debian/0000775000000000000000000000000012271635053007174 5ustar debian/copyright0000664000000000000000000000543212251427211011124 0ustar ADIOS is freely available under the terms of the BSD license given below. Copyright (c) 2008 - 2009. UT-BATTELLE, LLC. All rights reserved. Copyright (c) 2008 - 2009. Georgia Institute of Technology. All rights reserved. Produced at the National Center for Computational Sciences in Oak Ridge National Laboratory. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the disclaimer (as noted below) in the documentation and/or other materials provided with the distribution. * Neither the name of the UT-BATTELLE, LLC nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Additional BSD Notice 1. This notice is required to be provided under our contract with the U.S. Department of Energy (DOE). This work was produced at Oak Ridge National Laboratory under Contract No. DEAC05-00OR22725 with the DOE. 2. Neither the United States Government nor UT-BATTELLE, LLC nor any of their employees, makes any warranty, express or implied, or assumes any liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately-owned rights. 3. Also, reference herein to any specific commercial products, process, or services by trade name, trademark, manufacturer or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or UT-BATTELLE, LLC. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or UT-BATTELLE, LLC, and shall not be used for advertising or product endorsement purposes. debian/libadios-bin.dirs0000664000000000000000000000002012251427211012374 0ustar /etc/adios/skel debian/libadios-dev.install0000664000000000000000000000011112251427211013110 0ustar usr/include/* usr/lib/*/*.a usr/lib/*/python/* /usr/share/pyshared/adios debian/changelog0000664000000000000000000001176112271631704011053 0ustar adios (1.5.0-1ubuntu7) trusty; urgency=low * Add more netcdf fixes. -- Daniel T Chen Mon, 27 Jan 2014 23:09:51 -0500 adios (1.5.0-1ubuntu6) trusty; urgency=low * Fix netcdf underlinkage for ppc64el. -- Daniel T Chen Mon, 27 Jan 2014 17:42:42 -0500 adios (1.5.0-1ubuntu5) trusty; urgency=low * Use pkg-config to pull in the necessary libs for ppc64el. -- Daniel T Chen Mon, 27 Jan 2014 13:59:27 -0500 adios (1.5.0-1ubuntu4) trusty; urgency=low * Rearrange yet another missing lib to link for Ubuntu/ppc64el. -- Daniel T Chen Mon, 27 Jan 2014 13:08:57 -0500 adios (1.5.0-1ubuntu3) trusty; urgency=low * Add another missing lib to link for Ubuntu/ppc64el. -- Daniel T Chen Mon, 27 Jan 2014 12:53:17 -0500 adios (1.5.0-1ubuntu2) trusty; urgency=low * Rearrange missing libs to link for Ubuntu/ppc64el. -- Daniel T Chen Mon, 27 Jan 2014 12:19:40 -0500 adios (1.5.0-1ubuntu1) trusty; urgency=low * Use dh-autoreconf for newer arches. * Add missing curl lib to link (and its build-dependency aligned with Debian sid's build), resolving FTBFS on Ubuntu. -- Daniel T Chen Mon, 27 Jan 2014 11:38:45 -0500 adios (1.5.0-1) unstable; urgency=medium * New upstream. * Standards-Version: 3.9.5 * Include latest config.{sub,guess} * New watch file. * Create libadios-bin for binaries. -- Alastair McKinstry Mon, 09 Dec 2013 15:21:31 +0000 adios (1.4.1-1) unstable; urgency=low * New upstream. * update config.{sub,guess} for the AArch64 port. Closes: #727312. * Make python code python2-3 agnostic. -- Alastair McKinstry Thu, 24 Oct 2013 19:27:47 +0100 adios (1.3-11) unstable; urgency=low * Comment out lustre support (and remove dependency) as Wheezy will not ship with lustre-dev. Closes: #699262. * Standards-Version: 3.9.4. No changes required. * Update debhelper dependency to 9 for multiarch. -- Alastair McKinstry Tue, 29 Jan 2013 16:18:53 +0000 adios (1.3-10) unstable; urgency=low * Patch from Simon Ruderich for hardening flags. Closes: #663925, #663978. -- Alastair McKinstry Wed, 21 Mar 2012 10:20:55 +0000 adios (1.3-9) unstable; urgency=low * Move to Standards-Version: 3.9.3. No changes required. * Fixes to build with hardening flags. * Patch from Pino Toscano to fix FTBFS on Hurd. Closes: #660562. * Fix netcdf linking. Closes: #662995 * Change to Multiarch: foreign now we ship arch-dependent binaries in libadios-dev. -- Alastair McKinstry Fri, 09 Mar 2012 17:34:24 +0000 adios (1.3-8) unstable; urgency=low * Add -Wl,--as-needed to remove unnecessary dependencies. * Mult-Arch support. - No longer ship adios_config.flags. Instead recommend users use pkg-config, which Does The Right Thing in multi-arch. - adios_ -- Alastair McKinstry Wed, 14 Sep 2011 15:43:29 +0100 adios (1.3-7) unstable; urgency=low * Rename gpp to adiosxml2h. (Will be renamed by upstream in next release) Closes: #639257. * Move DH_COMPAT=8 -- Alastair McKinstry Thu, 25 Aug 2011 18:17:09 +0100 adios (1.3-6) unstable; urgency=low * LAM uses mpicc.lam, not mpicc. -- Alastair McKinstry Tue, 16 Aug 2011 17:18:36 +0100 adios (1.3-5) unstable; urgency=low * MPI_IN_PLACE patch is needed for adiso_mpi_lustre.c too, even though Lustre is not used in LAM environment. Sigh. -- Alastair McKinstry Tue, 16 Aug 2011 09:57:26 +0100 adios (1.3-4) unstable; urgency=low * Patch to stop compilation with dummy MPI if real parallel HDF5 is used. Closes: #637893. * make use of MPI_IN_PLACE conditional on MPI_IN_PLACE existing, as its not present in LAM MPI. Also, conditionally use mpicc. -- Alastair McKinstry Mon, 15 Aug 2011 17:57:34 +0100 adios (1.3-3) unstable; urgency=low * Make lustre support conditional to intel,amd64, powerpc archs. -- Alastair McKinstry Mon, 15 Aug 2011 16:56:23 +0100 adios (1.3-2) unstable; urgency=low * Set CC=mpicc to ensure new C code gets built with MPI. Closes: #637714. * Add lustre support. -- Alastair McKinstry Sun, 14 Aug 2011 16:12:14 +0100 adios (1.3-1) unstable; urgency=low * New upstream release. * Ignore -little flag in configure to support SH4. Thanks to Nobuhiro Iwamatsu; Closes: #635908. -- Alastair McKinstry Tue, 09 Aug 2011 20:32:58 +0100 adios (1.2.1-2) unstable; urgency=low * Use MPIFC=mpif77 during build, to work on LAM-based MPI systems. -- Alastair McKinstry Sun, 10 Jul 2011 00:33:10 +0100 adios (1.2.1-1) unstable; urgency=low * Initial release. (Closes: #624371). -- Alastair McKinstry Wed, 27 Apr 2011 19:16:12 +0100 debian/libadios-dev.dirs0000664000000000000000000000003212251427211012405 0ustar /usr/share/pyshared/adios debian/libadios-dev.docs0000664000000000000000000000004412251427211012377 0ustar KNOWN_BUGS AUTHORS TODO README NEWS debian/patches/0000775000000000000000000000000012271634707010630 5ustar debian/patches/nompi_flag.patch0000664000000000000000000000172112251427211013751 0ustar Description: bp2h5 pulls in a dummy mph.h which breaks if you use a real MPI-enabled HDF5. Author: Alastair McKinstry Last-Updated: 2011-08-15 Forwarded: no Index: adios-1.3/utils/bp2h5/Makefile.in =================================================================== --- adios-1.3.orig/utils/bp2h5/Makefile.in 2011-08-15 17:04:18.000000000 +0100 +++ adios-1.3/utils/bp2h5/Makefile.in 2011-08-15 17:04:22.000000000 +0100 @@ -312,7 +312,7 @@ INCLUDES = $(all_includes) -I$(top_builddir)/src AUTOMAKE_OPTIONS = no-dependencies bp2h5_SOURCES = bp2h5.c -bp2h5_CPPFLAGS = -DH5_USE_16_API $(ADIOSLIB_EXTRA_CPPFLAGS) $(ADIOSREADLIB_SEQ_CPPFLAGS) $(ADIOSREADLIB_SEQ_CFLAGS ) $(HDF5_CPPFLAGS) +bp2h5_CPPFLAGS = -DH5_USE_16_API $(ADIOSLIB_EXTRA_CPPFLAGS) $(ADIOSREADLIB_INT_CPPFLAGS) $(HDF5_CPPFLAGS) bp2h5_LDFLAGS = $(ADIOSREADLIB_SEQ_LDFLAGS) $(HDF5_LDFLAGS) bp2h5_LDADD = $(top_builddir)/src/libadiosread_nompi.a \ $(ADIOSREADLIB_SEQ_LDADD) $(HDF5_LIBS) debian/patches/debian_paths.patch0000664000000000000000000000673012251427211014264 0ustar Author: Alastair McKinstry Description: Change paths to match Debian and FHS Forwarded: no Last-Updated: 2013-12-09 Index: adios-1.5.0/utils/skel/lib/skel_makefile.py =================================================================== --- adios-1.5.0.orig/utils/skel/lib/skel_makefile.py 2013-12-09 20:26:51.000000000 +0000 +++ adios-1.5.0/utils/skel/lib/skel_makefile.py 2013-12-09 20:26:51.000000000 +0000 @@ -34,7 +34,7 @@ makefile_template_name = '~/.skel/templates/Makefile.default.tpl' makefile_template = open(os.path.expanduser(makefile_template_name), 'r') - include_statement = "" + os.path.dirname (sys.argv[0]) + '/../etc/skel/compiler_fragment.mk' + include_statement = '/etc/adios/skel/compiler_fragment.mk' for template_line in makefile_template: @@ -72,10 +72,10 @@ # Makefile generation no longer depends on the target, just using default here. #makefile_template_name = os.path.dirname (sys.argv[0]) + '/../etc/skel/templates/Makefile.' + platform + '.tpl' - makefile_template_name = os.path.dirname (sys.argv[0]) + '/../etc/skel/templates/Makefile.default.tpl' + makefile_template_name = '/etc/adios/skel/templates/Makefile.default.tpl' makefile_template = open(os.path.expanduser(makefile_template_name), 'r') - include_statement = "" + os.path.dirname (sys.argv[0]) + '/../etc/skel/compiler_fragment.mk' + include_statement = "" + '/etc/adios/skel/compiler_fragment.mk' for template_line in makefile_template: Index: adios-1.5.0/utils/skel/lib/skel_settings.py =================================================================== --- adios-1.5.0.orig/utils/skel/lib/skel_settings.py 2013-12-09 20:26:51.000000000 +0000 +++ adios-1.5.0/utils/skel/lib/skel_settings.py 2013-12-09 20:26:51.000000000 +0000 @@ -54,7 +54,7 @@ skel_settings_dir_name = os.path.expanduser ('~/.skel') if not os.path.exists (skel_settings_dir_name): bindir = os.path.dirname (sys.argv[0]) - shutil.copytree (bindir + '/../etc/skel', skel_settings_dir_name) + shutil.copytree ('/etc/adios/skel', skel_settings_dir_name) print('Created ' + skel_settings_dir_name) Index: adios-1.5.0/utils/gpp/ad_config.py =================================================================== --- adios-1.5.0.orig/utils/gpp/ad_config.py 2013-12-09 20:26:49.000000000 +0000 +++ adios-1.5.0/utils/gpp/ad_config.py 2013-12-09 20:27:16.000000000 +0000 @@ -1,3 +1,4 @@ +#!/usr/bin/env python from __future__ import absolute_import, division, print_function, unicode_literals import xml.dom.minidom import type_mapper Index: adios-1.5.0/utils/gpp/type_mapper.py =================================================================== --- adios-1.5.0.orig/utils/gpp/type_mapper.py 2013-12-09 20:02:59.000000000 +0000 +++ adios-1.5.0/utils/gpp/type_mapper.py 2013-12-09 20:28:56.000000000 +0000 @@ -1,4 +1,4 @@ - +#!/usr/bin/env python c_types = { 'string' : 'string', Index: adios-1.5.0/utils/skel/bin/skel_extract.py =================================================================== --- adios-1.5.0.orig/utils/skel/bin/skel_extract.py 2013-12-09 20:26:49.000000000 +0000 +++ adios-1.5.0/utils/skel/bin/skel_extract.py 2013-12-09 20:56:22.000000000 +0000 @@ -113,7 +113,7 @@ # check the selected fields for field in selected_fields: if not field in keys: - print 'Invalid selection, field ' + field + print('Invalid selection, field ' + field) return #Print the header debian/patches/security.patch0000664000000000000000000000303712251427211013507 0ustar Index: adios.git/utils/bpls/bpls.c =================================================================== --- adios.git.orig/utils/bpls/bpls.c 2013-12-09 18:45:05.000000000 +0000 +++ adios.git/utils/bpls/bpls.c 2013-12-09 18:45:04.000000000 +0000 @@ -374,7 +374,7 @@ #define PRINT_DIMS(str, v, n, loopvar) printf("%s = { ", str); \ - for (loopvar=0; loopvar Description: Make sure bp2ncd is linked against NetCDF. Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=662995 Forwarded: no Last-Updated: 2012-03-09 Index: adios.git/utils/bp2ncd/Makefile.in =================================================================== --- adios.git.orig/utils/bp2ncd/Makefile.in 2013-12-09 18:45:09.000000000 +0000 +++ adios.git/utils/bp2ncd/Makefile.in 2013-12-09 18:45:08.000000000 +0000 @@ -98,12 +98,12 @@ ACLOCAL = @ACLOCAL@ ADIOSLIB_CFLAGS = @ADIOSLIB_CFLAGS@ ADIOSLIB_CPPFLAGS = @ADIOSLIB_CPPFLAGS@ -ADIOSLIB_EXTRA_CPPFLAGS = @ADIOSLIB_EXTRA_CPPFLAGS@ + ADIOSLIB_INT_CFLAGS = @ADIOSLIB_INT_CFLAGS@ ADIOSLIB_INT_CPPFLAGS = @ADIOSLIB_INT_CPPFLAGS@ ADIOSLIB_INT_LDADD = @ADIOSLIB_INT_LDADD@ ADIOSLIB_INT_LDFLAGS = @ADIOSLIB_INT_LDFLAGS@ -ADIOSLIB_LDADD = @ADIOSLIB_LDADD@ +ADIOSLIB_LDADD = @ADIOSLIB_LDADD@ @NETCDF_LIBS@ ADIOSLIB_LDFLAGS = @ADIOSLIB_LDFLAGS@ ADIOSLIB_SEQ_CFLAGS = @ADIOSLIB_SEQ_CFLAGS@ ADIOSLIB_SEQ_CPPFLAGS = @ADIOSLIB_SEQ_CPPFLAGS@ @@ -325,7 +325,7 @@ @USE_PARALLEL_COMPILER_TRUE@bp2ncd_LDFLAGS = $(ADIOSLIB_LDFLAGS) -static-libtool-libs @USE_PARALLEL_COMPILER_FALSE@bp2ncd_LDADD = $(top_builddir)/src/libadios_internal_nompi.a \ @USE_PARALLEL_COMPILER_FALSE@ $(ADIOSLIB_INT_LDADD) -@USE_PARALLEL_COMPILER_TRUE@bp2ncd_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +@USE_PARALLEL_COMPILER_TRUE@bp2ncd_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) EXTRA_DIST = bp2ncd.h all: all-am debian/patches/mpi_in_place.patch0000664000000000000000000000535012251427211014257 0ustar Description: LAM MPI does not have MPI_IN_PLACE, so make its use optional. Author: Alastair McKinstry Last-Updated: 2013-04-10 Forwarded: no Index: adios.git/src/write/adios_mpi_lustre.c =================================================================== --- adios.git.orig/src/write/adios_mpi_lustre.c 2013-12-09 18:44:57.000000000 +0000 +++ adios.git/src/write/adios_mpi_lustre.c 2013-12-09 18:44:57.000000000 +0000 @@ -744,7 +744,11 @@ ,fd->group->name, md->old_pg_root ); MPI_Scatter (offsets, 3, MPI_LONG_LONG +#ifdef MPI_IN_PLACE ,MPI_IN_PLACE, 3, MPI_LONG_LONG +#else + ,offsets, 3, MPI_LONG_LONG +#endif ,0, md->group_comm ); md->b.read_pg_offset = offsets [0]; @@ -838,7 +842,11 @@ else offsets [0] = fd->write_size_bytes; +#ifdef MPI_IN_PLACE MPI_Gather (MPI_IN_PLACE, 1, MPI_LONG_LONG +#else + MPI_Gather (offsets, 1, MPI_LONG_LONG +#endif ,offsets, 1, MPI_LONG_LONG ,0, md->group_comm ); @@ -861,7 +869,11 @@ md->b.pg_index_offset = offsets [md->size - 1] + last_offset; MPI_Scatter (offsets, 1, MPI_LONG_LONG +#ifdef MPI_IN_PLACE ,MPI_IN_PLACE, 1, MPI_LONG_LONG +#else + ,offsets, 1, MPI_LONG_LONG +#endif ,0, md->group_comm ); fd->base_offset = offsets [0]; @@ -1140,7 +1152,11 @@ else offsets [0] = fd->write_size_bytes; +#ifdef MPI_IN_PLACE MPI_Gather (MPI_IN_PLACE, 1, MPI_LONG_LONG +#else + MPI_Gather (offsets, 1, MPI_LONG_LONG +#endif ,offsets, 1, MPI_LONG_LONG ,0, md->group_comm ); @@ -1156,7 +1172,11 @@ md->b.pg_index_offset = offsets [md->size - 1] + last_offset; MPI_Scatter (offsets, 1, MPI_LONG_LONG +#ifdef MPI_IN_PLACE ,MPI_IN_PLACE, 1, MPI_LONG_LONG +#else + ,offsets, 1, MPI_LONG_LONG +#endif ,0, md->group_comm ); fd->base_offset = offsets [0]; debian/patches/python3.patch0000664000000000000000000005013112251427211013241 0ustar Author: Alastair McKinstry Description: Make the python code python2-3 agnostic. Last-Updated:2013-12-09 Forwarded: no Index: adios-1.5.0/utils/skel/bin/skel =================================================================== --- adios-1.5.0.orig/utils/skel/bin/skel 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/utils/skel/bin/skel 2013-12-09 19:59:55.000000000 +0000 @@ -1,5 +1,7 @@ #!