Update tree.

dcaliste · dcaliste · commit c16a076b9341 · 2015-06-02T10:05:50.000+02:00
diff --git a/ChangeLog b/ChangeLog
@@ -1,6 +1,7 @@
-* Fri Nov 25 2011 Yann Pouillon <yann.pouillon@ehu.es> 1.0.4
+* Thu Sep 19 2013 Yann Pouillon <yann.pouillon@ehu.es> and Damien Caliste <damien.caliste@cea.fr> 1.0.4
 - Upgrade configure.ac to correct different badly written autoconf tests.
 - Modify NetCDF detection for enhanced results.
+- Add support for parallel I/O introduced in NetCDF 4.
 
 * Mon Mar 29 2010 Damien Caliste <damien.caliste@cea.fr> 1.0.3
 - Correct configure.ac and Makefile.am for aclocal to always run with its
diff --git a/config/etsf/template.Makefile.am b/config/etsf/template.Makefile.am
@@ -9,12 +9,20 @@ else
 module_DATA = etsf_io.@MODULE_EXT@
 endif
 
-AM_FCFLAGS = -I$(top_builddir)/src/low_level -I$(srcdir) -I@NETCDF_CFLAGS@
+CLEANFILES = $(module_DATA)
 
-libetsf_io_a_SOURCES = etsf_io.f90
+if HAVE_PARALLEL_IO
+NETCDF_WRAPPERS = $(top_builddir)/src/low_level/netcdf4_wrappers.o
+else
+NETCDF_WRAPPERS = $(top_builddir)/src/low_level/netcdf3_wrappers.o
+endif
 
-libetsf_io_a_LIBADD = $(top_builddir)/src/low_level/etsf_io_low_level.o
+AM_FCFLAGS = -I$(top_builddir)/src/low_level -I$(srcdir) @NETCDF_INCLUDES@
+
+libetsf_io_a_SOURCES = etsf_io.f90
 
+libetsf_io_a_LIBADD = $(top_builddir)/src/low_level/etsf_io_low_level.o \
+	$(NETCDF_WRAPPERS)
 
 #dependencies
 etsf_io.o: etsf_io.f90 \
diff --git a/config/etsf/template.tests_init b/config/etsf/template.tests_init
@@ -20,9 +20,9 @@ contains
     type(etsf_io_low_error), intent(in) :: error
     
     if (lstat) then
-      write(*, "(A,A,A,A)") "== ", name, repeat(" ", 68 - len(name)), "OK     =="
+      write(*, "(A,A,A,A)") "== ", name, repeat(" ", 78 - len(name)), "OK     =="
     else
-      write(*, "(A,A,A,A)") "== ", name, repeat(" ", 68 - len(name)), "Failed =="
+      write(*, "(A,A,A,A)") "== ", name, repeat(" ", 78 - len(name)), "Failed =="
       call etsf_io_low_error_handle(error)
     end if
   end subroutine tests_write_status
diff --git a/config/etsf/template.utils_Makefile.am b/config/etsf/template.utils_Makefile.am
@@ -16,7 +16,9 @@ else
 module_DATA = etsf_io_file.@MODULE_EXT@ etsf_io_tools.@MODULE_EXT@
 endif
 
-AM_FCFLAGS = -I$(top_builddir)/src/low_level -I$(top_builddir)/src/group_level  -I@NETCDF_CFLAGS@
+CLEANFILES = $(module_DATA)
+
+AM_FCFLAGS = -I$(top_builddir)/src/low_level -I$(top_builddir)/src/group_level @NETCDF_INCLUDES@
 
 libetsf_io_utils_a_SOURCES = etsf_io_file.f90 \
 	etsf_io_tools.f90
diff --git a/configure.ac b/configure.ac
@@ -78,7 +78,7 @@ AC_ARG_WITH([netcdf-libs],
   AS_HELP_STRING([--with-netcdf-libs],
     [NetCDF link flags.]),
   [ac_netcdf_libs="$withval"],
-  [ac_netcdf_libs=""])
+  [ac_netcdf_libs="-lnetcdff -lnetcdf"])
 AC_ARG_WITH([netcdf-prefix],
   AS_HELP_STRING([--with-netcdf-prefix],
     [Prefix directory where to look for NetCDF components.]),
@@ -133,6 +133,24 @@ if test "$withnetcdf" = "no" ; then
   AC_MSG_ERROR(["No 'NetCDF' library found."])
 fi
 
+dnl Check whether NetCDF has the comm argument for parallel IO
+AC_MSG_CHECKING([for parallel IO with NetCDF])
+FCFLAGS_SVG="$FCFLAGS"
+LIBS_SVG="$LIBS"
+FCFLAGS="$FCFLAGS $ac_netcdf_incs"
+LIBS="$ac_netcdf_libs $LIBS"
+AC_LINK_IFELSE([
+program main
+  use netcdf
+  integer :: s, ncid
+  s = nf90_open(path = "", mode = NF90_NOWRITE, ncid = ncid, comm = 1, info = 1)
+end program main
+], withpio="yes", withpio="no")
+AC_MSG_RESULT([$withpio])
+LIBS="$LIBS_SVG"
+FCFLAGS="$FCFLAGS_SVG"
+AM_CONDITIONAL(HAVE_PARALLEL_IO, test "$withpio" = "yes")
+
 dnl Test if only the library must be built
 ac_build_tutorials="no"
 AC_ARG_ENABLE(build-tutorials,
diff --git a/debian/changelog b/debian/changelog
@@ -1,7 +1,40 @@
+etsf-io (1.0.4-1) unstable; urgency=low
+
+  [ Damien Caliste ]
+  * New minor upstream release with parallel IO support introduced by NetCDF 4.
+
+ -- Sylvestre Ledru <sylvestre@debian.org>  Thu, 19 Sep 2013 10:50:37 +0200
+
+etsf-io (1.0.3-5) unstable; urgency=low
+
+  [ Damien Caliste ]
+  * Standards-Version updated to version 3.9.4
+  * Add a -fPIC compilation flag to allow to build .so libraries
+    from the static libraries of ETSF_IO.
+
+ -- Sylvestre Ledru <sylvestre@debian.org>  Tue, 19 Feb 2013 10:46:37 +0100
+
+etsf-io (1.0.3-4) unstable; urgency=low
+
+  [ Sylvestre Ledru ]
+  * Team upload
+  * Man page added
+  * Lintian warning removed
+
+  [ Damien Caliste ]
+  * Standards-Version updated to version 3.9.2
+  * Add a missing dependency for the devel package on NetCDF
+    (Closes: #618168, #615652)
+  * Add a pkg-config configuration file for ease of use.
+
+ -- Sylvestre Ledru <sylvestre@debian.org>  Sat, 19 Nov 2011 13:58:37 +0100
+
 etsf-io (1.0.3-3) unstable; urgency=low
 
+  * Team upload
   * Remove myself from uploaders
   * Standards-Version updated to version 3.9.1
+
    [ Damien Caliste ]
   * Correct wrong copyright notice (LP: #676077).
 
diff --git a/debian/compat b/debian/compat
@@ -0,0 +1 @@
+5
diff --git a/debian/control b/debian/control
@@ -4,7 +4,7 @@ Priority: optional
 Maintainer: Debian Science Team <debian-science-maintainers@lists.alioth.debian.org>
 Uploaders:  Damien Caliste <damien.caliste@cea.fr>
 Build-Depends: debhelper (>= 5), cdbs, autotools-dev, gfortran, libnetcdf-dev, texinfo
-Standards-Version: 3.9.1
+Standards-Version: 3.9.4
 Homepage: http://www.etsf.eu/resources/software/libraries_and_tools
 Vcs-Svn: svn://svn.debian.org/svn/debian-science/packages/etsf-io/
 Vcs-Browser: http://svn.debian.org/viewsvn/debian-science/packages/etsf-io/
@@ -51,7 +51,7 @@ Description: Developer documentation API and tutorials for ETSF_IO
 Package: libetsf-io-dev
 Section: libdevel
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}, libnetcdf-dev
 Suggests: libetsf-io-doc
 Description: Static libraries and Fortran module files of ETSF_IO
  ETSF_IO is a library of F90 routines to read/write the ETSF file format.
diff --git a/debian/etsf-io.manpages b/debian/etsf-io.manpages
@@ -0,0 +1 @@
+debian/tmp/usr/share/man/man1/etsf_io.1
diff --git a/debian/etsf_io.pc b/debian/etsf_io.pc
@@ -0,0 +1,13 @@
+prefix=/usr
+exec_prefix=${prefix}
+libdir=${exec_prefix}/lib
+includedir=${prefix}/include
+fc=gfortran
+fcflags=-I${includedir}
+
+Name: etsf_io
+Description: ETSF_IO library, read / write library for NetCDF electronic structure files
+Version: 1.0.4
+Libs: -L${libdir} -letsf_io
+# To be activated later when Debian upgrade to NetCDF 4.2 or later.
+#Requires: netcdf-fortran
diff --git a/debian/etsf_io_utils.pc b/debian/etsf_io_utils.pc
@@ -0,0 +1,12 @@
+prefix=/usr
+exec_prefix=${prefix}
+libdir=${exec_prefix}/lib
+includedir=${prefix}/include
+fc=gfortran
+fcflags=-I${includedir}
+
+Name: etsf_io_utils
+Description: ETSF_IO library, read / write library for NetCDF electronic structure files
+Version: 1.0.4
+Libs: -L${libdir} -letsf_io_utils
+Requires: etsf_io
diff --git a/debian/libetsf-io-dev.install b/debian/libetsf-io-dev.install
@@ -1,2 +1,4 @@
 debian/tmp/usr/include/*
 debian/tmp/usr/lib
+debian/etsf_io.pc /usr/lib/pkgconfig
+debian/etsf_io_utils.pc /usr/lib/pkgconfig
diff --git a/debian/rules b/debian/rules
@@ -1,11 +1,10 @@
 #!/usr/bin/make -f
-# Copyright 2010 Damien Caliste <damien.caliste@cea.fr>
+# Copyright 2010-2013 Damien Caliste <damien.caliste@cea.fr>
 
 include /usr/share/cdbs/1/rules/debhelper.mk
 include /usr/share/cdbs/1/class/autotools.mk
-include /usr/share/cdbs/1/rules/simple-patchsys.mk
 
-DEB_CONFIGURE_USER_FLAGS := --docdir=\$${prefix}/share/doc/libetsf-io-doc --with-moduledir=\$${includedir}
+DEB_CONFIGURE_USER_FLAGS := --docdir=\$${prefix}/share/doc/libetsf-io-doc --with-moduledir=\$${includedir} FCFLAGS="-O2 -fPIC"
 DEB_MAKE_INSTALL_TARGET  := install DESTDIR=$(DEB_DESTDIR)
 DEB_INSTALL_DOCS_etsf-io := -XTODO
 DEB_INSTALL_DOCS_libetsf-io-doc := -XAUTHORS -XREADME -XNEWS -XTODO
diff --git a/debian/watch b/debian/watch
@@ -1,4 +1,4 @@
 version=3
-opts=filenamemangle=s/.*etsf_io-(.*).tar_.gz/etsf-io_$1.orig.tar.gz/,downloadurlmangle=s/tar_/tar/ \
-  http://www.etsf.eu/resources/software/libraries_and_tools/etsfio_history \
-  http://www.etsf.eu/sites/default/files/etsf_io-(.*)\.tar_\.gz
+opts=filenamemangle=s/.*etsf_io-(.*).tar_?.gz/etsf-io_$1.orig.tar.gz/,downloadurlmangle=s/tar_/tar/ \
+  http://www.etsf.eu/resources/software/libraries_and_tools \
+  /system/files/etsf_io-(.*)\.tar\.gz
diff --git a/doc/etsf_io.1 b/doc/etsf_io.1
@@ -1,91 +1,52 @@
-
-.\"                                      Hey, EMACS: -*- nroff -*-
-.\" First parameter, NAME, should be all caps
-.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
-.\" other parameters are allowed: see man(7), man(1)
-.TH "ETSF_IO" "1" "Feb 22, 2011"
-.\" Please adjust this date whenever revising the manpage.
-.\"
-.\" Some roff macros, for reference:
-.\" .nh        disable hyphenation
-.\" .hy        enable hyphenation
-.\" .ad l      left justify
-.\" .ad b      justify to both left and right margins
-.\" .nf        disable filling
-.\" .fi        enable filling
-.\" .br        insert line break
-.\" .sp <n>    insert n+1 empty lines
-.\" for manpage-specific macros, see man(7)
+.\" It was generated by help2man 1.40.4.
+.\" then modified by Damien Caliste.
+.TH ETSF_IO "1" "November 2011" "etsf_io" "User Commands"
 .SH NAME
-etsf_io \- a command-line tool to handle ETSF files
+ETSF_IO library \- manual page for etsf_io command line tool
+
 .SH SYNOPSIS
 .B etsf_io
-.B [-h
-.B ]
-.B [-a
-.I action
-.B ]
-.B [-i
-.I file
-.B ]
-.B [-f
-.I flag
-.B ]
-.B [-o
-.I file
-.B ]
-.B [arguments
-.B ]
+[\fI-h | -a action\fR] [[\fI-i file\fR]...] [[\fI-f flag\fR]...]
+[\-o file] [arguments]
+
+.SH DESCRIPTION
 .PP
-This manual page documents briefly the
-.B etsf_io
-commands. It is a software to handle NetCDF files following ETSF specifications.
-.SH OPTIONS
+Handle ETSF files, see \fB\-\-action\fR option.
 .PP
-This program follows the usual GNU command line syntax, with long
-options starting with two dashes (`-').
+\fB\-h\fR \fB\-\-help\fR             : show this little help.
 .PP
-A complete list of options is included below.
-    
-.TP
-.B \-h, \-\-help
-show this little help.
-
-.TP
-.B \-a, \-\-action value
-give the action to perform. Possible action may be:
- * 'merge' to gather several files that have been splitted.
- * 'content' to get the name of specifications the file matches.
- * 'check' to check the validity of the file against specifications.
-
-.TP
-.B \-o, \-\-output-file file
-give the path to the output ETSF file in case of merge action.
-
-.TP
-.B \-i, \-\-input-file file
-give the path for an input file. This option can be used one or several times.
-
-.TP
-.B \-l, \-\-list
-when action is check, it give the list of available flags.
-
-.TP
-.B \-f, \-\-flag value
-give a flag name (get valid names from -l option).
-
+\fB\-a\fR \fB\-\-action\fR value     : give the action to perform.
+.PP
+Possible action may be:
+.PP
+         * 'merge' to gather several files that have been splitted.
+.PP
+         * 'content' to get the name of specifications the file matches.
+.PP
+         * 'check' to check the validity of the file against specifications.
+.PP
+\fB\-o\fR \fB\-\-output\-file\fR file : give the path to the output ETSF file.
+.PP
+\fB\-i\fR \fB\-\-input\-file\fR file  : give the path for an input file.
+                        This option can be used one or several times.
+.PP
+\fB\-l\fR \fB\-\-list\fR             : when action is check, it give the list of available flags.
+.PP
+\fB\-f\fR \fB\-\-flag\fR value       : give a flag name (get valid names from \fB\-l\fR option).
 
 .SH EXAMPLES
-Merge three files, etsf_io -a merge -i file1.nc -i file2.nc -i file3.nc -o output.nc
-
-Get the contents of file test.nc, etsf_io -a content test.nc
-
-Get the list of flags for validity checks, etsf_io -a check -l
-
-Checks with two flags, etsf_io -a check -f flag1 -f flag2 test.nc
+Merge three files, etsf_io \fB\-a\fR merge \fB\-i\fR file1.nc \fB\-i\fR file2.nc
+\fB\-i\fR file3.nc \fB\-o\fR output.nc
+.PP
+Get the contents of file test.nc, etsf_io \fB\-a\fR content test.nc
+.PP
+Get the list of flags for validity checks, etsf_io \fB\-a\fR check \fB\-l\fR
+.PP
+Checks with two flags, etsf_io \fB\-a\fR check \fB\-f\fR flag1 \fB\-f\fR flag2 test.nc
 
 .SH AUTHOR
-etsf_io was written by Damien Caliste.
+ETSF_IO library was written by Damien Caliste, Valerio Oleva, Yann Pouillon
+and Matthieu Verstaete.
 .PP
 This manual page was written by Damien Caliste <damien.caliste@cea.fr>.
-    
+
diff --git a/src/low_level/Makefile.am b/src/low_level/Makefile.am
@@ -14,9 +14,16 @@ endif
 
 AM_FCFLAGS = @NETCDF_INCLUDES@ -I$(srcdir)
 
-libetsf_io_low_level_a_SOURCES = etsf_io_low_level.f90
+if HAVE_PARALLEL_IO
+NETCDF_WRAPPERS = netcdf4_wrappers.f90
+else
+NETCDF_WRAPPERS = netcdf3_wrappers.f90
+endif
 
+libetsf_io_low_level_a_SOURCES = etsf_io_low_level.f90 \
+	$(NETCDF_WRAPPERS)
 
+CLEANFILES = $(module_DATA)
 
 #dependencies
 etsf_io_low_level.o: etsf_io_low_level.f90 \
@@ -27,3 +34,5 @@ etsf_io_low_level.o: etsf_io_low_level.f90 \
 	write_routines_auto.f90
 
 etsf_io_low_level.@MODULE_EXT@ ETSF_IO_LOW_LEVEL.@MODULE_EXT@: etsf_io_low_level.o
+
+netcdf3_wrappers.o netcdf4_wrappers.o: etsf_io_low_level.o
diff --git a/src/low_level/etsf_io_low_level.f90 b/src/low_level/etsf_io_low_level.f90
diff --git a/src/low_level/netcdf3_wrappers.f90 b/src/low_level/netcdf3_wrappers.f90
diff --git a/src/low_level/netcdf4_wrappers.f90 b/src/low_level/netcdf4_wrappers.f90
diff --git a/src/low_level/write_routines.f90 b/src/low_level/write_routines.f90
diff --git a/tests/group_level/Makefile.am b/tests/group_level/Makefile.am
diff --git a/tests/group_level/tests_module.f90 b/tests/group_level/tests_module.f90
diff --git a/tests/low_level/Makefile.am b/tests/low_level/Makefile.am

-Original file line number
+Diff line change
@@ @@ -1,6 +1,7 @@ @@
 -* Fri Nov 25 2011 Yann Pouillon <[email protected]> 1.0.4
 +* Thu Sep 19 2013 Yann Pouillon <[email protected]> and Damien Caliste <[email protected]> 1.0.4
 - Upgrade configure.ac to correct different badly written autoconf tests.
 - Modify NetCDF detection for enhanced results.
 +- Add support for parallel I/O introduced in NetCDF 4.
 * Mon Mar 29 2010 Damien Caliste <[email protected]> 1.0.3
 - Correct configure.ac and Makefile.am for aclocal to always run with its
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+debian/tmp/usr/share/man/man1/etsf_io.1`