function
          called ``MPI_Wtime()`` that calls ``gettimeofday()``.  If your
          operating system does not support ``gettimeofday()``, you will
          need to insert code to call another timer.  Note that the

doc/src/Build_link.rst

@@ -20,16 +20,8 @@ the suffix ``.so.0`` (or some other number).
 .. note::
 
    Care should be taken to use the same MPI library for the calling code
-   and the LAMMPS library.  The ``library.h`` file includes ``mpi.h``
-   and uses definitions from it so those need to be available and
-   consistent.  When LAMMPS is compiled with the included STUBS MPI
-   library, then its ``mpi.h`` file needs to be included.  While it is
-   technically possible to use a full MPI library in the calling code
-   and link to a serial LAMMPS library compiled with MPI STUBS, it is
-   recommended to use the *same* MPI library for both, and then use
-   ``MPI_Comm_split()`` in the calling code to pass a suitable
-   communicator with a subset of MPI ranks to the function creating the
-   LAMMPS instance.
+   and the LAMMPS library unless LAMMPS is to be compiled without (real)
+   MPI support using the include STUBS MPI library.
 
 Link with LAMMPS as a static library
 ------------------------------------
@@ -110,7 +102,7 @@ executable, that are also required to link the LAMMPS executable.
 
       .. code-block:: bash
 
-         gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
+         gcc -c -O -I${HOME}/lammps/src -caller.c
          g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
                       -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src \
                       -llammps_serial -lpoems -lmpi_stubs
@@ -174,7 +166,7 @@ the POEMS package installed becomes:
 
       .. code-block:: bash
 
-         gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
+         gcc -c -O -I${HOME}/lammps/src -caller.c
          g++ -o caller caller.o -L${HOME}/lammps/src -llammps_serial
 
 Locating liblammps.so at runtime

python/lammps/core.py

@@ -286,15 +286,16 @@ class lammps(object):
     self.lib.lammps_fix_external_set_energy_global = [c_void_p, c_char_p, c_double]
     self.lib.lammps_fix_external_set_virial_global = [c_void_p, c_char_p, POINTER(c_double)]
 
-    # detect if Python is using version of mpi4py that can pass a communicator
-
+    # detect if Python is using a version of mpi4py that can pass communicators
+    # only needed if LAMMPS has been compiled with MPI support.
     self.has_mpi4py = False
-    try:
-      from mpi4py import __version__ as mpi4py_version
-      # tested to work with mpi4py versions 2 and 3
-      self.has_mpi4py = mpi4py_version.split('.')[0] in ['2','3']
-    except:
-      pass
+    if self.has_mpi_support:
+      try:
+        from mpi4py import __version__ as mpi4py_version
+        # tested to work with mpi4py versions 2 and 3
+        self.has_mpi4py = mpi4py_version.split('.')[0] in ['2','3']
+      except:
+        pass
 
     # if no ptr provided, create an instance of LAMMPS
     #   don't know how to pass an MPI communicator from PyPar
@@ -307,23 +308,27 @@ class lammps(object):
 
     if not ptr:
 
-      # with mpi4py v2, can pass MPI communicator to LAMMPS
+      # with mpi4py v2+, we can pass MPI communicators to LAMMPS
       # need to adjust for type of MPI communicator object
       # allow for int (like MPICH) or void* (like OpenMPI)
-      if self.has_mpi4py and self.has_mpi_support:
+      if self.has_mpi_support and self.has_mpi4py:
         from mpi4py import MPI
         self.MPI = MPI
 
       if comm:
-        if not self.has_mpi4py:
-          raise Exception('Python mpi4py version is not 2 or 3')
         if not self.has_mpi_support:
           raise Exception('LAMMPS not compiled with real MPI library')
+        if not self.has_mpi4py:
+          raise Exception('Python mpi4py version is not 2 or 3')
         if self.MPI._sizeof(self.MPI.Comm) == sizeof(c_int):
           MPI_Comm = c_int
         else:
           MPI_Comm = c_void_p
 
+        # Detect whether LAMMPS and mpi4py definitely use different MPI libs
+        if sizeof(MPI_Comm) != self.lib.lammps_config_has_mpi_support():
+          raise Exception('Inconsistent MPI library in LAMMPS and mpi4py')
+
         narg = 0
         cargs = None
         if cmdargs:

src/STUBS/Makefile

@@ -11,13 +11,13 @@ SHELL = /bin/sh
 
 # Files
 
-SRC =		mpi.c
+SRC =		mpi.cpp
 INC =		mpi.h
 
 # Definitions
 
 EXE =		libmpi_stubs.a
-OBJ = 		$(SRC:.c=.o)
+OBJ = 		$(SRC:.cpp=.o)
 
 # System-specific settings
 
@@ -36,7 +36,7 @@ clean:
 
 # Compilation rules
 
-.c.o:
+.cpp.o:
 	$(CC) $(CCFLAGS) -c $<
 
 # Individual dependencies

src/STUBS/Makefile.mingw32-cross

@@ -5,17 +5,17 @@ SHELL = /bin/sh
 
 # Files
 
-SRC =		mpi.c
+SRC =		mpi.cpp
 INC =		mpi.h
 
 # Definitions
 
 EXE =		libmpi_mingw32.a
-OBJ = 		$(SRC:%.c=%_mingw32.o)
+OBJ = 		$(SRC:%.cpp=%_mingw32.o)
 
 # System-specific settings
 
-CC =	        i686-w64-mingw32-gcc
+CC =	        i686-w64-mingw32-g++
 CCFLAGS =	-O2 -Wall -march=i686 -mtune=generic -mfpmath=387 -mpc64 -I.
 ARCHIVE =	i686-w64-mingw32-ar
 ARCHFLAG =	rs

src/STUBS/Makefile.mingw64-cross

@@ -5,17 +5,17 @@ SHELL = /bin/sh
 
 # Files
 
-SRC =		mpi.c
+SRC =		mpi.cpp
 INC =		mpi.h
 
 # Definitions
 
 EXE =		libmpi_mingw64.a
-OBJ = 		$(SRC:%.c=%_mingw64.o)
+OBJ = 		$(SRC:%.cpp=%_mingw64.o)
 
 # System-specific settings
 
-CC =	        x86_64-w64-mingw32-gcc
+CC =	        x86_64-w64-mingw32-g++
 CCFLAGS =	-O2 -Wall -march=core2 -mtune=core2 -msse2 -mpc64 -I.
 ARCHIVE =	x86_64-w64-mingw32-ar
 ARCHFLAG =	rs

src/STUBS/mpi.h

@@ -16,12 +16,17 @@
 
 #include <stdlib.h>
 
-/* use C bindings for MPI interface */
+/* We compile STUBS with C++ so the symbols embedded
+ * the serial shared library will not collide with any
+ * corresponding symbols from a real MPI library (which
+ * uses C bindings). As a consequence the header *must*
+ * enforce compiling with C++ only. */
 
-#ifdef __cplusplus
-extern "C" {
+#ifndef __cplusplus
+#error "MPI STUBS must be compiled with a C++ compiler"
 #endif
 
+
 /* Dummy defs for MPI stubs */
 
 #define MPI_COMM_WORLD 0
@@ -176,8 +181,4 @@ int MPI_Alltoallv(void *sendbuf, int *sendcounts, int *sdispls,
                   MPI_Datatype recvtype, MPI_Comm comm);
 /* ---------------------------------------------------------------------- */
 
-#ifdef __cplusplus
-}
-#endif
-
 #endif

src/library.cpp

@@ -4128,16 +4128,18 @@ void lammps_get_os_info(char *buffer, int buf_size)
 /* ---------------------------------------------------------------------- */
 
 /** This function is used to query whether LAMMPS was compiled with
- *  a real MPI library or in serial.
+ *  a real MPI library or in serial. For the real MPI library it
+ *  reports the size of the MPI communicator in bytes (4 or 8),
+ *  which allows to check for compatibility with a hosting code.
  *
- * \return 0 when compiled with MPI STUBS, otherwise 1 */
+ * \return 0 when compiled with MPI STUBS, otherwise the MPI_Comm size in bytes */
 
 int lammps_config_has_mpi_support()
 {
 #ifdef MPI_STUBS
   return 0;
 #else
-  return 1;
+  return sizeof(MPI_Comm);
 #endif
 }
 

unittest/c-library/test_library_config.cpp

@@ -74,7 +74,7 @@ TEST(LAMMPSConfig, package_name)
         EXPECT_EQ(lammps_config_package_name(numpkgs + 10, buf, 128), 0);
         EXPECT_THAT(buf, StrEq(""));
     } else {
-        EXPECT_EQ(lammps_config_package_name(0, buf, 128), 1);
+        EXPECT_EQ(lammps_config_package_name(0, buf, 128), 0);
         EXPECT_THAT(buf, StrEq(""));
     }
 };
@@ -200,7 +200,10 @@ TEST(LAMMPSConfig, exceptions)
 
 TEST(LAMMPSConfig, mpi_support)
 {
-    EXPECT_EQ(lammps_config_has_mpi_support(), LAMMPS_HAS_MPI);
+    if (LAMMPS_HAS_MPI)
+        EXPECT_GT(lammps_config_has_mpi_support(), 0);
+    else
+        EXPECT_EQ(lammps_config_has_mpi_support(), 0);
 };
 
 TEST(LAMMPSConfig, png_support)

unittest/python/python-open.py

@@ -37,7 +37,7 @@ class PythonOpen(unittest.TestCase):
         lmp=lammps(name=self.machine)
         self.assertIsNot(lmp.lmp,None)
         self.assertEqual(lmp.opened,1)
-        self.assertEqual(has_mpi4py,lmp.has_mpi4py)
+        self.assertEqual(has_mpi and has_mpi4py,lmp.has_mpi4py)
         self.assertEqual(has_mpi,lmp.has_mpi_support)
         lmp.close()
         self.assertIsNone(lmp.lmp,None)