Merge branch 'ejh_async2'

E3SM-Project · May 27, 2016 · eecde10 · eecde10
2 parents 24a34ff + 696d403
commit eecde10
Show file tree

Hide file tree

Showing 16 changed files with 8,398 additions and 13,783 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -14,18 +14,28 @@ mark_as_advanced(VERSION_MAJOR VERSION_MINOR VERSION_PATCH)
 #===== Library Options =====
 option (PIO_ENABLE_FORTRAN   "Enable the Fortran library builds"            ON)
 option (PIO_ENABLE_TIMING    "Enable the use of the GPTL timing library"    ON)
+option (PIO_ENABLE_ASYNC     "Enable the use of asychronus IO operations"   OFF)
+option (PIO_ENABLE_LOGGING   "Enable debug logging (large output possible)" OFF)
 option (PIO_TEST_BIG_ENDIAN  "Enable test to see if machine is big endian"  ON)
 option (PIO_USE_MPIIO        "Enable support for MPI-IO auto detect"        ON)
 option (PIO_USE_MPISERIAL    "Enable mpi-serial support (instead of MPI)"   OFF)
 option (PIO_USE_MALLOC       "Use native malloc (instead of bget package)"  OFF)
 option (WITH_PNETCDF         "Require the use of PnetCDF"                   ON)
 
+# Set a variable that appears in the config.h.in file.
 if(PIO_USE_MALLOC)
   set(USE_MALLOC 1)
 else()
   set(USE_MALLOC 0)
 endif()
 
+# Set a variable that appears in the config.h.in file.
+if(PIO_ENABLE_LOGGING)
+  set(ENABLE_LOGGING 1)
+else()
+  set(ENABLE_LOGGING 0)
+endif()
+
 #===== Library Variables =====
 set (PIO_FILESYSTEM_HINTS IGNORE CACHE STRING "Filesystem hints (lustre or gpfs)")
 

diff --git a/src/clib/CMakeLists.txt b/src/clib/CMakeLists.txt
@@ -15,14 +15,20 @@ set (PIO_C_SRCS topology.c
                 pio_spmd.c
                 pio_rearrange.c
                 pio_darray.c
+		pio_nc4.c
                 bget.c)
 
-set (PIO_GENNC_SRCS ${CMAKE_CURRENT_BINARY_DIR}/pio_nc.c
-  ${CMAKE_CURRENT_BINARY_DIR}/pio_nc4.c
-  ${CMAKE_CURRENT_BINARY_DIR}/pio_put_nc.c 
-  ${CMAKE_CURRENT_BINARY_DIR}/pio_get_nc.c)
+set (PIO_GENNC_SRCS ${CMAKE_CURRENT_BINARY_DIR}/pio_put_nc.c
+  ${CMAKE_CURRENT_BINARY_DIR}/pio_get_nc.c
+  ${CMAKE_CURRENT_BINARY_DIR}/pio_nc.c)
 
-add_library (pioc ${PIO_C_SRCS} ${PIO_GENNC_SRCS})
+if (PIO_ENABLE_ASYNC)
+  set (PIO_ADDL_SRCS pio_nc_async.c pio_put_nc_async.c pio_get_nc_async.c pio_msg.c pio_varm.c)
+else ()
+  set (PIO_ADDL_SRCS ${PIO_GENNC_SRCS})
+endif ()
+
+add_library (pioc ${PIO_C_SRCS} ${PIO_ADDL_SRCS})
 
 # set up include-directories
 include_directories(
@@ -196,12 +202,9 @@ else ()
                                              pio_get_nc.c
             COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/pio_nc.c
                                              pio_nc.c
-            COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/pio_nc4.c
-                                             pio_nc4.c
             DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/pio_put_nc.c
                     ${CMAKE_CURRENT_SOURCE_DIR}/pio_get_nc.c
-                    ${CMAKE_CURRENT_SOURCE_DIR}/pio_nc.c
-                    ${CMAKE_CURRENT_SOURCE_DIR}/pio_nc4.c)
+                    ${CMAKE_CURRENT_SOURCE_DIR}/pio_nc.c)
 endif ()
 
 

diff --git a/src/clib/config.h.in b/src/clib/config.h.in
@@ -19,4 +19,7 @@
  * will use the included bget() package for memory management. */
 #define PIO_USE_MALLOC @USE_MALLOC@
 
+/** Set to non-zero to turn on logging. Output may be large. */
+#define PIO_ENABLE_LOGGING @ENABLE_LOGGING@
+
 #endif /* _PIO_CONFIG_ */
diff --git a/src/clib/pio.h b/src/clib/pio.h
@@ -259,6 +259,10 @@ typedef struct file_desc_t
   int mode;
   struct wmulti_buffer buffer;
   struct file_desc_t *next;
+
+  /** True if this task should participate in IO (only true for one
+   * task with netcdf serial files. */
+  int do_io;
 } file_desc_t;
 
