Removed OpenMP because I/O is not thread safe

Version:2.0.7

README.rst

@@ -12,6 +12,8 @@ directory. This main directory contains subdirectories, which contain
 files. Each file corresponds to a data. For atomic data the file is a
 plain text file, and for array data the file is a gzipped text file.
 
+Starting with version 2.0, EZFIO produces Python3 files.
+
 Download
 ========
 

make.config

@@ -1,9 +1,9 @@
-VERSION ?= 1.4.0
+VERSION ?= 2.0.7
 RANLIB  ?= ranlib
 IRPF90  ?= irpf90
 CC      ?= gcc
-FC      ?= gfortran -g -ffree-line-length-none -fPIC # -fopenmp
+FC      ?= gfortran -g -ffree-line-length-none -fPIC
 FCFLAGS ?= -fPIC
-AR      ?= ar
+ARCHIVE ?= ar crs
 RANLIB  ?= ranlib
 PYTHON  ?= python3

src/Makefile

@@ -50,13 +50,12 @@ IRPF90_temp/system_f.o: system_f.f90
 
 ../lib/libezfio.a: IRPF90_temp/irpf90.a
 	rm -f ../lib/libezfio.a
-	$(AR) cru ../lib/libezfio.a IRPF90_temp/system_f.o IRPF90_temp/system.o $(OBJ1)  
+	$(ARCHIVE) ../lib/libezfio.a IRPF90_temp/system_f.o IRPF90_temp/system.o $(OBJ1)  
 	$(RANLIB) ../lib/libezfio.a
 
 ../lib/libezfio_irp.a: ../lib/libezfio.a
 	rm -f ../lib/libezfio_irp.a
-	cp ../lib/libezfio.a ../lib/libezfio_irp.a
-	$(AR) dv ../lib/libezfio_irp.a irp_stack.irp.o
+	$(ARCHIVE) ../lib/libezfio_irp.a IRPF90_temp/system_f.o IRPF90_temp/system.o $(filter-out IRPF90_temp/irp_stack.irp.o, $(OBJ1) )
 	$(RANLIB) ../lib/libezfio_irp.a
 
 

src/create_ocaml.py

@@ -46,7 +46,7 @@ def run():
   
   for group in groups.keys():
      for var,type,dims,command in groups[group]:
-       if command is not "":
+       if command != "":
          continue
        dims_py = str(dims)
        for g in groups.keys():

src/ezfio-head.py

@@ -102,7 +102,7 @@ def get_conv(type):
       else:
         raise TypeError
   elif type == "ch":
-    conv = lambda x: x.strip()
+    conv = lambda x: x.decode('utf-8').strip() if isinstance(x,bytes) else x.strip()
   else:
     raise TypeError
   return conv

src/ezfio.ml

@@ -1,26 +1,26 @@
 (*
     EZFIO is an automatic generator of I/O libraries
     Copyright (C) 2009 Anthony SCEMAMA, CNRS
- 
+
     This program is free software; you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
     the Free Software Foundation; either version 2 of the License, or
     (at your option) any later version.
- 
+
     This program is distributed in the hope that it will be useful,
     but WITHOUT ANY WARRANTY; without even the implied warranty of
     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     GNU General Public License for more details.
- 
+
     You should have received a copy of the GNU General Public License along
     with this program; if not, write to the Free Software Foundation, Inc.,
     51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- 
+
     Anthony Scemama
     LCPQ - IRSAMC - CNRS
     Universite Paul Sabatier
-    118, route de Narbonne      
-    31062 Toulouse Cedex 4      
+    118, route de Narbonne
+    31062 Toulouse Cedex 4
     scemama@irsamc.ups-tlse.fr
 *)
 
@@ -40,7 +40,7 @@ State variables
 let read_only = ref false
 let ezfio_filename = ref "EZFIO_File"
 
-(* 
+(*
 Helper functions
 =================
 *)
@@ -54,7 +54,7 @@ let exists path =
   let filename = Filename.concat path ".version" in
   Sys.file_exists filename
 
- 
+
 let has group name =
   let dirname = Filename.concat !ezfio_filename group in
   if (exists dirname) then
@@ -82,14 +82,14 @@ let create_group group =
 
 
 
-let maxval l = 
+let maxval l =
   match l with
   | [] -> None
   | [a] -> Some a
   | hd::tail -> Some (List.fold_left max hd tail)
 
 
-let minval l = 
+let minval l =
   match l with
   | [] -> None
   | [a] -> Some a
@@ -105,10 +105,10 @@ let size (_) = 0
 let n_count_ch (str,_,v) =
   let rec do_work accu = function
   | 0 -> accu
-  | i -> 
-    let newaccu = 
+  | i ->
+    let newaccu =
       if str.[i-1] == v then accu+1
-      else accu 
+      else accu
     in do_work newaccu (i-1)
   in do_work 0 (String.length str)
 
@@ -116,15 +116,15 @@ let n_count_ch (str,_,v) =
 let n_count (l,_,v) =
   let rec do_work accu = function
   | []  -> accu
-  | h::tail -> 
-    let newaccu = 
+  | h::tail ->
+    let newaccu =
       if h == v then accu+1
-      else accu 
+      else accu
     in do_work newaccu tail
   in do_work 0 l
 
 
-(* 
+(*
 Scalars
 =======
 *)
@@ -156,7 +156,7 @@ let fortran_string_of_bool = function
  | false-> "F\n"
 
 
-let read_int   = read_scalar   int_of_string 
+let read_int   = read_scalar   int_of_string
 let read_int64 = read_scalar Int64.of_string
 let read_float = read_scalar float_of_string
 let read_string= read_scalar (fun (x:string) -> x)
@@ -183,7 +183,7 @@ let write_scalar print_fun group name s =
      close_out out_channel
   end
 
-  
+
 let write_int    = write_scalar print_int
 let write_int64  = write_scalar print_int64
 let write_float  = write_scalar print_float
@@ -199,7 +199,7 @@ Arrays
 *)
 
 type 'a ezfio_data =
-| Ezfio_item of 'a array 
+| Ezfio_item of 'a array
 | Ezfio_data of ('a ezfio_data) array
 
 
@@ -210,13 +210,37 @@ type 'a ezfio_array =
   data : 'a ezfio_data ;
 }
 
+let ezfio_array_of_array ~rank ~dim ~data =
+  assert (rank > 0);
+  let read_1d data nmax =
+    (Ezfio_item (Array.sub data 0 nmax), Array.sub data nmax ((Array.length data) - nmax))
+  in
+  let rec read_nd data = function
+    | m when m<1 -> raise (Failure "dimension should not be <1")
+    | 1 -> read_1d data dim.(0)
+    | m ->
+      let rec do_work accu data = function
+      | 0 -> (Array.of_list (List.rev accu), data)
+      | n ->
+        let (newlist,rest) = read_nd data (m-1) in
+        do_work (newlist::accu) rest (n-1)
+      in
+      let (data,rest) = do_work [] data dim.(m-1) in
+      (Ezfio_data data,rest)
+  in
+  let (result,_) = read_nd data rank in
+  { rank= rank;
+    dim=  dim;
+    data=result;
+  }
+
 
 let ezfio_array_of_list ~rank ~dim ~data =
   assert (rank > 0);
   let read_1d data nmax =
     let rec do_work accu data = function
     | 0 -> (Array.of_list (List.rev accu), data)
-    | n -> 
+    | n ->
       begin
         match data with
         | x::rest -> do_work (x::accu) rest (n-1)
@@ -237,8 +261,8 @@ let ezfio_array_of_list ~rank ~dim ~data =
         do_work (newlist::accu) rest (n-1)
       in
       let (data,rest) = do_work [] data dim.(m-1) in
-      (Ezfio_data data,rest) 
-  in    
+      (Ezfio_data data,rest)
+  in
   let (result,_) = read_nd data rank in
   { rank= rank;
     dim=  dim;
@@ -250,12 +274,12 @@ let ezfio_array_of_list ~rank ~dim ~data =
 let ezfio_get_element { rank=r ; dim=d ; data=data } coord =
   (*assert ((List.length coord) == r);*)
   let rec do_work buffer = function
-  | [c] -> 
+  | [c] ->
     begin match buffer with
     | Ezfio_item buffer -> buffer.(c)
     | Ezfio_data buffer -> raise (Failure "Error in ezfio_get_element")
     end
-  | c::tail -> 
+  | c::tail ->
     begin match buffer with
     | Ezfio_item buffer -> raise (Failure "Error in ezfio_get_element")
     | Ezfio_data buffer -> do_work buffer.(c) tail
@@ -299,7 +323,7 @@ Read
 
 let read_rank in_channel =
     let trimmed_line = String.trim (input_line in_channel) in
-    int_of_string trimmed_line 
+    int_of_string trimmed_line
 
 
 let read_dimensions in_channel =
@@ -317,7 +341,7 @@ let read_array type_conversion group name : 'a ezfio_array =
   let in_filename = (Filename.concat !ezfio_filename @@ Filename.concat group name) ^ ".gz" in
   let in_channel = Unix.open_process_in ("zcat "^in_filename) in
   (* Read rank *)
-  let rank = read_rank in_channel                                                             
+  let rank = read_rank in_channel
   (* Read dimensions *)
   and dimensions = read_dimensions in_channel
   in
@@ -334,7 +358,7 @@ let read_array type_conversion group name : 'a ezfio_array =
       let rec read_nd = function
         | m when m<1 -> raise (Failure "dimension should not be <1")
         | 1 -> read_1d dimensions.(0)
-        | m -> 
+        | m ->
           let rec do_work accu = function
           | 0 -> Array.of_list (List.rev accu)
           | n ->
@@ -342,19 +366,19 @@ let read_array type_conversion group name : 'a ezfio_array =
             do_work (newlist::accu) (n-1)
           in
           Ezfio_data (do_work [] dimensions.(m-1))
-      in    
+      in
       let result = {
          rank = rank ;
          dim = dimensions ;
          data = read_nd rank ;
-      }  
-      in 
+      }
+      in
       match Unix.close_process_in in_channel with
         | Unix.WEXITED _ -> result
-        | _ -> failwith ("Failed in reading compressed file "^in_filename)   
+        | _ -> failwith ("Failed in reading compressed file "^in_filename)
   end
 
-  
+
 let read_int_array    = read_array          int_of_string
 let read_int64_array  = read_array        Int64.of_string
 let read_float_array  = read_array        float_of_string
@@ -375,7 +399,7 @@ let write_array print_fun group name a =
   let out_channel = Unix.open_process_out command in
   let { rank=rank ; dim=dimensions ; data=data } = a in
   let data = flattened_ezfio a in
-  begin                                                                                       
+  begin
      (* Write rank *)
      Printf.fprintf out_channel "%3d\n" rank;
      (* Write dimensions *)
@@ -384,7 +408,7 @@ let write_array print_fun group name a =
      Array.iter (print_fun out_channel) data;
      match Unix.close_process_out out_channel with
       | Unix.WEXITED _ -> ()
-      | _ -> failwith ("Failed writing compressed file "^out_filename)   
+      | _ -> failwith ("Failed writing compressed file "^out_filename)
   end
 
 

src/f_types.py

@@ -27,7 +27,7 @@ format= {
  'integer'         : ["'(I20)'", "%20d"],
  'real'            : ["'(E24.15)'","%24.15E"],
  'double precision': ["'(E24.15)'","%24.15E"],
- 'logical'         : ["'(L)'","%c"],
+ 'logical'         : ["'(L1)'","%c"],
  'character*(*)'   : ["'(A)'","%s"]
  }
 

src/groups.py

@@ -49,8 +49,8 @@ for group in list(groups.keys()):
     command_py = command
     dims_py = str(dims)
     for g in list(groups.keys()):
-      command_py = command_py.replace(g,'self.'+g)
-      dims_py = dims_py.replace(g,'self.'+g)
+      command_py = re.sub("(\W)"+g, r"\1self."+g, command_py)
+      dims_py = dims_py.replace("(\W)"+g,r'\1self.'+g)
     var = var.lower()
     group = group.lower()
     strdims = tuple(['('+str(x)+')' for x in dims])
@@ -107,7 +107,7 @@ for group in list(groups.keys()):
       declar_loop = declar_loop[:-1]
       for k,d in enumerate(dims):
         dims_loop += "  dims("+str(k+1)+") = "+str(d)+"\n"
-        dims_loop_py += "    dims["+str(k)+"] = "+str(d)+"\n"
+        dims_loop_py += "    dims["+str(k)+"] = int("+str(d)+")\n"
       for k,d in enumerate(dims):
         copy_loop += k*" "+"  do i"+str(k+1)+"=1,"+str(d)+'\n'
       copy_loop += (k+1)*" "+"  %(var)s ("

src/groups_templates.py

@@ -58,23 +58,23 @@ BEGIN_PROVIDER [ %(type)s, %(group)s_%(var)s ]
 
 END_PROVIDER
 
-subroutine ezfio_set_%(group)s_%(var)s(%(var)s)
+subroutine ezfio_set_%(group)s_%(var)s(v)
   implicit none
   BEGIN_DOC
 ! Sets the %(group)s/%(var)s attribute
   END_DOC
-  %(type_set)s :: %(var)s
-  call ezfio_write_%(type_short)s(path_%(group)s,'%(var)s',%(var)s)
+  %(type_set)s :: v
+  call ezfio_write_%(type_short)s(path_%(group)s,'%(var)s',v)
   FREE %(group)s_%(var)s
 end subroutine
 
-subroutine ezfio_get_%(group)s_%(var)s(%(var)s)
+subroutine ezfio_get_%(group)s_%(var)s(v)
   implicit none
   BEGIN_DOC
 ! Gets the %(group)s/%(var)s attribute
   END_DOC
-  %(type)s :: %(var)s
-  %(var)s = %(group)s_%(var)s
+  %(type)s :: v
+  v = %(group)s_%(var)s
 end subroutine
 
 subroutine ezfio_has_%(group)s_%(var)s(result)
@@ -111,30 +111,30 @@ BEGIN_PROVIDER [ %(type)s, %(group)s_%(var)s, %(dims)s ]
 
 END_PROVIDER
 
-subroutine ezfio_set_%(group)s_%(var)s(%(var)s)
+subroutine ezfio_set_%(group)s_%(var)s(v)
   implicit none
   BEGIN_DOC
 ! Sets the %(group)s/%(var)s attribute
   END_DOC
-  %(type_set)s :: %(var)s (*)
+  %(type_set)s :: v (*)
   integer :: rank, dim_max, i
   integer :: dims(10)
   rank = %(rank)s
   character*(1024) :: message
 %(dims_loop)s
   call ezfio_write_array_%(type_short)s(path_%(group)s,'%(var)s', &
-   rank,dims,%(dim_max)s,%(var)s)
+   rank,dims,%(dim_max)s,v)
   FREE %(group)s_%(var)s
 end subroutine
 
-subroutine ezfio_get_%(group)s_%(var)s(%(var)s)
+subroutine ezfio_get_%(group)s_%(var)s(v)
   implicit none
   BEGIN_DOC
 ! Gets the %(group)s/%(var)s attribute
   END_DOC
-  %(type)s, intent(out) :: %(var)s (*)
+  %(type)s, intent(out) :: v (*)
   character*(1024) :: message
-  %(var)s(1: %(dim_max)s ) = reshape ( %(group)s_%(var)s, (/ %(dim_max)s /) )
+  v(1: %(dim_max)s ) = reshape ( %(group)s_%(var)s, (/ %(dim_max)s /) )
 end subroutine
 
 subroutine ezfio_has_%(group)s_%(var)s(result)
@@ -163,13 +163,13 @@ BEGIN_PROVIDER [ %(type)s, %(group)s_%(var)s ]
  %(group)s_%(var)s = %(expr)s
 END_PROVIDER
 
-subroutine ezfio_get_%(group)s_%(var)s(%(var)s)
+subroutine ezfio_get_%(group)s_%(var)s(v)
   implicit none
   BEGIN_DOC
 ! Gets the %(group)s/%(var)s attribute
   END_DOC
-  %(type)s, intent(out) :: %(var)s
-  %(var)s = %(group)s_%(var)s
+  %(type)s, intent(out) :: v
+  v = %(group)s_%(var)s
 end
 
 subroutine ezfio_free_%(group)s_%(var)s()

src/libezfio_util.irp.f

@@ -220,11 +220,9 @@ subroutine ezfio_read_array_%(type_short)s(dir,fil,rank,dims,dim_max,dat)
     
     allocate (buffer(dim_max))
     read(libezfio_iunit,'(A)') buffer(1:dim_max)
-    !$OMP PARALLEL DO PRIVATE(i)
     do i=1,dim_max
       read(buffer(i),%(fmt)s) dat(i)
     enddo
-    !$OMP END PARALLEL DO
     deallocate(buffer)
     call libezfio_closez(trim(l_filename),'r')
     return
@@ -262,12 +260,10 @@ subroutine ezfio_write_array_%(type_short)s(dir,fil,rank,dims,dim_max,dat)
     write(libezfio_iunit,'(30(I20,X))') dims(1:rank)
     close(unit=libezfio_iunit)
     allocate (buffer(dim_max))
-    !$OMP PARALLEL DO PRIVATE(i)
     do i=1,dim_max
       write(buffer(i)(1:24), %(fmt)s) dat(i)
       buffer(i)(25:25) = ACHAR(10)
     enddo
-    !$OMP END PARALLEL DO
     call libezfio_reopenz_unformatted(trim(l_filename(1)),'wb',err)
     write(libezfio_iunit) buffer
     call libezfio_closez(trim(l_filename(1)),'w')

src/test.py

@@ -44,7 +44,7 @@ values = []
 isize = 5
 EZFIO.open_read_ao_two_int()
 indices,values = EZFIO.read_buffer(isize)
-print indices
-print values
+print(indices)
+print(values)
 EZFIO.close_read_ao_two_int()
 

version

@@ -1 +1 @@
-VERSION=2.0.1
+VERSION=2.0.7