add -nonbuf / -nb command line flag to disable buffering for screen and logfile

doc/src/Run_options.rst

@@ -14,6 +14,7 @@ letter abbreviation can be used:
 * :ref:`-m or -mpicolor <mpicolor>`
 * :ref:`-c or -cite <cite>`
 * :ref:`-nc or -nocite <nocite>`
+* :ref:`-nb or -nonbuf <nonbuf>`
 * :ref:`-pk or -package <package>`
 * :ref:`-p or -partition <partition>`
 * :ref:`-pl or -plog <plog>`
@@ -257,6 +258,23 @@ Disable generating a citation reminder (see above) at all.
 
 ----------
 
+.. _nonbuf:
+
+**-nonbuf**
+
+Turn off buffering for screen and logfile output.  For performance
+reasons, output to the screen and logfile is usually buffered, i.e.
+output is only generated if a buffer - typically 4096 bytes - has been
+filled.  However, when LAMMPS crashes, that can mean that there is
+important output missing.  When using this flag, this buffering is
+turned off (only for screen and logfile output).  Note that when running
+in parallel with MPI, the screen output may still be buffered by the MPI
+library which cannot be changed by LAMMPS.  This flag should only be
+used for debugging and not for production simulations as the performance
+impact can be significant, especially for large parallel runs.
+
+----------
+
 .. _package:
 
 **-package style args ....**

src/lammps.cpp

@@ -196,6 +196,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
   int citelogfile = CiteMe::VERBOSE;
   char *citefile = nullptr;
   int helpflag = 0;
+  int nonbufflag = 0;
 
   suffix = suffix2 = suffixp = nullptr;
   suffix_enable = 0;
@@ -298,6 +299,11 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
       citeflag = 0;
       iarg++;
 
+    } else if (strcmp(arg[iarg],"-nonbuf") == 0 ||
+               strcmp(arg[iarg],"-nb") == 0) {
+      nonbufflag = 1;
+      iarg++;
+
     } else if (strcmp(arg[iarg],"-package") == 0 ||
                strcmp(arg[iarg],"-pk") == 0) {
       if (iarg+2 > narg)
@@ -520,7 +526,6 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
       utils::flush_buffers(this);
     }
 
-
   // universe is one or more worlds, as setup by partition switch
   // split universe communicator into separate world communicators
   // set world screen, logfile, communicator, infile
@@ -540,6 +545,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
           screen = fopen(str.c_str(),"w");
           if (screen == nullptr)
             error->one(FLERR,"Cannot open screen file {}: {}",str,utils::getsyserror());
+          setvbuf(screen, NULL, _IONBF, 0);
         } else if (strcmp(arg[screenflag],"none") == 0) {
           screen = nullptr;
         } else {
@@ -563,6 +569,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
           logfile = fopen(str.c_str(),"w");
           if (logfile == nullptr)
             error->one(FLERR,"Cannot open logfile {}: {}",str, utils::getsyserror());
+          setbuf(logfile, NULL);
         } else if (strcmp(arg[logflag],"none") == 0) {
           logfile = nullptr;
         } else {
@@ -587,6 +594,15 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
       }
     }
 
+    // make all screen and logfile output unbuffered for debugging crashes
+
+    if (nonbufflag) {
+      if (universe->uscreen) setbuf(universe->uscreen, nullptr);
+      if (universe->ulogfile) setbuf(universe->ulogfile, nullptr);
+      if (screen) setbuf(screen, nullptr);
+      if (logfile) setbuf(logfile, nullptr);
+    }
+
     // screen and logfile messages for universe and world
 
     if ((universe->me == 0) && (!helpflag)) {