option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
option(GMX_SOFTWARE_INVSQRT "Use GROMACS software 1/sqrt" ON)
mark_as_advanced(GMX_SOFTWARE_INVSQRT)
-option(GMX_POWERPC_INVSQRT "Use PowerPC hardware 1/sqrt" OFF)
-mark_as_advanced(GMX_POWERPC_INVSQRT)
option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
mark_as_advanced(GMX_FAHCORE)
if(GMX_SOFTWARE_INVSQRT)
set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
endif(GMX_SOFTWARE_INVSQRT)
-if(GMX_POWERPC_INVSQRT)
- set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_POWERPC_INVSQRT")
-endif(GMX_POWERPC_INVSQRT)
########################################################################
#Process MPI settings
set(BUILD_SHARED_LIBS OFF CACHE BOOL "Shared libraries not compatible with BlueGene/L, disabled!" FORCE)
endif (${CMAKE_SYSTEM_NAME} STREQUAL "BlueGeneL")
set(GMX_SOFTWARE_INVSQRT OFF CACHE BOOL "Do not use software reciprocal square root on BlueGene" FORCE)
- set(GMX_POWERPC_INVSQRT ON CACHE BOOL "Use hardware reciprocal square root on BlueGene" FORCE)
set(GMX_X11 OFF CACHE BOOL "X11 not compatible with BlueGene, disabled!" FORCE)
set(GMX_THREAD_MPI OFF CACHE BOOL "Thread-MPI not compatible with BlueGene, disabled!" FORCE)
set(GMX_MPI ON CACHE BOOL "Use MPI on BlueGene" FORCE)
# The automatic testing for endianness does not work for the BlueGene cross-compiler
set(GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER 1 CACHE INTERNAL "BlueGene has big endian FP byte order (by default)" FORCE)
set(GMX_IEEE754_BIG_ENDIAN_WORD_ORDER 1 CACHE INTERNAL "BlueGene has big endian FP word order (by default)" FORCE)
-elseif(${GMX_CPU_ACCELERATION} STREQUAL "POWER6")
- set(GMX_POWER6 1)
- set(GMX_SOFTWARE_INVSQRT OFF CACHE BOOL "Do not use software reciprocal square root on Power6" FORCE)
- set(GMX_POWERPC_INVSQRT ON CACHE BOOL "Use hardware reciprocal square root on Power6" FORCE)
else(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
MESSAGE(FATAL_ERROR "Unrecognized option for accelerated kernels: ${GMX_CPU_ACCELERATION}. Pick one of None, SSE2, SSE4.1, AVX_128_FMA, AVX_256, BlueGene")
endif(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
/* we put all of these on their own cache line by padding the data structure
to the size of a cache line on x86 (64 bytes): */
+#define TMPI_SIZEOF_X86_CACHE_LINE 64
typedef struct tMPI_Atomic
{
int value;
- char padding[64-sizeof(int)];
+ char padding[TMPI_SIZEOF_X86_CACHE_LINE-sizeof(int)];
} tMPI_Atomic_t;
typedef struct tMPI_Atomic_ptr
{
void* value;
- char padding[64-sizeof(void*)];
+ char padding[TMPI_SIZEOF_X86_CACHE_LINE-sizeof(void*)];
} tMPI_Atomic_ptr_t;
typedef struct tMPI_Spinlock
{
unsigned int lock;
- char padding[64-sizeof(unsigned int)];
+ char padding[TMPI_SIZEOF_X86_CACHE_LINE-sizeof(unsigned int)];
} tMPI_Spinlock_t;
as the 486, and gcc on some Linux versions still target 80386 by default).
We also specifically check for icc, because intrinsics are not always
- supported there. */
-#if ( (TMPI_GCC_VERSION >= 40100) && defined(__x86_64__) && \
- !defined(__INTEL_COMPILER) )
+ supported there.
+
+ llvm has issues with inline assembly and also in 32 bits has support for
+ the gcc intrinsics */
+#if ( ( (TMPI_GCC_VERSION >= 40100) && defined(__x86_64__) && \
+ !defined(__INTEL_COMPILER) ) || defined(__llvm__) )
#include "gcc_intrinsics.h"
#else
__asm__ __volatile__("lock ; xaddl %0, %1;"
:"=r"(i) :"m"(a->value), "0"(i) : "memory");
return i + __i;
-}
+}
static inline int tMPI_Atomic_fetch_add(tMPI_Atomic_t *a, int i)
{
static inline int tMPI_Atomic_cas(tMPI_Atomic_t *a, int oldval, int newval)
{
- unsigned int prev;
+ int prev;
__asm__ __volatile__("lock ; cmpxchgl %1,%2"
: "=a"(prev)
#define INVSQRT_DONE
#endif /* gmx_invsqrt */
-#ifdef GMX_POWERPC_SQRT
-static real gmx_powerpc_invsqrt(real x)
-{
- const real half=0.5;
- const real three=3.0;
- t_convert result,bit_pattern;
- unsigned int exp,fract;
- real lu;
- real y;
-#ifdef GMX_DOUBLE
- real y2;
-#endif
-
- lu = __frsqrte((double)x);
-
- y=(half*lu*(three-((x*lu)*lu)));
-
-#if (GMX_POWERPC_SQRT==2)
- /* Extra iteration required */
- y=(half*y*(three-((x*y)*y)));
-#endif
-
-#ifdef GMX_DOUBLE
- y2=(half*y*(three-((x*y)*y)));
-
- return y2; /* 10 Flops */
-#else
- return y; /* 5 Flops */
-#endif
-}
-#define gmx_invsqrt(x) gmx_powerpc_invsqrt(x)
-#define INVSQRT_DONE
-#endif /* powerpc_invsqrt */
-
#ifndef INVSQRT_DONE
# ifdef GMX_DOUBLE
# ifdef HAVE_RSQRT
# If you only use one shell you can copy that GMXRC.* instead.
-# only csh/tcsh understand 'set'
-set is_csh = 123
-test "$is_csh" = 123 && goto CSH
+# only csh/tcsh set the variable $shell (note: lower case!)