/usr/bin/env python +from __future__ import absolute_import, division, print_function, unicode_literals + import sys import os.path @@ -61,7 +63,7 @@ try: config = adios.adiosConfig (args.project + '_skel.xml') except (IOError): - print "Error reading " + args.project + "_skel.xml. Try running skel xml " + args.project + " first." + print( "Error reading " + args.project + "_skel.xml. Try running skel xml " + args.project + " first.")/ return 1 if args.subcommand == 'params': @@ -72,8 +74,8 @@ try: params = skelconf.skelConfig (args.project + '_params.xml') except (IOError): - print "Error reading " + args.project + "_params.xml. Try running skel params " + args.project + " first," - print "then copy the generated " + args.project + "_params.xml.default, and edit to suit your needs." + print("Error reading " + args.project + "_params.xml. Try running skel params " + args.project + " first,") + print("then copy the generated " + args.project + "_params.xml.default, and edit to suit your needs.") return 1 if args.subcommand == 'makefile': @@ -92,7 +94,7 @@ skel_submit.generate_submit_scripts (params) return 0 - print 'Unknown subcommand, exiting.' + print('Unknown subcommand, exiting.') if __name__ == "__main__": Index: adios-1.5.0/utils/skel/bin/skel_extract.py =================================================================== --- adios-1.5.0.orig/utils/skel/bin/skel_extract.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/utils/skel/bin/skel_extract.py 2013-12-09 19:59:55.000000000 +0000 @@ -1,5 +1,6 @@ #!/usr/bin/env python +from __future__ import absolute_import, division, print_function, unicode_literals import argparse import xml.dom.minidom import sys @@ -46,7 +47,7 @@ # check the selected fields for field in selected_fields: if not field in keys: - print 'Invalid selection, field ' + field + print('Invalid selection, field ' + field) return #Print the header Index: adios-1.5.0/utils/skel/lib/skelconf.py =================================================================== --- adios-1.5.0.orig/utils/skel/lib/skelconf.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/utils/skel/lib/skelconf.py 2013-12-09 19:59:55.000000000 +0000 @@ -1,5 +1,5 @@ +from __future__ import absolute_import, division, print_function, unicode_literals import xml.dom.minidom - import skel_settings import skel_have_adios_timing @@ -10,7 +10,7 @@ nodes = doc.childNodes if (nodes.length != 1): - print 'malformed param file, should contain only a single skel-config element' + print('malformed param file, should contain only a single skel-config element') raise SystemExit self.config_node = nodes[0] Index: adios-1.5.0/utils/gpp/ad_config.py =================================================================== --- adios-1.5.0.orig/utils/gpp/ad_config.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/utils/gpp/ad_config.py 2013-12-09 19:59:55.000000000 +0000 @@ -1,3 +1,4 @@ +from __future__ import absolute_import, division, print_function, unicode_literals import xml.dom.minidom import type_mapper @@ -11,7 +12,7 @@ doc = xml.dom.minidom.parse (config_file_name) nodes = doc.childNodes if (nodes.length != 1): - print 'malformed adios config file, should contain only a single adios-config element' + print('malformed adios config file, should contain only a single adios-config element') raise SystemExit self.config_node = nodes[0] @@ -41,7 +42,7 @@ def get_buffer (self): #return the buffer info - print 'get_buffer is not yet implemented' + print('get_buffer is not yet implemented') def get_host_language (self): return self.config_node.getAttribute ('host-language') @@ -100,7 +101,7 @@ # Returns the variable from this group with the specified name, or None def get_var (self, varname): - if self.vardict.has_key (varname): + if varname in self.vardict: return self.vardict [varname] return None @@ -164,7 +165,7 @@ return None else: # place the dimensions in a list and remove the time-index if it is there. - dims = filter (lambda x : x != self.time_index, self.var_node.getAttribute ('dimensions').split(',') ) + dims = [x for x in self.var_node.getAttribute ('dimensions').split(',') if x != self.time_index] cleandims = [] for d in dims: Index: adios-1.5.0/utils/gpp/gpp.py =================================================================== --- adios-1.5.0.orig/utils/gpp/gpp.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/utils/gpp/gpp.py 2013-12-09 19:59:55.000000000 +0000 @@ -1,5 +1,5 @@ #!/usr/bin/env python - +from __future__ import absolute_import, division, print_function, unicode_literals import sys import os @@ -17,10 +17,10 @@ if rv == 0: return 'success' elif rv == 32512: # System unable to find adios_lint command - print "Unable to find adios_lint. Proceeding with code generation." + print("Unable to find adios_lint. Proceeding with code generation.") return 'success' else: - print "gpp.py failed." + print("gpp.py failed.") return 'failure' @@ -235,7 +235,7 @@ # Must be called with one argument, the name of the xml file if len (sys.argv) != 2: - print 'Usage: gpp.py \n' + print('Usage: gpp.py \n') return 1 @@ -256,7 +256,7 @@ elif lang == 'c' or lang == 'cpp': generate_c (config) else: - print "Fatal: Language unknown or unspecified" + print("Fatal: Language unknown or unspecified") raise SystemExit Index: adios-1.5.0/utils/skel/lib/adios.py =================================================================== --- adios-1.5.0.orig/utils/skel/lib/adios.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/utils/skel/lib/adios.py 2013-12-09 19:59:55.000000000 +0000 @@ -1,5 +1,5 @@ +from __future__ import print_function import xml.dom.minidom - import typeMapper class adiosConfig: @@ -12,7 +12,7 @@ doc = xml.dom.minidom.parse (config_file_name) nodes = doc.childNodes if (nodes.length != 1): - print 'malformed adios config file, should contain only a single adios-config element' + print('malformed adios config file, should contain only a single adios-config element') raise SystemExit self.config_node = nodes[0] @@ -47,7 +47,7 @@ def get_buffer (self): #return the buffer info - print 'implement get_buffer' + print('implement get_buffer') def get_host_language (self): return self.host_language @@ -141,7 +141,7 @@ return None else: # place the dimensions in a list and remove the time-index if it is there. - dims = filter (lambda x : x != self.time_index, self.var_node.getAttribute ('dimensions').split(',') ) + dims = [x for x in self.var_node.getAttribute ('dimensions').split(',') if x != self.time_index] cleandims = [] for d in dims: Index: adios-1.5.0/utils/skel/lib/argparse.py =================================================================== --- adios-1.5.0.orig/utils/skel/lib/argparse.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/utils/skel/lib/argparse.py 2013-12-09 19:59:55.000000000 +0000 @@ -81,7 +81,6 @@ 'ZERO_OR_MORE', ] - import copy as _copy import os as _os import re as _re Index: adios-1.5.0/utils/skel/lib/skel_install.py =================================================================== --- adios-1.5.0.orig/utils/skel/lib/skel_install.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/utils/skel/lib/skel_install.py 2013-12-09 19:59:55.000000000 +0000 @@ -1,5 +1,5 @@ #!/usr/bin/env python - +from __future__ import absolute_import, division, print_function, unicode_literals import skel_settings def main(argv=None): Index: adios-1.5.0/utils/skel/lib/skel_makefile.py =================================================================== --- adios-1.5.0.orig/utils/skel/lib/skel_makefile.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/utils/skel/lib/skel_makefile.py 2013-12-09 19:59:55.000000000 +0000 @@ -1,5 +1,7 @@ #!/usr/bin/env python +# from __future__ import absolute_import, division, print_function, unicode_literals +from __future__ import print_function import argparse import os import sys @@ -121,10 +123,10 @@ lang = config.get_host_language () if 'c' == lang or 'C' == lang: - print 'generating C flavored Makefile' + print('generating C flavored Makefile') generate_makefiles_c (params) else: - print 'generating fortran flavored Makefile' + print('generating fortran flavored Makefile') generate_makefiles_fortran (params) Index: adios-1.5.0/utils/skel/lib/skel_params.py =================================================================== --- adios-1.5.0.orig/utils/skel/lib/skel_params.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/utils/skel/lib/skel_params.py 2013-12-09 19:59:55.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/env python +from __future__ import absolute_import, division, print_function, unicode_literals import sys import os import argparse Index: adios-1.5.0/utils/skel/lib/skel_settings.py =================================================================== --- adios-1.5.0.orig/utils/skel/lib/skel_settings.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/utils/skel/lib/skel_settings.py 2013-12-09 19:59:55.000000000 +0000 @@ -1,5 +1,5 @@ #!/usr/bin/env python - +from __future__ import absolute_import, division, print_function import sys import os.path import shutil @@ -20,8 +20,8 @@ continue split_line = line.split('=') if not len (split_line) == 2: - print 'Malformed configuration line: ' + line - print 'Ignoring' + print('Malformed configuration line: ' + line) + print('Ignoring') continue self.settings_dict[split_line[0]] = split_line[1] @@ -55,7 +55,7 @@ if not os.path.exists (skel_settings_dir_name): bindir = os.path.dirname (sys.argv[0]) shutil.copytree (bindir + '/../etc/skel', skel_settings_dir_name) - print 'Created ' + skel_settings_dir_name + print('Created ' + skel_settings_dir_name) def main(argv=None): Index: adios-1.5.0/utils/skel/lib/skel_source.py =================================================================== --- adios-1.5.0.orig/utils/skel/lib/skel_source.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/utils/skel/lib/skel_source.py 2013-12-09 20:01:16.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/env python +from __future__ import absolute_import, division, print_function, unicode_literals import sys import os import argparse @@ -83,25 +84,25 @@ # same program var (as is done by genarray) c_file.write ('\n\n// Scalar declarations') declarations = set() - for v in filter (lambda x : x.is_scalar(), g.get_vars() ): + for v in [x for x in g.get_vars() if x.is_scalar()]: declarations.add (adios.cFormatter.get_declaration (v, params.get_group (g.get_name() ) ) ) for d in declarations: c_file.write (d) # Now the initializations - for v in filter (lambda x : x.is_scalar(), g.get_vars() ): + for v in [x for x in g.get_vars() if x.is_scalar()]: c_file.write (adios.cFormatter.get_initialization (v, params.get_group (g.get_name() ) ) ) c_file.write ('\n\n// Array declarations') declarations = set() - for v in filter (lambda x : not x.is_scalar(), g.get_vars() ): + for v in [x for x in g.get_vars() if not x.is_scalar()]: declarations.add (adios.cFormatter.get_declaration (v, params.get_group (g.get_name() ) ) ) for d in declarations: c_file.write ('\n' + d) - for v in filter (lambda x : not x.is_scalar(), g.get_vars() ): + for v in [x for x in g.get_vars() if not x.is_scalar()]: c_file.write (adios.cFormatter.get_initialization (v, params.get_group (g.get_name() ) ) ) if measure.use_sleep_before_open(): @@ -197,9 +198,9 @@ if measure.use_adios_timing(): - print "Use adios timing" + print("Use adios timing") else: - print "Don't use adios timing" + print("Don't use adios timing") # Detailed reporting disabled, use adios timing instead. @@ -230,7 +231,7 @@ # free the array memory c_file.write ('\n\n// Free the arrays') frees = set() - for v in filter (lambda x : not x.is_scalar(), g.get_vars() ): + for v in [x for x in g.get_vars() if not x.is_scalar()]: frees.add ('\nfree (' + v.get_gwrite() + ');') for f in frees: @@ -307,7 +308,7 @@ # same program var (as is done by genarray) f_file.write ('\n\n! Scalar declarations') declarations = set() - for v in filter (lambda x : x.is_scalar(), g.get_vars() ): + for v in [x for x in g.get_vars() if x.is_scalar()]: declarations.add (adios.fortranFormatter.get_declaration (v, params.get_group (g.get_name() ) ) ) for d in declarations: @@ -315,7 +316,7 @@ f_file.write ('\n\n! Array declarations') declarations = set() - for v in filter (lambda x : not x.is_scalar(), g.get_vars() ): + for v in [x for x in g.get_vars() if not x.is_scalar()]: declarations.add (adios.fortranFormatter.get_declaration (v, params.get_group (g.get_name() ) ) ) for d in declarations: @@ -345,13 +346,13 @@ # For now, just do the numerical values first, then come back and do the more # complicated ones. This won't cover something like a depends on b, b depends on c, # but it will work for the moment - for v in filter (lambda x : x.is_scalar(), g.get_vars() ): + for v in [x for x in g.get_vars() if x.is_scalar()]: #split at the spaces, just print the ones where the third element is a number init_str = adios.fortranFormatter.get_initialization (v, params.get_group (g.get_name() ) ) if init_str.split (None, 2)[2].isdigit(): f_file.write (init_str) - for v in filter (lambda x : x.is_scalar(), g.get_vars() ): + for v in [x for x in g.get_vars() if x.is_scalar()]: #split at the spaces, just print the ones where the third element is a number init_str = adios.fortranFormatter.get_initialization (v, params.get_group (g.get_name() ) ) if not init_str.split (None, 2)[2].isdigit(): @@ -360,7 +361,7 @@ f_file.write ('\n\n! Initialize the arrays') # And the vector initializations - for v in filter (lambda x : not x.is_scalar(), g.get_vars() ): + for v in [x for x in g.get_vars() if not x.is_scalar()]: f_file.write (adios.fortranFormatter.get_initialization (v, params.get_group (g.get_name() ) ) ) @@ -545,7 +546,7 @@ # same program var (as is done by genarray) c_file.write ('\n\n// Scalar declarations') declarations = set() - for v in filter (lambda x : x.is_scalar(), g.get_vars() ): + for v in [x for x in g.get_vars() if x.is_scalar()]: declarations.add (adios.cFormatter.get_declaration (v, params.get_group (g.get_name() ) ) ) for d in declarations: @@ -553,7 +554,7 @@ c_file.write ('\n\n// Array declarations') declarations = set() - for v in filter (lambda x : not x.is_scalar(), g.get_vars() ): + for v in [x for x in g.get_vars() if not x.is_scalar()]: declarations.add (adios.cFormatter.get_declaration (v, params.get_group (g.get_name() ) ) ) for d in declarations: @@ -630,7 +631,7 @@ # free the array memory c_file.write ('\n\n// Free the arrays') frees = set() - for v in filter (lambda x : not x.is_scalar(), g.get_vars() ): + for v in [x for x in g.get_vars() if not x.is_scalar()]: frees.add ('\nfree (' + v.get_gwrite() + ');') for f in frees: Index: adios-1.5.0/utils/skel/lib/skel_submit.py =================================================================== --- adios-1.5.0.orig/utils/skel/lib/skel_submit.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/utils/skel/lib/skel_submit.py 2013-12-09 19:59:56.000000000 +0000 @@ -1,5 +1,5 @@ #!/usr/bin/env python - +from __future__ import absolute_import, division, print_function, unicode_literals import argparse import os Index: adios-1.5.0/utils/skel/lib/skel_xml.py =================================================================== --- adios-1.5.0.orig/utils/skel/lib/skel_xml.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/utils/skel/lib/skel_xml.py 2013-12-09 19:59:56.000000000 +0000 @@ -1,5 +1,6 @@ #!/usr/bin/env python +from __future__ import absolute_import, division, print_function, unicode_literals import argparse import xml.dom.minidom Index: adios-1.5.0/wrappers/numpy/example/ncdf2bp.py =================================================================== --- adios-1.5.0.orig/wrappers/numpy/example/ncdf2bp.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/wrappers/numpy/example/ncdf2bp.py 2013-12-09 19:59:56.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/env python +from __future__ import absolute_import, division, print_function, unicode_literals from adios import * from scipy.io import netcdf import numpy as np Index: adios-1.5.0/wrappers/numpy/test/adios_noxml_test.py =================================================================== --- adios-1.5.0.orig/wrappers/numpy/test/adios_noxml_test.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/wrappers/numpy/test/adios_noxml_test.py 2013-12-09 19:59:57.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/env python +from __future__ import absolute_import, division, print_function, unicode_literals from adios import * import numpy as np @@ -17,7 +18,7 @@ size = 1 rank = 0 groupsize = 4 + 4 + 4 + 8 * 1 * NX -t = np.array(range(NX), dtype=np.float64) +t = np.array(list(range(NX)), dtype=np.float64) set_group_size(fd, groupsize) write_int(fd, "NX", NX) write_int(fd, "size", size) Index: adios-1.5.0/wrappers/numpy/test/adios_read_test.py =================================================================== --- adios-1.5.0.orig/wrappers/numpy/test/adios_read_test.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/wrappers/numpy/test/adios_read_test.py 2013-12-09 19:59:57.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/env python + from adios import * import numpy as np @@ -9,6 +10,6 @@ v = g.var["/temperature"] v.printself() -print v.read() +print(v.read()) f.close() Index: adios-1.5.0/wrappers/numpy/test/adios_write_test.py =================================================================== --- adios-1.5.0.orig/wrappers/numpy/test/adios_write_test.py 2013-12-09 19:59:57.000000000 +0000 +++ adios-1.5.0/wrappers/numpy/test/adios_write_test.py 2013-12-09 19:59:57.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/env python +from __future__ import absolute_import, division, print_function, unicode_literals import adios import numpy as np @@ -9,7 +10,7 @@ size = 1 rank = 0 groupsize = 4 + 4 + 4 + 8 * 1 * NX -t = np.array(range(NX), dtype=np.float64) +t = np.array(list(range(NXi)), dtype=np.float64) adios.set_group_size(fd, groupsize) adios.write_int(fd, "NX", NX) adios.write_int(fd, "size", size) debian/patches/series0000664000000000000000000000016112271505444012036 0ustar sh4.patch mpi_in_place.patch security.patch netcdf-fix.patch python3.patch debian_paths.patch underlinkage.patch debian/patches/sh4.patch0000664000000000000000000000153712251427211012341 0ustar Description: Support for SH-4 Architecture Origin: vendor, http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=635908 Bug-Debian: http://bugs.debian.org/635908 Forwarded: not-needed Author: Nobuhiro Iwamatsu Last-Updated: 2011-08-09 Index: adios-1.4.1/configure =================================================================== --- adios-1.4.1.orig/configure 2013-04-08 19:30:42.000000000 +0100 +++ adios-1.4.1/configure 2013-04-08 19:31:18.000000000 +0100 @@ -7111,7 +7111,7 @@ ;; # Ignore these flags. - -lang* | -lcrt*.o | -lc | -lgcc* | -lSystem | -libmil | -LANG:=* | -LIST:* | -LNO:*) + -lang* | -lcrt*.o | -lc | -lgcc* | -lSystem | -libmil | -LANG:=* | -LIST:* | -little | -LNO:*) ;; -lkernel32) test x"$CYGWIN" != xyes && ac_cv_fc_libs="$ac_cv_fc_libs $ac_arg" debian/patches/errno.patch0000664000000000000000000000265612251427211012773 0ustar Bug-Debian: http://bugs.debian.org/660562 Description: Fix errrno conflict on Hurd-i386. Last-Updated: 2012-02-21 Forwarded: no Author: Pino Toscano --- a/src/adios_error.c +++ b/src/adios_error.c @@ -29,19 +29,19 @@ return aerr; } -void adios_error (enum ADIOS_ERRCODES errno, char *fmt, ...) +void adios_error (enum ADIOS_ERRCODES aerrno, char *fmt, ...) { va_list ap; - adios_errno = (int)errno; + adios_errno = (int)aerrno; va_start(ap, fmt); (void) vsnprintf(aerr, ERRMSG_MAXLEN, fmt, ap); va_end(ap); } -void adios_error_at_line (enum ADIOS_ERRCODES errno, const char* filename, unsigned int linenum, char *fmt, ...) +void adios_error_at_line (enum ADIOS_ERRCODES aerrno, const char* filename, unsigned int linenum, char *fmt, ...) { va_list ap; - adios_errno = (int)errno; + adios_errno = (int)aerrno; va_start(ap, fmt); (void) vsnprintf(aerr, ERRMSG_MAXLEN, fmt, ap); va_end(ap); --- a/src/adios_error.h +++ b/src/adios_error.h @@ -35,8 +35,8 @@ ,err_unspecified }; -void adios_error (enum ADIOS_ERRCODES errno, char *fmt, ...); -void adios_error_at_line (enum ADIOS_ERRCODES errno, const char* filename, unsigned int linenum, char *fmt, ...); +void adios_error (enum ADIOS_ERRCODES aerrno, char *fmt, ...); +void adios_error_at_line (enum ADIOS_ERRCODES aerrno, const char* filename, unsigned int linenum, char *fmt, ...); const char* adios_get_last_errmsg (void); debian/patches/underlinkage.patch0000664000000000000000000007145012271634707014330 0ustar Index: adios-1.5.0/utils/bp2bp/Makefile.am =================================================================== --- adios-1.5.0.orig/utils/bp2bp/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/utils/bp2bp/Makefile.am 2014-01-27 11:38:35.699607836 -0500 @@ -8,7 +8,7 @@ bp2bp_SOURCES = bp2bp.c bp2bp_CPPFLAGS = ${MACRODEFFLAG}ADIOS_USE_READ_API_1 $(ADIOSLIB_CPPFLAGS) $(ADIOSLIB_CFLAGS) $(ADIOSLIB_EXTRA_CPPFLAGS) bp2bp_LDFLAGS = $(ADIOSLIB_LDFLAGS) -bp2bp_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +bp2bp_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) -lcurl #if USE_PARALLEL_COMPILER Index: adios-1.5.0/utils/bp2ncd/Makefile.am =================================================================== --- adios-1.5.0.orig/utils/bp2ncd/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/utils/bp2ncd/Makefile.am 2014-01-27 17:53:15.166901933 -0500 @@ -13,7 +13,7 @@ bp2ncd_CPPFLAGS = $(ADIOSLIB_EXTRA_CPPFLAGS) $(ADIOSLIB_CPPFLAGS) bp2ncd_CFLAGS = $(ADIOSLIB_CFLAGS) bp2ncd_LDFLAGS = $(ADIOSLIB_LDFLAGS) -static-libtool-libs - bp2ncd_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) + bp2ncd_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) else bp2ncd_CPPFLAGS = $(ADIOSLIB_EXTRA_CPPFLAGS) $(ADIOSLIB_INT_CPPFLAGS) $(ADIOSLIB_INT_CFLAGS) bp2ncd_LDFLAGS = $(ADIOSLIB_INT_LDFLAGS) -static-libtool-libs Index: adios-1.5.0/tests/C/Makefile.am =================================================================== --- adios-1.5.0.orig/tests/C/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/tests/C/Makefile.am 2014-01-27 18:00:48.835586527 -0500 @@ -8,7 +8,7 @@ adios_test_c_SOURCES = adios_test_c.c adios_test_c_CPPFLAGS = $(ADIOSLIB_CPPFLAGS) adios_test_c_CFLAGS = $(ADIOSLIB_CFLAGS) -adios_test_c_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +adios_test_c_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) adios_test_c_LDFLAGS = $(ADIOSLIB_LDFLAGS) CLEANFILES = restart.bp Index: adios-1.5.0/tests/Fortran/Makefile.am =================================================================== --- adios-1.5.0.orig/tests/Fortran/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/tests/Fortran/Makefile.am 2014-01-27 23:11:55.568911749 -0500 @@ -10,12 +10,12 @@ adios_test_f_CPPFLAGS = $(ADIOSLIB_CPPFLAGS) adios_test_f_CFLAGS = $(ADIOSLIB_CFLAGS) adios_test_f_LDFLAGS = $(ADIOSLIB_LDFLAGS) -adios_test_f_LDADD = $(top_builddir)/src/libadiosf.a $(ADIOSLIB_LDADD) +adios_test_f_LDADD = $(top_builddir)/src/libadiosf.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) FC=$(MPIFC) FCLINK = \ $(LIBTOOL) --mode=link --tag F77 $(FC) \ - $(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) -o $@ + $(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) $(NETCDF_LIBS) -o $@ EXTRA_DIST = config_fortran.xml Index: adios-1.5.0/tests/bp_read/Makefile.am =================================================================== --- adios-1.5.0.orig/tests/bp_read/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/tests/bp_read/Makefile.am 2014-01-27 23:38:09.768550088 -0500 @@ -14,27 +14,27 @@ genbp_SOURCES = genbp.c genbp_CPPFLAGS = $(ADIOSLIB_CPPFLAGS) genbp_CFLAGS = $(ADIOSLIB_CFLAGS) -genbp_LDADD = $(top_builddir)/src/libadios.a $(top_builddir)/src/libadiosread.a $(ADIOSLIB_LDADD) +genbp_LDADD = $(top_builddir)/src/libadios.a $(top_builddir)/src/libadiosread.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) genbp_LDFLAGS = $(ADIOSLIB_LDFLAGS) if BUILD_FORTRAN bp_read_f_SOURCES = bp_read_f.F90 bp_read_f_CPPFLAGS = $(ADIOSLIB_CPPFLAGS) bp_read_f_CFLAGS = $(ADIOSLIB_CFLAGS) -bp_read_f_LDADD = $(top_builddir)/src/libadiosreadf.a $(ADIOSREADLIB_LDADD) +bp_read_f_LDADD = $(top_builddir)/src/libadiosreadf.a $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) bp_read_f_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) bp_read_f_v1_SOURCES = bp_read_f_v1.F90 bp_read_f_v1_CPPFLAGS = $(ADIOSLIB_CPPFLAGS) bp_read_f_v1_CFLAGS = $(ADIOSLIB_CFLAGS) -bp_read_f_v1_LDADD = $(top_builddir)/src/libadiosreadf_v1.a $(ADIOSREADLIB_LDADD) +bp_read_f_v1_LDADD = $(top_builddir)/src/libadiosreadf_v1.a $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) bp_read_f_v1_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) endif bp_read_c_SOURCES = bp_read_c.c bp_read_c_CPPFLAGS = -DADIOS_USE_READ_API_1 $(ADIOSLIB_CPPFLAGS) bp_read_c_CFLAGS = $(ADIOSLIB_CFLAGS) -bp_read_c_LDADD = $(top_builddir)/src/libadiosread.a $(ADIOSREADLIB_LDADD) +bp_read_c_LDADD = $(top_builddir)/src/libadiosread.a $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) bp_read_c_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) FC=$(MPIFC) @@ -42,7 +42,7 @@ FCLINK = \ $(LIBTOOL) --mode=link --tag F77 $(FC) \ - $(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) -o $@ + $(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) $(NETCDF_LIBS) -o $@ if BUILD_FORTRAN CLEANFILES = *.o bp_read_c bp_read_f genbp read_coords read_phi read_parts_global Index: adios-1.5.0/tests/genarray/Makefile.am =================================================================== --- adios-1.5.0.orig/tests/genarray/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/tests/genarray/Makefile.am 2014-01-27 23:39:10.383799863 -0500 @@ -8,25 +8,25 @@ genarray_SOURCES = genarray.F90 genarray_CPPFLAGS = $(ADIOSLIB_CPPFLAGS) genarray_CFLAGS = $(ADIOSLIB_CFLAGS) -genarray_LDADD = $(top_builddir)/src/libadiosf.a $(ADIOSLIB_LDADD) +genarray_LDADD = $(top_builddir)/src/libadiosf.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) genarray_LDFLAGS = $(ADIOSLIB_LDFLAGS) genarray2D_SOURCES = genarray2D.F90 genarray2D_CPPFLAGS = $(ADIOSLIB_CPPFLAGS) genarray2D_CFLAGS = $(ADIOSLIB_CFLAGS) -genarray2D_LDADD = $(top_builddir)/src/libadiosf.a $(ADIOSLIB_LDADD) +genarray2D_LDADD = $(top_builddir)/src/libadiosf.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) genarray2D_LDFLAGS = $(ADIOSLIB_LDFLAGS) copyarray_SOURCES = copyarray.F90 copyarray_CPPFLAGS = $(ADIOSLIB_CPPFLAGS) copyarray_CFLAGS = $(ADIOSLIB_CFLAGS) -copyarray_LDADD = $(top_builddir)/src/libadiosf.a $(ADIOSLIB_LDADD) +copyarray_LDADD = $(top_builddir)/src/libadiosf.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) copyarray_LDFLAGS = $(ADIOSLIB_LDFLAGS) copyarray2D_SOURCES = copyarray2D.F90 copyarray2D_CPPFLAGS = $(ADIOSLIB_CPPFLAGS) copyarray2D_CFLAGS = $(ADIOSLIB_CFLAGS) -copyarray2D_LDADD = $(top_builddir)/src/libadiosf.a $(ADIOSLIB_LDADD) +copyarray2D_LDADD = $(top_builddir)/src/libadiosf.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) copyarray2D_LDFLAGS = $(ADIOSLIB_LDFLAGS) FC=$(MPIFC) @@ -43,7 +43,7 @@ FCLINK = \ $(LIBTOOL) --mode=link --tag F77 $(FC) \ - $(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) -o $@ + $(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) $(NETCDF_LIBS) -o $@ CLEANFILES = genarray_comm.mod genarray2d_comm.mod gwrite_genarray.fh gread_genarray.fh Index: adios-1.5.0/examples/C/arrays/Makefile.am =================================================================== --- adios-1.5.0.orig/examples/C/arrays/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/examples/C/arrays/Makefile.am 2014-01-27 23:48:47.822199921 -0500 @@ -6,10 +6,10 @@ noinst_PROGRAMS = arrays_write arrays_read arrays_write_SOURCES = arrays_write.c -arrays_write_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +arrays_write_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) arrays_write_LDFLAGS = $(ADIOSLIB_LDFLAGS) arrays_read_SOURCES = arrays_read.c -arrays_read_LDADD = $(top_builddir)/src/libadiosread.a $(ADIOSREADLIB_LDADD) +arrays_read_LDADD = $(top_builddir)/src/libadiosread.a $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) arrays_read_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) CLEANFILES = *.bp Index: adios-1.5.0/examples/C/attributes/Makefile.am =================================================================== --- adios-1.5.0.orig/examples/C/attributes/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/examples/C/attributes/Makefile.am 2014-01-27 23:50:29.738782281 -0500 @@ -8,11 +8,11 @@ attributes_write_SOURCES = attributes_write.c attributes_write_LDADD = $(top_builddir)/src/libadios.a attributes_write_LDFLAGS = $(ADIOSLIB_LDFLAGS) -attributes_write_LDADD += $(ADIOSLIB_LDADD) +attributes_write_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) attributes_read_SOURCES = attributes_read.c attributes_read_LDADD = $(top_builddir)/src/libadiosread.a attributes_read_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) -attributes_read_LDADD += $(ADIOSREADLIB_LDADD) +attributes_read_LDADD += $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) CLEANFILES = *.bp CC=$(MPICC) Index: adios-1.5.0/examples/C/flexpath_arrays/global_range_select/Makefile.am =================================================================== --- adios-1.5.0.orig/examples/C/flexpath_arrays/global_range_select/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/examples/C/flexpath_arrays/global_range_select/Makefile.am 