 /**
@@ -409,8 +413,8 @@ int PIOc_inq_varnatts (int ncid, int varid, int *nattsp);
 int PIOc_def_var (int ncid, const char *name, nc_type xtype,  int ndims, const int *dimidsp, int *varidp);
 int PIOc_def_var_deflate(int ncid, int varid, int shuffle, int deflate,
 			 int deflate_level);
-int PIOc_inq_var_deflate(int ncid, int varid, int *shufflep,
-			 int *deflatep, int *deflate_levelp);
+int PIOc_inq_var_deflate(int ncid, int varid, int *shufflep, int *deflatep,
+			 int *deflate_levelp);
 int PIOc_inq_var_szip(int ncid, int varid, int *options_maskp, int *pixels_per_blockp);
 int PIOc_def_var_chunking(int ncid, int varid, int storage, const PIO_Offset *chunksizesp);
 int PIOc_inq_var_chunking(int ncid, int varid, int *storagep, PIO_Offset *chunksizesp);
@@ -481,6 +485,8 @@ int PIOc_InitDecomp(const int iosysid, const int basetype,const int ndims, const
 int PIOc_Init_Intracomm(const MPI_Comm comp_comm, 
 			  const int num_iotasks, const int stride, 
 			  const int base, const int rearr, int *iosysidp);
+int PIOc_Init_Intercomm(int component_count, MPI_Comm peer_comm, MPI_Comm *comp_comms,
+			MPI_Comm io_comm, int *iosysidp);
 int PIOc_closefile(int ncid);
 int PIOc_createfile(const int iosysid, int *ncidp,  int *iotype,
 		    const char *fname, const int mode);
@@ -586,10 +592,11 @@ int PIOc_set_blocksize(const int newblocksize);
   int PIOc_put_vars_longlong (int ncid, int varid, const PIO_Offset start[], const PIO_Offset count[], const PIO_Offset stride[], const long long *op);  
   int PIOc_put_vara_double (int ncid, int varid, const PIO_Offset start[], const PIO_Offset count[], const double *op);  
   int PIOc_put_vars (int ncid, int varid, const PIO_Offset start[], const PIO_Offset count[], const PIO_Offset stride[], const void *buf, PIO_Offset bufcount, MPI_Datatype buftype);  
+  int PIOc_put_vars_tc(int ncid, int varid, const PIO_Offset start[], const PIO_Offset count[], const PIO_Offset stride[], nc_type xtype, const void *buf);  
   int PIOc_put_var_uchar (int ncid, int varid, const unsigned char *op); 
   int PIOc_put_var_long (int ncid, int varid, const long *op); 
   int PIOc_put_varm_longlong (int ncid, int varid, const PIO_Offset start[], const PIO_Offset count[], const PIO_Offset stride[], const PIO_Offset imap[], const long long *op);
- int PIOc_get_vara_int (int ncid, int varid, const PIO_Offset start[], const PIO_Offset count[], int *buf);
+  int PIOc_get_vara_int (int ncid, int varid, const PIO_Offset start[], const PIO_Offset count[], int *buf);
   int PIOc_get_var1_float (int ncid, int varid, const PIO_Offset index[], float *buf); 
   int PIOc_get_var1_short (int ncid, int varid, const PIO_Offset index[], short *buf); 
   int PIOc_get_vars_int (int ncid, int varid, const PIO_Offset start[], const PIO_Offset count[], const PIO_Offset stride[], int *buf);                      
@@ -641,11 +648,15 @@ int PIOc_set_blocksize(const int newblocksize);
   int PIOc_get_vars_text (int ncid, int varid, const PIO_Offset start[], const PIO_Offset count[], const PIO_Offset stride[], char *buf);  
   int PIOc_get_var1_uchar (int ncid, int varid, const PIO_Offset index[], unsigned char *buf); 
   int PIOc_get_vars (int ncid, int varid, const PIO_Offset start[], const PIO_Offset count[], const PIO_Offset stride[], void *buf, PIO_Offset bufcount, MPI_Datatype buftype);  
+  int PIOc_get_vars_tc(int ncid, int varid, const PIO_Offset start[], const PIO_Offset count[], const PIO_Offset stride[], nc_type xtype, void *buf);  
   int PIOc_get_varm_short (int ncid, int varid, const PIO_Offset start[], const PIO_Offset count[], const PIO_Offset stride[], const PIO_Offset imap[], short *buf);  
   int PIOc_get_varm_ulonglong (int ncid, int varid, const PIO_Offset start[], const PIO_Offset count[], const PIO_Offset stride[], const PIO_Offset imap[], unsigned long long *buf);  
   int PIOc_get_var_schar (int ncid, int varid, signed char *buf); 
   int PIOc_iotype_available(const int iotype);
-
+  int PIOc_set_log_level(int level);
+  int PIOc_put_att(int ncid, int varid, const char *name, nc_type xtype, PIO_Offset len, const void *op);
+  int PIOc_get_att(int ncid, int varid, const char *name, void *ip);
+  int PIOc_inq_type(int ncid, nc_type xtype, char *name, PIO_Offset *sizep);    
 #if defined(__cplusplus)
 }
 #endif