git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11100 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/output.cpp

@@ -762,13 +762,13 @@ void Output::create_restart(int narg, char **arg)
       error->all(FLERR,"Both restart files must have '%' or neither");
   }
 
-  int mpiio;
+  int mpiioflag;
-  if (strstr(arg[1],".mpi")) mpiio = 1;
+  if (strstr(arg[1],".mpi")) mpiioflag = 1;
-  else mpiio = 0;
+  else mpiioflag = 0;
   if (nfile == 2) {
-    if (mpiio && !strstr(arg[2],".mpi")) 
+    if (mpiioflag && !strstr(arg[2],".mpi")) 
       error->all(FLERR,"Both restart files must use MPI-IO or neither");
-    if (!mpiio && strstr(arg[2],".mpi"))
+    if (!mpiioflag && strstr(arg[2],".mpi"))
       error->all(FLERR,"Both restart files must use MPI-IO or neither");
   }
 
@@ -777,7 +777,7 @@ void Output::create_restart(int narg, char **arg)
   delete restart;
   restart = new WriteRestart(lmp);
   int iarg = nfile+1;
-  restart->multiproc_options(multiproc,mpiio,narg-iarg,&arg[iarg]);
+  restart->multiproc_options(multiproc,mpiioflag,narg-iarg,&arg[iarg]);
 }
 
 /* ----------------------------------------------------------------------

src/read_restart.cpp

@@ -35,6 +35,7 @@
 #include "improper.h"
 #include "special.h"
 #include "universe.h"
+#include "mpiio.h"
 #include "memory.h"
 #include "error.h"
 
@@ -96,13 +97,20 @@ void ReadRestart::command(int narg, char **arg)
 
   if (strchr(arg[0],'%')) multiproc = 1;
   else multiproc = 0;
-  if (strstr(arg[0],".mpi")) mpiio = 1;
+  if (strstr(arg[0],".mpi")) mpiioflag = 1;
-  else mpiio = 0;
+  else mpiioflag = 0;
 
-  if (multiproc && mpiio) 
+  if (multiproc && mpiioflag) 
     error->all(FLERR,
                "Read restart MPI-IO output not allowed with '%' in filename");
 
+  if (mpiioflag) {
+    mpiio = new RestartMPIIO(lmp);
+    if (!mpiio->mpiio_exists) 
+      error->all(FLERR,"Reading from MPI-IO filename when "
+                 "MPIIO package is not installed");
+  }
+
   // open single restart file or base file for multiproc case
 
   if (me == 0) {
@@ -170,19 +178,37 @@ void ReadRestart::command(int narg, char **arg)
 
   if (me == 0) fclose(fp);
 
-  // single file:
-  // nprocs_file = # of chunks in file
-  // proc 0 reads a chunk and bcasts it to other procs
-  // each proc unpacks the atoms, saving ones in it's sub-domain
-  // check for atom in sub-domain differs for orthogonal vs triclinic box
-
   AtomVec *avec = atom->avec;
 
   int maxbuf = 0;
   double *buf = NULL;
   int m;
 
-  if (multiproc == 0) {
+  // MPI-IO input from single file
+
+  if (mpiioflag) {
+    // add calls to RestartMPIIO class
+    // reopen header file
+    // perform reads
+    // allow for different # of procs reading than wrote the file
+
+    // mpiio->open(file);
+    // mpiio->read();
+    // mpiio->close();
+
+    // then process atom info as
+
+    //m = 0;
+    //while (m < n) m += avec->unpack_restart(&buf[m]);
+  }
+
+  // input of single native file
+  // nprocs_file = # of chunks in file
+  // proc 0 reads a chunk and bcasts it to other procs
+  // each proc unpacks the atoms, saving ones in it's sub-domain
+  // check for atom in sub-domain differs for orthogonal vs triclinic box
+
+  else if (multiproc == 0) {
 
     int triclinic = domain->triclinic;
     double *x,lamda[3];
@@ -225,13 +251,14 @@ void ReadRestart::command(int narg, char **arg)
     }
 
     if (me == 0) fclose(fp);
+  }
 
-  // multiple files with procs <= files
+  // input of multiple native files with procs <= files
   // # of files = multiproc_file
   // each proc reads a subset of files, striding by nprocs
   // each proc keeps all atoms in all perproc chunks in its files
 
-  } else if (nprocs <= multiproc_file) {
+  else if (nprocs <= multiproc_file) {
 
     char *procfile = new char[strlen(file) + 16];
     char *ptr = strchr(file,'%');
@@ -275,15 +302,16 @@ void ReadRestart::command(int narg, char **arg)
     }
 
     delete [] procfile;
+  }
 
-  // multiple files with procs > files
+  // input of multiple native files with procs > files
   // # of files = multiproc_file
   // cluster procs based on # of files
   // 1st proc in each cluster reads per-proc chunks from file
   // sends chunks round-robin to other procs in its cluster
   // each proc keeps all atoms in its perproc chunks in file
 
-  } else {
+  else {
 
     // nclusterprocs = # of procs in my cluster that read from one file
     // filewriter = 1 if this proc reads file, else 0
@@ -382,10 +410,10 @@ void ReadRestart::command(int narg, char **arg)
   delete [] file;
   memory->destroy(buf);
 
-  // for multiproc files:
+  // for multiproc or MPI-IO files:
   // perform irregular comm to migrate atoms to correct procs
 
-  if (multiproc) {
+  if (multiproc || mpiioflag) {
 
     // create a temporary fix to hold and migrate extra atom info
     // necessary b/c irregular will migrate atoms
@@ -899,13 +927,16 @@ void ReadRestart::file_layout()
         error->all(FLERR,"Restart file is a multi-proc file");
 
     } else if (flag = MPIIO) {
-      int mpiio_file = read_int();
+      int mpiioflag_file = read_int();
-      if (mpiio == 0 && mpiio_file)
+      if (mpiioflag == 0 && mpiioflag_file)
         error->all(FLERR,"Restart file is a MPI-IO file");
-      if (mpiio && mpiio_file == 0)
+      if (mpiioflag && mpiioflag_file == 0)
         error->all(FLERR,"Restart file is not a MPI-IO file");
     }
 
+    // NOTE: could add reading of MPI-IO specific fields to header here
+    // e.g. read vector of PERPROCSIZE values
+
     flag = read_int();
   }
 }

src/read_restart.h

@@ -35,10 +35,12 @@ class ReadRestart : protected Pointers {
   FILE *fp;
   int nfix_restart_global,nfix_restart_peratom;
 
-  int mpiio;                 // 1 for MPIIO output, else 0
   int multiproc;             // 0 = proc 0 writes for all
                              // else # of procs writing files
 
+  int mpiioflag;               // 1 for MPIIO output, else 0
+  class RestartMPIIO *mpiio;   // MPIIO for restart file input
+
   void file_search(char *, char *);
   void header(int);
   void type_arrays();

src/write_restart.cpp

@@ -34,6 +34,7 @@
 #include "comm.h"
 #include "output.h"
 #include "thermo.h"
+#include "mpiio.h"
 #include "memory.h"
 #include "error.h"
 
@@ -96,17 +97,24 @@ void WriteRestart::command(int narg, char **arg)
 
   if (strchr(arg[0],'%')) multiproc = nprocs;
   else multiproc = 0;
-  if (strstr(arg[0],".mpi")) mpiio = 1;
+  if (strstr(arg[0],".mpi")) mpiioflag = 1;
-  else mpiio = 0;
+  else mpiioflag = 0;
 
-  if (multiproc && mpiio) 
+  if (multiproc && mpiioflag) 
     error->all(FLERR,
                "Write restart MPI-IO output not allowed with '%' in filename");
 
+  if (mpiioflag) {
+    mpiio = new RestartMPIIO(lmp);
+    if (!mpiio->mpiio_exists) 
+      error->all(FLERR,"Writing to MPI-IO filename when "
+                 "MPIIO package is not installed");
+  }
+
   // setup output style and process optional args
   // also called by Output class for periodic restart files
 
-  multiproc_options(multiproc,mpiio,narg-1,&arg[1]);
+  multiproc_options(multiproc,mpiioflag,narg-1,&arg[1]);
 
   // init entire system since comm->exchange is done
   // comm::init needs neighbor::init needs pair::init needs kspace::init, etc
@@ -136,11 +144,11 @@ void WriteRestart::command(int narg, char **arg)
 /* ----------------------------------------------------------------------
 ------------------------------------------------------------------------- */
 
