Flush reports when having gap junctions (#311)

* Flush reports when having gap junctions
* Load neuron module due to issue with cmake build system of neuron : neuronsimulator/nrn#567

Co-authored-by: Blanco Alonso Jorge <[email protected]>
Co-authored-by: Ioannis Magkanaris <[email protected]>

Author: 3 people

coreneuron/sim/fadvance_core.cpp

@@ -80,6 +80,10 @@ void nrn_fixed_step_minimal() { /* not so minimal anymore with gap junctions */
         nrn_spike_exchange(nrn_threads);
     }
 #endif
+
+#ifdef ENABLE_REPORTING
+    nrn_flush_reports(nrn_threads[0]._t);
+#endif
     t = nrn_threads[0]._t;
 }
 

tests/jenkins/run_neuron.sh

@@ -2,6 +2,7 @@
 
 set -e
 source ${JENKINS_DIR:-.}/_env_setup.sh
+module load neuron/develop
 
 set -x
 TEST_DIR="$1"
@@ -14,15 +15,27 @@ if [ "${TEST_DIR}" = "testcorenrn" ]; then
     mkdir test${TEST}dat
     mkdir ${TEST}
     mpirun -n ${MPI_RANKS} ./x86_64/special -mpi -c sim_time=100 test${TEST}.hoc
+    if [ ! -f out${TEST}.dat ]; then
+      echo "Neuron simulation didn't run correctly"
+      exit 1
+    fi
     cat out${TEST}.dat | sort -k 1n,1n -k 2n,2n > ${TEST}/out_nrn_${TEST}.spk
     rm out${TEST}.dat
 elif [ "${TEST_DIR}" = "ringtest" ]; then
     mkdir ${TEST}
     mpirun -n 6 ./x86_64/special ringtest.py -mpi
+    if [ ! -f coredat/spk6.std ]; then
+      echo "Neuron simulation didn't run correctly"
+      exit 1
+    fi
     cat coredat/spk6.std | sort -k 1n,1n -k 2n,2n > ${TEST}/out_nrn_${TEST}.spk
 elif [ "${TEST_DIR}" = "tqperf" ]; then
     mkdir ${TEST}
     mpirun -n ${MPI_RANKS} ./x86_64/special -c tstop=50 run.hoc -mpi
+    if [ ! -f spk000.dat ]; then
+      echo "Neuron simulation didn't run correctly"
+      exit 1
+    fi
     cat spk000.dat | sort -k 1n,1n -k 2n,2n > ${TEST}/out_nrn_${TEST}.spk
 else
     echo "Not a valid TEST"