struct execResult_t execGetReturnCode(const char **aArguments) { struct execResult_t execResult; char **argcopy = argCopy(aArguments); pid_t pid; int status; memset(&execResult, 0, sizeof(execResult)); execResult.success = true; pid = fork(); if (pid == -1) { perror("fork"); execResult.success = false; return execResult; } if (pid > 0) { char commandLineBuffer[256]; convertCommandLine(commandLineBuffer, sizeof(commandLineBuffer), aArguments); logmsg(LLVL_DEBUG, "Subprocess [PID %d]: Will execute '%s'\n", pid, commandLineBuffer); } if (pid == 0) { /* Child */ if (getLogLevel() < LLVL_DEBUG) { /* Shut up the child if user did not request debug output */ close(1); close(2); } execvp(aArguments[0], argcopy); perror("execvp"); logmsg(LLVL_ERROR, "Execution of %s in forked child process failed at execvp: %s\n", aArguments[0], strerror(errno)); /* Exec failed, terminate chExec failed, terminate child process * (parent will catch this as the return code) */ exit(EXIT_FAILURE); } if (waitpid(pid, &status, 0) == (pid_t)-1) { perror("waitpid"); execResult.success = false; return execResult; } freeArgCopy(argcopy); execResult.returnCode = WEXITSTATUS(status); logmsg(LLVL_DEBUG, "Subprocess [PID %d]: %s returned %d\n", pid, aArguments[0], execResult.returnCode); return execResult; }
/** Loop over all filenames in replica_filenames, set up TrajectoryIO. */ int TrajIOarray::SetupIOarray(ArgList& argIn, TrajFrameCounter& counter, CoordinateInfo& cInfo, Topology* trajParm) { // Sanity check if (!IOarray_.empty()) { mprinterr("Internal Error: SetupIOarray() has been called twice.\n"); return 1; } // Save arguments that have not been processed so they can be passed // to each replica in turn. Only the lowest replica will use argIn. ArgList argCopy( argIn ); bool lowestRep = true; int rep0Frames = TrajectoryIO::TRAJIN_UNK; // Total frames in replica 0 int totalFrames = TrajectoryIO::TRAJIN_UNK; // Total # frames to be read from ensemble TrajectoryFile::TrajFormatType lastRepFmt = TrajectoryFile::UNKNOWN_TRAJ; // Right now enforce that all replicas have the same metadata as lowest // replica, e.g. if replica 0 has temperature, replica 1 does too etc. for (File::NameArray::const_iterator repfile = replica_filenames_.begin(); repfile != replica_filenames_.end(); ++repfile) { // Detect format TrajectoryFile::TrajFormatType repformat = TrajectoryFile::UNKNOWN_TRAJ; TrajectoryIO* replica0 = TrajectoryFile::DetectFormat( *repfile, repformat ); if ( replica0 == 0 ) { mprinterr("Error: Could not set up replica file %s\n", repfile->full()); return 1; } if (repformat != lastRepFmt) mprintf("\tReading '%s' as %s\n", repfile->full(), TrajectoryFile::FormatString(repformat)); lastRepFmt = repformat; replica0->SetDebug( debug_ ); // Pushing replica0 here allows the destructor to handle it on errors IOarray_.push_back( replica0 ); // Process format-specific read args. Do not exit on error in case // replicas have different formats supporting different args. if (lowestRep) { replica0->processReadArgs( argIn ); } else { ArgList argtmp( argCopy ); replica0->processReadArgs( argtmp ); } // Set up replica for reading and get the number of frames. int nframes = replica0->setupTrajin( *repfile, trajParm ); if (nframes == TrajectoryIO::TRAJIN_ERR) { mprinterr("Error: Could not set up %s for reading.\n", repfile->full()); return 1; } // TODO: Do not allow unknown number of frames? if (lowestRep) { cInfo = replica0->CoordInfo(); rep0Frames = nframes; totalFrames = nframes; if (cInfo.ReplicaDimensions().Ndims() > 0) { mprintf("\tReplica dimensions:\n"); for (int rd = 0; rd < cInfo.ReplicaDimensions().Ndims(); rd++) mprintf("\t\t%i: %s\n", rd+1, cInfo.ReplicaDimensions().Description(rd)); } } else { // Check total frames in this replica against lowest rep. if (nframes != rep0Frames) mprintf("Warning: Replica %s frames (%i) does not match # frames in first replica (%i).\n", repfile->base(), nframes, rep0Frames); //if (repframes < 0) { // mprinterr("Error: RemdTraj: Unknown # of frames in replica.\n"); // return 1; //} if (nframes < totalFrames) { totalFrames = nframes; mprintf("Warning: Setting total # of frames to read from replica ensemble to %i\n", totalFrames); } // Check box info against lowest rep. if ( replica0->CoordInfo().HasBox() != cInfo.HasBox() ) { mprinterr("Error: Replica %s box info does not match first replica.\n", repfile->full()); return 1; } // TODO: Check specific box type // Check velocity info against lowest rep. if ( replica0->CoordInfo().HasVel() != cInfo.HasVel() ) { mprinterr("Error: Replica %s velocity info does not match first replica.\n", repfile->full()); return 1; } // Check # dimensions and types against lowest rep if ( replica0->CoordInfo().ReplicaDimensions() != cInfo.ReplicaDimensions() ) { mprinterr("Error: Replica %s dimension info does not match first replica.\n", repfile->full()); ReplicaDimArray const& thisRepDims = replica0->CoordInfo().ReplicaDimensions(); for (int rd = 0; rd < thisRepDims.Ndims(); rd++) mprinterr("\t\t%i: %s\n", rd+1, thisRepDims.Description(rd)); return 1; } // If temperature/time info does not match set to false. if (cInfo.HasTemp() != replica0->CoordInfo().HasTemp()) cInfo.SetTemperature( false ); if (cInfo.HasTime() != replica0->CoordInfo().HasTime()) cInfo.SetTime( false ); } lowestRep = false; } // Check how many frames will actually be read if (counter.CheckFrameArgs( totalFrames, argIn )) return 1; // Check for errors. if (IOarray_.empty()) { mprinterr("Error: No replica trajectories set up.\n"); return 1; } if (IOarray_.size() != replica_filenames_.size()) { // SANITY CHECK mprinterr("Error: Not all replica files were set up.\n"); return 1; } // Update ensemble size cInfo.SetEnsembleSize( (int)IOarray_.size() ); if (debug_ > 0) cInfo.PrintCoordInfo( replica_filenames_[0].full(), trajParm->c_str() ); return 0; }