From cba8e8237ae754cd842e4440a1d555c7be3fbbfa Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 13 Aug 2021 06:25:21 -0400
Subject: [PATCH] avoid memory leak with MPI-IO

---
 src/read_restart.cpp | 41 ++++++++++++++++++++---------------------
 1 file changed, 20 insertions(+), 21 deletions(-)

diff --git a/src/read_restart.cpp b/src/read_restart.cpp
index faf9fd1620..e42bb59272 100644
--- a/src/read_restart.cpp
+++ b/src/read_restart.cpp
@@ -44,7 +44,7 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-ReadRestart::ReadRestart(LAMMPS *lmp) : Command(lmp) {}
+ReadRestart::ReadRestart(LAMMPS *lmp) : Command(lmp), mpiio(nullptr) {}
 
 /* ---------------------------------------------------------------------- */
 
@@ -110,8 +110,7 @@ void ReadRestart::command(int narg, char **arg)
     }
     fp = fopen(hfile.c_str(),"rb");
     if (fp == nullptr)
-      error->one(FLERR,"Cannot open restart file {}: {}",
-                                   hfile, utils::getsyserror());
+      error->one(FLERR,"Cannot open restart file {}: {}", hfile, utils::getsyserror());
   }
 
   // read magic string, endian flag, format revision
@@ -336,8 +335,7 @@ void ReadRestart::command(int narg, char **arg)
       procfile.replace(procfile.find("%"),1,fmt::format("{}",icluster));
       fp = fopen(procfile.c_str(),"rb");
       if (fp == nullptr)
-        error->one(FLERR,"Cannot open restart file {}: {}",
-                                     procfile, utils::getsyserror());
+        error->one(FLERR,"Cannot open restart file {}: {}", procfile, utils::getsyserror());
     }
 
     int procsperfile;
@@ -401,7 +399,7 @@ void ReadRestart::command(int narg, char **arg)
 
   // clean-up memory
 
-  delete [] file;
+  delete[] file;
   memory->destroy(buf);
 
   // for multiproc or MPI-IO files:
@@ -525,8 +523,9 @@ void ReadRestart::command(int narg, char **arg)
   MPI_Barrier(world);
 
   if (comm->me == 0)
-    utils::logmesg(lmp,"  read_restart CPU = {:.3f} seconds\n",
-                   MPI_Wtime()-time1);
+    utils::logmesg(lmp,"  read_restart CPU = {:.3f} seconds\n",MPI_Wtime()-time1);
+
+  delete mpiio;
 }
 
 /* ----------------------------------------------------------------------
@@ -599,7 +598,7 @@ void ReadRestart::header()
       if (me == 0)
         utils::logmesg(lmp,"  restart file = {}, LAMMPS = {}\n",
                        version,lmp->version);
-      delete [] version;
+      delete[] version;
 
       // we have no forward compatibility, thus exit with error
 
@@ -638,7 +637,7 @@ void ReadRestart::header()
     } else if (flag == UNITS) {
       char *style = read_string();
       if (strcmp(style,update->unit_style) != 0) update->set_units(style);
-      delete [] style;
+      delete[] style;
 
     } else if (flag == NTIMESTEP) {
       update->ntimestep = read_bigint();
@@ -772,9 +771,9 @@ void ReadRestart::header()
       atom->create_avec(style,nargcopy,argcopy,1);
       if (comm->me ==0)
         utils::logmesg(lmp,"  restoring atom style {} from restart\n",style);
-      for (int i = 0; i < nargcopy; i++) delete [] argcopy[i];
-      delete [] argcopy;
-      delete [] style;
+      for (int i = 0; i < nargcopy; i++) delete[] argcopy[i];
+      delete[] argcopy;
+      delete[] style;
 
     } else if (flag == NATOMS) {
       atom->natoms = read_bigint();
@@ -889,7 +888,7 @@ void ReadRestart::type_arrays()
       double *mass = new double[atom->ntypes+1];
       read_double_vec(atom->ntypes,&mass[1]);
       atom->set_mass(mass);
-      delete [] mass;
+      delete[] mass;
 
     } else error->all(FLERR,
                       "Invalid flag in type arrays section of restart file");
@@ -910,7 +909,7 @@ void ReadRestart::force_fields()
     if (flag == PAIR) {
       style = read_string();
       force->create_pair(style,1);
-      delete [] style;
+      delete[] style;
       if (comm->me ==0)
         utils::logmesg(lmp,"  restoring pair style {} from restart\n",
                        force->pair_style);
@@ -926,7 +925,7 @@ void ReadRestart::force_fields()
     } else if (flag == BOND) {
       style = read_string();
       force->create_bond(style,1);
-      delete [] style;
+      delete[] style;
       if (comm->me ==0)
         utils::logmesg(lmp,"  restoring bond style {} from restart\n",
                        force->bond_style);
@@ -935,7 +934,7 @@ void ReadRestart::force_fields()
     } else if (flag == ANGLE) {
       style = read_string();
       force->create_angle(style,1);
-      delete [] style;
+      delete[] style;
       if (comm->me ==0)
         utils::logmesg(lmp,"  restoring angle style {} from restart\n",
                        force->angle_style);
@@ -944,7 +943,7 @@ void ReadRestart::force_fields()
     } else if (flag == DIHEDRAL) {
       style = read_string();
       force->create_dihedral(style,1);
-      delete [] style;
+      delete[] style;
       if (comm->me ==0)
         utils::logmesg(lmp,"  restoring dihedral style {} from restart\n",
                        force->dihedral_style);
@@ -953,7 +952,7 @@ void ReadRestart::force_fields()
     } else if (flag == IMPROPER) {
       style = read_string();
       force->create_improper(style,1);
-      delete [] style;
+      delete[] style;
       if (comm->me ==0)
         utils::logmesg(lmp,"  restoring improper style {} from restart\n",
                        force->improper_style);
@@ -1117,7 +1116,7 @@ void ReadRestart::magic_string()
   MPI_Bcast(str,n,MPI_CHAR,0,world);
   if (strcmp(str,MAGIC_STRING) != 0)
     error->all(FLERR,"Invalid LAMMPS restart file");
-  delete [] str;
+  delete[] str;
 }
 
 /* ----------------------------------------------------------------------
@@ -1164,7 +1163,7 @@ void ReadRestart::check_eof_magic()
   if (strcmp(str,MAGIC_STRING) != 0)
     error->all(FLERR,"Incomplete or corrupted LAMMPS restart file");
 
-  delete [] str;
+  delete[] str;
 }
 
 /* ----------------------------------------------------------------------