TestArray.h File Reference

#include <type_traits>

Go to the source code of this file.

Functions
void	NAMD_die (const char *)
int	TestArray_write_helper (const char *filename, const char *label, const void *array, int elemsize, int length, int isfp)
template<typename T >
int	TestArray_write (const char *filename, const char *label, const T *array, int length)

Function Documentation

NAMD_die()

void NAMD_die

(

const char *

)

Definition at line 148 of file common.C.

References Node::Object().

Referenced by Controller::adaptTempInit(), ConfigList::add_element(), ComputeMsmMgr::addPotential(), after_backend_init(), Sequencer::algorithm(), Controller::algorithm(), CollectiveDeviceBuffer< T >::allocate_no_check(), AnisoElem::AnisoElem(), msm::PatchData::anterpolation(), msm::PatchData::anterpolationC1Hermite(), Parameters::assign_angle_index(), Parameters::assign_bond_index(), Parameters::assign_crossterm_index(), Parameters::assign_dihedral_index(), Parameters::assign_improper_index(), Parameters::assign_vdw_index(), WorkDistrib::assignNodeToPatch(), Molecule::build_go_arrays(), Molecule::build_go_params(), Molecule::build_go_sigmas(), Molecule::build_go_sigmas2(), Molecule::build_gridforce_params(), buildBondData(), HomePatch::buildRattleList(), ReductionMgr::buildSpanTree(), ParallelIOMgr::calcAtomsInEachPatch(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), GlobalMasterTest::calculate(), GlobalMasterTcl::calculate(), GlobalMaster::calculate(), ComputeQMMgr::calcUSR(), Calloc(), GlobalMaster::check(), GroupRestraintParam::CheckParam(), ComputeMsmMgr::compute(), PmeRealSpace::compute_forces(), LjPmeRealSpace::compute_scaledForces(), OneFourNbTholeElem::computeForce(), AngleElem::computeForce(), LjPmeCompute::computeLJpotential(), ComputeTclBC::ComputeTclBC(), ConfigList::ConfigList(), NamdState::configListInit(), ConfigList::ConfigListNode::ConfigListNode(), Sequencer::correctMomentum(), Controller::correctMomentum(), WorkDistrib::createAtomLists(), cuda_errcheck(), cuda_getargs(), CudaComputeNonbonded::CudaComputeNonbonded(), cudaDie(), CudaGlobalMaster::CUDAGM_NS::CudaGlobalMasterClient::CudaGlobalMasterClient(), CudaGlobalMasterServer::CudaGlobalMasterServer(), curandDie(), ComputeMsmMgr::d_stencil_1d(), Molecule::delete_qm_bonded(), ComputeGridForce::doForce(), ComputeNonbondedSelf::doForce(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), Parameters::done_reading_files(), ComputeFullDirect::doWork(), ComputeTclBC::doWork(), ARestraint::EarlyExit(), Node::earlyExit(), GlobalMasterMisc::easy_calc(), msm::Array< msm::PatchDiagram >::elem(), msm::GridFixed< T, N >::elem(), msm::Grid< Vtype >::elem(), colvarproxy_namd::error(), ScriptTcl::eval(), PmeZPencil::fft_init(), PmeYPencil::fft_init(), PmeXPencil::fft_init(), LjPmeRealSpace::fill_charges(), PmeRealSpace::fill_charges(), Ambertoppar::get(), Molecule::get_atom_from_index_in_residue(), Molecule::get_atom_from_name(), Molecule::get_atomtype(), Parameters::get_dihedral_params(), Molecule::get_fep_bonded_type(), Parameters::get_improper_params(), Molecule::get_residue_size(), Parameters::get_vdw_params(), IndexFile::getAllElements(), ComputeLjPmeSerialMgr::getLJparameters(), OneFourNbTholeElem::getMoleculePointers(), AngleElem::getMoleculePointers(), ImproperElem::getMoleculePointers(), CrosstermElem::getMoleculePointers(), DihedralElem::getMoleculePointers(), TholeElem::getMoleculePointers(), AnisoElem::getMoleculePointers(), ExclElem::getMoleculePointers(), BondElem::getMoleculePointers(), GromacsPairElem::getMoleculePointers(), IndexFile::getNElements(), OneFourNbTholeElem::getTupleInfo(), TholeElem::getTupleInfo(), AnisoElem::getTupleInfo(), GlobalMasterIMD::GlobalMasterIMD(), GlobalMasterSymmetry::GlobalMasterSymmetry(), LjPmeMgr::gridCalculation(), GromacsTopFile::GromacsTopFile(), IndexFile::IndexFile(), BackEnd::init(), LjPmeCompute::initialize(), LjPmeMgr::initialize(), LdbCoordinator::initialize(), DeviceCUDA::initialize(), GridforceFullMainGrid::initialize(), GridforceFullSubGrid::initialize(), GridforceLiteGrid::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize(), SimParameters::initialize_config_data(), msm::PatchData::interpolation(), msm::PatchData::interpolationC1Hermite(), LjPmeKSpace::LjPmeKSpace(), ScriptTcl::load(), NamdState::loadStructure(), ludcmp(), main::main(), Malloc(), Node::mallocTest(), WorkDistrib::mapComputes(), HomePatch::minimize_rattle2(), Molecule::Molecule(), HomePatch::mollyAverage(), HomePatch::mollyMollify(), NAMD_new_handler(), NAMD_read_int(), NAMD_read_line(), NAMD_seek(), NAMD_write(), ComputeMsmMgr::ndsplitting(), OneFourNbTholeElem::OneFourNbTholeElem(), IndexFile::open(), LjPmeMgr::optimizeFFT(), Node::outputPatchComputeMaps(), MGridforceParamsList::pack_data(), WorkDistrib::patchMapInit(), PDB::PDB(), PDBUnknown::PDBUnknown(), Ambertoppar::preadln(), Molecule::prepare_qm(), ProblemParsing(), MsmBlockProxyMsg::put(), MsmC1HermiteBlockProxyMsg::put(), HomePatch::rattle1old(), HomePatch::rattle2(), Molecule::read_alch_unpert_angles(), Molecule::read_alch_unpert_bonds(), Molecule::read_alch_unpert_dihedrals(), read_binary_file(), Parameters::read_charmm_parameter_file(), Parameters::read_ener_table(), Parameters::read_energy_type(), Parameters::read_energy_type_bothcubspline(), Parameters::read_energy_type_cubspline(), Molecule::read_go_file(), Parameters::read_parameter_file(), Parameters::read_parm(), SimParameters::readExtendedSystem(), AmberParm7Reader::readparm(), GridforceFullBaseGrid::readSubgridHierarchy(), Realloc(), CollectiveDeviceBuffer< T >::reallocate_no_check(), RecBisection::RecBisection(), Molecule::receive_GoMolecule(), Parameters::receive_Parameters(), CollectionMaster::receiveDataStream(), ParallelIOMgr::recvAtomsCntPerPatch(), Controller::recvCheckpointReq(), HomePatch::recvCheckpointReq(), ComputeMgr::recvComputeDPMEData(), ComputeMgr::recvComputeDPMEResults(), ComputeMgr::recvComputeEwaldData(), ComputeMgr::recvComputeEwaldResults(), ComputeMgr::recvComputeGlobalData(), ComputeMgr::recvComputeGlobalResults(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), ComputeLjPmeSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeMgr::recvCudaGlobalMasterCreateMsg(), ComputeMgr::recvCudaGlobalMasterRemoveMsg(), ComputeMgr::recvCudaGlobalMasterUpdateMsg(), SynchronousCollectives::recvIndexData(), ComputeQMMgr::recvPartQM(), ComputeQMMgr::recvPntChrg(), Output::recvReplicaDcdData(), Node::reloadCharges(), Node::reloadGridforceGrid(), ReductionMgr::remoteRegister(), ReductionMgr::remoteUnregister(), ReductionSet::removeData(), Sequencer::rescaleaccelMD(), Controller::rescaleaccelMD(), ScriptTcl::run(), ComputeMsm::saveResults(), SimParameters::scriptSet(), ComputeNonbondedUtil::select(), GlobalMasterIMD::send_box(), GlobalMasterIMD::send_energies(), GlobalMasterIMD::send_fcoords(), GlobalMasterIMD::send_forces(), Molecule::send_GoMolecule(), Parameters::send_Parameters(), GlobalMasterIMD::send_time(), GlobalMasterIMD::send_velocities(), ComputeMgr::sendComputeDPMEData(), ComputeMgr::sendComputeEwaldData(), StringList::set(), GroupRestraintParam::SetGroup1AtomFileIndices(), GroupRestraintParam::SetGroup1AtomListIndices(), GroupRestraintParam::SetGroup1RefPosition(), GroupRestraintParam::SetGroup2AtomFileIndices(), GroupRestraintParam::SetGroup2AtomListIndices(), GroupRestraintParam::SetGroupName(), msm::Array< msm::PatchDiagram >::setmax(), GroupRestraintParam::SetResCenter(), GroupRestraintParam::SetResDirection(), ComputeMsmMgr::setup_hgrid_1d(), ComputeMsmMgr::setup_periodic_blocksize(), SimParameters::setupIDWS(), PatchMap::sizeGrid(), ComputeMsmMgr::splitting(), ComputeMsmMgr::stencil_1d(), NamdCentLB::Strategy(), StringList::StringList(), ScriptTcl::tclmain(), TestArray_write(), TholeElem::TholeElem(), ComputeLonepairsCUDA::updateAtoms(), Node::updateGridScale(), ReductionMgr::willRequire(), and ReductionMgr::willSubmit().

{
  if ( ! err_msg ) err_msg = "(unknown error)";
  CkPrintf("FATAL ERROR: %s\n", err_msg);
  fflush(stdout);
  char repstr[24] = "";
  if (CmiNumPartitions() > 1 || 
      (Node::Object()->simParameters != 0 &&
       Node::Object()->simParameters->CUDASOAintegrateMode)) {
    sprintf(repstr,"REPLICA %d ", CmiMyPartition());
    // CkAbort ensures that all replicas die
    CkAbort("%sFATAL ERROR: %s\n", repstr, err_msg);
  }
  CkError("%sFATAL ERROR: %s\n", repstr, err_msg);
#if CHARM_VERSION < 61000
  CkExit();
#else
  CkExit(1);
#endif
}

TestArray_write()

template<typename T >

int TestArray_write	(	const char *	filename,
		const char *	label,
		const T *	array,
		int	length
	)

Write an array to file for later analysis. The array type needs to be a standard arithmetic type, as designated true by std::is_arithmetic<T>.

File format is:

• label is padded to 116 characters including null terminator
• nonzero 4-byte int if array is floating point
• number of bytes per element stored as 4-byte int
• length of the array stored as 4-byte int
• the array data

Returns zero for success or nonzero for error.

Parameters

filename	save to file name
label	label for array (truncated to 120 characters)
array	points to the array to save
length	length of the array

Definition at line 32 of file TestArray.h.

References NAMD_die(), and TestArray_write_helper().

      {
  if ( ! std::is_arithmetic<T>::value ) {
    NAMD_die("Called TestArray_write with non-aritmetic type");
  }
  int isfp = std::is_floating_point<T>::value;
  return TestArray_write_helper(filename, label,
      (const void *)array, sizeof(T), length, isfp);
}

TestArray_write_helper()

int TestArray_write_helper	(	const char *	filename,
		const char *	label,
		const void *	array,
		int	elemsize,
		int	length,
		int	isfp
	)

Definition at line 10 of file TestArray.C.

References LABEL_SIZE.

Referenced by TestArray_write().

      {
  const char *stype = "unknown";
  if      (  isfp && elemsize==8 ) stype = "double";
  else if (  isfp && elemsize==4 ) stype = "float";
  else if ( !isfp && elemsize==8 ) stype = "int64";
  else if ( !isfp && elemsize==4 ) stype = "int32";
  else if ( !isfp && elemsize==2 ) stype = "int16";
  else if ( !isfp && elemsize==1 ) stype = "int8";
  printf("Writing %s array of length %d to binary file %s\n",
      stype, length, filename);
  FILE *fp = fopen(filename, "wb");
  if ( fp == 0 ) return -1;
  char padbuf[LABEL_SIZE] = { 0 };
  strncpy(padbuf, label, LABEL_SIZE-1);
  fwrite(padbuf, 1, LABEL_SIZE, fp);
  fwrite(&isfp, sizeof(int), 1, fp);
  fwrite(&elemsize, sizeof(int), 1, fp);
  fwrite(&length, sizeof(int), 1, fp);
  fwrite(array, elemsize, length, fp);
  fclose(fp);
  fflush(stdout);
  return 0;
}