cleanup a bunch of code and stale comments

darshan-posix-log-format.h

@@ -177,11 +177,4 @@ struct darshan_posix_file
     double fcounters[POSIX_F_NUM_INDICES];
 };
 
-/* This macro can be used to identify files that have been opened using
- * pnetcdf, hdf5, or mpi-io, but were never opened at the posix level.  As a
- * result the record will not necessarily have all of the expected fields
- * populated.
- */
-#define POSIX_FILE_PARTIAL(__file)((((__file)->counters[POSIX_OPENS] || (__file)->counters[POSIX_FOPENS] || (__file)->counters[POSIX_STATS]) ? 0 : 1))
-
 #endif /* __DARSHAN_POSIX_LOG_FORMAT_H */

darshan-runtime/Makefile.in

@@ -33,12 +33,12 @@ CFLAGS_SHARED = -DDARSHAN_CONFIG_H=\"darshan-runtime-config.h\" -I . -I$(srcdir)
 
 LIBS = -lz @LIBBZ2@
 
-static-mod-objs = lib/darshan-posix.o lib/darshan-mpiio.o lib/darshan-hdf5.o lib/darshan-pnetcdf.o
-dynamic-mod-objs = lib/darshan-posix.po lib/darshan-mpiio.po lib/darshan-hdf5.po lib/darshan-pnetcdf.po
+DARSHAN_STATIC_MOD_OBJS = lib/darshan-posix.o lib/darshan-mpiio.o lib/darshan-hdf5.o lib/darshan-pnetcdf.o
+DARSHAN_DYNAMIC_MOD_OBJS = lib/darshan-posix.po lib/darshan-mpiio.po lib/darshan-hdf5.po lib/darshan-pnetcdf.po
 
 ifdef DARSHAN_USE_BGQ
-static-mod-objs += lib/darshan-bgq.o
-dynamic-mod-objs += lib/darshan-bgq.po
+DARSHAN_STATIC_MOD_OBJS += lib/darshan-bgq.o
+DARSHAN_DYNAMIC_MOD_OBJS += lib/darshan-bgq.po
 CFLAGS += -DDARSHAN_BGQ
 CFLAGS_SHARED += -DDARSHAN_BGQ
 endif
@@ -118,10 +118,10 @@ lib/lookup8.o: lib/lookup8.c
 lib/lookup8.po: lib/lookup8.c
 	$(CC) $(CFLAGS_SHARED) -c $< -o $@
 
-lib/libdarshan.a: lib/darshan-core-init-finalize.o lib/darshan-core.o lib/darshan-common.o $(static-mod-objs) lib/lookup3.o lib/lookup8.o
+lib/libdarshan.a: lib/darshan-core-init-finalize.o lib/darshan-core.o lib/darshan-common.o $(DARSHAN_STATIC_MOD_OBJS) lib/lookup3.o lib/lookup8.o
 	ar rcs $@ $^
 
-lib/libdarshan.so: lib/darshan-core-init-finalize.po lib/darshan-core.po lib/darshan-common.po $(dynamic-mod-objs) lib/lookup3.po lib/lookup8.po
+lib/libdarshan.so: lib/darshan-core-init-finalize.po lib/darshan-core.po lib/darshan-common.po $(DARSHAN_DYNAMIC_MOD_OBJS) lib/lookup3.po lib/lookup8.po
 	$(CC) $(CFLAGS_SHARED) $(LDFLAGS) -o $@ $^ -lpthread -lrt -lz -ldl
 