+test $shell && goto CSH
# if we got here, shell is bsh/bash/zsh/ksh
# bsh cannot remove part of a variable with %%
/* Use the GROMACS software 1/sqrt(x) */
#cmakedefine GMX_SOFTWARE_INVSQRT
-/* Use the PowerPC hardware 1/sqrt(x) */
-#cmakedefine GMX_POWERPC_INVSQRT
-
/* Use sub-counters */
#cmakedefine GMX_CYCLE_SUBCOUNTERS
/* We tried again, and this time there was a copied buffer.
We use that, and indicate that we're not reading from the
regular buf. This case should be pretty rare. */
- tMPI_Atomic_fetch_add(&(cev->met[rank].buf_readcount),-1);
+ tMPI_Atomic_add_return(&(cev->met[rank].buf_readcount),-1);
tMPI_Atomic_memory_barrier_acq();
srcbuf=try_again_srcbuf;
}
{
/* we decrement the read count; potentially releasing the buffer. */
tMPI_Atomic_memory_barrier_rel();
- tMPI_Atomic_fetch_add( &(cev->met[rank].buf_readcount), -1);
+ tMPI_Atomic_add_return( &(cev->met[rank].buf_readcount), -1);
}
#endif
}
else
{
/* wait until everybody else is done copying the original buffer.
- We use fetch_add because we want to be sure of coherency.
+ We use atomic add-return because we want to be sure of coherency.
This wait is bound to be very short (otherwise it wouldn't
be double-buffering) so we always spin here. */
/*tMPI_Atomic_memory_barrier_rel();*/
-100000))
#endif
#if 0
- while (tMPI_Atomic_fetch_add( &(cev->met[myrank].buf_readcount), 0)
+ while (tMPI_Atomic_add_return( &(cev->met[myrank].buf_readcount), 0)
!= 0)
#endif
#if 1
tMPI_Atomic_memory_barrier_rel();
/* signal that we're done */
- tMPI_Atomic_fetch_add(&(cev->coll.current_sync), 1);
+ tMPI_Atomic_add_return(&(cev->coll.current_sync), 1);
/* we need to keep being in sync */
csync->syncs++;
}
tMPI_Error(TMPI_COMM_WORLD, TMPI_ERR_INIT);
}
}
- /* the main thread now also runs start_fn if we don't want
+ /* the main thread also runs start_fn if we don't want
it to return */
if (!main_returns)
tMPI_Thread_starter((void*)&(threads[0]));
tMPI_Trace_print("tMPI_Init(%p, %p, %p)", argc, argv, start_function);
#endif
-
if (TMPI_COMM_WORLD==0) /* we're the main process */
{
int N=0;
tMPI_Get_N(argc, argv, "-nt", &N);
- tMPI_Start_threads(FALSE, N, TMPI_AFFINITY_ALL_CORES, argc, argv,
+ tMPI_Start_threads(TRUE, N, TMPI_AFFINITY_ALL_CORES, argc, argv,
NULL, NULL, start_function);
}
else
# disabling GMX_BUILD_OWN_FFTW changes dependencies correctly.
add_dependencies(md gmxfftw)
endif()
-set_target_properties(md PROPERTIES OUTPUT_NAME "md${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
+option(GMX_PREFIX_LIBMD "Change install name of libmd to libgmxmd to avoid collision with BSD's/Martin Hinner's libmd, which is used in X11 and zfs" OFF)
+mark_as_advanced(GMX_PREFIX_LIBMD)
+if (GMX_PREFIX_LIBMD)
+ set(MD_PREFIX "gmx")
+else()
+ set(MD_PREFIX)
+endif()
+set_target_properties(md PROPERTIES OUTPUT_NAME "${MD_PREFIX}md${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
COMPILE_FLAGS "${OpenMP_C_FLAGS}")
install(TARGETS md DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libmd.pc.cmakein ${CMAKE_CURRENT_BINARY_DIR}/libmd.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libmd.pc
DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
- RENAME "libmd${GMX_LIBS_SUFFIX}.pc"
+ RENAME "lib${MD_PREFIX}md${GMX_LIBS_SUFFIX}.pc"
COMPONENT development)
Version: @PROJECT_VERSION@
Requires: libgmx@GMX_LIBS_SUFFIX@ @PKG_FFT@
Libs.private: -lm @CMAKE_THREAD_LIBS_INIT@
-Libs: -L${libdir} -lmd@GMX_LIBS_SUFFIX@ @PKG_FFT_LIBS@
+Libs: -L${libdir} -l@MD_PREFIX@md@GMX_LIBS_SUFFIX@ @PKG_FFT_LIBS@
Cflags: -I${includedir} @PKG_CFLAGS@
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff