// Slow-path append string
private void append2slowstr() {
// In case of all NAs and then a string, convert NAs to string NAs
if (_xs != null) {
_xs = null;
_ls = null;
alloc_str_indices(sparseLen());
Arrays.fill(_is, -1);
}
if (_is != null && _is.length > 0) {
// Check for sparseness
if (_id == null) {
int nzs = 0; // assume one non-null for the element currently being stored
for (int i : _is) if (i != -1) ++nzs;
if ((nzs + 1) * _sparseRatio < _len) set_sparse(nzs);
} else {
if ((_sparseRatio * (_sparseLen) >> 1) > _len) cancel_sparse();
else _id = MemoryManager.arrayCopyOf(_id, _sparseLen << 1);
}
_is = MemoryManager.arrayCopyOf(_is, sparseLen() << 1);
/* initialize the memory extension with -1s */
for (int i = sparseLen(); i < _is.length; i++) _is[i] = -1;
} else {
_is = MemoryManager.malloc4(4);
/* initialize everything with -1s */
for (int i = 0; i < _is.length; i++) _is[i] = -1;
if (sparse()) alloc_indices(4);
}
assert sparseLen() == 0 || _is.length > sparseLen()
: "_ls.length = " + _is.length + ", _len = " + sparseLen();
}
// Slow-path append data
private void append2slow() {
if (_len > Vec.CHUNK_SZ) throw new ArrayIndexOutOfBoundsException(_len);
assert _ds == null;
if (_len2 == _len) { // Check for sparse-ness now & then
int nzcnt = 0;
for (int i = 0; i < _len; i++) {
if (_ls[i] != 0) nzcnt++;
if (_xs[i] != 0) {
nzcnt = Vec.CHUNK_SZ;
break;
} // Only non-specials sparse
}
if (_len >= 32 && nzcnt * 8 <= _len) { // Heuristic for sparseness
_len = 0;
for (int i = 0; i < _len2; i++)
if (_ls[i] != 0) {
_xs[_len] = i; // Row number in xs
_ls[_len++] = _ls[i]; // Sparse value in ls
}
return; // Compressed, so lots of room now
}
}
_xs = _ls == null ? MemoryManager.malloc4(4) : MemoryManager.arrayCopyOf(_xs, _len << 1);
_ls = _ls == null ? MemoryManager.malloc8(4) : MemoryManager.arrayCopyOf(_ls, _len << 1);
}
public Submodel(
double lambda,
double[] beta,
double[] norm_beta,
long run_time,
int iteration,
boolean sparseCoef) {
this.lambda_value = lambda;
this.run_time = run_time;
this.iteration = iteration;
int r = 0;
if (beta != null) {
final double[] b = norm_beta != null ? norm_beta : beta;
// grab the indeces of non-zero coefficients
for (double d : beta) if (d != 0) ++r;
idxs = MemoryManager.malloc4(sparseCoef ? r : beta.length);
int j = 0;
for (int i = 0; i < beta.length; ++i) if (!sparseCoef || beta[i] != 0) idxs[j++] = i;
j = 0;
this.beta = MemoryManager.malloc8d(idxs.length);
for (int i : idxs) this.beta[j++] = beta[i];
if (norm_beta != null) {
j = 0;
this.norm_beta = MemoryManager.malloc8d(idxs.length);
for (int i : idxs) this.norm_beta[j++] = norm_beta[i];
}
} else idxs = null;
rank = r;
this.sparseCoef = sparseCoef;
}
protected void cancel_sparse() {
if (sparseLen() != _len) {
if (_is != null) {
int[] is = MemoryManager.malloc4(_len);
for (int i = 0; i < _len; i++) is[i] = -1;
for (int i = 0; i < sparseLen(); i++) is[_id[i]] = _is[i];
_is = is;
} else if (_ds == null) {
int[] xs = MemoryManager.malloc4(_len);
long[] ls = MemoryManager.malloc8(_len);
for (int i = 0; i < sparseLen(); ++i) {
xs[_id[i]] = _xs[i];
ls[_id[i]] = _ls[i];
}
_xs = xs;
_ls = ls;
} else {
double[] ds = MemoryManager.malloc8d(_len);
for (int i = 0; i < sparseLen(); ++i) ds[_id[i]] = _ds[i];
_ds = ds;
}
set_sparseLen(_len);
}
_id = null;
}
public Row(boolean sparse, int nNums, int nBins, int nresponses, double etaOffset) {
binIds = MemoryManager.malloc4(nBins);
numVals = MemoryManager.malloc8d(nNums);
response = MemoryManager.malloc8d(nresponses);
if (sparse) numIds = MemoryManager.malloc4(nNums);
this.etaOffset = etaOffset;
this.nNums = sparse ? 0 : nNums;
}
private void cancel_sparse() {
long ls[] = MemoryManager.malloc8(_len2 + 1);
for (int i = 0; i < _len; i++) // Inflate ls to hold values
ls[_xs[i]] = _ls[i];
_ls = ls;
_xs = MemoryManager.malloc4(_len2 + 1);
_len = _len2; // Not compressed now!
}
public Row(boolean sparse, int nNums, int nBins, int nresponses, int i, long start) {
binIds = MemoryManager.malloc4(nBins);
numVals = MemoryManager.malloc8d(nNums);
response = MemoryManager.malloc8d(nresponses);
if (sparse) numIds = MemoryManager.malloc4(nNums);
this.nNums = sparse ? 0 : nNums;
cid = i;
rid = start + i;
}
private void append_ss(String str) {
if (_ss == null) {
_ss = MemoryManager.malloc1((str.length() + 1) * 4);
}
while (_ss.length < (_sslen + str.length() + 1)) {
_ss = MemoryManager.arrayCopyOf(_ss, _ss.length << 1);
}
for (byte b : str.getBytes()) _ss[_sslen++] = b;
_ss[_sslen++] = (byte) 0; // for trailing 0;
}
public void setPredictorTransform(TransformType t) {
_predictor_transform = t;
if (t == TransformType.NONE) {
_normMul = null;
_normSub = null;
} else {
_normMul = MemoryManager.malloc8d(_nums);
_normSub = MemoryManager.malloc8d(_nums);
setTransform(t, _normMul, _normSub, _cats, _nums);
}
}
public void setResponseTransform(TransformType t) {
_response_transform = t;
if (t == TransformType.NONE) {
_normRespMul = null;
_normRespSub = null;
} else {
_normRespMul = MemoryManager.malloc8d(_responses);
_normRespSub = MemoryManager.malloc8d(_responses);
setTransform(t, _normRespMul, _normRespSub, _adaptedFrame.numCols() - _responses, _responses);
}
}
private void append_ss(String str) {
byte[] bytes = str.getBytes(Charsets.UTF_8);
// Allocate memory if necessary
if (_ss == null) _ss = MemoryManager.malloc1((bytes.length + 1) * 4);
while (_ss.length < (_sslen + bytes.length + 1))
_ss = MemoryManager.arrayCopyOf(_ss, _ss.length << 1);
// Copy bytes to _ss
for (byte b : bytes) _ss[_sslen++] = b;
_ss[_sslen++] = (byte) 0; // for trailing 0;
}
@Override
NewChunk inflate_impl(NewChunk nc) {
double dx = Math.log10(_scale);
assert DParseTask.fitsIntoInt(dx);
Arrays.fill(nc._xs = MemoryManager.malloc4(_len), (int) dx);
nc._ls = MemoryManager.malloc8(_len);
for (int i = 0; i < _len; i++) {
int res = UDP.get2(_mem, (i << 1) + OFF);
if (res == C2Chunk._NA) nc.setNA_impl2(i);
else nc._ls[i] = res + _bias;
}
return nc;
}
private void append_ss(BufferedString str) {
int strlen = str.length();
int off = str.getOffset();
byte b[] = str.getBuffer();
if (_ss == null) {
_ss = MemoryManager.malloc1((strlen + 1) * 4);
}
while (_ss.length < (_sslen + strlen + 1)) {
_ss = MemoryManager.arrayCopyOf(_ss, _ss.length << 1);
}
for (int i = off; i < off + strlen; i++) _ss[_sslen++] = b[i];
_ss[_sslen++] = (byte) 0; // for trailing 0;
}
private final double[] contractVec(double[] beta, final int[] activeCols) {
double[] res = MemoryManager.malloc8d(activeCols.length + 1);
int i = 0;
for (int c : activeCols) res[i++] = beta[c];
res[res.length - 1] = beta[beta.length - 1];
return res;
}
// Compute a sparse float buffer
private byte[] bufD(final int valsz) {
int log = 0;
while ((1 << log) < valsz) ++log;
assert (1 << log) == valsz;
final int ridsz = _len >= 65535 ? 4 : 2;
final int elmsz = ridsz + valsz;
int off = CXDChunk._OFF;
byte[] buf = MemoryManager.malloc1(off + sparseLen() * elmsz, true);
for (int i = 0; i < sparseLen(); i++, off += elmsz) {
if (ridsz == 2) UnsafeUtils.set2(buf, off, (short) _id[i]);
else UnsafeUtils.set4(buf, off, _id[i]);
final double dval =
_ds == null ? isNA2(i) ? Double.NaN : _ls[i] * PrettyPrint.pow10(_xs[i]) : _ds[i];
switch (valsz) {
case 4:
UnsafeUtils.set4f(buf, off + ridsz, (float) dval);
break;
case 8:
UnsafeUtils.set8d(buf, off + ridsz, dval);
break;
default:
throw H2O.fail();
}
}
assert off == buf.length;
return buf;
}
public ModelDataAdaptor(OldModel M, int yCol, int[] cols, int[][] catMap) {
this.M = M;
_yCol = yCol;
_row = MemoryManager.malloc8d(cols.length);
_xCols = cols;
_catMap = catMap;
}
private double[] setNewBeta(final double[] newBeta) {
final double[] fullBeta;
if (_activeCols != null) {
fullBeta = MemoryManager.malloc8d(_dinfo.fullN() + 1);
int j = 0;
for (int i : _activeCols) fullBeta[i] = newBeta[j++];
assert j == newBeta.length - 1;
fullBeta[fullBeta.length - 1] = newBeta[j];
} else {
assert newBeta.length == _dinfo.fullN() + 1;
fullBeta = newBeta;
}
final double[] newBetaDeNorm;
if (_dinfo._standardize) {
newBetaDeNorm = fullBeta.clone();
double norm = 0.0; // Reverse any normalization on the intercept
// denormalize only the numeric coefs (categoricals are not normalized)
final int numoff = _dinfo.numStart();
for (int i = numoff; i < fullBeta.length - 1; i++) {
double b = newBetaDeNorm[i] * _dinfo._normMul[i - numoff];
norm += b * _dinfo._normSub[i - numoff]; // Also accumulate the intercept adjustment
newBetaDeNorm[i] = b;
}
newBetaDeNorm[newBetaDeNorm.length - 1] -= norm;
} else newBetaDeNorm = null;
_model.setLambdaSubmodel(
_lambdaIdx,
newBetaDeNorm == null ? fullBeta : newBetaDeNorm,
newBetaDeNorm == null ? null : fullBeta,
(_iter + 1));
_model.clone().update(self());
return fullBeta;
}
// Slow-path append data
private void append2slowd() {
assert _ls == null;
if (_ds != null && _ds.length > 0) {
if (_id == null) { // check for sparseness
int nzs = 0; // assume one non-zero for the element currently being stored
for (double d : _ds) if (d != 0) ++nzs;
if ((nzs + 1) * _sparseRatio < _len) set_sparse(nzs);
} else _id = MemoryManager.arrayCopyOf(_id, sparseLen() << 1);
_ds = MemoryManager.arrayCopyOf(_ds, sparseLen() << 1);
} else {
alloc_doubles(4);
if (sparse()) alloc_indices(4);
}
assert sparseLen() == 0 || _ds.length > sparseLen()
: "_ds.length = " + _ds.length + ", _len = " + sparseLen();
}
// filter the current active columns using the strong rules
// note: strong rules are update so tha they keep all previous coefficients in, to prevent issues
// with line-search
private int[] activeCols(final double l1, final double l2, final double[] grad) {
final double rhs = alpha[0] * (2 * l1 - l2);
int[] cols = MemoryManager.malloc4(_dinfo.fullN());
int selected = 0;
int j = 0;
if (_activeCols == null) _activeCols = new int[] {-1};
for (int i = 0; i < _dinfo.fullN(); ++i)
if ((j < _activeCols.length && i == _activeCols[j]) || grad[i] > rhs || grad[i] < -rhs) {
cols[selected++] = i;
if (j < _activeCols.length && i == _activeCols[j]) ++j;
}
if (!strong_rules_enabled || selected == _dinfo.fullN()) {
_activeCols = null;
_activeData._adaptedFrame = _dinfo._adaptedFrame;
_activeData = _dinfo;
} else {
_activeCols = Arrays.copyOf(cols, selected);
_activeData = _dinfo.filterExpandedColumns(_activeCols);
}
Log.info(
"GLM2 strong rule at lambda="
+ l1
+ ", got "
+ selected
+ " active cols out of "
+ _dinfo.fullN()
+ " total.");
return _activeCols;
}
// Compute a compressed double buffer
private Chunk chunkD() {
HashMap<Long, Byte> hs = new HashMap<>(CUDChunk.MAX_UNIQUES);
Byte dummy = 0;
final byte[] bs = MemoryManager.malloc1(_len * 8, true);
int j = 0;
boolean fitsInUnique = true;
for (int i = 0; i < _len; ++i) {
double d = 0;
if (_id == null || _id.length == 0 || (j < _id.length && _id[j] == i)) {
d =
_ds != null
? _ds[j]
: (isNA2(j) || isCategorical(j)) ? Double.NaN : _ls[j] * PrettyPrint.pow10(_xs[j]);
++j;
}
if (fitsInUnique) {
if (hs.size() < CUDChunk.MAX_UNIQUES) // still got space
hs.put(
Double.doubleToLongBits(d),
dummy); // store doubles as longs to avoid NaN comparison issues during extraction
else
fitsInUnique =
(hs.size() == CUDChunk.MAX_UNIQUES)
&& // full, but might not need more space because of repeats
hs.containsKey(Double.doubleToLongBits(d));
}
UnsafeUtils.set8d(bs, 8 * i, d);
}
assert j == sparseLen() : "j = " + j + ", _len = " + sparseLen();
if (fitsInUnique && CUDChunk.computeByteSize(hs.size(), len()) < 0.8 * bs.length)
return new CUDChunk(bs, hs, len());
else return new C8DChunk(bs);
}
private double[] scoreRow(Row r, double o, double[] preds) {
if (_parms._family == Family.multinomial) {
if (_eta == null) _eta = new ThreadLocal<>();
double[] eta = _eta.get();
if (eta == null) _eta.set(eta = MemoryManager.malloc8d(_output.nclasses()));
final double[][] bm = _output._global_beta_multinomial;
double sumExp = 0;
double maxRow = 0;
for (int c = 0; c < bm.length; ++c) {
eta[c] = r.innerProduct(bm[c]) + o;
if (eta[c] > maxRow) maxRow = eta[c];
}
for (int c = 0; c < bm.length; ++c) sumExp += eta[c] = Math.exp(eta[c] - maxRow); // intercept
sumExp = 1.0 / sumExp;
for (int c = 0; c < bm.length; ++c) preds[c + 1] = eta[c] * sumExp;
preds[0] = ArrayUtils.maxIndex(eta);
} else {
double mu = _parms.linkInv(r.innerProduct(beta()) + o);
if (_parms._family == Family.binomial) { // threshold for prediction
preds[0] = mu >= defaultThreshold() ? 1 : 0;
preds[1] = 1.0 - mu; // class 0
preds[2] = mu; // class 1
} else preds[0] = mu;
}
return preds;
}
// Append all of 'nc' onto the current NewChunk. Kill nc.
public void add(NewChunk nc) {
assert _cidx >= 0;
assert sparseLen() <= _len;
assert nc.sparseLen() <= nc._len : "_len = " + nc.sparseLen() + ", _len2 = " + nc._len;
if (nc._len == 0) return;
if (_len == 0) {
_ls = nc._ls;
nc._ls = null;
_xs = nc._xs;
nc._xs = null;
_id = nc._id;
nc._id = null;
_ds = nc._ds;
nc._ds = null;
_is = nc._is;
nc._is = null;
_ss = nc._ss;
nc._ss = null;
set_sparseLen(nc.sparseLen());
set_len(nc._len);
return;
}
if (nc.sparse() != sparse()) { // for now, just make it dense
cancel_sparse();
nc.cancel_sparse();
}
if (_ds != null) throw H2O.fail();
while (sparseLen() + nc.sparseLen() >= _xs.length)
_xs = MemoryManager.arrayCopyOf(_xs, _xs.length << 1);
_ls = MemoryManager.arrayCopyOf(_ls, _xs.length);
System.arraycopy(nc._ls, 0, _ls, sparseLen(), nc.sparseLen());
System.arraycopy(nc._xs, 0, _xs, sparseLen(), nc.sparseLen());
if (_id != null) {
assert nc._id != null;
_id = MemoryManager.arrayCopyOf(_id, _xs.length);
System.arraycopy(nc._id, 0, _id, sparseLen(), nc.sparseLen());
for (int i = sparseLen(); i < sparseLen() + nc.sparseLen(); ++i) _id[i] += _len;
} else assert nc._id == null;
set_sparseLen(sparseLen() + nc.sparseLen());
set_len(_len + nc._len);
nc._ls = null;
nc._xs = null;
nc._id = null;
nc.set_sparseLen(nc.set_len(0));
assert sparseLen() <= _len;
}
private final double[] expandVec(double[] beta, final int[] activeCols) {
if (activeCols == null) return beta;
double[] res = MemoryManager.malloc8d(_dinfo.fullN() + 1);
int i = 0;
for (int c : activeCols) res[c] = beta[i++];
res[res.length - 1] = beta[beta.length - 1];
return res;
}
void addNullSubmodel(double lmax, double icept, GLMValidation val) {
assert _submodels == null;
double[] beta = MemoryManager.malloc8d(_coefficient_names.length);
beta[beta.length - 1] = icept;
_submodels =
new Submodel[] {new Submodel(lmax, beta, beta, 0, 0, _coefficient_names.length > 750)};
_submodels[0].validation = val;
}
Col(String s, int rows, boolean isClass) {
_name = s;
_isClass = isClass;
_rawB = MemoryManager.malloc1(rows);
_isFloat = false;
_isByte = true;
_colBinLimit = 0;
}
// Slow-path append data
private void append2slowUUID() {
if (_ds == null && _ls != null) { // This can happen for columns with all NAs and then a UUID
_xs = null;
alloc_doubles(sparseLen());
Arrays.fill(_ls, C16Chunk._LO_NA);
Arrays.fill(_ds, Double.longBitsToDouble(C16Chunk._HI_NA));
}
if (_ls != null && _ls.length > 0) {
_ls = MemoryManager.arrayCopyOf(_ls, sparseLen() << 1);
_ds = MemoryManager.arrayCopyOf(_ds, sparseLen() << 1);
} else {
alloc_mantissa(4);
alloc_doubles(4);
}
assert sparseLen() == 0 || _ls.length > sparseLen()
: "_ls.length = " + _ls.length + ", _len = " + sparseLen();
}
@Override
public byte[] atomic(byte[] bits1) {
byte[] mem = DKV.get(_key).get();
int len = Math.max(_dst_off + mem.length, bits1 == null ? 0 : bits1.length);
byte[] bits2 = MemoryManager.malloc1(len);
if (bits1 != null) System.arraycopy(bits1, 0, bits2, 0, bits1.length);
System.arraycopy(mem, 0, bits2, _dst_off, mem.length);
return bits2;
}
Col(String s, int rows, boolean isClass, int binLimit, boolean isFloat) {
_name = s;
_isFloat = isFloat;
_isClass = isClass;
_colBinLimit = binLimit;
_isByte = false;
_raw = MemoryManager.malloc4f(rows);
_ignored = false;
}
private static void addFolder(FileSystem fs, Path p, JsonArray succeeded, JsonArray failed) {
try {
if (fs == null) return;
for (FileStatus file : fs.listStatus(p)) {
Path pfs = file.getPath();
if (file.isDir()) {
addFolder(fs, pfs, succeeded, failed);
} else {
Key k = Key.make(pfs.toString());
long size = file.getLen();
Value val = null;
if (pfs.getName().endsWith(Extensions.JSON)) {
JsonParser parser = new JsonParser();
JsonObject json = parser.parse(new InputStreamReader(fs.open(pfs))).getAsJsonObject();
JsonElement v = json.get(Constants.VERSION);
if (v == null) throw new RuntimeException("Missing version");
JsonElement type = json.get(Constants.TYPE);
if (type == null) throw new RuntimeException("Missing type");
Class c = Class.forName(type.getAsString());
OldModel model = (OldModel) c.newInstance();
model.fromJson(json);
} else if (pfs.getName().endsWith(Extensions.HEX)) { // Hex file?
