mark_as_advanced(GMX_INSTALL_PREFIX)
include(gmxBuildTypeReference)
+include(gmxBuildTypeThreadSanitizer)
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference." FORCE)
+ # There's no need to offer a user the choice of ThreadSanitizer
# Set the possible values of build type for cmake-gui
set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
"MinSizeRel" "RelWithDebInfo")
set(MPI_IN_PLACE_EXISTS 1)
endif(GMX_THREAD_MPI)
tmpi_get_source_list(THREAD_MPI_SRC)
+# If atomics are manually disabled a define is needed because atomics.h doesn't depend on config.h
+if (TMPI_ATOMICS_DISABLED)
+ add_definitions(-DTMPI_ATOMICS_DISABLED)
+endif()
if(GMX_GPU)
# now that we have detected the dependencies, do the second configure pass
include(CheckFunctionExists)
include(CheckCSourceCompiles)
-# sets TMPI_ATOMICS to 1 if atomic operations are found, 0 otherwise
+# sets TMPI_ATOMICS to 1 if atomic operations are found, undef otherwise
# Options:
# include directory for thread_mpi/atomic.h
MACRO(TMPI_TEST_ATOMICS INCDIR)
if (NOT DEFINED TMPI_ATOMICS)
try_compile(TEST_ATOMICS "${CMAKE_BINARY_DIR}"
"${CMAKE_SOURCE_DIR}/cmake/TestAtomics.c"
- COMPILE_DEFINITIONS "-I${INCDIR}")
+ COMPILE_DEFINITIONS "-I${INCDIR} -DTMPI_ATOMICS")
if (TEST_ATOMICS)
message(STATUS "Atomic operations found")
+ # If the check fails, we want to be able to check again,
+ # in case the user has been able to fix this without
+ # needing to delete the cache. Thus we only cache
+ # positive results.
+ set(TMPI_ATOMICS ${TEST_ATOMICS} CACHE INTERNAL "Whether atomic operations are found")
+ set(TMPI_ATOMICS_INCDIR ${INCDIR} CACHE INTERNAL "Atomic operations check include dir")
else (TEST_ATOMICS)
message(STATUS "Atomic operations not found")
+ undef(TEST_ATOMICS)
endif(TEST_ATOMICS)
- set(TMPI_ATOMICS ${TEST_ATOMICS} CACHE INTERNAL "Whether atomic operations are found")
- set(TMPI_ATOMICS_INCDIR ${INCDIR} CACHE INTERNAL "Atomic operations check include dir")
endif(NOT DEFINED TMPI_ATOMICS)
ENDMACRO(TMPI_TEST_ATOMICS VARIABLE)
# Turns on thread_mpi MPI functions.
MACRO(TMPI_ENABLE)
- # first check whether threads and atomics are available.
- if(NOT TMPI_ATOMICS)
- # check again, to allow the user to fix this.
- unset(TMPI_ATOMICS CACHE)
- TMPI_TEST_ATOMICS(${TMPI_ATOMICS_INCDIR})
- endif(NOT TMPI_ATOMICS)
- if(NOT TMPI_ATOMICS)
+ TMPI_TEST_ATOMICS(TMPI_ATOMICS_INCDIR)
+ if(NOT DEFINED TMPI_ATOMICS)
message(WARNING "Atomic operations not found for this CPU+compiler combination. Thread support will be unbearably slow: disable threads. Atomic operations should work on all but the most obscure CPU+compiler combinations; if your system is not obscure -- like, for example, x86 with gcc -- please contact the developers.")
- endif(NOT TMPI_ATOMICS)
+ endif()
set(TMPI_ENABLED 1)
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+# Custom build type "ThreadSanitizer", to be used for compiling GROMACS
+# with clang 3.4 or gcc 4.8 (currently pre-release) with ThreadSanitizer
+# (aka "TSan") turned on, so that the tests can be run to detect data races.
+#
+# The main advantage of the clang version is that there can be a
+# suppressions file that acts at compile time, though there is no use of
+# that yet. The main advantage of the gcc version is that it can be used
+# with a OpenMP (if gomp is compiled with --disable-linux-futex).
+#
+# Unfortunately, out of the box Thread-MPI provokes several false
+# positives. One example is that tMPI_Event_t contains an atomic int
+# field "sync" that is initialized before thread spawn. During a
+# collective, this is atomically updated by the source thread, and the
+# update is observed by sink threads in tMPI_Event_wait, which do a
+# yield wait when no change has occured. This means the read can
+# happen before the write (by design, whether or not the read is
+# atomic), but the surrounding logic prevents action until the write
+# has happened. There is no way for the sink thread(s) to avoid
+# reading until the write has happened - that is the point of the
+# implementation.
+#
+# This ought to be able to be suppressed, but my attempts to apply
+# suppressions on individual functions don't suppress reporting of the
+# race event. Applying the suppression to the whole thread-MPI library
+# might work, but seems to defeat the point. We want to be able to
+# detect mis-use of the primitives provided by thread-MPI.
+#
+# This means there needs to be a way for this build type to trigger
+# the use of the generic mutex-based fallback implementation within
+# thread-MPI.
