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common.C File Reference

#include <unistd.h>
#include <errno.h>
#include <string.h>
#include <sys/stat.h>
#include <ctype.h>
#include "common.h"
#include "InfoStream.h"
#include "charm++.h"

Go to the source code of this file.

Functions

char * NAMD_stringdup (const char *s)
void NAMD_quit (const char *err_msg)
void NAMD_die (const char *err_msg)
void NAMD_err (const char *err_msg)
void NAMD_bug (const char *err_msg)
void NAMD_backup_file (const char *filename, const char *extension)
void NAMD_write (int fd, const char *buf, size_t count)
FILE * Fopen (const char *filename, const char *mode)
int Fclose (FILE *fout)

Function Documentation

int Fclose (  FILE *  fout  ) 
 

Definition at line 255 of file common.C.

Referenced by ConfigList::ConfigList(), parm::genclose(), PDB::PDB(), read_binary_file(), Parameters::read_parameter_file(), and Molecule::read_psf_file().

00256 {
00257   int rc = -1;
00258 #if !defined(NOCOMPRESSED)
00259   rc = pclose(fout);
00260 #endif
00261   if (rc == -1) // stream not associated with a popen()
00262     {
00263     rc = fclose(fout);
00264     }
00265   return rc;
00266 } /* Fclose() */

FILE* Fopen (  const char *  filename,
const char *  mode
) 
 

Definition at line 170 of file common.C.

References iout.

Referenced by ConfigList::ConfigList(), parm::genopen(), GridforceGrid::initialize(), PDB::PDB(), read_binary_file(), Parameters::read_parameter_file(), and Molecule::read_psf_file().

00171 {
00172   struct stat buf;
00173   // check if basic filename exists (and not a directory)
00174 
00175 #if defined(NOCOMPRESSED)
00176   if (!stat(filename,&buf))
00177     {
00178       return(fopen(filename,mode));
00179     }
00180 #else
00181   if (!stat(filename,&buf))
00182     {
00183       if (!S_ISDIR(buf.st_mode))
00184         return(fopen(filename,mode));
00185     }
00186   // check for a compressed file
00187   char *realfilename;
00188   char *command;
00189   FILE *fout;
00190   command = (char *)malloc(strlen(filename)+25);
00191   // check for .Z (unix compress)
00192   sprintf(command,"zcat %s.Z",filename);
00193   realfilename = command+5;
00194   iout << "Command = " << command << "\n" << endi;
00195   iout << "Filename.Z = " << realfilename << "\n" << endi;
00196   if (!stat(realfilename,&buf))
00197         {
00198         if (!S_ISDIR(buf.st_mode))
00199                 {
00200                 fout = popen(command,mode);
00201                 // on HP-UX, the first character(s) out of pipe may be
00202                 // garbage!  (Argh!)
00203                 int C;
00204                 do
00205                   {
00206                   C = fgetc(fout);
00207                   // iout << "C is " << C << "\n" << endi;
00208                   if (isalnum(C) || isspace(C))
00209                         {
00210                         ungetc(C,fout);
00211                         C = -1; // outta loop
00212                         }
00213                   } while(C != -1);
00214                 free(command);
00215                 return(fout);
00216                 }
00217         }
00218   // check for .gz (gzip)
00219   sprintf(command,"gzip -d -c %s.gz",filename);
00220   realfilename = command+11;
00221   iout << "Command = " << command << "\n" << endi;
00222   iout << "Filename.gz = " << realfilename << "\n" << endi;
00223   if (!stat(realfilename,&buf))
00224         {
00225         if (!S_ISDIR(buf.st_mode))
00226                 {
00227                 fout = popen(command,mode);
00228                 // on HP-UX, the first character(s) out of pipe may be
00229                 // garbage!  (Argh!)
00230                 int C;
00231                 do
00232                   {
00233                   C = fgetc(fout);
00234                   // iout << "C is " << C << "\n" << endi;
00235                   if (isalnum(C) || isspace(C))
00236                         {
00237                         ungetc(C,fout);
00238                         C = -1; // outta loop
00239                         }
00240                   } while(C != -1);
00241                 free(command);
00242                 return(fout);
00243                 }
00244         }
00245   free(command);
00246 #endif /* !defined(NOCOMPRESSED) */
00247 
00248   return(NULL);
00249 } /* Fopen() */

void NAMD_backup_file (  const char *  filename,
const char *  extension
) 
 

Definition at line 117 of file common.C.

References iERROR(), and iout.

Referenced by Controller::outputExtendedSystem(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), and CollectionMaster::receiveDataStream().

00118 {
00119   struct stat sbuf;
00120   if (stat(filename, &sbuf) == 0) {
00121     if ( ! extension ) extension = ".BAK";
00122     char *backup = new char[strlen(filename)+strlen(extension)+1];
00123     strcpy(backup, filename);
00124     strcat(backup, extension);
00125 #if defined(WIN32) && !defined(__CYGWIN__)
00126     remove(backup);
00127 #endif
00128     if ( rename(filename,backup) )
00129     {
00130       char *sys_err_msg = strerror(errno);
00131       if ( ! sys_err_msg ) sys_err_msg = "(unknown error)";
00132       iout << iERROR << "Error on renaming file " << filename
00133         << " to " << backup << ": " << sys_err_msg << "\n" << endi;
00134       fflush(stdout);
00135       // char errmsg[256];
00136       // sprintf(errmsg, "Error on renaming file %s to %s",filename,backup);
00137       // NAMD_err(errmsg);
00138     }
00139     delete [] backup;
00140   }
00141 }

void NAMD_bug (  const char *  err_msg  ) 
 

Definition at line 103 of file common.C.

Referenced by LdbCoordinator::barrier(), HomePatch::buildSpanningTree(), ComputeNonbondedUtil::calc_error(), checkSum(), Controller::compareChecksums(), ComputeTclBC::ComputeTclBC(), NamdState::configListInit(), WorkDistrib::createAtomLists(), ComputePme::doWork(), WorkDistrib::enqueueAngles(), WorkDistrib::enqueueBonds(), WorkDistrib::enqueueCrossterms(), WorkDistrib::enqueueDihedrals(), WorkDistrib::enqueueImpropers(), WorkDistrib::enqueuePme(), WorkDistrib::enqueueSelfA(), WorkDistrib::enqueueSelfB(), WorkDistrib::enqueueWork(), WorkDistrib::enqueueWorkA(), WorkDistrib::enqueueWorkB(), WorkDistrib::enqueueWorkC(), WorkDistrib::fillOnePatchAtoms(), Communicate::getMessage(), ComputeHomePatch::initialize(), ComputePatch::initialize(), ComputePmeMgr::initialize(), ScriptTcl::load(), WorkDistrib::messageEnqueueWork(), NAMD_write(), Node::Node(), Controller::printDynamicsEnergies(), ProxyMgr::ProxyMgr(), HomePatch::rattle1(), HomePatch::rattle2(), Sequencer::reassignVelocities(), BroadcastMgr::recvBroadcast(), ComputePmeMgr::recvGrid(), ProxyMgr::recvResults(), ComputePmeMgr::recvUngrid(), registerUserEventsForAllComputeObjs(), CollectionMaster::CollectVectorInstance::reset(), CollectionMgr::CollectVectorInstance::reset(), ComputeNonbondedUtil::select(), SELF(), Communicate::sendMessage(), SimpleBroadcastObject< Tensor >::SimpleBroadcastObject(), Node::startup(), and wrap_coor_int().

00105 {
00106    const char *bug_msg = 
00107      "FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html";
00108    char *new_err_msg = new char[strlen(err_msg) + 20 + strlen(bug_msg)];
00109    sprintf(new_err_msg,"FATAL ERROR: %s\n%s\n",err_msg,bug_msg);
00110    CkPrintf(new_err_msg);
00111    fflush(stdout);
00112    CmiAbort(new_err_msg);
00113    delete [] new_err_msg;
00114 }

void NAMD_die (  const char *  err_msg  ) 
 

Definition at line 75 of file common.C.

Referenced by ConfigList::add_element(), Controller::algorithm(), 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_constant_forces(), Molecule::build_constorque_params(), Molecule::build_constraint_params(), Molecule::build_exPressure_atoms(), Molecule::build_extra_bonds(), Molecule::build_fep_flags(), Molecule::build_fixed_atoms(), Molecule::build_gridforce_params(), Molecule::build_langevin_params(), Molecule::build_movdrag_params(), Molecule::build_rotdrag_params(), Molecule::build_stirred_atoms(), GlobalMaster::calculate(), GlobalMasterTcl::calculate(), GlobalMasterTest::calculate(), GlobalMaster::check(), ComputeTclBC::ComputeTclBC(), ConfigList::ConfigList(), NamdState::configListInit(), ConfigList::ConfigListNode::ConfigListNode(), Controller::correctMomentum(), Sequencer::correctMomentum(), ReductionSet::delData(), ComputeNonbondedSelf::doForce(), HomePatch::doMarginCheck(), Parameters::done_reading_files(), ComputeTclBC::doWork(), ARestraint::EarlyExit(), GlobalMasterMisc::easy_calc(), CollectionMasterHandler::enqueuePositions(), CollectionMasterHandler::enqueueVelocities(), PmeZPencil::fft_init(), PmeYPencil::fft_init(), PmeXPencil::fft_init(), parm::get(), Molecule::get_atom_from_index_in_residue(), Molecule::get_atom_from_name(), Molecule::get_atomtype(), Parameters::get_dihedral_params(), Parameters::get_improper_params(), Molecule::get_residue_size(), getAcceptorData(), getAngleData(), getAtomData(), getBondData(), getCrosstermData(), getDihedralData(), getDonorData(), getExclusionData(), getExtraBonds(), getImproperData(), AngleElem::getMoleculePointers(), BondElem::getMoleculePointers(), CrosstermElem::getMoleculePointers(), DihedralElem::getMoleculePointers(), ImproperElem::getMoleculePointers(), GlobalMasterIMD::GlobalMasterIMD(), GromacsTopFile::GromacsTopFile(), ComputePmeMgr::initialize(), GridforceGrid::initialize(), LdbCoordinator::initialize(), SimParameters::initialize_config_data(), ScriptTcl::load(), ComputeHomeTuples< BondElem, Bond, BondValue >::loadTuples(), ludcmp(), main(), WorkDistrib::mapComputes(), HomePatch::mollyAverage(), HomePatch::mollyMollify(), NAMD_new_handler(), NAMD_read_int(), NAMD_read_line(), NAMD_write(), Vector::operator[](), outputPsfFile(), PDB::PDB(), PDBUnknown::PDBUnknown(), parm::preadln(), ProblemParsing(), GlobalMaster::processData(), HomePatch::rattle2(), read_binary_file(), Parameters::read_charmm_parameter_file(), Parameters::read_parameter_file(), Molecule::read_parm(), Parameters::read_parm(), Molecule::read_psf_file(), readPsfFile(), RecBisection::RecBisection(), Parameters::receive_Parameters(), CollectionMaster::receiveDataStream(), ComputeMgr::recvComputeDPMEData(), ComputeMgr::recvComputeDPMEResults(), ComputeMgr::recvComputeEwaldData(), ComputeMgr::recvComputeEwaldResults(), ComputeMgr::recvComputeGlobalConfig(), ComputeMgr::recvComputeGlobalData(), ComputeMgr::recvComputeGlobalResults(), ComputeExtMgr::recvCoord(), GlobalMasterServer::recvData(), Molecule::reloadCharges(), Node::reloadCharges(), ReductionMgr::remoteRegister(), ReductionMgr::remoteUnregister(), ScriptTcl::run(), SimParameters::scriptSet(), ComputeNonbondedUtil::select(), Molecule::send_Molecule(), Parameters::send_Parameters(), SimParameters::send_SimParameters(), Node::sendCharmArrProxies(), ComputeMgr::sendComputeDPMEData(), ComputeMgr::sendComputeEwaldData(), PatchMap::sizeGrid(), StringList::StringList(), ComputeMap::unpack(), ReductionMgr::willRequire(), and ReductionMgr::willSubmit().

00077 {
00078    char *new_err_msg = new char[strlen(err_msg) + 20];
00079    sprintf(new_err_msg,"FATAL ERROR: %s\n",err_msg);
00080    CkPrintf(new_err_msg);
00081    fflush(stdout);
00082    CmiAbort(new_err_msg);
00083    delete [] new_err_msg;
00084 }

void NAMD_err (  const char *  err_msg  ) 
 

Definition at line 88 of file common.C.

Referenced by Molecule::build_extra_bonds(), getExtraBonds(), Controller::outputExtendedSystem(), PDB::PDB(), and PDB::write().

00090 {
00091    char *sys_err_msg = strerror(errno);
00092    if ( ! sys_err_msg ) sys_err_msg = "(unknown error)";
00093    char *new_err_msg = new char[strlen(err_msg) + 20 + strlen(sys_err_msg)];
00094    sprintf(new_err_msg,"FATAL ERROR: %s: %s\n",err_msg, sys_err_msg);
00095    CkPrintf(new_err_msg);
00096    fflush(stdout);
00097    CmiAbort(new_err_msg);
00098    delete [] new_err_msg;
00099 }

void NAMD_quit (  const char *  err_msg  ) 
 

Definition at line 62 of file common.C.

Referenced by GlobalMasterIMD::get_vmd_forces().

00064 {
00065    char *new_err_msg = new char[strlen(err_msg) + 20];
00066    sprintf(new_err_msg,"EXITING: %s\n",err_msg);
00067    CkPrintf(new_err_msg);
00068    fflush(stdout);
00069    CmiAbort(new_err_msg);
00070    delete [] new_err_msg;
00071 }

char* NAMD_stringdup (  const char *  s  ) 
 

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 48 of file common.C.

00048                                     {
00049   char *rs;
00050 
00051   if(!s)
00052     return NULL;
00053 
00054   rs = new char[strlen(s) + 1];
00055   strcpy(rs,s);
00056 
00057   return rs;
00058 }

void NAMD_write (  int  fd,
const char *  buf,
size_t  count
) 
 

Definition at line 144 of file common.C.

References NAMD_bug(), and NAMD_die().

00144                                                        {
00145   while ( count ) {
00146 #if defined(WIN32) && !defined(__CYGWIN__)
00147     long retval = _write(fd,buf,count);
00148 #else
00149     ssize_t retval = write(fd,buf,count);
00150 #endif
00151     if ( retval < 0 ) NAMD_die(strerror(errno));
00152     if ( retval > count ) NAMD_bug("extra bytes written in NAMD_write()");
00153     buf += retval;
00154     count -= retval;
00155   }
00156 }

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