FSDataInputStream s = fs.open(pfs);
int sz = (int) Math.min(1L << 20, size); // Read up to the 1st meg
byte[] mem = MemoryManager.malloc1(sz);
s.readFully(mem);
// Convert to a ValueArray (hope it fits in 1Meg!)
ValueArray ary = new ValueArray(k, 0).read(new AutoBuffer(mem));
val = new Value(k, ary, Value.HDFS);
} else if (size >= 2 * ValueArray.CHUNK_SZ) {
val =
new Value(
k,
new ValueArray(k, size),
Value.HDFS); // ValueArray byte wrapper over a large file
} else {
val = new Value(k, (int) size, Value.HDFS); // Plain Value
val.setdsk();
}
DKV.put(k, val);
Log.info("PersistHdfs: DKV.put(" + k + ")");
JsonObject o = new JsonObject();
o.addProperty(Constants.KEY, k.toString());
o.addProperty(Constants.FILE, pfs.toString());
o.addProperty(Constants.VALUE_SIZE, file.getLen());
succeeded.add(o);
}
}
} catch (Exception e) {
Log.err(e);
JsonObject o = new JsonObject();
o.addProperty(Constants.FILE, p.toString());
o.addProperty(Constants.ERROR, e.getMessage());
failed.add(o);
}
}
// private constructor called by filterExpandedColumns
private DataInfo(
DataInfo dinfo,
Frame fr,
double[] normMul,
double[] normSub,
int[][] catLevels,
int[] catModes) {
_fullCatOffsets = dinfo._catOffsets;
if (!dinfo._useAllFactorLevels) {
_fullCatOffsets = dinfo._catOffsets.clone();
for (int i = 0; i < _fullCatOffsets.length; ++i)
_fullCatOffsets[i] += i; // add for the skipped zeros.
}
_offset = dinfo._offset;
_weights = dinfo._weights;
_fold = dinfo._fold;
_valid = false;
_interactions = dinfo._interactions;
_interactionVecs = dinfo._interactionVecs;
assert dinfo._predictor_transform != null;
assert dinfo._response_transform != null;
_predictor_transform = dinfo._predictor_transform;
_response_transform = dinfo._response_transform;
_skipMissing = dinfo._skipMissing;
_imputeMissing = dinfo._imputeMissing;
_adaptedFrame = fr;
_catOffsets = MemoryManager.malloc4(catLevels.length + 1);
_catMissing = new boolean[catLevels.length];
Arrays.fill(_catMissing, !(dinfo._imputeMissing || dinfo._skipMissing));
int s = 0;
for (int i = 0; i < catLevels.length; ++i) {
_catOffsets[i] = s;
s += catLevels[i].length;
}
_catLvls = catLevels;
_catOffsets[_catOffsets.length - 1] = s;
_responses = dinfo._responses;
_cats = catLevels.length;
_nums =
fr.numCols()
- _cats
- dinfo._responses
- (_offset ? 1 : 0)
- (_weights ? 1 : 0)
- (_fold ? 1 : 0);
_numOffsets = _nums == 0 ? new int[0] : dinfo._numOffsets.clone();
int diff = _numOffsets.length > 0 ? _numOffsets[0] - s : 0;
for (int i = 0; i < _numOffsets.length; i++) // need to shift everyone down by the offset!
_numOffsets[i] -= diff;
_useAllFactorLevels = true; // dinfo._useAllFactorLevels;
_numMeans = new double[_nums];
_normMul = normMul;
_normSub = normSub;
_catModes = catModes;
for (int i = 0; i < _nums; i++) _numMeans[i] = _adaptedFrame.vec(_cats + i).mean();
}