+#
+# Later, if a blacklist is needed, use something like
+# "-fsanitize-blacklist=${CMAKE_SOURCE_DIR}/cmake/thread-sanitizer.supp"
+# TODO find a better home for this and other suppression files
+set(_flags "-O1 -g -fsanitize=thread")
+
+foreach(_language C CXX)
+
+ string(REPLACE "X" "+" _human_readable_language ${_language})
+
+ if (CMAKE_${_language}_COMPILER_ID MATCHES "GNU")
+ set(CMAKE_${_language}_FLAGS_THREADSANITIZER "${_flags} -pie -fPIE" CACHE STRING "${_human_readable_language} flags for thread sanitizer")
+ else()
+ set(CMAKE_${_language}_FLAGS_THREADSANITIZER ${_flags} CACHE STRING "${_human_readable_language} flags for thread sanitizer")
+ endif()
+ mark_as_advanced(CMAKE_${_language}_FLAGS_THREADSANITIZER)
+ string(TOUPPER "${CMAKE_BUILD_TYPE}" _cmake_build_type)
+ if (_cmake_build_type STREQUAL THREADSANITIZER)
+ set(TMPI_ATOMICS_DISABLED 1)
+ set(TMPI_ATOMICS 0)
+ if (NOT((CMAKE_${_language}_COMPILER_ID MATCHES "Clang" AND
+ CMAKE_${_language}_COMPILER_VERSION VERSION_GREATER 3.2.999)
+ OR (CMAKE_${_language}_COMPILER_ID MATCHES "GNU" AND
+ CMAKE_${_language}_COMPILER_VERSION VERSION_GREATER 4.7.999)))
+ message(FATAL_ERROR "The ThreadSanitizer build is only available with clang ${_human_readable_language} >=3.3 and gnu ${_human_readable_language} >=4.8.")
+ endif()
+ endif()
+
+endforeach()
} /* Avoids screwing up auto-indentation */
#endif
+/* Setting TMPI_ATOMICS_DISABLED permits the build to enforce that no
+ * atomic operations are used. This is used when building to run
+ * ThreadSanitzer.
+ *
+ * It could also be useful as a temporary measure on some
+ * compiler+hardware for which the detection below fails to produce a
+ * correct result. Performance will be greatly improved by using
+ * whatever atomic operations are available, so make sure such a
+ * measure is only temporary! */
+#ifdef TMPI_ATOMICS_DISABLED
+
+#ifndef DOXYGEN
+#define TMPI_NO_ATOMICS
+#endif
+
+#else
+
/* first check for gcc/icc platforms.
Some compatible compilers, like icc on linux+mac will take this path,
too */
#else
+
+#ifndef DOXYGEN
+/** Indicates that no support for atomic operations is present. */
+#define TMPI_NO_ATOMICS
+#endif
+
+#endif /* platform-specific checks */
+
+#endif /* TMPI_NO_ATOMICS */
+
+#ifdef TMPI_NO_ATOMICS
+
/* No atomic operations, use mutex fallback. Documentation is in x86 section */
#ifdef TMPI_CHECK_ATOMICS
#error No atomic operations implemented for this cpu/compiler combination.
#endif
-#ifndef DOXYGEN
-/** Indicates that no support for atomic operations is present. */
-#define TMPI_NO_ATOMICS
-#endif
/** Memory barrier operation
void tMPI_Spinlock_wait(tMPI_Spinlock_t *x);
-#endif /* platform-specific checks */
+#endif /* TMPI_NO_ATOMICS */
/* now define all the atomics that are not avaible natively. These
are done on the assumption that a native CAS does exist. */
real max_hours;
const char *deviceOptions;
unsigned long Flags;
- int ret; /* return value */
};
fplog = mc.fplog;
}
- mda->ret = mdrunner(&mc.hw_opt, fplog, cr, mc.nfile, fnm, mc.oenv,
- mc.bVerbose, mc.bCompact, mc.nstglobalcomm,
- mc.ddxyz, mc.dd_node_order, mc.rdd,
- mc.rconstr, mc.dddlb_opt, mc.dlb_scale,
- mc.ddcsx, mc.ddcsy, mc.ddcsz,
- mc.nbpu_opt, mc.nstlist_cmdline,
- mc.nsteps_cmdline, mc.nstepout, mc.resetstep,
- mc.nmultisim, mc.repl_ex_nst, mc.repl_ex_nex, mc.repl_ex_seed, mc.pforce,
- mc.cpt_period, mc.max_hours, mc.deviceOptions, mc.Flags);
+ mdrunner(&mc.hw_opt, fplog, cr, mc.nfile, fnm, mc.oenv,
+ mc.bVerbose, mc.bCompact, mc.nstglobalcomm,
+ mc.ddxyz, mc.dd_node_order, mc.rdd,
+ mc.rconstr, mc.dddlb_opt, mc.dlb_scale,
+ mc.ddcsx, mc.ddcsy, mc.ddcsz,
+ mc.nbpu_opt, mc.nstlist_cmdline,
+ mc.nsteps_cmdline, mc.nstepout, mc.resetstep,
+ mc.nmultisim, mc.repl_ex_nst, mc.repl_ex_nex, mc.repl_ex_seed, mc.pforce,
+ mc.cpt_period, mc.max_hours, mc.deviceOptions, mc.Flags);
}
/* called by mdrunner() to start a specific number of threads (including
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff