Examples with EquationSet gov.sandia.n2a.eqset.EquationSet used on opensource projects

Example 41 with EquationSet

use of gov.sandia.n2a.eqset.EquationSet in project n2a by frothga.

the class ChangeVariable method emitPath.

public static String emitPath(EquationSet home, EquationSet target, String name) {
    // If there is an unambiguous path up to "name", then emit nothing.
    EquationSet e = home;
    while (e != target) {
        if (isVisible(e, name))
            break;
        e = e.container;
    }
    if (e == target)
        return "";
    // If there is an unambiguous path to the container of "name", then use that.
    if (// Only do this if not top-level container, as that container can't be referenced explicitly.
    target.container != null) {
        // Count depth to decide between using this method or $up. For a single level, $up is a nicer choice. For many levels, an explicit part name is more concise.
        int depth = 0;
        e = home;
        while (e != target) {
            depth++;
            if (isVisible(e, target.name))
                break;
            e = e.container;
        }
        if (e == target && depth > 1)
            return target.name + ".";
    }
    // Otherwise, use $up.
    String result = "";
    e = home;
    while (e != target) {
        result += "$up.";
        e = e.container;
    }
    return result;
}

Example 42 with EquationSet

use of gov.sandia.n2a.eqset.EquationSet in project n2a by frothga.

the class ExportJob method fakeConnectionTarget.

/**
 *        Replace any entries of the form A=connect() with A=N2A_fakePart.
 */
public static boolean fakeConnectionTarget(EquationSet s) {
    boolean result = false;
    for (Variable v : s.variables) {
        if (// may be due to unreadable part names in connect()
        v.equations.size() == 0) {
            String value = s.source.get(v.nameString());
            if (!Operator.containsConnect(value))
                continue;
            try {
                v.add(new EquationEntry("N2A_fakePart"));
                result = true;
            } catch (Exception e) {
            }
        } else if (// could be a properly-parsed connect() line
        v.equations.size() == 1) {
            EquationEntry e = v.equations.first();
            // connect() appears like AccessElement during initial parse
            if (!(e.expression instanceof AccessElement))
                continue;
            AccessElement ae = (AccessElement) e.expression;
            AccessVariable av = (AccessVariable) ae.operands[0];
            if (!av.name.equals("connect"))
                continue;
            av.name = "N2A_fakePart";
            e.expression = av;
            result = true;
        }
    }
    for (EquationSet p : s.parts) if (fakeConnectionTarget(p))
        result = true;
    return result;
}

Example 43 with EquationSet

use of gov.sandia.n2a.eqset.EquationSet in project n2a by frothga.

the class ExportJob method process.

public void process(MPart source) {
    if (source.get("$metadata", "backend", "lems", "part").isEmpty()) {
        for (EquationSet p : equations.parts) topLevelPart((MPart) p.source);
    } else {
        topLevelPart(source);
    }
    // Simulation
    if (simulation != null) {
        simulation.findOutputs();
        if (simulation.score() > 0)
            simulation.append();
    }
    // ComponentTypes
    if (componentTypes.size() > 0) {
        try {
            // Rebuild equations, this time without the aggressive constant folding.
            MPart mpart = (MPart) equations.source;
            equations = new EquationSet(mpart);
            makeExecutable(equations, false);
            for (ComponentType ct : componentTypes) ct.append();
        }// Shouldn't be any exceptions, since we already built this equation set once.
         catch (Exception e) {
        }
    }
    appendUnits(requiresNML);
    // Collate
    Element root;
    if (componentTypes.isEmpty() && !forBackend) {
        suffix = "nml";
        root = doc.createElement("neuroml");
        root.setAttribute("xmlns", "http://www.neuroml.org/schema/neuroml2");
        root.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance");
        root.setAttribute("xsi:schemaLocation", "http://www.neuroml.org/schema/neuroml2 ../Schemas/NeuroML2/NeuroML_v2beta4.xsd");
        root.setAttribute("id", modelName);
    } else {
        suffix = "xml";
        root = doc.createElement("Lems");
        if (requiresNML) {
            Element include = addElement("Include", elements);
            include.setAttribute("file", "Cells.xml");
            include = addElement("Include", elements);
            include.setAttribute("file", "Networks.xml");
            if (simulation != null) {
                include = addElement("Include", elements);
                include.setAttribute("file", "Simulation.xml");
                Element target = addElement("Target", elements);
                target.setAttribute("component", simulation.id);
            }
        } else {
        // TODO: set Target for pure LEMS file (one with no NeuroML elements at all).
        }
    }
    sequencer.append(root, elements);
    doc.appendChild(root);
}

Example 44 with EquationSet

use of gov.sandia.n2a.eqset.EquationSet in project n2a by frothga.

the class JobSTACS method run.

public void run() {
    localJobDir = Host.getJobDir(Host.getLocalResourceDir(), job);
    Path errPath = localJobDir.resolve("err");
    try {
        Backend.err.set(new PrintStream(new FileOutputStream(errPath.toFile(), true), false, "UTF-8"));
    } catch (Exception e) {
    }
    try {
        Files.createFile(localJobDir.resolve("started"));
        MNode model = NodeJob.getModel(job);
        env = Host.get(job);
        // remote or local
        Path resourceDir = env.getResourceDir();
        // Unlike localJobDir (which is created by MDir), this may not exist until we explicitly create it.
        jobDir = Host.getJobDir(resourceDir, job);
        // digestModel() might write to a remote file (params), so we need to ensure the dir exists first.
        Files.createDirectories(jobDir);
        digestedModel = new EquationSet(model);
        InternalBackend.digestModel(digestedModel);
        String duration = digestedModel.metadata.get("duration");
        if (!duration.isEmpty())
            job.set(duration, "duration");
        seed = model.getOrDefault(System.currentTimeMillis(), "$metadata", "seed");
        job.set(seed, "seed");
        int cores = 1;
        if (!(env instanceof Remote))
            cores = env.getProcessorTotal();
        cores = job.getOrDefault(cores, "host", "cores");
        int nodes = job.getOrDefault(1, "host", "nodes");
        processes = cores * nodes;
        generateConfigs();
        // The simulator could append to the same error file, so we need to close the file before submitting.
        PrintStream ps = Backend.err.get();
        if (ps != System.err) {
            ps.close();
            Backend.err.remove();
            job.set(Host.size(errPath), "errSize");
        }
        List<List<String>> commands = new ArrayList<List<String>>();
        List<String> charmrun = new ArrayList<String>();
        charmrun.add("charmrun");
        charmrun.add("+p" + processes);
        List<String> command = new ArrayList<String>(charmrun);
        command.add(env.config.getOrDefault("genet", "backend", "stacs", "genet"));
        command.add("config.yml");
        commands.add(command);
        command = new ArrayList<String>(charmrun);
        command.add(env.config.getOrDefault("stacs", "backend", "stacs", "stacs"));
        command.add("config.yml");
        commands.add(command);
        env.submitJob(job, true, commands);
    } catch (Exception e) {
        if (!(e instanceof AbortRun))
            e.printStackTrace(Backend.err.get());
        try {
            Files.copy(new ByteArrayInputStream("failure".getBytes("UTF-8")), localJobDir.resolve("finished"));
        } catch (Exception f) {
        }
    }
    // If an exception occurred, the error file will still be open.
    PrintStream ps = Backend.err.get();
    if (ps != System.err)
        ps.close();
}

Example 45 with EquationSet

use of gov.sandia.n2a.eqset.EquationSet in project n2a by frothga.

the class XyceBackend method analyze.

public void analyze(EquationSet s) {
    for (EquationSet p : s.parts) analyze(p);
    XyceBackendData bed = new XyceBackendData();
    bed.internal = (InternalBackendData) s.backendData;
    s.backendData = bed;
    bed.analyze(s);
}