 lib/libdarshan-stubs.a: lib/darshan-hdf5-stubs.o lib/darshan-pnetcdf-stubs.o

darshan-runtime/darshan.h

@@ -115,17 +115,17 @@ void darshan_core_unregister_module(
 
 /* darshan_core_register_record()
  *
- * Register the Darshan record given by 'name' with the darshan-core
- * runtime, allowing it to be properly tracked and (potentially)
- * correlated with records from other modules. 'len' is the size of
- * the name pointer (string length for string names), and 'printable_flag'
- * indicates whether the name is a string. 'mod_limit_flag' is set if
- * the calling module is out of memory (to prevent darshan-core from
- * creating new records and to just search existing records)  and 'mod_id'
- * is the identifier of the calling module. 'rec_id' is an output pointer
- * storing the correspoing Darshan record identifier and 'file_alignment'
- * is an output pointer storing the file system alignment value for the
- * given record.
+ * Register a record with the darshan-core runtime, allowing it to be
+ * properly tracked and (potentially) correlated with records from other
+ * modules. 'name' is the the name of the Darshan record (e.g., the full
+ * file path) and 'len' is the size of the name pointer (string length
+ * for string names). 'mod_id' is the identifier of the calling module,
+ * 'printable_flag' indicates whether the name is a string, and 
+ * 'mod_limit_flag' is set if the calling module is out of memory (to
+ * prevent darshan-core from creating new records and to just search
+ * through existing records). 'rec_id' is an output pointer storing the
+ * correspoing Darshan record identifier and 'file_alignment' is an output
+ * pointer storing the file system alignment value for the given record.
  */
 void darshan_core_register_record(
     void *name,

darshan-runtime/lib/darshan-bgq.c

@@ -50,7 +50,7 @@ static int instrumentation_disabled = 0;
 static int my_rank = -1;
 static int darshan_mem_alignment = 1;
 
-/* internal helper functions for the "NULL" module */
+/* internal helper functions for the BGQ module */
 void bgq_runtime_initialize(void);
 
 /* forward declaration for module functions needed to interface with darshan-core */
@@ -58,7 +58,7 @@ static void bgq_begin_shutdown(void);
 static void bgq_get_output_data(MPI_Comm mod_comm, darshan_record_id *shared_recs, int shared_rec_count, void **buffer, int *size);
 static void bgq_shutdown(void);
 
-/* macros for obtaining/releasing the "NULL" module lock */
+/* macros for obtaining/releasing the BGQ module lock */
 #define BGQ_LOCK() pthread_mutex_lock(&bgq_runtime_mutex)
 #define BGQ_UNLOCK() pthread_mutex_unlock(&bgq_runtime_mutex)
 
@@ -133,13 +133,15 @@ void bgq_runtime_initialize()
     if(mem_limit == 0)
     {
         instrumentation_disabled = 1;
+        BGQ_UNLOCK();
         return;
     }
 
-    /* no enough memory to fit bgq module */
+    /* not enough memory to fit bgq module */
     if (mem_limit < sizeof(*bgq_runtime))
     {
         instrumentation_disabled = 1;
+        BGQ_UNLOCK();
         return;
     }
 
@@ -148,6 +150,7 @@ void bgq_runtime_initialize()
     if(!bgq_runtime)
     {
         instrumentation_disabled = 1;
+        BGQ_UNLOCK();
         return;
     }
     memset(bgq_runtime, 0, sizeof(*bgq_runtime));
@@ -180,7 +183,7 @@ void bgq_runtime_initialize()
     return;
 }
 
-/* Perform any necessary steps prior to shutting down for the "NULL" module. */
+/* Perform any necessary steps prior to shutting down for the BGQ module. */
 static void bgq_begin_shutdown()
 {
     BGQ_LOCK();
@@ -204,7 +207,7 @@ static int cmpr(const void *p1, const void *p2)
     return ((*a == *b) ?  0 : ((*a < *b) ? -1 : 1));
 }
 
-/* Pass output data for the "BGQ" module back to darshan-core to log to file. */
+/* Pass output data for the BGQ module back to darshan-core to log to file. */
 static void bgq_get_output_data(
     MPI_Comm mod_comm,
     darshan_record_id *shared_recs,
@@ -212,7 +215,7 @@ static void bgq_get_output_data(
     void **buffer,
     int *size)
 {
-    /* Just set the output buffer to point at the array of the "BGQ" module's
+    /* Just set the output buffer to point at the array of the BGQ module's
      * I/O records, and set the output size according to the number of records
      * currently being tracked.
      */
@@ -273,7 +276,7 @@ static void bgq_get_output_data(
     return;
 }
 
