Edits to k-buffering and new features in pp_ser.py (#245)

This PR contains  two minor changes to the k-buffering feature used by `pp_ser.py` and implemented in `utils_ppser_kbuff.f90` (increase in maximum number of buffers, more verbose error message in case of a problem) and adds two new features to `pp_ser.py`.

For the latter, the changes are located in `pp_ser.py` and `utils_ppser.f90` only and entail:
- When initializing `pp_ser.py` with reference data one can specify another directory where the data is located. If this is not available, new data will be serialized into the same directory as the reference data which can lead to conflicts or corrupt data.
- Up to now, the directive syntax for specifying a savepoint was `!$ser savepoint gugus` where gugus was the name of the savepoint. This syntax does not allow the dynamic generation of savepoint names (e.g. from runtime information such as timestep or a unique ID). A new command line option to `pp_ser.py` named `-s` or `--sp-as-var` allows to use `!$ser savepoint "gugus"` or `!$ser savepoint my_string` where `my_string` is a variable.

Author: ofuhrer

src/serialbox-fortran/utils_ppser.f90

@@ -63,20 +63,27 @@ MODULE utils_ppser
 
 !============================================================================
 
-SUBROUTINE ppser_initialize(directory, prefix, mode, prefix_ref, mpi_rank, rprecision, rperturb, realtype, archive, unique_id)
+SUBROUTINE ppser_initialize(directory, prefix, mode, directory_ref, prefix_ref, &
+                mpi_rank, rprecision, rperturb, realtype, archive, unique_id)
   CHARACTER(LEN=*), INTENT(IN)           :: directory, prefix
   INTEGER, OPTIONAL, INTENT(IN)          :: mode
-  CHARACTER(LEN=*), OPTIONAL, INTENT(IN) :: prefix_ref
+  CHARACTER(LEN=*), OPTIONAL, INTENT(IN) :: directory_ref, prefix_ref ! use a different serializer for reading (optional)
   INTEGER, OPTIONAL, INTENT(IN)          :: mpi_rank
   REAL(KIND=8), OPTIONAL, INTENT(IN)     :: rprecision, rperturb
   INTEGER, OPTIONAL, INTENT(IN)          :: realtype
   CHARACTER(LEN=*), INTENT(IN), OPTIONAL :: archive
   LOGICAL, INTENT(IN), OPTIONAL          :: unique_id
 
+  CHARACTER(LEN=256)                     :: dir_ref
   CHARACTER(LEN=1), DIMENSION(128)       :: buffer
   CHARACTER(LEN=15)                      :: suffix
   INTEGER                                :: intvalue
 
+  IF (PRESENT(directory_ref)) THEN
+    dir_ref = directory_ref
+  ELSE
+    dir_ref = directory
+  ENDIF
 
   ! Initialize serializer and savepoint
   IF ( .NOT. ppser_initialized ) THEN
@@ -102,15 +109,15 @@ SUBROUTINE ppser_initialize(directory, prefix, mode, prefix_ref, mpi_rank, rprec
       ppser_hasref = .true.
       IF ( PRESENT(mpi_rank) ) THEN
         IF ( PRESENT(archive) ) THEN
-          CALL fs_create_serializer(directory, TRIM(prefix_ref)//TRIM(suffix), 'r', ppser_serializer_ref, archive)
+          CALL fs_create_serializer(dir_ref, TRIM(prefix_ref)//TRIM(suffix), 'r', ppser_serializer_ref, archive)
         ELSE
-          CALL fs_create_serializer(directory, TRIM(prefix_ref)//TRIM(suffix), 'r', ppser_serializer_ref)
+          CALL fs_create_serializer(dir_ref, TRIM(prefix_ref)//TRIM(suffix), 'r', ppser_serializer_ref)
         END IF
       ELSE
         IF ( PRESENT(archive) ) THEN
-          CALL fs_create_serializer(directory, TRIM(prefix_ref), 'r', ppser_serializer_ref, archive)
+          CALL fs_create_serializer(dir_ref, TRIM(prefix_ref), 'r', ppser_serializer_ref, archive)
         ELSE
-          CALL fs_create_serializer(directory, TRIM(prefix_ref), 'r', ppser_serializer_ref)
+          CALL fs_create_serializer(dir_ref, TRIM(prefix_ref), 'r', ppser_serializer_ref)
         END IF
       END IF
     END IF

src/serialbox-fortran/utils_ppser_kbuff.f90

@@ -59,7 +59,7 @@ MODULE utils_ppser_kbuff
     LOGICAL, ALLOCATABLE :: ok(:)                 ! has this k-level been written?
   END TYPE kbuff_type
 
-  INTEGER, PARAMETER :: max_kbuff = 999           ! increase in case you get errors
+  INTEGER, PARAMETER :: max_kbuff = 9999           ! increase in case you get errors
   TYPE(kbuff_type) :: kbuff(max_kbuff)            ! array containing buffers
 
   ! overload interface for different types and dimensions
@@ -113,6 +113,9 @@ SUBROUTINE finalize_kbuff()
   DO idx = 1, max_kbuff
     IF (kbuff(idx)%in_use) THEN
       WRITE(0,*) 'ERROR in utils_ppser_kbuff: finalize called before all buffers have been flushed'
+      WRITE(0,*) 'savepoint_name: ', TRIM(kbuff(idx)%savepoint_name)
+      WRITE(0,*) 'name of partially empty field: ', TRIM(kbuff(idx)%fieldname)
+      WRITE(0,*) 'vertical indices filled boolean: ', kbuff(idx)%ok(:)
       STOP
     END IF
     kbuff(idx)%fieldname = ""

src/serialbox-python/pp_ser/pp_ser.py

@@ -77,7 +77,7 @@ class PpSer:
 
     def __init__(self, infile, outfile='', ifdef='SERIALIZE', real='ireals',
                  module='m_serialize', identical=True, verbose=False,
-                 acc_prefix=True, acc_if='', modules=''):
+                 acc_prefix=True, acc_if='', modules='', sp_as_var=False):
 
         # public variables
         self.verbose = verbose
@@ -89,6 +89,7 @@ def __init__(self, infile, outfile='', ifdef='SERIALIZE', real='ireals',
         self.identical = identical    # write identical files (no preprocessing done)?
         self.acc_prefix = acc_prefix  # generate preprocessing marco for ACC_PREFIX
         self.acc_if = acc_if          # generate IF clause after OpenACC update
+        self.sp_as_var = sp_as_var    # Syntax for savepoints using variable instead of string
 
         # setup (also public)
         self.methods = {
@@ -460,7 +461,10 @@ def __ser_savepoint(self, args):
 
         self.__calls.add(self.methods['savepoint'])
         self.__calls.add(self.methods['spinfo'])
-        l += tab + 'call ' + self.methods['savepoint'] + '(\'' + name + '\', ppser_savepoint)\n'
+        if not self.sp_as_var:
+            l += tab + 'call ' + self.methods['savepoint'] + '(\'' + name + '\', ppser_savepoint)\n'
+        else:
+            l += tab + 'call ' + self.methods['savepoint'] + '(' + name + ', ppser_savepoint)\n'
         for k, v in zip(keys, values):
             l += tab + 'call ' + self.methods['spinfo'] + '(ppser_savepoint, \'' + k + '\', ' + v + ')\n'
 
@@ -1057,6 +1061,8 @@ def parse_args():
                       default='', type=str, dest='acc_if')
     parser.add_option('-m', '--module', help='Extra MODULE to be add to the use statement',
                       default='', type=str, dest='modules')
+    parser.add_option('-s', '--sp-as-var', help='Savepoint specified as variable instead of string',
+                      default=False, action='store_true', dest='sp_as_var')
     (options, args) = parser.parse_args()
     if len(args) < 1:
         parser.error('Need at least one source file to process')
@@ -1098,5 +1104,5 @@ def parse_args():
             print('Processing file', infile)
             ser = PpSer(infile, real='wp', outfile=outfile, identical=(not options.ignore_identical),
                         verbose=options.verbose, acc_prefix=options.acc_prefix, acc_if=options.acc_if,
-                        modules=options.modules)
+                        modules=options.modules, sp_as_var=options.sp_as_var)
             ser.preprocess()