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iomaganarispramodk
iomaganaris
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pramodk
committed
Added neuron direct test in CoreNeuron Jenkins pipeline (#187)
 - Install with spack neuron master branch and run all the tests requiring neuron with it - Added neuron_direct.py script for direct checking
1 parent b858a08 commit 9fff9e0

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-26
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7 files changed

+164
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‎tests/jenkins/Jenkinsfile‎

Lines changed: 42 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -4,21 +4,33 @@ pipeline {
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}
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stages {
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stage('install Spack'){
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steps {
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sh 'source $WORKSPACE/tests/jenkins/spack_setup.sh'
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}
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}
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stage('spack install neuron@develop'){
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steps {
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sh 'sh tests/jenkins/install_neuron.sh'
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}
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}
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stage('build corenrn AoS'){
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steps {
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sh 'sh tests/jenkins/install.sh AoS'
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sh 'sh tests/jenkins/install_coreneuron.sh AoS'
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}
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}
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stage('build corenrn SoA'){
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steps {
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sh 'sh tests/jenkins/install.sh SoA'
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sh 'sh tests/jenkins/install_coreneuron.sh SoA'
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}
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}
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stage('build corenrn GPU'){
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steps {
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sh 'sh tests/jenkins/install.sh GPU'
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sh 'sh tests/jenkins/install_coreneuron.sh GPU'
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}
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}
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@@ -42,6 +54,21 @@ pipeline {
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}
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}
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stage('neuron_direct'){
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parallel{
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stage('AoS'){
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steps{
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sh 'sh tests/jenkins/run_neuron_direct.sh AoS'
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}
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}
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stage('SoA'){
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steps{
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sh 'sh tests/jenkins/run_neuron_direct.sh SoA'
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}
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}
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}
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}
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stage('checkout testcorenrn and ringtest'){
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steps{
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dir('testcorenrn'){
@@ -94,17 +121,17 @@ pipeline {
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stages{
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stage('neuron'){
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steps{
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sh 'sh tests/jenkins/run_neuron.sh testcorenrn deriv 6'
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sh 'sh tests/jenkins/run_neuron.sh testcorenrn deriv 1'
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}
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}
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stage('corenrn AoS'){
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steps{
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sh 'sh tests/jenkins/run_corenrn.sh testcorenrn AoS deriv 6'
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sh 'sh tests/jenkins/run_corenrn.sh testcorenrn AoS deriv 1'
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}
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}
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stage('corenrn SoA'){
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steps{
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sh 'sh tests/jenkins/run_corenrn.sh testcorenrn SoA deriv 6'
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sh 'sh tests/jenkins/run_corenrn.sh testcorenrn SoA deriv 1'
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}
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}
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}
@@ -132,17 +159,17 @@ pipeline {
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stages{
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stage('neuron'){
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steps{
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sh 'sh tests/jenkins/run_neuron.sh testcorenrn kin 6'
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sh 'sh tests/jenkins/run_neuron.sh testcorenrn kin 1'
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}
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}
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stage('corenrn AoS'){
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steps{
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sh 'sh tests/jenkins/run_corenrn.sh testcorenrn AoS kin 6'
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sh 'sh tests/jenkins/run_corenrn.sh testcorenrn AoS kin 1'
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}
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}
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stage('corenrn SoA'){
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steps{
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sh 'sh tests/jenkins/run_corenrn.sh testcorenrn SoA kin 6'
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sh 'sh tests/jenkins/run_corenrn.sh testcorenrn SoA kin 1'
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}
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}
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}
@@ -151,17 +178,17 @@ pipeline {
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stages{
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stage('neuron'){
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steps{
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sh 'sh tests/jenkins/run_neuron.sh testcorenrn conc 6'
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sh 'sh tests/jenkins/run_neuron.sh testcorenrn conc 1'
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}
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}
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stage('corenrn AoS'){
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steps{
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sh 'sh tests/jenkins/run_corenrn.sh testcorenrn AoS conc 6'
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sh 'sh tests/jenkins/run_corenrn.sh testcorenrn AoS conc 1'
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}
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}
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stage('corenrn SoA'){
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steps{
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sh 'sh tests/jenkins/run_corenrn.sh testcorenrn SoA conc 6'
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sh 'sh tests/jenkins/run_corenrn.sh testcorenrn SoA conc 1'
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}
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}
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}
@@ -189,17 +216,17 @@ pipeline {
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stages{
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stage('neuron'){
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steps{
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sh 'sh tests/jenkins/run_neuron.sh testcorenrn bbcore 6'
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sh 'sh tests/jenkins/run_neuron.sh testcorenrn bbcore 1'
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}
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}
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stage('corenrn AoS'){
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steps{
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sh 'sh tests/jenkins/run_corenrn.sh testcorenrn AoS bbcore 6'
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sh 'sh tests/jenkins/run_corenrn.sh testcorenrn AoS bbcore 1'
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}
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}
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stage('corenrn SoA'){
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steps{
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sh 'sh tests/jenkins/run_corenrn.sh testcorenrn SoA bbcore 6'
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sh 'sh tests/jenkins/run_corenrn.sh testcorenrn SoA bbcore 1'
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}
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}
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}

tests/jenkins/install.sh renamed to tests/jenkins/install_coreneuron.sh

File renamed without changes.

‎tests/jenkins/install_neuron.sh‎

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#!/usr/bin/bash
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set -x
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set -e
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export SPACK_INSTALL_PREFIX="${SPACK_INSTALL_PREFIX:-${WORKSPACE}/INSTALL_HOME}"
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source $WORKSPACE/BUILD_HOME/spack/share/spack/setup-env.sh
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source /gpfs/bbp.cscs.ch/apps/hpc/jenkins/config/modules.sh
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export PATH=$WORKSPACE/BUILD_HOME/spack/bin:/usr/bin:$PATH
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export MODULEPATH=$SPACK_INSTALL_PREFIX/modules/tcl/$(spack arch):$MODULEPATH
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unset $(env|awk -F= '/^(PMI|SLURM)_/ {if ($1 != "SLURM_ACCOUNT") print $1}')
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spack install neuron@develop
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module av neuron

‎tests/jenkins/neuron_direct.py‎

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from neuron import h, gui
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import sys
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h('''create soma''')
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h.soma.L=5.6419
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h.soma.diam=5.6419
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h.soma.insert("hh")
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ic = h.IClamp(h.soma(.5))
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ic.delay = .5
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ic.dur = 0.1
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ic.amp = 0.3
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v = h.Vector()
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v.record(h.soma(.5)._ref_v, sec = h.soma)
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tv = h.Vector()
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tv.record(h._ref_t, sec=h.soma)
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h.run()
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vstd = v.cl()
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tvstd = tv.cl()
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#h.CoreNeuronRun[0].run()
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pc = h.ParallelContext()
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h.cvode.cache_efficient(1)
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h.stdinit()
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pc.nrncore_run("-e %g"%h.tstop, 0)
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if not bool(tv.eq(tvstd)):
28+
print("Voltage times are different")
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sys.exit(-1)
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if v.cl().sub(vstd).abs().max() >= 1e-10:
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print("Voltage difference greater than or equal to 1e-10")
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sys.exit(-1)
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print("Voltage times are same and difference is less than 1e-10")
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h.quit()

‎tests/jenkins/nrnivmodl.sh‎

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@@ -1,22 +1,15 @@
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#!/usr/bin/bash
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set -e
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set +x
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TEST_DIR="$1"
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. /gpfs/bbp.cscs.ch/apps/hpc/jenkins/config/modules.sh
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module load intel
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export SPACK_INSTALL_PREFIX="${SPACK_INSTALL_PREFIX:-${WORKSPACE}/INSTALL_HOME}"
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export PATH=$WORKSPACE/BUILD_HOME/spack/bin:/usr/bin:$PATH
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export MODULEPATH=$SPACK_INSTALL_PREFIX/modules/tcl/$(spack arch):$MODULEPATH
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11-
neuron_version=$(module av neuron 2>&1 | grep -o -m 1 '^neuron.*/parallel$' | awk -F' ' '{print $1}')
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if [[ $neuron_version ]]; then
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module load $neuron_version
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module list
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else
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echo "Error: no compatible neuron version found." >&2
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module list
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exit 1
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fi
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module load intel neuron
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unset $(env|awk -F= '/^(PMI|SLURM)_/ {if ($1 != "SLURM_ACCOUNT") print $1}')
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‎tests/jenkins/run_neuron_direct.sh‎

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#!/usr/bin/bash
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set -e
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set -x
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CORENRN_TYPE="$1"
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unset MODULEPATH
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. /gpfs/bbp.cscs.ch/apps/hpc/jenkins/config/modules.sh
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export SPACK_INSTALL_PREFIX="${SPACK_INSTALL_PREFIX:-${WORKSPACE}/INSTALL_HOME}"
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export PATH=$WORKSPACE/BUILD_HOME/spack/bin:/usr/bin:$PATH
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export MODULEPATH=$SPACK_INSTALL_PREFIX/modules/tcl/$(spack arch):$MODULEPATH
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module load hpe-mpi neuron
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export CORENEURONLIB=$WORKSPACE/install_${CORENRN_TYPE}/lib64/libcoreneuron.so
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unset $(env|awk -F= '/^(PMI|SLURM)_/ {if ($1 != "SLURM_ACCOUNT") print $1}')
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nrniv -python $WORKSPACE/tests/jenkins/neuron_direct.py

‎tests/jenkins/spack_setup.sh‎

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#!/bin/bash
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# Based on spack_setup.sh from blueconfigs repo
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echo "
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=====================================================================
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Preparing spack environment...
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====================================================================="
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export SPACK_INSTALL_PREFIX="${SPACK_INSTALL_PREFIX:-${WORKSPACE}/INSTALL_HOME}"
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export SOFTS_DIR_PATH=$SPACK_INSTALL_PREFIX # Deprecated, but might still be reqd
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BUILD_HOME="${WORKSPACE}/BUILD_HOME"
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export SPACK_ROOT="${BUILD_HOME}/spack"
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# ENV SETUP
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# TODO: /usr/bin was added as a quickfix due to git dependencies probs
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export PATH=$SPACK_ROOT/bin/spack:/usr/bin:$PATH
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# MODULES
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# Use spack only modules. Last one is added by changing MODULEPATH since it might not exist yet
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module purge
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unset MODULEPATH
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source /gpfs/bbp.cscs.ch/apps/hpc/jenkins/config/modules.sh
26+
export MODULEPATH=$SPACK_INSTALL_PREFIX/modules/tcl/$(spack arch):$MODULEPATH
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############################# CLONE/SETUP REPOSITORY #############################
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install_spack() (
31+
set -e
32+
BASEDIR="$(dirname "$SPACK_ROOT")"
33+
mkdir -p $BASEDIR && cd $BASEDIR
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rm -rf .spack # CLEANUP SPACK CONFIGS
35+
SPACK_REPO=https://github.com/BlueBrain/spack.git
36+
SPACK_BRANCH=${SPACK_BRANCH:-"develop"}
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echo "Installing SPACK. Cloning $SPACK_REPO $SPACK_ROOT --depth 1 -b $SPACK_BRANCH"
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git clone $SPACK_REPO $SPACK_ROOT --depth 1 -b $SPACK_BRANCH
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# Use BBP configs
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mkdir -p $SPACK_ROOT/etc/spack/defaults/linux
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cp /gpfs/bbp.cscs.ch/apps/hpc/jenkins/config/*.yaml $SPACK_ROOT/etc/spack/
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)
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install_spack
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