add macro to detect partial posix file recs

darshan-posix-log-format.h

@@ -176,4 +176,11 @@ 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/lib/darshan-posix.c

@@ -1719,7 +1719,10 @@ static void posix_record_reduction_op(void* infile_v, void* inoutfile_v,
             tmp_file.counters[j] = infile->counters[j] + inoutfile->counters[j];
         }
 
-        tmp_file.counters[POSIX_MODE] = infile->counters[POSIX_MODE];
+        if(POSIX_FILE_PARTIAL(infile))
+            tmp_file.counters[POSIX_MODE] = inoutfile->counters[POSIX_MODE];
+        else
+            tmp_file.counters[POSIX_MODE] = infile->counters[POSIX_MODE];
 
         /* sum */
         for(j=POSIX_BYTES_READ; j<=POSIX_BYTES_WRITTEN; j++)
@@ -1742,8 +1745,10 @@ static void posix_record_reduction_op(void* infile_v, void* inoutfile_v,
             tmp_file.counters[j] = infile->counters[j] + inoutfile->counters[j];
         }
 
-        tmp_file.counters[POSIX_MEM_ALIGNMENT] = infile->counters[POSIX_MEM_ALIGNMENT];
-        tmp_file.counters[POSIX_FILE_ALIGNMENT] = infile->counters[POSIX_FILE_ALIGNMENT];
+        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];
 
         /* sum */
         for(j=POSIX_FILE_NOT_ALIGNED; j<=POSIX_FILE_NOT_ALIGNED; j++)
@@ -1751,6 +1756,11 @@ static void posix_record_reduction_op(void* infile_v, void* inoutfile_v,
             tmp_file.counters[j] = infile->counters[j] + inoutfile->counters[j];
         }
 
+        if(POSIX_PARTIAL_FILE(infile))
+            tmp_file.counters[POSIX_FILE_ALIGNMENT] = inoutfile->counters[POSIX_FILE_ALIGNMENT];
+        else
+            tmp_file.counters[POSIX_FILE_ALIGNMENT] = infile->counters[POSIX_FILE_ALIGNMENT];
+
         /* skip POSIX_MAX_*_TIME_SIZE; handled in floating point section */
 
         for(j=POSIX_SIZE_READ_0_100; j<=POSIX_SIZE_WRITE_1G_PLUS; j++)