// checkCheckPoint tests that a checkpoint happened at the requested delay
// in seconds (+/- margin)
func checkCheckPoint(testDir string, c *jsonParser.TestCase) error {
path := file.GetOutputDir(testDir)
stamp := filepath.Join(path, c.BaseName+".stamp")
stampi, err := os.Stat(stamp)
if err != nil {
return fmt.Errorf("Failed to stat file %s", stamp)
}
stampTime := stampi.ModTime()
checkpt := filepath.Join(path, c.BaseName+".cp")
checkpti, err := os.Stat(checkpt)
if err != nil {
return fmt.Errorf("Failed to stat file %s", checkpt)
}
checkTime := checkpti.ModTime()
if checkTime.Sub(stampTime).Seconds() < c.Delay-c.Margin {
return fmt.Errorf("Realtime checkpoint scheduled for %f seconds but "+
"time between timestamp and checkpoint is less than %f seconds",
c.Delay, c.Delay-c.Margin)
}
if checkTime.Sub(stampTime).Seconds() > c.Delay+c.Margin {
return fmt.Errorf("Realtime checkpoint scheduled for %f seconds but "+
"time between timestamp and checkpoint exceeds %f seconds", c.Delay,
c.Delay+c.Margin)
}
return nil
}
// createSimJobs is responsible for filling a worker queue with
// jobs to be run via the simulation tool. It parses the test
// description, assembles a TestDescription struct and adds it
// to the simulation job queue.
func createSimJobs(includePath string, testPaths []string,
simJobs chan *jsonParser.TestDescription) {
runID := 0
for _, testDir := range testPaths {
testFile := filepath.Join(testDir, "test_description.json")
testDescription, err := jsonParser.Parse(testFile, includePath)
if err != nil {
log.Printf("Error parsing test description in %s: %v", testDir, err)
continue
}
// create output directory
outputDir := file.GetOutputDir(testDir)
if err := os.Mkdir(outputDir, 0744); err != nil {
log.Print(err)
continue
}
// set path and pick a Seed value for run
testDescription.Path = testDir
testDescription.Run.RunID = runID
// schedule requested number of Seeds; if there is just a single
// Seed requested we pick one randomly
switch testDescription.Run.NumSeeds {
case 0: // user didn't set number of Seeds -- assume single Seed
testDescription.Run.NumSeeds = 1
testDescription.Run.Seed = rng.Intn(10000)
case 1:
testDescription.Run.Seed = rng.Intn(10000)
default:
for i := 1; i < testDescription.Run.NumSeeds; i++ {
newTest := testDescription.Copy()
newTest.Run.Seed = i
testDescription.Run.Seed = i + 1
simJobs <- newTest
}
}
simJobs <- testDescription
runID++
}
close(simJobs)
}
// checkDREAMMV3MolsBin checks the layout for molecule viz data as part of the
// binary DREAMM v3 format
func checkDREAMMV3MolsBin(testDir string, c *jsonParser.TestCase) error {
s, err := misc.CreateMolMeshIters(c.AllIters, c.SurfPosIters, c.SurfOrientIters,
c.SurfStateIters)
if err != nil {
return err
}
v, err := misc.CreateMolMeshIters(c.AllIters, c.VolPosIters, c.VolOrientIters,
c.VolStateIters)
if err != nil {
return err
}
molIters := s.AllCombined.Clone().Union(v.AllCombined)
dataPath := filepath.Join(file.GetOutputDir(testDir), c.VizPath)
lastSurfPos := -1
lastSurfOrient := -1
lastSurfState := -1
lastVolPos := -1
lastVolOrient := -1
lastVolState := -1
for _, i := range s.All {
iterPath := filepath.Join(dataPath, "frame_data", "iteration_%d")
hadFrame := false
// surface positions
surfPosFile := filepath.Join(iterPath, "surface_molecules_positions.bin")
if err := misc.CheckDREAMMV3IterItems(s.Pos, molIters, i, lastSurfPos,
c.SurfEmpty, surfPosFile); err != nil {
return err
}
if s.Pos.Contains(i) {
lastSurfPos = i
hadFrame = true
}
// surface orientations
surfOrientFile := filepath.Join(iterPath, "surface_molecules_orientations.bin")
if err := misc.CheckDREAMMV3IterItems(s.Others, molIters, i, lastSurfOrient,
c.SurfEmpty, surfOrientFile); err != nil {
return err
}
if s.Others.Contains(i) {
lastSurfOrient = i
hadFrame = true
}
// surface states
surfStateFile := filepath.Join(iterPath, "surface_molecules_states.bin")
if err := misc.CheckDREAMMV3IterItems(s.States, molIters, i, lastSurfState,
c.SurfEmpty, surfStateFile); err != nil {
return err
}
if s.States.Contains(i) {
lastSurfState = i
hadFrame = true
}
surfTemplate := filepath.Join(iterPath, "surface_molecules.dx")
if err := misc.CheckDREAMMV3DXItems(i, lastSurfPos, lastSurfOrient, lastSurfState,
hadFrame, surfTemplate); err != nil {
return err
}
// volume positions
hadFrame = false
volPosFile := filepath.Join(iterPath, "volume_molecules_positions.bin")
if err := misc.CheckDREAMMV3IterItems(v.Pos, molIters, i, lastVolPos,
c.VolEmpty, volPosFile); err != nil {
return err
}
if v.Pos.Contains(i) {
lastVolPos = i
hadFrame = true
}
// volume orientations
volOrientFile := filepath.Join(iterPath, "volume_molecules_orientations.bin")
if err := misc.CheckDREAMMV3IterItems(v.Others, molIters, i, lastVolOrient,
c.VolEmpty, volOrientFile); err != nil {
return err
}
if v.Others.Contains(i) {
lastVolOrient = i
hadFrame = true
}
// volume states
volStateFile := filepath.Join(iterPath, "volume_molecules_states.bin")
if err := misc.CheckDREAMMV3IterItems(v.States, molIters, i, lastVolState,
c.SurfEmpty, volStateFile); err != nil {
return err
}
if v.States.Contains(i) {
lastVolState = i
hadFrame = true
}
volTemplate := filepath.Join(iterPath, "volume_molecules.dx")
if err := misc.CheckDREAMMV3DXItems(i, lastVolPos, lastVolOrient, lastVolState,
hadFrame, volTemplate); err != nil {
return err
}
}
return nil
}
// checkDREAMMV3Grouped checks the layout for DREAMM V3 grouped format
func checkDREAMMV3Grouped(testDir, dataDir string, numIters, numTimes int,
haveMeshPos, haveRgnIdx, haveMeshState, noMeshes, haveMolPos, haveMolOrient,
haveMolState, noMols bool) error {
dataPath := filepath.Join(file.GetOutputDir(testDir), dataDir)
// meshes
meshPath := dataPath + ".mesh_positions.1.bin"
if err := misc.CheckDREAMMV3GroupedItem(meshPath, haveMeshPos, noMeshes); err != nil {
return err
}
regionPath := dataPath + ".region_indices.1.bin"
if err := misc.CheckDREAMMV3GroupedItem(regionPath, haveRgnIdx, noMeshes); err != nil {
return err
}
meshStatesPath := dataPath + ".mesh_states.1.bin"
if err := misc.CheckDREAMMV3GroupedItem(meshStatesPath, haveMeshState,
noMeshes); err != nil {
return err
}
// molecules
molPath := dataPath + ".molecule_positions.1.bin"
if err := misc.CheckDREAMMV3GroupedItem(molPath, haveMolPos, noMols); err != nil {
return err
}
orientPath := dataPath + ".molecule_orientations.1.bin"
if err := misc.CheckDREAMMV3GroupedItem(orientPath, haveMolOrient, noMols); err != nil {
return err
}
molStatesPath := dataPath + ".molecule_states.1.bin"
if err := misc.CheckDREAMMV3GroupedItem(molStatesPath, haveMolState, noMols); err != nil {
return err
}
// iterations
iterPath := dataPath + ".iteration_numbers.1.bin"
if numIters != 0 {
ok, err := file.HasSize(iterPath, int64(numIters*12))
if err != nil {
return err
}
if !ok {
return fmt.Errorf("file %s has incorrect file size", iterPath)
}
} else {
ok, err := file.IsNonEmpty(iterPath)
if err != nil {
return err
}
if !ok {
return fmt.Errorf("file %s is not non-empty", iterPath)
}
}
// times
timePath := dataPath + ".time_values.1.bin"
if numTimes != 0 {
ok, err := file.HasSize(timePath, int64(numTimes*8))
if err != nil {
return err
}
if !ok {
return fmt.Errorf("file %s has incorrect file size", timePath)
}
} else {
ok, err := file.IsNonEmpty(timePath)
if err != nil {
return err
}
if !ok {
return fmt.Errorf("file %s is not non-empty", timePath)
}
}
return nil
}
// checkDREAMMV3MeshASCII checks the layout for mesh related data within the
// DREAMM v3 viz format
func checkDREAMMV3MeshASCII(testDir, dataDir string, allIters, posIters,
regionIters, stateIters jsonParser.IntList, meshEmpty bool, objects,
objectRegions []string) error {
m, err := misc.CreateMolMeshIters(allIters, posIters, regionIters, stateIters)
if err != nil {
return err
}
if len(objectRegions) == 0 {
objectRegions = objects
}
dataPath := filepath.Join(file.GetOutputDir(testDir), dataDir)
lastPos := -1
lastRegion := -1
lastState := -1
for _, i := range m.All {
iterPath := filepath.Join(dataPath, "frame_data", "iteration_%d")
hadFrame := false
// positions
for _, obj := range objects {
posFile := filepath.Join(iterPath, obj+".positions.dat")
if err := misc.CheckDREAMMV3IterItems(m.Pos, m.Combined, i, lastPos,
meshEmpty, posFile); err != nil {
return err
}
conFile := filepath.Join(iterPath, obj+".connections.dat")
if err := misc.CheckDREAMMV3IterItems(m.Pos, m.Combined, i, lastPos,
meshEmpty, conFile); err != nil {
return err
}
}
if m.Pos.Contains(i) {
lastPos = i
misc.UnsetTrackers(i, &lastPos, &lastRegion, &lastState)
hadFrame = true
}
// regions
for _, obj := range objectRegions {
regionFile := filepath.Join(iterPath, obj+".region_indices.dat")
if err := misc.CheckDREAMMV3IterItems(m.Others, m.States, i, lastRegion,
meshEmpty, regionFile); err != nil {
return err
}
}
if m.Others.Contains(i) {
lastRegion = i
misc.UnsetTrackers(i, &lastPos, &lastRegion, &lastState)
hadFrame = true
}
// states
for _, obj := range objects {
statesFile := filepath.Join(iterPath, obj+".states.bin")
emptySet := set.NewIntSet()
if err := misc.CheckDREAMMV3IterItems(m.States, emptySet, i, lastState,
meshEmpty, statesFile); err != nil {
return err
}
}
if m.States.Contains(i) {
lastState = i
misc.UnsetTrackers(i, &lastPos, &lastRegion, &lastState)
hadFrame = true
}
template := filepath.Join(iterPath, "meshes.dx")
if err := misc.CheckDREAMMV3DXItems(i, lastPos, lastRegion, lastState,
hadFrame, template); err != nil {
return err
}
}
return nil
}
// checkDREAMMV3MolsASCII checks the layout for molecule viz data as part of the
// ASCII DREAMM v3 format
func checkDREAMMV3MolsASCII(testDir string, c *jsonParser.TestCase) error {
m, err := misc.CreateMolMeshIters(c.AllIters, c.PosIters, c.OrientIters, c.StateIters)
if err != nil {
return err
}
dataPath := filepath.Join(file.GetOutputDir(testDir), c.VizPath)
lastPos := -1
lastOrient := -1
lastState := -1
for _, i := range m.All {
iterPath := filepath.Join(dataPath, "frame_data", "iteration_%d")
hadFrame := false
// positions
for _, obj := range c.MolNames {
posFile := filepath.Join(iterPath, obj+".positions.dat")
if err := misc.CheckDREAMMV3IterItems(m.Pos, m.Combined, i, lastPos,
true, posFile); err != nil {
return err
}
}
if m.Pos.Contains(i) {
lastPos = i
misc.UnsetTrackers(i, &lastPos, &lastOrient, &lastState)
hadFrame = true
}
// orientations
for _, obj := range c.MolNames {
orientFile := filepath.Join(iterPath, obj+".orientations.dat")
if err := misc.CheckDREAMMV3IterItems(m.Others, m.Combined, i, lastOrient,
true, orientFile); err != nil {
return err
}
}
if m.Others.Contains(i) {
lastOrient = i
misc.UnsetTrackers(i, &lastPos, &lastOrient, &lastState)
hadFrame = true
}
// states
for _, obj := range c.MolNames {
stateFile := filepath.Join(iterPath, obj+".states.dat")
if err := misc.CheckDREAMMV3IterItems(m.States, m.Combined, i, lastState,
true, stateFile); err != nil {
return err
}
}
if m.States.Contains(i) {
lastState = i
misc.UnsetTrackers(i, &lastPos, &lastOrient, &lastState)
hadFrame = true
}
volTemplate := filepath.Join(iterPath, "volume_molecules.dx")
if err := misc.CheckDREAMMV3DXItems(i, lastPos, lastOrient, lastState,
hadFrame, volTemplate); err != nil {
return err
}
surfTemplate := filepath.Join(iterPath, "surface_molecules.dx")
if err := misc.CheckDREAMMV3DXItems(i, lastPos, lastOrient, lastState,
hadFrame, surfTemplate); err != nil {
return err
}
}
return nil
}
// simRunner runs mcell on the mdl file passed in as an
// absolute path. The working directory is set to the base path
// of the mdl file.
func simRunner(mcellPath string, test *jsonParser.TestDescription,
output chan *jsonParser.TestDescription) {
outputDir := file.GetOutputDir(test.Path)
for i, runFile := range test.Run.MdlFiles {
// create run command
mdlPath := filepath.Join(test.Path, runFile)
runLog := fmt.Sprintf("run_%d.%d.log", test.Run.Seed, i)
errLog := fmt.Sprintf("err_%d.%d.log", test.Run.Seed, i)
argList := append(test.Run.CommandlineOpts, "-seed", strconv.Itoa(test.Run.Seed),
"-logfile", runLog, "-errfile", errLog, mdlPath)
cmd := exec.Command(mcellPath, argList...)
cmd.Dir = outputDir
if err := misc.WriteCmdLine(mcellPath, outputDir, argList); err != nil {
test.SimStatus = append(test.SimStatus,
jsonParser.RunStatus{false, fmt.Sprint(err), "", -1})
output <- test
return
}
// connect stdout and stderr
stdOutPath := fmt.Sprintf("stdout_%d.%d.log", test.Run.Seed, i)
stdOut, err := os.Create(filepath.Join(outputDir, stdOutPath))
if err != nil {
test.SimStatus = append(test.SimStatus,
jsonParser.RunStatus{false, fmt.Sprint(err), "", -1})
output <- test
return
}
defer stdOut.Close()
cmd.Stdout = stdOut
stdErrPath := fmt.Sprintf("stderr_%d.%d.log", test.Run.Seed, i)
stdErr, err := os.Create(filepath.Join(outputDir, stdErrPath))
if err != nil {
test.SimStatus = append(test.SimStatus,
jsonParser.RunStatus{false, fmt.Sprint(err), "", -1})
output <- test
return
}
defer stdErr.Close()
cmd.Stderr = stdErr
err = cmd.Run()
if err != nil {
stdErrContent, _ := ioutil.ReadFile(filepath.Join(outputDir, errLog))
exitCode, err := misc.DetermineExitCode(err)
if err != nil {
exitCode = -1
}
test.SimStatus = append(test.SimStatus,
jsonParser.RunStatus{false, fmt.Sprint(err),
string(stdErrContent), exitCode})
} else {
test.SimStatus = append(test.SimStatus,
jsonParser.RunStatus{true, "", "", 0})
}
}
output <- test
}