From 8234a2aea4d45c75d73d9cf85f1e13a3fc68ff74 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@gmx.com>
Date: Wed, 12 Jul 2017 00:11:34 +0200
Subject: [PATCH 1/3] Revert "Add hostname in temporary filename (problem on
 clusters)"

---
 Bash/ezfio.sh           | 22 +++++------
 C/.empty                |  0
 Makefile                |  2 +-
 bin/archive_ezfio.py    |  2 +-
 configure.py            |  7 ++--
 src/Makefile            | 87 ++++++++++++++++++-----------------------
 src/f_types.py          |  2 +-
 src/groups.py           |  9 -----
 src/groups_templates.py | 68 ++++++++++++--------------------
 src/libezfio_file.irp.f | 10 ++---
 src/libezfio_util.irp.f | 17 +++-----
 11 files changed, 91 insertions(+), 135 deletions(-)
 delete mode 100644 C/.empty

diff --git a/Bash/ezfio.sh b/Bash/ezfio.sh
index 991688d..9d36360 100644
--- a/Bash/ezfio.sh
+++ b/Bash/ezfio.sh
@@ -4,7 +4,7 @@ EZFIO_ROOT=$( cd $(dirname "${BASH_SOURCE}")/..  ; pwd -P )
 
 function _ezfio_py()
 {
-  python "${EZFIO_ROOT}/Python/ezfio.py" $@
+  python ${EZFIO_ROOT}/Python/ezfio.py $@
 }
 
 
@@ -84,11 +84,11 @@ function _ezfio_set_file()
 {
   _require_first_argument $@ || return 1
 
-  if [[ ! -d "$1" ]]
+  if [[ ! -d $1 ]]
   then
-    mkdir -p "$1" || return 1
+    mkdir -p $1 || return 1
   fi
-  export EZFIO_FILE="$1"
+  export EZFIO_FILE=$1
   _ezfio_info "Set file ${EZFIO_FILE}"
   return 0
 }
@@ -106,12 +106,12 @@ function _ezfio_has()
   _require_ezfio_file        || return 1
   _require_first_argument $@ || return 1
   
-  if [[ ! -d "${EZFIO_FILE}/${1,,}" ]]
+  if [[ ! -d ${EZFIO_FILE}/${1,,} ]]
   then
       return 1
   fi
   
-  if [[ -z "$2" ]]
+  if [[ -z $2 ]]
   then
       return 0
   fi
@@ -123,14 +123,14 @@ function _ezfio_get()
 {
   _require_ezfio_file        || return 1
 
-  if [[ -z "$1" ]] 
+  if [[ -z $1 ]] 
   then
     ls ${EZFIO_FILE} && return 0 || return 1
   fi
 
-  if [[ -z "$2" ]]
+  if [[ -z $2 ]]
   then
-      ls "${EZFIO_FILE}/${1,,}" && return 0 || return 1
+      ls ${EZFIO_FILE}/${1,,} && return 0 || return 1
   fi
 
   _ezfio_py get $@ && return 0 || return 1
@@ -142,11 +142,11 @@ function _ezfio_set()
   _require_first_argument  $@ || return 1
   _require_second_argument $@ || return 2
 
-  if [[ -z "$3" ]]
+  if [[ -z $3 ]]
   then
     _ezfio_py set $@ || return 1
   else
-    echo "$3" | _ezfio_py set "$1" "$2" || return 1
+    echo $3 | _ezfio_py set $1 $2 || return 1
   fi
   return 0
 }
diff --git a/C/.empty b/C/.empty
deleted file mode 100644
index e69de29..0000000
diff --git a/Makefile b/Makefile
index 88b078f..5ac6182 100644
--- a/Makefile
+++ b/Makefile
@@ -28,7 +28,7 @@ include make.config
 .PHONY: default clean veryclean archive 
 
 default: make.config
-	cd src && BUILD_SYSTEM=make $(MAKE)
+	cd src && $(MAKE)
 
 clean:
 	- bash -c "[[ -f lib/libezfio.a ]] && rm $$PWD/lib/*"
diff --git a/bin/archive_ezfio.py b/bin/archive_ezfio.py
index cb09c9f..82a5140 100755
--- a/bin/archive_ezfio.py
+++ b/bin/archive_ezfio.py
@@ -37,7 +37,7 @@ def main():
     f_name = f[4:]
     try:
       exec """d['%s'] = ezfio.%s"""%(f_name,f_name)
-    except IOError:
+    except:
       if do_verbose:
         print "%-40s [%5s]"%(f_name, "Empty")
     else:
diff --git a/configure.py b/configure.py
index 0f86bb3..86e8773 100755
--- a/configure.py
+++ b/configure.py
@@ -26,7 +26,7 @@ d_default = {
   "FCFLAGS" : '-O2',
   "RANLIB" : 'ranlib',
   "AR" : 'ar',
-  "BUILD_SYSTEM" : 'make'
+  "NINJA" : 'ninja',
 }
 
 CONFIG_FILES=' '.join([ os.path.join("config",x) for x in os.listdir('config') if x != '.empty'])
@@ -112,7 +112,7 @@ rule build_libezfio_a
    description = Building libezfio.a
 
 rule build_libezfio_irp_a
-   command = cp lib/libezfio.a lib/libezfio_irp.a ; {RANLIB} lib/libezfio_irp.a
+   command = cp lib/libezfio.a lib/libezfio_irp.a ; {AR} dv lib/libezfio_irp.a irp_stack.irp.o > /dev/null ; {RANLIB} lib/libezfio_irp.a
    description = Building libezfio_irp.a
 
 rule build_python
@@ -141,4 +141,5 @@ build Ocaml/ezfio.ml: build_ocaml | lib/libezfio.a
 
 
 if __name__ == '__main__':
-	create_build_ninja()
+
+    create_build_ninja()
diff --git a/src/Makefile b/src/Makefile
index 66cdeb5..91f9ae6 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -1,71 +1,60 @@
-.EXPORT_ALL_VARIABLES:
+#   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      
+#   scemama@irsamc.ups-tlse.fr
+
+DEFAULT_TARGET: all
+
 include ../make.config
+export
 
-# Dark magic below modify with caution!
-# "You are Not Expected to Understand This"
-#                     .
-#           /^\     .
-#      /\   "V",
-#     /__\   I      O  o
-#    //..\\  I     .
-#    \].`[/  I
-#    /l\/j\  (]    .  O
-#   /. ~~ ,\/I          .
-#   \\L__j^\/I       o
-#    \/--v}  I     o   .
-#    |    |  I   _________
-#    |    |  I c(`       ')o
-#    |    l  I   \.     ,/
-#  _/j  L l\_!  _//^---^\\_
+include irpf90.make
 
+irpf90.make: $(wildcard *.irp.f) ../config/* 
+	$(IRPF90)
 
-ifeq ($(BUILD_SYSTEM),ninja)
-	BUILD_FILE=IRPF90_temp/build.ninja
-	IRPF90FLAGS += -j
-else ifeq ($(BUILD_SYSTEM),make)
-	BUILD_FILE=IRPF90_temp/build.make
-	BUILD_SYSTEM += -j
-else
-DUMMY:
-	$(error 'Wrong BUILD_SYSTEM: $(BUILD_SYSTEM)')
-endif
-
-define run_and_touch
-        $(BUILD_SYSTEM) -C $(dir $(1) ) -f $(notdir $(1) ) $(addprefix $(CURDIR)/, $(2)) && touch $(2)
-endef
-
-export PYTHONPATH:=$(CURDIR):$(PYTHONPATH)
-
+include ../version
 
 .PHONY: static all
 
 all: static ../Python/ezfio.py ../Ocaml/ezfio.ml
+
 static: ../lib/libezfio.a ../lib/libezfio_irp.a
 
 ../lib/libezfio.a: IRPF90_temp/irpf90.a
 	rm -f ../lib/libezfio.a
-	cp  IRPF90_temp/irpf90.a ../lib/libezfio.a
+	$(AR) cru ../lib/libezfio.a $(OBJ1)
 	$(RANLIB) ../lib/libezfio.a
 
-#No more irp_stack
 ../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
+	$(RANLIB) ../lib/libezfio_irp.a
 
-../Python/ezfio.py: ../lib/libezfio.a
+../Python/ezfio.py:
 	python create_python.py
 
-../Ocaml/ezfio.ml: ../lib/libezfio.a
+../Ocaml/ezfio.ml:
 	python create_ocaml.py
 
-IRPF90_temp/irpf90.a: $(BUILD_FILE)
-	$(call run_and_touch, $<, $@)
 
-$(BUILD_FILE): $(shell find .  -maxdepth 2 -path ./IRPF90_temp -prune -o -name '*.irp.f' -print) ../config/*
-	$(IRPF90) $(IRPF90FLAGS)
-
-clean:
-	rm -f -- $(BUILD_FILE) $(shell find IRPF90_temp -type f \( -name "*.o" -o -name "*.mod" -name "*.a" \)  -delete;)
-	rm -f ../lib/libezfio.a ../lib/libezfio_irp.a
-
-veryclean: clean
-	rm -rf IRPF90_temp/ IRPF90_man/ irpf90_entities dist tags
diff --git a/src/f_types.py b/src/f_types.py
index b70bfd2..d1c5d43 100644
--- a/src/f_types.py
+++ b/src/f_types.py
@@ -27,7 +27,7 @@ format= {
  'integer'         : ["'(I20)'", "%20d"],
  'real'            : ["'(E24.15)'","%24.15E"],
  'double precision': ["'(E24.15)'","%24.15E"],
- 'logical'         : ["'(L1)'","%c"],
+ 'logical'         : ["'(L)'","%c"],
  'character*(*)'   : ["'(A)'","%s"]
  }
 
diff --git a/src/groups.py b/src/groups.py
index 27f69c8..83dd175 100644
--- a/src/groups.py
+++ b/src/groups.py
@@ -40,9 +40,6 @@ print >>file_py, """
   version = property(fset=None,fget=get_version)
 """%(v)
 
-file_c = open("../C/ezfio.h","w")
-print >>file_c, c_header
-
 import sys
 
 for group in groups.keys():
@@ -80,7 +77,6 @@ for group in groups.keys():
               'group': group,
               'dims': strdims}
         print attributes%d
-        print >>file_c, attributes_c%d
         print >>file_py, attributes_py%d
       else:
         d = { 'type': type,
@@ -100,7 +96,6 @@ for group in groups.keys():
             'dims_py': dims_py,
             'dims': dims }
       print buffered%d
-      print >>file_c, buffered_c%d
       print >>file_py, buffered_py%d
     else:
       dims_loop = ''
@@ -147,9 +142,5 @@ for group in groups.keys():
             'declar_loop' : declar_loop}
       print attributes_arr%d
       print >>file_py, attributes_arr_py%d
-      print >>file_c, attributes_arr_c%d
 
-print >>file_c, c_footer
 file_py.close()
-file_c.close()
-
diff --git a/src/groups_templates.py b/src/groups_templates.py
index 1150088..4e14c24 100644
--- a/src/groups_templates.py
+++ b/src/groups_templates.py
@@ -239,48 +239,38 @@ end
 #---------
 
 attributes_c = """
-void ezfio_set_%(group)s_%(var)s(%(ctype)s %(var)s)
+void ezfio_set_%(group)s_%(var)s(%(type)s %(var)s)
 {
   ezfio_set_%(group)s_%(var)s_(&%(var)s);
 }
-
-void ezfio_get_%(group)s_%(var)s(%(ctype)s *%(var)s)
-{
-  ezfio_get_%(group)s_%(var)s_(%(var)s);
-}
-
-int ezfio_has_%(group)s_%(var)s()
-{
-  ezfio_has_%(group)s_%(var)s_();
-}
 """
 
-attributes_arr_c = """
-void ezfio_set_%(group)s_%(var)s(%(ctype)s %(var)s)
-{
-  ezfio_set_%(group)s_%(var)s_(&%(var)s);
-}
-
-void ezfio_get_%(group)s_%(var)s(%(ctype)s *%(var)s)
-{
-  ezfio_get_%(group)s_%(var)s_(%(var)s);
-}
-
-int ezfio_has_%(group)s_%(var)s()
-{
-  ezfio_has_%(group)s_%(var)s_();
-}
-"""
-
-calculated_c = attributes_c
-
-c_header = """#ifndef EZFIO_H\n#define EZFIO_H
-
-#include <string.h>
+c_header = """
+#ifndef EZFIO_H
+#define EZFIO_H
 
 #ifdef __cplusplus
 extern "C" {
 #endif
+"""
+
+c_footer = """
+#ifdef  __cplusplus
+}
+#endif
+#endif
+"""
+
+
+file_h = [c_header]
+file_h +=[ """
+void ezfio_set_file_(char* filename, long filename_size);
+
+void ezfio_read_buffer_(int* indices,double* values, int* isize);
+void ezfio_write_buffer_(int* indices,double* values, int* isize);
+"""]
+
+file_c = [ """
 
 typedef struct
 {
@@ -292,7 +282,7 @@ void ezfio_set_file(char* filename)
 {
   long len;
   len = strlen(filename);
-  ezfio_set_file_(filename,len);
+  ezfio_set_file_(filename,mlen);
 }
 
 sparse ezfio_read_buffer(int isize)
@@ -307,15 +297,7 @@ void ezfio_write_buffer(sparse data, int isize)
   ezfio_write_buffer_(data.indices,data.values,&isize);
 }
 
-"""
-
-c_footer = """
-#ifdef  __cplusplus
-}
-#endif
-#endif
-"""
-
+""" ]
 
 
 
diff --git a/src/libezfio_file.irp.f b/src/libezfio_file.irp.f
index 9334a2a..860eb8e 100644
--- a/src/libezfio_file.irp.f
+++ b/src/libezfio_file.irp.f
@@ -128,16 +128,16 @@ logical function exists(path)
   character*(*) :: path
   character*(32) :: V
   inquire(file=trim(path)//'/.version',exist=exists)
-!  if (exists) then
-!    open(libezfio_iunit,file=trim(path)//'/.version')
-!    read(libezfio_iunit,*) V
-!    close(libezfio_iunit)
+  if (exists) then
+    open(libezfio_iunit,file=trim(path)//'/.version')
+    read(libezfio_iunit,*) V
+    close(libezfio_iunit)
 !   integer :: char_to_version
 !   if (char_to_version(V) > char_to_version(libezfio_version)) then
 !     call ezfio_error(irp_here, 'This file was generated with version '//trim(V)//&
 !     '  but the current installed version is '//trim(libezfio_version)//'')
 !   endif
-!  endif
+  endif
 end function
 
 subroutine ezfio_set_file(filename_in)
diff --git a/src/libezfio_util.irp.f b/src/libezfio_util.irp.f
index 1ab88b4..3d6a9b0 100644
--- a/src/libezfio_util.irp.f
+++ b/src/libezfio_util.irp.f
@@ -23,21 +23,14 @@
 !   scemama@irsamc.ups-tlse.fr
 
  BEGIN_PROVIDER [ integer, PID ]
-&BEGIN_PROVIDER [ character*(256), PID_str ]
+&BEGIN_PROVIDER [ character*(8), PID_str ]
   implicit none
   BEGIN_DOC
   ! Current process ID
   END_DOC
   integer                        :: getpid
-  character*(240) :: hostname
   PID = getpid()
   write(PID_str,'(I8.8)') PID
-  call HOSTNM(hostname)
-  write(PID_str,'(A,''.'',I8.8,X)') trim(hostname), PID
-  PID_str = trim(PID_str)
-  print *,  PID_str
-  call sleep(1)
-
 END_PROVIDER
 
 logical function ezfio_exists(path)
@@ -82,7 +75,7 @@ subroutine libezfio_openz(filename,mode,err)
  character*(*)                  :: filename, mode
  character*(1024)               :: fifo
  integer                        :: err
- fifo = trim(filename)//'.'//trim(PID_str)
+ fifo = trim(filename)//'.'//PID_str
  err=1
  
  if (mode(1:1) == 'r') then
@@ -104,7 +97,7 @@ subroutine libezfio_closez(filename,mode)
   END_DOC
  character*(*)                  :: filename, mode
  character*(1024)               :: fifo
- fifo = trim(filename)//'.'//trim(PID_str)
+ fifo = trim(filename)//'.'//PID_str
  if (mode(1:1) == 'w') then
    close(unit=libezfio_iunit)
    call system('gzip -c < '//trim(fifo)//' > '//trim(filename))
@@ -148,7 +141,7 @@ subroutine ezfio_write_%(type_short)s(dir,fil,dat)
   if (libezfio_read_only) then
     call ezfio_error(irp_here,'Read-only file.')
   endif
-  l_filename(1)=trim(dir)//'/.'//fil//'.'//trim(PID_str)
+  l_filename(1)=trim(dir)//'/.'//fil//'.'//PID_str
   l_filename(2)=trim(dir)//'/'//fil
   open(unit=libezfio_iunit,file=l_filename(1),form='FORMATTED',action='WRITE')
   write(libezfio_iunit,%(fmt)s) dat
@@ -223,7 +216,7 @@ subroutine ezfio_write_array_%(type_short)s(dir,fil,rank,dims,dim_max,dat)
   if (libezfio_read_only) then
     call ezfio_error(irp_here,'Read-only file.')
   endif
-  l_filename(1)=trim(dir)//'/.'//fil//trim(PID_str)//'.gz'
+  l_filename(1)=trim(dir)//'/.'//fil//PID_str//'.gz'
   l_filename(2)=trim(dir)//'/'//fil//'.gz'
   
   err = 0

From c826c47c13abd188fd73843bfdafd576fd55b0bc Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@gmx.com>
Date: Wed, 12 Jul 2017 00:18:23 +0200
Subject: [PATCH 2/3] Add hostname in temporary filename

 Problem on KNL clusters
---
 src/libezfio_util.irp.f | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/libezfio_util.irp.f b/src/libezfio_util.irp.f
index 3d6a9b0..a23ca35 100644
--- a/src/libezfio_util.irp.f
+++ b/src/libezfio_util.irp.f
@@ -29,8 +29,12 @@
   ! Current process ID
   END_DOC
   integer                        :: getpid
+  character*(240)                :: hostname
   PID = getpid()
   write(PID_str,'(I8.8)') PID
+  call HOSTNM(hostname)
+  write(PID_str,'(A,''.'',I8.8,X)') trim(hostname), PID
+  PID_str = trim(PID_str)
 END_PROVIDER
 
 logical function ezfio_exists(path)
@@ -75,7 +79,7 @@ subroutine libezfio_openz(filename,mode,err)
  character*(*)                  :: filename, mode
  character*(1024)               :: fifo
  integer                        :: err
- fifo = trim(filename)//'.'//PID_str
+ fifo = trim(filename)//'.'//trim(PID_str)
  err=1
  
  if (mode(1:1) == 'r') then
@@ -97,7 +101,7 @@ subroutine libezfio_closez(filename,mode)
   END_DOC
  character*(*)                  :: filename, mode
  character*(1024)               :: fifo
- fifo = trim(filename)//'.'//PID_str
+ fifo = trim(filename)//'.'//trim(PID_str)
  if (mode(1:1) == 'w') then
    close(unit=libezfio_iunit)
    call system('gzip -c < '//trim(fifo)//' > '//trim(filename))
@@ -141,7 +145,7 @@ subroutine ezfio_write_%(type_short)s(dir,fil,dat)
   if (libezfio_read_only) then
     call ezfio_error(irp_here,'Read-only file.')
   endif
-  l_filename(1)=trim(dir)//'/.'//fil//'.'//PID_str
+  l_filename(1)=trim(dir)//'/.'//fil//'.'//trim(PID_str)
   l_filename(2)=trim(dir)//'/'//fil
   open(unit=libezfio_iunit,file=l_filename(1),form='FORMATTED',action='WRITE')
   write(libezfio_iunit,%(fmt)s) dat
@@ -216,7 +220,7 @@ subroutine ezfio_write_array_%(type_short)s(dir,fil,rank,dims,dim_max,dat)
   if (libezfio_read_only) then
     call ezfio_error(irp_here,'Read-only file.')
   endif
-  l_filename(1)=trim(dir)//'/.'//fil//PID_str//'.gz'
+  l_filename(1)=trim(dir)//'/.'//fil//trim(PID_str)//'.gz'
   l_filename(2)=trim(dir)//'/'//fil//'.gz'
   
   err = 0

From fc447ed41e7502ac4fdd8bc3fb5fe757c626ac51 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@gmx.com>
Date: Wed, 12 Jul 2017 01:49:13 +0200
Subject: [PATCH 3/3] 8 - 256

---
 src/libezfio_util.irp.f | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/libezfio_util.irp.f b/src/libezfio_util.irp.f
index a23ca35..3a3a573 100644
--- a/src/libezfio_util.irp.f
+++ b/src/libezfio_util.irp.f
@@ -23,7 +23,7 @@
 !   scemama@irsamc.ups-tlse.fr
 
  BEGIN_PROVIDER [ integer, PID ]
-&BEGIN_PROVIDER [ character*(8), PID_str ]
+&BEGIN_PROVIDER [ character*(256), PID_str ]
   implicit none
   BEGIN_DOC
   ! Current process ID