/*
* Helper for the freeLocalsHelpers which does the actual work of decrementing
* a value's refcount or releasing it.
*
* This helper is reached via call from the various freeLocalHelpers. It
* expects `tv' to be the address of a TypedValue with refcounted type `type'
* (though it may be static, and we will do nothing in that case).
*
* The `live' registers must be preserved across any native calls (and
* generally left untouched).
*/
static TCA emitDecRefHelper(CodeBlock& cb, DataBlock& data, CGMeta& fixups,
PhysReg tv, PhysReg type, RegSet live) {
return vwrap(cb, data, fixups, [&] (Vout& v) {
// Set up frame linkage to avoid an indirect fixup.
v << pushp{rlr(), rfp()};
v << copy{rsp(), rfp()};
// We use the first argument register for the TV data because we might pass
// it to the native release call. It's not live when we enter the helper.
auto const data = rarg(0);
v << load{tv[TVOFF(m_data)], data};
auto const sf = v.makeReg();
v << cmplim{1, data[FAST_REFCOUNT_OFFSET], sf};
ifThen(v, CC_NL, sf, [&] (Vout& v) {
// The refcount is positive, so the value is refcounted. We need to
// either decref or release.
ifThen(v, CC_NE, sf, [&] (Vout& v) {
// The refcount is greater than 1; decref it.
v << declm{data[FAST_REFCOUNT_OFFSET], v.makeReg()};
// Pop FP/LR and return
v << popp{rfp(), rlr()};
v << ret{live};
});
// Note that the stack is aligned since we called to this helper from an
// stack-unaligned stub.
PhysRegSaver prs{v, live};
// The refcount is exactly 1; release the value.
// Avoid 'this' pointer overwriting by reserving it as an argument.
v << callm{lookupDestructor(v, type), arg_regs(1)};
// Between where %rsp is now and the saved RIP of the call into the
// freeLocalsHelpers stub, we have all the live regs we pushed, plus the
// saved RIP of the call from the stub to this helper.
v << syncpoint{makeIndirectFixup(prs.dwordsPushed())};
// fallthru
});
// Either we did a decref, or the value was static.
// Pop FP/LR and return
v << popp{rfp(), rlr()};
v << ret{live};
});
}
/*
* Helper for the freeLocalsHelpers which does the actual work of decrementing
* a value's refcount or releasing it.
*
* This helper is reached via call from the various freeLocalHelpers. It
* expects `tv' to be the address of a TypedValue with refcounted type `type'
* (though it may be static, and we will do nothing in that case).
*
* The `live' registers must be preserved across any native calls (and
* generally left untouched).
*/
static TCA emitDecRefHelper(CodeBlock& cb, DataBlock& data, CGMeta& fixups,
PhysReg tv, PhysReg type, RegSet live) {
return vwrap(cb, data, fixups, [&] (Vout& v) {
// Set up frame linkage to avoid an indirect fixup.
v << stublogue{true};
v << copy{rsp(), rfp()};
// We use the first argument register for the TV data because we might pass
// it to the native release call. It's not live when we enter the helper.
auto const data = rarg(0);
v << load{tv[TVOFF(m_data)], data};
auto destroy = [&](Vout& v) {
// Note that the stack is aligned since we called to this helper from an
// stack-unaligned stub.
PhysRegSaver prs{v, live};
// The refcount is exactly 1; release the value.
// Avoid 'this' pointer overwriting by reserving it as an argument.
// There's no need for a fixup, because we setup a frame on the c++
// stack.
v << callm{lookupDestructor(v, type), arg_regs(1)};
// fallthru
};
auto const sf = emitCmpRefCount(v, OneReference, data);
if (one_bit_refcount) {
ifThen(v, CC_E, sf, destroy);
} else {
ifThen(v, CC_NL, sf, [&] (Vout& v) {
// The refcount is positive, so the value is refcounted. We need to
// either decref or release.
ifThen(v, CC_NE, sf, [&] (Vout& v) {
// The refcount is greater than 1; decref it.
emitDecRefCount(v, data);
v << stubret{live, true};
});
destroy(v);
});
}
// Either we did a decref, or the value was static.
v << stubret{live, true};
});
}
static int restoreProc( const SubCmd::Args &args )
{
if ( args.size() != 3 )
{
printf( "gitfs restore tag dest\n" );
return 1;
}
path_init( args[1] );
boost::spirit::classic::file_iterator<char> fi( args[1] );
if ( !fi )
std::cout << "error" << std::endl;
else
{
std::auto_ptr<GitbkFs> rfp( fromItem( &*fi, args[2] ) );
RunMt( rfp.get( ) );
}
return 0;
}
Function simpleIRK(Function f, int N, int order, const std::string& scheme,
const std::string& solver,
const Dict& solver_options) {
// Consistency check
casadi_assert_message(N>=1, "Parameter N (number of steps) must be at least 1, but got "
<< N << ".");
casadi_assert_message(f.n_in()==2, "Function must have two inputs: x and p");
casadi_assert_message(f.n_out()==1, "Function must have one outputs: dot(x)");
// Obtain collocation points
std::vector<double> tau_root = collocation_points(order, scheme);
tau_root.insert(tau_root.begin(), 0);
// Retrieve collocation interpolating matrices
std::vector < std::vector <double> > C;
std::vector < double > D;
collocationInterpolators(tau_root, C, D);
// Inputs of constructed function
MX x0 = MX::sym("x0", f.sparsity_in(0));
MX p = MX::sym("p", f.sparsity_in(1));
MX h = MX::sym("h");
// Time step
MX dt = h/N;
// Implicitly defined variables
MX v = MX::sym("v", repmat(x0.sparsity(), order));
std::vector<MX> x = vertsplit(v, x0.size1());
x.insert(x.begin(), x0);
// Collect the equations that implicitly define v
std::vector<MX> V_eq, f_in(2), f_out;
for (int j=1; j<order+1; ++j) {
// Expression for the state derivative at the collocation point
MX xp_j = 0;
for (int r=0; r<=order; ++r) xp_j+= C[j][r]*x[r];
// Collocation equations
f_in[0] = x[j];
f_in[1] = p;
f_out = f(f_in);
V_eq.push_back(dt*f_out.at(0)-xp_j);
}
// Root-finding function
Function rfp("rfp", {v, x0, p, h}, {vertcat(V_eq)});
// Create a implicit function instance to solve the system of equations
Function ifcn = rootfinder("ifcn", solver, rfp, solver_options);
// Get state at end time
MX xf = x0;
for (int k=0; k<N; ++k) {
std::vector<MX> ifcn_out = ifcn({repmat(xf, order), xf, p, h});
x = vertsplit(ifcn_out[0], x0.size1());
// State at end of step
xf = D[0]*x0;
for (int i=1; i<=order; ++i) {
xf += D[i]*x[i-1];
}
}
// Form discrete-time dynamics
return Function("F", {x0, p, h}, {xf}, {"x0", "p", "h"}, {"xf"});
}
TCA emitFreeLocalsHelpers(CodeBlock& cb, DataBlock& data, UniqueStubs& us) {
// The address of the first local is passed in the second argument register.
// We use the third and fourth as scratch registers.
auto const local = rarg(1);
auto const last = rarg(2);
auto const type = rarg(3);
CGMeta fixups;
TCA freeLocalsHelpers[kNumFreeLocalsHelpers];
TCA freeManyLocalsHelper;
// This stub is very hot; keep it cache-aligned.
align(cb, &fixups, Alignment::CacheLine, AlignContext::Dead);
auto const release =
emitDecRefHelper(cb, data, fixups, local, type, local | last);
auto const decref_local = [&] (Vout& v) {
auto const sf = v.makeReg();
// We can't use emitLoadTVType() here because it does a byte load, and we
// need to sign-extend since we use `type' as a 32-bit array index to the
// destructor table.
v << loadzbl{local[TVOFF(m_type)], type};
emitCmpTVType(v, sf, KindOfRefCountThreshold, type);
ifThen(v, CC_G, sf, [&] (Vout& v) {
v << call{release, arg_regs(3)};
});
};
auto const next_local = [&] (Vout& v) {
v << addqi{static_cast<int>(sizeof(TypedValue)),
local, local, v.makeReg()};
};
alignJmpTarget(cb);
freeManyLocalsHelper = vwrap(cb, data, [&] (Vout& v) {
// We always unroll the final `kNumFreeLocalsHelpers' decrefs, so only loop
// until we hit that point.
v << lea{rvmfp()[localOffset(kNumFreeLocalsHelpers - 1)], last};
// Set up frame linkage to avoid an indirect fixup.
v << copy{rsp(), rfp()};
doWhile(v, CC_NZ, {},
[&] (const VregList& in, const VregList& out) {
auto const sf = v.makeReg();
decref_local(v);
next_local(v);
v << cmpq{local, last, sf};
return sf;
}
);
});
for (auto i = kNumFreeLocalsHelpers - 1; i >= 0; --i) {
freeLocalsHelpers[i] = vwrap(cb, data, [&] (Vout& v) {
decref_local(v);
if (i != 0) next_local(v);
});
}
// All the stub entrypoints share the same ret.
vwrap(cb, data, fixups, [] (Vout& v) {
v << popp{rfp(), rlr()};
v << ret{};
});
// Create a table of branches
us.freeManyLocalsHelper = vwrap(cb, data, [&] (Vout& v) {
v << pushp{rlr(), rfp()};
// rvmfp() is needed by the freeManyLocalsHelper stub above, so frame
// linkage setup is deferred until after its use in freeManyLocalsHelper.
v << jmpi{freeManyLocalsHelper};
});
for (auto i = kNumFreeLocalsHelpers - 1; i >= 0; --i) {
us.freeLocalsHelpers[i] = vwrap(cb, data, [&] (Vout& v) {
// We set up frame linkage to avoid an indirect fixup.
v << pushp{rlr(), rfp()};
v << copy{rsp(), rfp()};
v << jmpi{freeLocalsHelpers[i]};
});
}
// FIXME: This stub is hot, so make sure to keep it small.
#if 0
always_assert(Stats::enabled() ||
(cb.frontier() - release <= 4 * x64::cache_line_size()));
#endif
fixups.process(nullptr);
return release;
}
Protein* PeptideBuilder::construct()
{
if (fragment_db_ == 0)
{
Log.warn() << "PeptideBuilder::construct(): no FragmengDB given!" << std::endl;
return 0;
}
if (sequence_.empty())
{
Log.warn() << "PeptideBuilder::construct(): no amino acid sequence specified." << std::endl;
return 0;
}
int id = 1;
Protein *protein = new Protein(proteinname_);
Chain *chain = new Chain(chainname_);
// create the first residue
Residue* residue = createResidue_(sequence_[0].getType(), id);
chain->insert(*residue);
Residue* residueold = residue;
std::vector<AminoAcidDescriptor>::iterator i = sequence_.begin();
++id;
// consistency check for empty sequences and sequences of length < 2!!
// loop for the remaining residues ;
for (++i; i != sequence_.end(); ++i)
{
// We have to take care of two special cases:
// - the residue we are looking at is proline
// - the last residue was proline
String type = (i-1)->getType();
type.toUpper();
// special case: residue is a proline
type = i->getType();
type.toUpper();
is_proline_ = (type == "PRO") ? true : false;
Residue* residue2 = createResidue_(i->getType(), id);
insert_(*residue2, *residueold);
chain->insert(*residue2);
// set the torsion angle
transform_(i->getPhi(), (i-1)->getPsi(),*residueold, *residue2);
peptide_(*residueold,*residue2);
// set the peptide bond angle omega
setOmega_(*residueold, *residue2, i->getOmega());
residueold=residue2;
++id;
}
protein->insert(*chain);
// read the names for a unique nomenclature
protein->apply(fragment_db_->normalize_names);
// add missing bonds and atoms (including side chains!)
ReconstructFragmentProcessor rfp(*fragment_db_);
protein->apply(rfp);
protein->apply(fragment_db_->build_bonds);
return protein;
}
