Merge branch 'master' into magkanar/fix_pdata

Author: iomaganaris

.github/workflows/test-as-submodule.yml

@@ -42,6 +42,7 @@ jobs:
       - name: Install apt packages
         if: startsWith(matrix.os, 'ubuntu')
         run: |
+          sudo apt-get update
           sudo apt-get install bison cython3 flex libfl-dev libopenmpi-dev \
             ninja-build openmpi-bin python3-dev python3-numpy python3-pytest \
             python3-pytest-cov
@@ -54,7 +55,8 @@ jobs:
           GITHUB_PR_BODY: ${{ github.event.pull_request.body }}
         run: |
           nrn_branch=`echo "${GITHUB_PR_BODY}" | grep "^CI_BRANCHES" \
-                      | awk -v FS="(NEURON_BRANCH=|,)" '{print $2}'`
+                      | awk -v FS="NEURON_BRANCH=" '{print $2}'` \
+                      | awk -v FS="," '{print $1}'
           if [ -z "$nrn_branch" ]; then
               nrn_branch=master
           fi

.gitlab-ci.yml

@@ -13,11 +13,18 @@ variables:
   NMODL_BRANCH:
     description: Branch of NMODL to build CoreNEURON against (NMODL_COMMIT and NMODL_TAG also possible)
     value: master
+  SPACK_BRANCH:
+    description: Branch of BlueBrain Spack to use for the CI pipeline
+    value: develop
+  SPACK_DEPLOYMENT_SUFFIX:
+    description: Extra path component used when finding deployed software. Set to something like `pulls/1497` use software built for https://github.com/BlueBrain/spack/pull/1497. You probably want to set SPACK_BRANCH to the branch used in the relevant PR if you set this.
+    value: ''
 
 # Set up Spack
 spack_setup:
   extends: .spack_setup_ccache
   variables:
+    CORENEURON_COMMIT: ${CI_COMMIT_SHA}
     # Enable fetching GitHub PR descriptions and parsing them to find out what
     # branches to build of other projects.
     PARSE_GITHUB_PR_DESCRIPTIONS: "true"
@@ -26,18 +33,12 @@ simulation_stack:
   stage: .pre
   # Take advantage of GitHub PR description parsing in the spack_setup job.
   needs: [spack_setup]
-  variables:
-    CORENEURON_BRANCH: $CI_COMMIT_BRANCH
-    MODELS_COMMON_BRANCH: $MODELS_COMMON_BRANCH
-    NEURON_BRANCH: $NEURON_BRANCH
-    PYNEURODAMUS_BRANCH: $PYNEURODAMUS_BRANCH
-    REPORTINGLIB_BRANCH: $REPORTINGLIB_BRANCH
-    SPACK_BRANCH: $SPACK_BRANCH
-    SYNAPSETOOL_BRANCH: $SYNAPSETOOL_BRANCH
   trigger:
     project: hpc/sim/blueconfigs
     # CoreNEURON CI status depends on the BlueConfigs CI status.
     strategy: depend
+  variables:
+    SPACK_ENV_FILE_URL: $SPACK_SETUP_COMMIT_MAPPING_URL
 
 # Performance seems to be terrible when we get too many jobs on a single node.
 .build:
@@ -82,22 +83,20 @@ build:coreneuron:mod2c:nvhpc:acc:
   extends: [.build, .spack_nvhpc]
   variables:
     SPACK_PACKAGE: coreneuron
-    # +report pulls in a lot of dependencies and the tests fail.
     # See https://github.com/BlueBrain/CoreNeuron/issues/518 re: build_type
-    SPACK_PACKAGE_SPEC: +gpu+openmp+tests~legacy-unit~report build_type=RelWithDebInfo
+    SPACK_PACKAGE_SPEC: +gpu+openmp+tests~legacy-unit build_type=RelWithDebInfo
 
 # Build CoreNEURON with Unified Memory on GPU
 build:coreneuron:mod2c:nvhpc:acc:unified:
   extends: [.build, .spack_nvhpc]
   variables:
     SPACK_PACKAGE: coreneuron
-    # +report pulls in a lot of dependencies and the tests fail.
     # See https://github.com/BlueBrain/CoreNeuron/issues/518 re: build_type
-    SPACK_PACKAGE_SPEC: +gpu+unified+openmp+tests~legacy-unit~report build_type=RelWithDebInfo
+    SPACK_PACKAGE_SPEC: +gpu+unified+openmp+tests~legacy-unit build_type=RelWithDebInfo
 
 .build_coreneuron_nmodl:
   extends: [.build]
-  before_script:
+  variables:
     # NEURON depends on py-mpi4py, most of whose dependencies are pulled in by
     # nmodl%gcc, with the exception of MPI, which is pulled in by
     # coreneuron%{nvhpc,intel}. hpe-mpi is an external package anyway, so
@@ -106,26 +105,23 @@ build:coreneuron:mod2c:nvhpc:acc:unified:
     # means that in the NEURON step an existing py-mpi4py%gcc can be used.
     # Otherwise a new py-mpi4py with hpe-mpi%{nvhpc,intel} will be built.
     # TODO: fix this more robustly so we don't have to play so many games.
-    - SPACK_PACKAGE_DEPENDENCIES="${SPACK_PACKAGE_DEPENDENCIES}^hpe-mpi%gcc"
-    - !reference [.spack_build, before_script]
+    SPACK_PACKAGE_DEPENDENCIES: ^hpe-mpi%gcc
 