-void WriteRestart::multiproc_options(int multiproc_caller, int mpiio_caller,
+void WriteRestart::multiproc_options(int multiproc_caller, int mpiioflag_caller,
                                      int narg, char **arg)
 {
   multiproc = multiproc_caller;
-  mpiio = mpiio_caller;
+  mpiioflag = mpiioflag_caller;
 
   // defaults for multiproc file writing
 
@@ -363,33 +371,50 @@ void WriteRestart::write(char *file)
     }
   }
 
+  // MPI-IO output to single file
+
+  if (mpiioflag) {
+    // add calls to RestartMPIIO class
+    // reopen header file in append mode
+    // perform writes
+
+    // mpiio->open(file);
+    // mpiio->write(send_size,buf);
+    // mpiio->close();
+  }
+
+  // output of one or more native files
   // filewriter = 1 = this proc writes to file
   // ping each proc in my cluster, receive its data, write data to file
   // else wait for ping from fileproc, send my data to fileproc
 
-  int tmp,recv_size;
+  else {
-  MPI_Status status;
+    int tmp,recv_size;
-  MPI_Request request;
+    MPI_Status status;
+    MPI_Request request;
 
-  if (filewriter) {
+    if (filewriter) {
-    write_int(PROCSPERFILE,nclusterprocs);
+      write_int(PROCSPERFILE,nclusterprocs);
-    for (int iproc = 0; iproc < nclusterprocs; iproc++) {
+      for (int iproc = 0; iproc < nclusterprocs; iproc++) {
-      if (iproc) {
+        if (iproc) {
-        MPI_Irecv(buf,max_size,MPI_DOUBLE,me+iproc,0,world,&request);
+          MPI_Irecv(buf,max_size,MPI_DOUBLE,me+iproc,0,world,&request);
-        MPI_Send(&tmp,0,MPI_INT,me+iproc,0,world);
+          MPI_Send(&tmp,0,MPI_INT,me+iproc,0,world);
-        MPI_Wait(&request,&status);
+          MPI_Wait(&request,&status);
-        MPI_Get_count(&status,MPI_DOUBLE,&recv_size);
+          MPI_Get_count(&status,MPI_DOUBLE,&recv_size);
-      } else recv_size = send_size;
+        } else recv_size = send_size;
+        
+        write_double_vec(PERPROC,recv_size,buf);
+      }
+      fclose(fp);
 
-      write_double_vec(PERPROC,recv_size,buf);
+    } else {
+      MPI_Recv(&tmp,0,MPI_INT,fileproc,0,world,&status);
+      MPI_Rsend(buf,send_size,MPI_DOUBLE,fileproc,0,world);
     }
-    fclose(fp);
-
-  } else {
-    MPI_Recv(&tmp,0,MPI_INT,fileproc,0,world,&status);
-    MPI_Rsend(buf,send_size,MPI_DOUBLE,fileproc,0,world);
   }
 
+  // clean up
+
   memory->destroy(buf);
 
   // invoke any fixes that write their own restart file
@@ -528,9 +553,12 @@ void WriteRestart::file_layout(int send_size)
 {
   if (me == 0) {
     write_int(MULTIPROC,multiproc);
-    write_int(MPIIO,mpiio);
+    write_int(MPIIO,mpiioflag);
   }
 
+  // NOTE: could add MPI-IO specific fields to header here
+  // e.g. gather send_size across all procs and call write_int_vec()
+
   // -1 flag signals end of file layout info
 
   if (me == 0) {

src/write_restart.h

@@ -37,7 +37,6 @@ class WriteRestart : protected Pointers {
   FILE *fp;
   bigint natoms;         // natoms (sum of nlocal) to write into file
 
-  int mpiio;                 // 1 for MPIIO output, else 0
   int multiproc;             // 0 = proc 0 writes for all
                              // else # of procs writing files
   int nclusterprocs;         // # of procs in my cluster that write to one file
@@ -45,6 +44,9 @@ class WriteRestart : protected Pointers {
   int fileproc;              // ID of proc in my cluster who writes to file
   int icluster;              // which cluster I am in
 
+  int mpiioflag;               // 1 for MPIIO output, else 0
+  class RestartMPIIO *mpiio;   // MPIIO for restart file output
+
   void header();
   void type_arrays();
   void force_fields();