-/* Shutdown the "BGQ" module by freeing up all data structures. */
+/* Shutdown the BGQ module by freeing up all data structures. */
 static void bgq_shutdown()
 {
     BGQ_LOCK();

darshan-runtime/lib/darshan-posix.c

@@ -39,8 +39,6 @@ typedef int64_t off64_t;
 #define aiocb64 aiocb
 #endif
 
-/* TODO: more libc, fgetc, etc etc etc. */
-
 DARSHAN_FORWARD_DECL(open, int, (const char *path, int flags, ...));
 DARSHAN_FORWARD_DECL(open64, int, (const char *path, int flags, ...));
 DARSHAN_FORWARD_DECL(creat, int, (const char* path, mode_t mode));
@@ -1728,10 +1726,7 @@ static void posix_record_reduction_op(void* infile_v, void* inoutfile_v,
             tmp_file.counters[j] = infile->counters[j] + inoutfile->counters[j];
         }
 
-        if(POSIX_FILE_PARTIAL(infile))
-            tmp_file.counters[POSIX_MODE] = inoutfile->counters[POSIX_MODE];
-        else
-            tmp_file.counters[POSIX_MODE] = infile->counters[POSIX_MODE];
+        tmp_file.counters[POSIX_MODE] = infile->counters[POSIX_MODE];
 
         /* sum */
         for(j=POSIX_BYTES_READ; j<=POSIX_BYTES_WRITTEN; j++)
@@ -1754,10 +1749,7 @@ static void posix_record_reduction_op(void* infile_v, void* inoutfile_v,
             tmp_file.counters[j] = infile->counters[j] + inoutfile->counters[j];
         }
 
-        if(POSIX_FILE_PARTIAL(infile))
-            tmp_file.counters[POSIX_MEM_ALIGNMENT] = inoutfile->counters[POSIX_MEM_ALIGNMENT];
-        else
-            tmp_file.counters[POSIX_MEM_ALIGNMENT] = infile->counters[POSIX_MEM_ALIGNMENT];
+        tmp_file.counters[POSIX_MEM_ALIGNMENT] = infile->counters[POSIX_MEM_ALIGNMENT];
 
         /* sum */
         for(j=POSIX_FILE_NOT_ALIGNED; j<=POSIX_FILE_NOT_ALIGNED; j++)
@@ -1765,10 +1757,7 @@ static void posix_record_reduction_op(void* infile_v, void* inoutfile_v,
             tmp_file.counters[j] = infile->counters[j] + inoutfile->counters[j];
         }
 
-        if(POSIX_FILE_PARTIAL(infile))
-            tmp_file.counters[POSIX_FILE_ALIGNMENT] = inoutfile->counters[POSIX_FILE_ALIGNMENT];
-        else
-            tmp_file.counters[POSIX_FILE_ALIGNMENT] = infile->counters[POSIX_FILE_ALIGNMENT];
+        tmp_file.counters[POSIX_FILE_ALIGNMENT] = infile->counters[POSIX_FILE_ALIGNMENT];
 
         /* skip POSIX_MAX_*_TIME_SIZE; handled in floating point section */
 

darshan-util/Makefile.in

@@ -15,6 +15,8 @@ pkgconfigdir = $(DESTDIR)$(libdir)/pkgconfig
 DARSHAN_LOG_FORMAT = $(srcdir)/../darshan-log-format.h
 DARSHAN_MOD_LOG_FORMATS = $(srcdir)/../darshan-posix-log-format.h $(srcdir)/../darshan-mpiio-log-format.h $(srcdir)/../darshan-hdf5-log-format.h $(srcdir)/../darshan-pnetcdf-log-format.h
 DARSHAN_MOD_LOGUTIL_HEADERS = darshan-posix-logutils.h darshan-mpiio-logutils.h darshan-hdf5-logutils.h darshan-pnetcdf-logutils.h
+DARSHAN_STATIC_MOD_OBJS = darshan-posix-logutils.o darshan-mpiio-logutils.o darshan-hdf5-logutils.o darshan-pnetcdf-logutils.o darshan-bgq-logutils.o
+DARSHAN_DYNAMIC_MOD_OBJS = darshan-posix-logutils.po darshan-mpiio-logutils.po darshan-hdf5-logutils.po darshan-pnetcdf-logutils.po darshan-bgq-logutils.po
 
