Callback from CoreNEURON to help transfer data to NEURON. (#717)

* Callback from CoreNEURON to help transfer data to NEURON. Help for the transfer of voltage, i_membrane_, and mechanism data. Strategy is to pass a pointer which is used by CoreNEURON to copy data which may have been reordered due to SoA and permutation. * After psolve uses nrn_core copy thread time to t. Add a more comprehensive data return test. * Handle artificial cells with multiple threads. Added artificial cell test. * Temporarily avoid non-deterministic segmentation fault from test. * CMAKE_CXX_STANDARD 11 allows greater clarity with "auto&". * Preserve CoreNEURON global and static data across invocations. * autotools STDCXX11 Co-authored-by: Alexandru Savulescu <[email protected]>
neuronsimulator · Aug 26, 2020 · 03400bf · 03400bf
1 parent 19cb091
commit 03400bf
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Showing 9 changed files with 1,322 additions and 19 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -6,7 +6,7 @@ project(NEURON C CXX)
 # =============================================================================
 set(PROJECT_VERSION_MAJOR 8)
 set(PROJECT_VERSION_MINOR 0)
-set(CMAKE_CXX_STANDARD 98)
+set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 

diff --git a/configure.ac b/configure.ac
@@ -16,6 +16,8 @@ AC_CONFIG_SRCDIR(src/memacs/main.c)
 AM_INIT_AUTOMAKE([foreign])
 AM_MAINTAINER_MODE([enable])
 
+AX_CXX_COMPILE_STDCXX(11, noext, mandatory)
+
 m4_pattern_allow([^AC_MSG_ERROR$])
 
 AC_PROG_CC_STDC

diff --git a/external/coreneuron b/external/coreneuron
+1 −0		coreneuron/CMakeLists.txt
+3 −0		coreneuron/apps/main1.cpp
+174 −0		coreneuron/io/core2nrn_data_return.cpp
+40 −0		coreneuron/io/core2nrn_data_return.hpp
+3 −0		coreneuron/io/nrn2core_direct.h
+3 −18		coreneuron/io/nrn_setup.cpp
+4 −10		coreneuron/io/output_spikes.cpp
+0 −6		coreneuron/io/phase1.cpp
+0 −4		coreneuron/io/phase1.hpp
+5 −2		coreneuron/mechanism/mech/enginemech.cpp
+20 −20		coreneuron/network/netcon.hpp
+24 −149		coreneuron/network/netpar.cpp
+26 −0		coreneuron/utils/nrnmutdec.h