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v2.6.0
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jougs committed Sep 30, 2015
1 parent 3ad9cad commit 1b8bb1e
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9 changes: 8 additions & 1 deletion Makefile.am
Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ dist-hook:
rm -rf $(distdir)/libltdl/.deps
rm -f $(distdir)/extras/logos/*.{ai,svg}
rm -f $(distdir)/extras/logos/nest-initiative-logo*.*
@PKGSRCDIR@/extras/create_rcsinfo.sh @PKGSRCDIR@ $(distdir)


.PHONY: doc fulldoc install-slidoc-recursive
Expand Down Expand Up @@ -55,7 +56,7 @@ if HAVE_PYTHON

# Python interpreter is discovered by AM_PATH_PYTHON and declared as a make variable by AC_SUBST
installcheck-local:
PATH="$(exec_prefix)/bin:$(PATH)" PYTHON="$(PYTHON)" PYTHONPATH="$(pyexecdir):$(PYTHONPATH)" \
PATH="$(exec_prefix)/bin:$(PATH)" PYTHON="$(PYTHON)" PYTHONPATH="$(pyexecdir):$(PYTHONPATH)" exec_prefix="$(exec_prefix)" \
/bin/sh $(DESTDIR)@PKGDATADIR@/extras/do_tests.sh --test-pynest --source-dir=$(top_srcdir)

else
Expand All @@ -76,11 +77,17 @@ install-data-hook: install-exec install-slidoc-recursive
-e "s:++PKGSRCDIR++:@PKGSRCDIR@:"\
$(DESTDIR)@PKGDATADIR@/extras/emacs/sli.el.in > $(DESTDIR)@PKGDATADIR@/extras/emacs/sli.el
rm $(DESTDIR)@PKGDATADIR@/extras/emacs/sli.el.in
\
@INSTALL_PROGRAM@ @PKGBUILDDIR@/extras/nest-config $(DESTDIR)$(exec_prefix)/bin/
@INSTALL_PROGRAM@ @PKGSRCDIR@/extras/nest_serial $(DESTDIR)$(exec_prefix)/bin/
@INSTALL_PROGRAM@ @PKGSRCDIR@/extras/nest_indirect $(DESTDIR)$(exec_prefix)/bin/
@INSTALL_PROGRAM@ @PKGBUILDDIR@/extras/nest_vars.sh $(DESTDIR)$(exec_prefix)/bin/
@INSTALL_PROGRAM@ -m 644 @PKGSRCDIR@/README $(DESTDIR)@PKGDOCDIR@/
@INSTALL_PROGRAM@ -m 644 @PKGSRCDIR@/NEWS $(DESTDIR)@PKGDOCDIR@/
\
@PKGSRCDIR@/extras/create_rcsinfo.sh @PKGSRCDIR@ @PKGBUILDDIR@
test -f @PKGBUILDDIR@/lib/sli/rcsinfo.sli \
&& @INSTALL_PROGRAM@ -m 644 @PKGBUILDDIR@/lib/sli/rcsinfo.sli $(DESTDIR)@PKGDATADIR@/sli

nobase_pkgdata_DATA=\
extras/emacs/sli.el.in \
Expand Down
58 changes: 2 additions & 56 deletions acinclude.m4
Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ echo "Platform: ${host}"
SLI_warningflags="-w1"
fi
if test "$SLI_optimize" = "set" -a -z "$SLI_optimizeflags"; then
SLI_optimizeflags="-O3 -mp"
SLI_optimizeflags="-O3 -fp-model precise"
fi
else
#real g++
Expand Down Expand Up @@ -357,7 +357,7 @@ echo "Platform: ${host}"
SLI_warningflags="-w1"
fi
if test "$SLI_optimize" = "set" -a -z "$SLI_optimizeflags"; then
SLI_optimizeflags="-O3 -mp"
SLI_optimizeflags="-O3 -fp-model precise"
fi
else
#real g++
Expand Down Expand Up @@ -692,60 +692,6 @@ fi
])



AC_DEFUN([SLI_ALPHA_CXX_PTHREAD_IGNORED],
[
AC_CACHE_CHECK(whether the compiler ignores symbols pthread.h,
sli_cv_alpha_cxx_pthread_ignored,
[AC_LANG_SAVE
pthread_help=$CXXFLAGS
CXXFLAGS=$AM_CXXFLAGS
AC_LANG_CPLUSPLUS
AC_TRY_COMPILE([
#include <pthread.h>
],,
sli_cv_alpha_cxx_pthread_ignored=no, sli_cv_alpha_cxx_pthread_ignored=yes)
CXXFLAGS=$pthread_help
AC_LANG_RESTORE
])
if test "$sli_cv_alpha_cxx_pthread_ignored" = yes; then
AC_DEFINE(HAVE_PTHREAD_IGNORED,,
[define if the compiler ignores symbolic names in pthread.h])
fi
])

AC_DEFUN([SLI_HAVE_PTHREAD_SETCONCURRENCY],
[
AC_CACHE_CHECK(whether pthread_setconcurrency is available,
sli_cv_have_pthread_setconcurrency,
[AC_LANG_SAVE
pthread_help=$CXXFLAGS
CXXFLAGS=$AM_CXXFLAGS
AC_LANG_CPLUSPLUS
AC_TRY_COMPILE([
#ifdef HAVE_PTHREAD_IGNORED
#undef __PURE_CNAME
#include <pthread.h>
#define __PURE_CNAME
#else
#include <pthread.h>
#endif
void foo()
{
unsigned int n=4;
int status = pthread_setconcurrency(n);
}
],,
sli_cv_have_pthread_setconcurrency=yes, sli_cv_have_pthread_setconcurrency=no)
CXXFLAGS=$pthread_help
AC_LANG_RESTORE
])
if test "$sli_cv_have_pthread_setconcurrency" = yes; then
AC_DEFINE(HAVE_PTHREAD_SETCONCURRENCY,,
[define if pthread_setconcurrency is available])
fi
])

AC_DEFUN([SLI_ALPHA_CXX_SIGUSR_IGNORED],
[
AC_CACHE_CHECK(whether the compiler ignores symbolic signal names in signal.h,
Expand Down
92 changes: 32 additions & 60 deletions configure.ac.in
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
#

AC_PREREQ(2.52)
AC_INIT([nest], [2.4.2], [[email protected]])
AC_INIT([nest], [2.6.0], [[email protected]])

# Prevent automatic rebuilding of Makefile.ins and configure if their
# content or timestamp changes. Not doing this lead to failing builds
Expand All @@ -19,8 +19,8 @@ AM_MAINTAINER_MODE([disable])
# The patchlevel is updated automatically by the script
# releasetools/buildnest
SLI_MAJOR=2
SLI_MINOR=4
SLI_PATCHLEVEL=2
SLI_MINOR=6
SLI_PATCHLEVEL=0

SLI_PRGNAME="nest-$SLI_MAJOR.$SLI_MINOR.$SLI_PATCHLEVEL"
SLI_VERSION=$SLI_MAJOR.$SLI_MINOR.$SLI_PATCHLEVEL
Expand Down Expand Up @@ -138,6 +138,11 @@ AC_ARG_WITH(vampir,[ --with-vampir Include support for the Vampir tool.],
fi])


# memory_thisjob_darwin needs the mach/mach.h header to get
# information about memory consumption
# 05 Nov 2014 Tammo Ippen
AC_CHECK_HEADERS(mach/mach.h)


bluegene_architecture="none"
configure_bluegene="no"
Expand Down Expand Up @@ -272,9 +277,15 @@ AC_ARG_WITH(libneurosim, [ --with-libneurosim[[=directory]] Request the u
[
if test "$withval" != "no"; then
if test "$withval" != "yes"; then
LIBNEUROSIM_LIBS="-L${withval}/lib -lneurosim"
LIBNEUROSIM_PY_LIBS="-lpyneurosim"
LIBNEUROSIM_INCLUDE="-I${withval}/include"
if test "x$configure_bluegene" = xyes; then
LIBNEUROSIM_LIBS="${withval}/lib/libneurosim.a"
LIBNEUROSIM_PY_LIBS="${withval}/lib/libpyneurosim.a"
LIBNEUROSIM_INCLUDE="-I${withval}/include"
else
LIBNEUROSIM_LIBS="-L${withval}/lib -lneurosim"
LIBNEUROSIM_PY_LIBS="-lpyneurosim"
LIBNEUROSIM_INCLUDE="-I${withval}/include"
fi
fi
HAVE_LIBNEUROSIM="yes"
else
Expand Down Expand Up @@ -617,29 +628,6 @@ AC_ARG_WITH([openmp], [AS_HELP_STRING([--without-openmp], [disable OpenMP multit
[with_openmp=$withval], # withval=yes, if configured with --with-openmp, no with --without-openmp
[with_openmp=default]) # withval would be yes, if configured without args

# Testing for POSIX threads
AC_ARG_WITH([pthread], [AS_HELP_STRING([--with-pthread], [enable POSIX threads])],
[with_pthread=$withval],
[with_pthread=no])

# This allows to override the default (OpenMP) by only using
# --with-pthread without also having to use --without-openmp
if test "$with_openmp" = default && test "$with_pthread" = yes; then
with_openmp=no
fi

# Force a sensible combination of --with-openmp and --with-pthread
if test "$with_openmp" = yes && test "$with_pthread" = yes; then
echo # we need a newline here because there won't be a result to print
AC_MSG_ERROR([Only one of OpenMP and POSIX threads can be enabled manually.])
fi

# On Blue Gene/L we can't use POSIX threads
if test "$with_pthread" = yes && test "x$bluegene_architecture" = xL; then
echo # we need a newline here because there won't be a result to print
AC_MSG_ERROR([POSIX threads are not available on Blue Gene/L, either use OpenMP, or no threading.])
fi

# Check if the OpenMP setup is usable
if test "$with_openmp" = yes || test "$with_openmp" = default; then
AC_MSG_RESULT(openmp)
Expand All @@ -659,21 +647,9 @@ if test "$with_openmp" = yes || test "$with_openmp" = default; then
AM_CXXFLAGS="$AM_CXXFLAGS $OPENMP_CXXFLAGS"
with_openmp=yes
else
# Check if the POSIX threads are usable
if test "$with_pthread" = yes; then
AC_MSG_RESULT(pthreads)
AC_CHECK_LIB(pthread, pthread_testcancel,
[SLI_LIBS="${SLI_LIBS} -lpthread"
SLI_THREAD_DEFS="-D_POSIX_C_SOURCE=199506L"
SLI_HAVE_PTHREADS="true"
AC_DEFINE(HAVE_PTHREADS,1,[pthreads are available])],\
[echo; AC_MSG_ERROR([No pthread library found, please use --without-pthread to disable.])])
else
AC_MSG_RESULT(none)
fi
AC_MSG_RESULT(none)
fi

AM_CONDITIONAL([LINK_PTHREAD], test "x$with_pthread" = xyes)
AM_CONDITIONAL([LINK_OPENMP], test "x$with_openmp" = xyes)

# End of thread library processing
Expand Down Expand Up @@ -710,6 +686,7 @@ AM_CONDITIONAL([HAVE_PYTHON], [test "x$have_python" = "xyes"])

AC_SUBST([HAVE_PYTHON])
AC_SUBST([PYNEST_SUBDIR])
AC_SUBST([PYEXECDIR], ${pyexecdir})

AC_SUBST([PYTHON])
AC_SUBST([PYTHON_VERSION])
Expand Down Expand Up @@ -750,12 +727,6 @@ SLI_CHECK_STATIC_TEMPLATE_DECLARATION

SLI_ALPHA_CMATH_MAKROS_IGNORED
SLI_ALPHA_CXX_SIGUSR_IGNORED
if test "$SLI_HAVE_PTHREADS" = "true"; then
SLI_ALPHA_CXX_PTHREAD_IGNORED

# must run aftr SLI_ALPHA_CXX_PTHREAD_IGNORED
SLI_HAVE_PTHREAD_SETCONCURRENCY
fi

SLI_CHECK_ISTREAM_HEADER
SLI_CHECK_OSTREAM_HEADER
Expand All @@ -779,9 +750,8 @@ LINKED_USER_MODULES=""
AC_ARG_WITH(modules,[ --with-modules = external modules to be linked in],
[
if test "$withval" != no; then
LINKED_USER_MODULES="-L$prefix/lib/nest"
for mod in $withval; do
LINKED_USER_MODULES="$LINKED_USER_MODULES -l$mod"
LINKED_USER_MODULES=" $prefix/lib/nest/lib$mod.la"
SLI_USER_MODULES="$SLI_USER_MODULES $mod"
done
fi
Expand Down Expand Up @@ -920,8 +890,6 @@ AC_SUBST(HAVE_M_E)
AC_SUBST(HAVE_M_PI)
AC_SUBST(HAVE_CMATH_MAKROS_IGNORED)
AC_SUBST(HAVE_SIGUSR_IGNORED)
AC_SUBST(HAVE_PTHREAD)
AC_SUBST(HAVE_PTHREAD_IGNORED)
AC_SUBST(HAVE_READLINE)
AC_SUBST(HAVE_VAMPIR)
AC_SUBST(VAMPIR_LIBS)
Expand Down Expand Up @@ -988,6 +956,8 @@ AC_SUBST(LINKED_USER_MODULES)
AC_CONFIG_HEADER(libnestutil/config.h)
AC_CONFIG_FILES(libnestutil/sliconfig.h)
AC_CONFIG_FILES(Makefile)
AC_CONFIG_FILES(doc/fulldoc.conf)
AC_CONFIG_FILES(doc/normaldoc.conf)
AC_CONFIG_FILES(doc/Makefile)
AC_CONFIG_FILES(examples/Makefile)
AC_CONFIG_FILES(examples/nest/Makefile)
Expand All @@ -1001,6 +971,7 @@ AC_CONFIG_FILES(nestkernel/Makefile)
AC_CONFIG_FILES(nest/Makefile)
AC_CONFIG_FILES(extras/nest-config)
AC_CONFIG_FILES(testsuite/do_tests.sh)
AC_CONFIG_FILES(extras/nest_vars.sh)

# conngen is special in that it might be omitted from build when
# libneurosim is not present, yet it always has to be configured
Expand Down Expand Up @@ -1107,11 +1078,7 @@ echo
if test "$with_openmp" = yes; then
echo "Use threading : Yes (OpenMP)"
else
if test "$with_pthread" = yes; then
echo "Use threading : Yes (POSIX threads)"
else
echo "Use threading : No"
fi
echo "Use threading : No"
fi

echo
Expand Down Expand Up @@ -1162,6 +1129,10 @@ if test "x$have_python" = "xyes"; then
printf " "; eval eval echo " ${pyexecdir}"
echo
fi
echo "To set necessary environment variables, add the following line"
echo "to your ~/.bashrc :"
printf " source "; eval eval echo "$exec_prefix/bin/nest_vars.sh"
echo
echo "--------------------------------------------------------------------------------"
echo

Expand Down Expand Up @@ -1196,9 +1167,10 @@ if test "$ac_have_gsl" != no; then
fi
else
echo
echo "You're about to compile NEST without the GNU Scientific"
echo "Library. Some models and random number generators will"
echo "not be available."
echo "ATTENTION!"
echo "You are about to compile NEST without the GNU Scientific"
echo "Library. This means that conductance-based neuron models"
echo "and some random number generators will not be available."
echo
echo "--------------------------------------------------------------------------------"
echo
Expand Down
8 changes: 4 additions & 4 deletions conngen/cg_connect.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ namespace nest
{
Node* const target_node = ConnectionGeneratorModule::get_network().get_node(target + target_offset);
const thread target_thread = target_node->get_thread();
ConnectionGeneratorModule::get_network().connect(source + source_offset, target + target_offset, target_node, target_thread, syn);
ConnectionGeneratorModule::get_network().connect(source + source_offset, target_node, target_thread, syn);
}
}
}
Expand All @@ -62,7 +62,7 @@ namespace nest
{
Node* const target_node = ConnectionGeneratorModule::get_network().get_node(target + target_offset);
const thread target_thread = target_node->get_thread();
ConnectionGeneratorModule::get_network().connect(source + source_offset, target + target_offset, target_node, target_thread, params[w_idx], params[d_idx], syn);
ConnectionGeneratorModule::get_network().connect(source + source_offset, target_node, target_thread, syn, params[d_idx], params[w_idx]);
}
}
}
Expand All @@ -88,7 +88,7 @@ namespace nest
{
Node* const target_node = ConnectionGeneratorModule::get_network().get_node(target_gids.at(target));
const thread target_thread = target_node->get_thread();
ConnectionGeneratorModule::get_network().connect(source_gids.at(source), target_gids.at(target), target_node, target_thread, syn);
ConnectionGeneratorModule::get_network().connect(source_gids.at(source), target_node, target_thread, syn);
}
}
}
Expand All @@ -108,7 +108,7 @@ namespace nest
{
Node* const target_node = ConnectionGeneratorModule::get_network().get_node(target_gids.at(target));
const thread target_thread = target_node->get_thread();
ConnectionGeneratorModule::get_network().connect(source_gids.at(source), target_gids.at(target), target_node, target_thread, params[w_idx], params[d_idx], syn);
ConnectionGeneratorModule::get_network().connect(source_gids.at(source), target_node, target_thread, syn, params[d_idx], params[w_idx]);
}
}
}
Expand Down
10 changes: 8 additions & 2 deletions doc/Makefile.am
Original file line number Diff line number Diff line change
Expand Up @@ -10,14 +10,20 @@

doc:
if DOXYGEN_AVAILABLE
TOPSRCDIR=$(top_srcdir) $(DOXYGEN) $(top_srcdir)/doc/normaldoc.conf

$(eval RCSINFO:=`@PKGSRCDIR@/extras/create_rcsinfo.sh @PKGSRCDIR@ /tmp`) \
$(SED) -i "/^PROJECT_NUMBER/ s/=.*/= @SLI_VERSION@, $(RCSINFO)/" @PKGBUILDDIR@/doc/normaldoc.conf
$(DOXYGEN) @PKGBUILDDIR@/doc/normaldoc.conf

endif

fulldoc:
if DOXYGEN_AVAILABLE
if DOT_AVAILABLE

TOPSRCDIR=$(top_srcdir) $(DOXYGEN) $(top_srcdir)/doc/fulldoc.conf
$(eval RCSINFO:=`@PKGSRCDIR@/extras/create_rcsinfo.sh @PKGSRCDIR@ /tmp`) \
$(SED) -i "/^PROJECT_NUMBER/ s/=.*/= @SLI_VERSION@, $(RCSINFO)/" @PKGBUILDDIR@/doc/fulldoc.conf
$(DOXYGEN) @PKGBUILDDIR@/doc/fulldoc.conf

## is it possible to issue a message here if DOT is not available?

Expand Down
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