 DARSHAN_ENABLE_SHARED=@DARSHAN_ENABLE_SHARED@
 
@@ -79,13 +81,12 @@ darshan-bgq-logutils.o: darshan-bgq-logutils.c darshan-logutils.h darshan-bgq-lo
 darshan-bgq-logutils.po: darshan-bgq-logutils.c darshan-logutils.h darshan-bgq-logutils.h $(DARSHAN_LOG_FORMAT) $(srcdir)/../darshan-bgq-log-format.h | uthash-1.9.2
 	$(CC) $(CFLAGS_SHARED) -c  $< -o $@
 
+libdarshan-util.a: darshan-logutils.o $(DARSHAN_STATIC_MOD_OBJS)
+	ar rcs libdarshan-util.a $^
 
-libdarshan-util.so: darshan-logutils.po darshan-posix-logutils.po darshan-mpiio-logutils.po darshan-hdf5-logutils.po darshan-pnetcdf-logutils.po darshan-bgq-logutils.po
+libdarshan-util.so: darshan-logutils.po $(DARSHAN_DYNAMIC_MOD_OBJS)
 	$(CC) $(CFLAGS_SHARED) $(LDFLAGS) -o $@ $^ $(LIBS)
 	
-libdarshan-util.a: darshan-logutils.o darshan-posix-logutils.o darshan-mpiio-logutils.o darshan-hdf5-logutils.o darshan-pnetcdf-logutils.o darshan-bgq-logutils.o
-	ar rcs libdarshan-util.a $^
-
 jenkins-hash-gen: jenkins-hash-gen.c lookup3.o
 	$(CC) $(CFLAGS) $(LDFLAGS) $^ -o $@ $(LIBS)
 

darshan-util/darshan-logutils.h

@@ -55,6 +55,9 @@ struct darshan_mod_logutil_funcs
     /* retrieve a single module record from the log file. 
      * return 1 on successful read of record, 0 on no more
      * module data, -1 on error
+     *      - 'fd' is the file descriptor to get record from
+     *      - 'buf' is the buffer to store the record in
+     *      - 'rec_id' is the corresponding darshan record id
      */
     int (*log_get_record)(
         darshan_fd fd,
@@ -63,13 +66,22 @@ struct darshan_mod_logutil_funcs
     );
     /* put a single module record into the log file.
      * return 0 on success, -1 on error
+     *      - 'fd' is the file descriptor to put record into
+     *      - 'buf' is the buffer containing the record data
+     *      - 'rec_id' is the corresponding darshan record id
      */
     int (*log_put_record)(
         darshan_fd fd,
         void *buf,
         int ver
     );
-    /* print the counters for a given log file record */
+    /* print the counters for a given log record
+     *      - 'file_rec' is the record's data buffer
+     *      - 'file_name' is the file path string for the record
+     *      - 'mnt-pt' is the file path mount point string
+     *      - 'fs_type' is the file system type string
+     *      - 'ver' is the version of the record
+     */
     void (*log_print_record)(
         void *file_rec,
         char *file_name,

darshan-util/darshan-null-logutils.c

@@ -51,7 +51,8 @@ struct darshan_mod_logutil_funcs null_logutils =
 
 /* retrieve a NULL record from log file descriptor 'fd', storing the
  * buffer in 'null_buf' and the corresponding Darshan record id in
- * 'rec_id'. Return 1 on successful record read, .
+ * 'rec_id'. Return 1 on successful record read, 0 on no more data,
+ * and -1 on error.
  */
 static int darshan_log_get_null_record(darshan_fd fd, void* null_buf, 
     darshan_record_id* rec_id)

darshan-util/darshan-parser.c

@@ -690,8 +690,7 @@ void posix_accum_file(struct darshan_posix_file *pfile,
         case POSIX_MODE:
         case POSIX_MEM_ALIGNMENT:
         case POSIX_FILE_ALIGNMENT:
-            if(POSIX_FILE_PARTIAL(tmp))
-                tmp->counters[i] = pfile->counters[i];
+            tmp->counters[i] = pfile->counters[i];
             break;
         case POSIX_MAX_BYTE_READ:
         case POSIX_MAX_BYTE_WRITTEN: