Merge pull request #10 from scemama/master

Add hostname in temporary filename (problem on clusters)

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
 }

Makefile

@@ -28,7 +28,7 @@ include make.config
 .PHONY: default clean veryclean archive 
 
 default: make.config
-	cd src && $(MAKE)
+	cd src && BUILD_SYSTEM=make $(MAKE)
 
 clean:
 	- bash -c "[[ -f lib/libezfio.a ]] && rm $$PWD/lib/*"

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:
+    except IOError:
       if do_verbose:
         print "%-40s [%5s]"%(f_name, "Empty")
     else:

configure.py

@@ -26,7 +26,7 @@ d_default = {
   "FCFLAGS" : '-O2',
   "RANLIB" : 'ranlib',
   "AR" : 'ar',
-  "NINJA" : 'ninja',
+  "BUILD_SYSTEM" : 'make'
 }
 
 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 ; {AR} dv lib/libezfio_irp.a irp_stack.irp.o > /dev/null ; {RANLIB} lib/libezfio_irp.a
+   command = cp lib/libezfio.a lib/libezfio_irp.a ; {RANLIB} lib/libezfio_irp.a
    description = Building libezfio_irp.a
 
 rule build_python
@@ -141,5 +141,4 @@ build Ocaml/ezfio.ml: build_ocaml | lib/libezfio.a
 
 
 if __name__ == '__main__':
-
+	create_build_ninja()
-    create_build_ninja()

src/Makefile

@@ -1,60 +1,71 @@
-#   EZFIO is an automatic generator of I/O libraries
+.EXPORT_ALL_VARIABLES:
-#   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
 
-include irpf90.make
+# 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\_!  _//^---^\\_
 
-irpf90.make: $(wildcard *.irp.f) ../config/* 
-	$(IRPF90)
 
-include ../version
+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)
+
 
 .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
-	$(AR) cru ../lib/libezfio.a $(OBJ1)
+	cp  IRPF90_temp/irpf90.a ../lib/libezfio.a
 	$(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:
+../Python/ezfio.py: ../lib/libezfio.a
 	python create_python.py
 
-../Ocaml/ezfio.ml:
+../Ocaml/ezfio.ml: ../lib/libezfio.a
 	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

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

@@ -40,6 +40,9 @@ 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():
@@ -77,6 +80,7 @@ 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,
@@ -96,6 +100,7 @@ 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 = ''
@@ -142,5 +147,9 @@ 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()
+

src/groups_templates.py

@@ -239,38 +239,48 @@ end
 #---------
 
 attributes_c = """
-void ezfio_set_%(group)s_%(var)s(%(type)s %(var)s)
+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_();
+}
 """
 
-c_header = """
+attributes_arr_c = """
-#ifndef EZFIO_H
+void ezfio_set_%(group)s_%(var)s(%(ctype)s %(var)s)
-#define EZFIO_H
+{
+  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>
 
 #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
 {
@@ -282,7 +292,7 @@ void ezfio_set_file(char* filename)
 {
   long len;
   len = strlen(filename);
-  ezfio_set_file_(filename,mlen);
+  ezfio_set_file_(filename,len);
 }
 
 sparse ezfio_read_buffer(int isize)
@@ -297,7 +307,15 @@ void ezfio_write_buffer(sparse data, int isize)
   ezfio_write_buffer_(data.indices,data.values,&isize);
 }
 
-""" ]
+"""
+
+c_footer = """
+#ifdef  __cplusplus
+}
+#endif
+#endif
+"""
+
 
 
 

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
+!  if (exists) then
-    open(libezfio_iunit,file=trim(path)//'/.version')
+!    open(libezfio_iunit,file=trim(path)//'/.version')
-    read(libezfio_iunit,*) V
+!    read(libezfio_iunit,*) V
-    close(libezfio_iunit)
+!    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)

src/libezfio_util.irp.f

@@ -23,14 +23,21 @@
 !   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
   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)
@@ -75,7 +82,7 @@ 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 +104,7 @@ 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 +148,7 @@ 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 +223,7 @@ 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