 build:coreneuron:nmodl:nvhpc:omp:
   extends: [.build_coreneuron_nmodl, .spack_nvhpc]
   variables:
     SPACK_PACKAGE: coreneuron
-    # +report pulls in a lot of dependencies and the tests fail.
     # See https://github.com/BlueBrain/CoreNeuron/issues/518 re: build_type
-    SPACK_PACKAGE_SPEC: +nmodl+openmp+gpu+tests~legacy-unit~report~sympy build_type=RelWithDebInfo
+    SPACK_PACKAGE_SPEC: +nmodl+openmp+gpu+tests~legacy-unit~sympy build_type=RelWithDebInfo
   needs: ["build:nmodl"]
 
 build:coreneuron:nmodl:nvhpc:acc:
   extends: [.build_coreneuron_nmodl, .spack_nvhpc]
   variables:
     SPACK_PACKAGE: coreneuron
-    # +report pulls in a lot of dependencies and the tests fail.
     # See https://github.com/BlueBrain/CoreNeuron/issues/518 re: build_type
     # Sympy + OpenMP target offload does not currently work with NVHPC
-    SPACK_PACKAGE_SPEC: +nmodl~openmp+gpu+tests~legacy-unit~report+sympy build_type=RelWithDebInfo
+    SPACK_PACKAGE_SPEC: +nmodl~openmp+gpu+tests~legacy-unit+sympy build_type=RelWithDebInfo
   needs: ["build:nmodl"]
 
 build:coreneuron:mod2c:intel:

CMakeLists.txt

@@ -433,6 +433,13 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${IGNORE_UNKNOWN_PRAGMA_FLAGS}")
 # =============================================================================
 add_subdirectory(coreneuron)
 
+if(CORENRN_ENABLE_GPU)
+  get_target_property(CORENRN_LINK_LIBRARIES coreneuron INTERFACE_LINK_LIBRARIES)
+  foreach(LIB ${CORENRN_LINK_LIBRARIES})
+    set_property(GLOBAL APPEND_STRING PROPERTY CORENEURON_LIB_LINK_FLAGS " ${LIB}")
+  endforeach()
+endif()
+
 include(MakefileBuildOptions)
 add_subdirectory(extra)
 

coreneuron/io/output_spikes.cpp

@@ -64,10 +64,10 @@ void spikevec_unlock() {
     mut.unlock();
 }
 
-void local_spikevec_sort(std::vector<double>& isvect,
-                         std::vector<int>& isvecg,
-                         std::vector<double>& osvect,
-                         std::vector<int>& osvecg) {
+static void local_spikevec_sort(std::vector<double>& isvect,
+                                std::vector<int>& isvecg,
+                                std::vector<double>& osvect,
+                                std::vector<int>& osvecg) {
     osvect.resize(isvect.size());
     osvecg.resize(isvecg.size());
     // first build a permutation vector
@@ -92,7 +92,7 @@ void local_spikevec_sort(std::vector<double>& isvect,
 
 #if NRNMPI
 
-void sort_spikes(std::vector<double>& spikevec_time, std::vector<int>& spikevec_gid) {
+static void sort_spikes(std::vector<double>& spikevec_time, std::vector<int>& spikevec_gid) {
     double lmin_time = std::numeric_limits<double>::max();
     double lmax_time = std::numeric_limits<double>::min();
     if (!spikevec_time.empty()) {
@@ -154,7 +154,7 @@ void sort_spikes(std::vector<double>& spikevec_time, std::vector<int>& spikevec_
 /** Split spikevec_time and spikevec_gid by populations
  *  Add spike data with population name and gid offset tolibsonatareport API
  */
-void output_spike_populations(
+static void output_spike_populations(
     const std::vector<std::pair<std::string, int>>& population_name_offset) {
     // Write spikes with default population name and offset
     if (population_name_offset.empty()) {
@@ -198,8 +198,9 @@ void output_spike_populations(
  *  \todo : MPI related code should be factored into nrnmpi.c
  *          Check spike record length which is set to 64 chars
  */
-void output_spikes_parallel(
+static void output_spikes_parallel(
     const char* outpath,
+    const char* filename,
     const std::vector<std::pair<std::string, int>>& population_name_offset) {
     std::stringstream ss;
     ss << outpath << "/out.dat";
@@ -210,7 +211,7 @@ void output_spikes_parallel(
         remove(fname.c_str());
     }
 #ifdef ENABLE_SONATA_REPORTS
-    sonata_create_spikefile(outpath);
+    sonata_create_spikefile(outpath, filename);
     output_spike_populations(population_name_offset);
     sonata_write_spike_populations();
     sonata_close_spikefile();
@@ -253,7 +254,7 @@ void output_spikes_parallel(
 }
 #endif
 
-void output_spikes_serial(const char* outpath) {
+static void output_spikes_serial(const char* outpath) {
     std::stringstream ss;
     ss << outpath << "/out.dat";
     std::string fname = ss.str();
@@ -288,7 +289,7 @@ void output_spikes(const char* outpath,
     }
 #if NRNMPI
     if (corenrn_param.mpi_enable && nrnmpi_initialized()) {
-        output_spikes_parallel(outpath, population_name_offset);
+        output_spikes_parallel(outpath, "out", population_name_offset);
     } else
 #endif
     {

coreneuron/mechanism/membfunc.hpp

@@ -120,6 +120,7 @@ extern double nrn_ghk(double v, double ci, double co, double z);
 nrn_pragma_omp(end declare target)
 extern void hoc_register_prop_size(int, int, int);
 extern void hoc_register_dparam_semantics(int type, int, const char* name);
+extern void hoc_reg_ba(int, mod_f_t, int);
 
 struct DoubScal {
     const char* name;