2014-01-27 23:48:13.783323913 -0500 @@ -6,10 +6,10 @@ noinst_PROGRAMS = arrays_write arrays_read arrays_write_SOURCES = arrays_write.c -arrays_write_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +arrays_write_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) arrays_write_LDFLAGS = $(ADIOSLIB_LDFLAGS) arrays_read_SOURCES = arrays_read.c -arrays_read_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +arrays_read_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) arrays_read_LDFLAGS = $(ADIOSLIB_LDFLAGS) CLEANFILES = *.bp Index: adios-1.5.0/examples/C/flexpath_arrays/process_select/Makefile.am =================================================================== --- adios-1.5.0.orig/examples/C/flexpath_arrays/process_select/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/examples/C/flexpath_arrays/process_select/Makefile.am 2014-01-27 23:48:29.310813056 -0500 @@ -6,10 +6,10 @@ noinst_PROGRAMS = arrays_write arrays_read arrays_write_SOURCES = arrays_write.c -arrays_write_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +arrays_write_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) arrays_write_LDFLAGS = $(ADIOSLIB_LDFLAGS) arrays_read_SOURCES = arrays_read.c -arrays_read_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +arrays_read_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) arrays_read_LDFLAGS = $(ADIOSLIB_LDFLAGS) CLEANFILES = *.txt Index: adios-1.5.0/examples/C/global-array-time/Makefile.am =================================================================== --- adios-1.5.0.orig/examples/C/global-array-time/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/examples/C/global-array-time/Makefile.am 2014-01-27 23:46:25.674541402 -0500 @@ -8,19 +8,19 @@ adios_globaltime_SOURCES = adios_globaltime.c adios_globaltime_LDADD = $(top_builddir)/src/libadios.a adios_globaltime_LDFLAGS = $(ADIOSLIB_LDFLAGS) -adios_globaltime_LDADD += $(ADIOSLIB_LDADD) +adios_globaltime_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) adios_globaltime_no_xml_SOURCES = adios_globaltime_no_xml.c adios_globaltime_no_xml_LDADD = $(top_builddir)/src/libadios.a adios_globaltime_no_xml_LDFLAGS = $(ADIOSLIB_LDFLAGS) -adios_globaltime_no_xml_LDADD += $(ADIOSLIB_LDADD) +adios_globaltime_no_xml_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) adios_read_globaltime_SOURCES = adios_read_globaltime.c adios_read_globaltime_LDADD = $(top_builddir)/src/libadiosread.a adios_read_globaltime_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) -adios_read_globaltime_LDADD += $(ADIOSREADLIB_LDADD) +adios_read_globaltime_LDADD += $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) adios_read_globaltime_streaming_SOURCES = adios_read_globaltime_streaming.c adios_read_globaltime_streaming_LDADD = $(top_builddir)/src/libadiosread.a adios_read_globaltime_streaming_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) -adios_read_globaltime_streaming_LDADD += $(ADIOSREADLIB_LDADD) +adios_read_globaltime_streaming_LDADD += $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) CLEANFILES = *.bp CC=$(MPICC) Index: adios-1.5.0/examples/C/global-array/Makefile.am =================================================================== --- adios-1.5.0.orig/examples/C/global-array/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/examples/C/global-array/Makefile.am 2014-01-27 23:50:16.627233737 -0500 @@ -8,43 +8,43 @@ adios_global_SOURCES = adios_global.c adios_global_LDADD = $(top_builddir)/src/libadios.a adios_global_LDFLAGS = $(ADIOSLIB_LDFLAGS) -adios_global_LDADD += $(ADIOSLIB_LDADD) +adios_global_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) adios_global_2files_SOURCES = adios_global_2files.c adios_global_2files_LDADD = $(top_builddir)/src/libadios.a adios_global_2files_LDFLAGS = $(ADIOSLIB_LDFLAGS) -adios_global_2files_LDADD += $(ADIOSLIB_LDADD) +adios_global_2files_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) adios_read_global_SOURCES = adios_read_global.c adios_read_global_LDADD = $(top_builddir)/src/libadiosread.a adios_read_global_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) -adios_read_global_LDADD += $(ADIOSREADLIB_LDADD) +adios_read_global_LDADD += $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) adios_read_writeblock_SOURCES = adios_read_writeblock.c adios_read_writeblock_LDADD = $(top_builddir)/src/libadiosread.a adios_read_writeblock_LDFLAGS = $(ADIOSLIB_LDFLAGS) -adios_read_writeblock_LDADD += $(ADIOSLIB_LDADD) +adios_read_writeblock_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) adios_read_chunk_SOURCES = adios_read_chunk.c adios_read_chunk_LDADD = $(top_builddir)/src/libadiosread.a adios_read_chunk_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) -adios_read_chunk_LDADD += $(ADIOSREADLIB_LDADD) +adios_read_chunk_LDADD += $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) adios_read_gpp_SOURCES = adios_read_gpp.c adios_read_gpp_LDADD = $(top_builddir)/src/libadiosread.a adios_read_gpp_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) -adios_read_gpp_LDADD += $(ADIOSREADLIB_LDADD) +adios_read_gpp_LDADD += $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) adios_global_no_xml_SOURCES = adios_global_no_xml.c adios_global_no_xml_LDADD = $(top_builddir)/src/libadios.a adios_global_no_xml_LDFLAGS = $(ADIOSLIB_LDFLAGS) -adios_global_no_xml_LDADD += $(ADIOSLIB_LDADD) +adios_global_no_xml_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) adios_read_global_no_xml_SOURCES = adios_read_global_no_xml.c adios_read_global_no_xml_LDADD = $(top_builddir)/src/libadiosread.a adios_read_global_no_xml_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) -adios_read_global_no_xml_LDADD += $(ADIOSREADLIB_LDADD) +adios_read_global_no_xml_LDADD += $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) no_xml_write_byid_SOURCES = no_xml_write_byid.c no_xml_write_byid_LDADD = $(top_builddir)/src/libadios.a no_xml_write_byid_LDFLAGS = $(ADIOSLIB_LDFLAGS) -no_xml_write_byid_LDADD += $(ADIOSLIB_LDADD) +no_xml_write_byid_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) read_no_xml_write_byid_SOURCES = read_no_xml_write_byid.c read_no_xml_write_byid_LDADD = $(top_builddir)/src/libadiosread.a read_no_xml_write_byid_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) -read_no_xml_write_byid_LDADD += $(ADIOSREADLIB_LDADD) +read_no_xml_write_byid_LDADD += $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) CLEANFILES = *.bp CC=$(MPICC) Index: adios-1.5.0/examples/C/manual/Makefile.am =================================================================== --- adios-1.5.0.orig/examples/C/manual/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/examples/C/manual/Makefile.am 2014-01-27 23:47:14.641176076 -0500 @@ -8,19 +8,19 @@ 1_nonadios_example_SOURCES = 1_nonadios_example.c 1_nonadios_example_LDADD = $(top_builddir)/src/libadios.a 1_nonadios_example_LDFLAGS = $(ADIOSLIB_LDFLAGS) -1_nonadios_example_LDADD += $(ADIOSLIB_LDADD) +1_nonadios_example_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) 2_adios_write_SOURCES = 2_adios_write.c 2_adios_write_LDADD = $(top_builddir)/src/libadios.a 2_adios_write_LDFLAGS = $(ADIOSLIB_LDFLAGS) -2_adios_write_LDADD += $(ADIOSLIB_LDADD) +2_adios_write_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) 3_adios_read_SOURCES = 3_adios_read.c 3_adios_read_LDADD = $(top_builddir)/src/libadios.a 3_adios_read_LDFLAGS = $(ADIOSLIB_LDFLAGS) -3_adios_read_LDADD += $(ADIOSLIB_LDADD) +3_adios_read_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) 4_adios_nfiles_SOURCES = 4_adios_nfiles.c 4_adios_nfiles_LDADD = $(top_builddir)/src/libadios.a 4_adios_nfiles_LDFLAGS = $(ADIOSLIB_LDFLAGS) -4_adios_nfiles_LDADD += $(ADIOSLIB_LDADD) +4_adios_nfiles_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) CLEANFILES = *.bp CC=$(MPICC) Index: adios-1.5.0/examples/C/read_all/Makefile.am =================================================================== --- adios-1.5.0.orig/examples/C/read_all/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/examples/C/read_all/Makefile.am 2014-01-27 23:46:41.550117031 -0500 @@ -9,10 +9,10 @@ read_all_CPPFLAGS = ${MACRODEFFLAG}_NOMPI read_all_LDADD = $(top_builddir)/src/libadiosread_nompi.a read_all_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) -read_all_LDADD += $(ADIOSREADLIB_LDADD) +read_all_LDADD += $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) read_all_v1_SOURCES = read_all_v1.c read_all_v1_CPPFLAGS = ${MACRODEFFLAG}_NOMPI ${MACRODEFFLAG}ADIOS_USE_READ_API_1 read_all_v1_LDADD = $(top_builddir)/src/libadiosread_nompi.a read_all_v1_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) -read_all_v1_LDADD += $(ADIOSREADLIB_LDADD) +read_all_v1_LDADD += $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) Index: adios-1.5.0/examples/C/scalars/Makefile.am =================================================================== --- adios-1.5.0.orig/examples/C/scalars/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/examples/C/scalars/Makefile.am 2014-01-27 23:45:55.667244116 -0500 @@ -8,15 +8,15 @@ scalars_write_SOURCES = scalars_write.c scalars_write_LDADD = $(top_builddir)/src/libadios.a scalars_write_LDFLAGS = $(ADIOSLIB_LDFLAGS) -scalars_write_LDADD += $(ADIOSLIB_LDADD) +scalars_write_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) scalars_read_SOURCES = scalars_read.c scalars_read_LDADD = $(top_builddir)/src/libadiosread.a scalars_read_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) -scalars_read_LDADD += $(ADIOSREADLIB_LDADD) +scalars_read_LDADD += $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) scalars_write_step_SOURCES = scalars_write.c scalars_write_step_LDADD = $(top_builddir)/src/libadios.a scalars_write_step_LDFLAGS = $(ADIOSLIB_LDFLAGS) -scalars_write_step_LDADD += $(ADIOSLIB_LDADD) +scalars_write_step_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) CLEANFILES = *.bp CC=$(MPICC) Index: adios-1.5.0/examples/C/schema/Makefile.am =================================================================== --- adios-1.5.0.orig/examples/C/schema/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/examples/C/schema/Makefile.am 2014-01-27 23:47:57.591835814 -0500 @@ -8,22 +8,22 @@ uniform_SOURCES = uniform.c uniform_LDADD = $(top_builddir)/src/libadios.a uniform_LDFLAGS = $(ADIOSLIB_LDFLAGS) -uniform_LDADD += $(ADIOSLIB_LDADD) +uniform_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) rectilinear_SOURCES = rectilinear.c rectilinear_LDADD = $(top_builddir)/src/libadios.a rectilinear_LDFLAGS = $(ADIOSLIB_LDFLAGS) -rectilinear_LDADD += $(ADIOSLIB_LDADD) +rectilinear_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) structured_SOURCES = structured.c structured_LDADD = $(top_builddir)/src/libadios.a structured_LDFLAGS = $(ADIOSLIB_LDFLAGS) -structured_LDADD += $(ADIOSLIB_LDADD) +structured_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) unstructured_SOURCES = unstructured.c unstructured_LDADD = $(top_builddir)/src/libadios.a unstructured_LDFLAGS = $(ADIOSLIB_LDFLAGS) -unstructured_LDADD += $(ADIOSLIB_LDADD) +unstructured_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) CLEANFILES = *.bp CC=$(MPICC) Index: adios-1.5.0/examples/C/stat/Makefile.am =================================================================== --- adios-1.5.0.orig/examples/C/stat/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/examples/C/stat/Makefile.am 2014-01-27 23:47:29.424720807 -0500 @@ -8,11 +8,11 @@ stat_write_SOURCES = stat_write.c stat_write_LDADD = $(top_builddir)/src/libadios.a stat_write_LDFLAGS = $(ADIOSLIB_LDFLAGS) -stat_write_LDADD += $(ADIOSLIB_LDADD) +stat_write_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) stat_read_SOURCES = stat_read.c stat_read_LDADD = $(top_builddir)/src/libadiosread.a stat_read_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) -stat_read_LDADD += $(ADIOSREADLIB_LDADD) +stat_read_LDADD += $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) CLEANFILES = *.bp CC=$(MPICC) Index: adios-1.5.0/examples/Fortran/arrays/Makefile.am =================================================================== --- adios-1.5.0.orig/examples/Fortran/arrays/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/examples/Fortran/arrays/Makefile.am 2014-01-27 23:51:32.992633791 -0500 @@ -8,12 +8,12 @@ arrays_write_SOURCES = arrays_write.F90 arrays_write_LDADD = $(top_builddir)/src/libadiosf.a arrays_write_LDFLAGS = $(ADIOSLIB_LDFLAGS) -arrays_write_LDADD += $(ADIOSLIB_LDADD) +arrays_write_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) arrays_read_SOURCES = arrays_read.F90 arrays_read_LDADD = $(top_builddir)/src/libadiosreadf.a arrays_read_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) -arrays_read_LDADD += $(ADIOSREADLIB_LDADD) +arrays_read_LDADD += $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) CLEANFILES = *.bp CC=$(MPICC) @@ -23,4 +23,4 @@ FCLINK = \ $(LIBTOOL) --mode=link --tag F77 $(FC) \ - $(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) -o $@ + $(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) $(NETCDF_LIBS) -o $@ Index: adios-1.5.0/examples/Fortran/global-array-time/Makefile.am =================================================================== --- adios-1.5.0.orig/examples/Fortran/global-array-time/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/examples/Fortran/global-array-time/Makefile.am 2014-01-27 23:51:16.641196887 -0500 @@ -8,7 +8,7 @@ adios_globaltime_SOURCES = adios_globaltime.F90 adios_globaltime_LDADD = $(top_builddir)/src/libadiosf.a adios_globaltime_LDFLAGS = $(ADIOSLIB_LDFLAGS) -adios_globaltime_LDADD += $(ADIOSLIB_LDADD) +adios_globaltime_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) CLEANFILES = *.bp CC=$(MPICC) @@ -16,6 +16,6 @@ FCLINK = \ $(LIBTOOL) --mode=link --tag F77 $(FC) \ - $(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) -o $@ + $(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) $(NETCDF_LIBS) -o $@ EXTRA_DIST = adios_globaltime.xml gread_restart.fh gwrite_restart.fh job.pbs Index: adios-1.5.0/examples/Fortran/global-array/Makefile.am =================================================================== --- adios-1.5.0.orig/examples/Fortran/global-array/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/examples/Fortran/global-array/Makefile.am 2014-01-27 23:51:59.943718066 -0500 @@ -8,17 +8,17 @@ adios_global_SOURCES = adios_global.F90 adios_global_LDADD = $(top_builddir)/src/libadiosf.a adios_global_LDFLAGS = $(ADIOSLIB_LDFLAGS) -adios_global_LDADD += $(ADIOSLIB_LDADD) +adios_global_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) adios_global_no_xml_SOURCES = adios_global_no_xml.F90 adios_global_no_xml_LDADD = $(top_builddir)/src/libadiosf.a adios_global_no_xml_LDFLAGS = $(ADIOSLIB_LDFLAGS) -adios_global_no_xml_LDADD += $(ADIOSLIB_LDADD) +adios_global_no_xml_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) no_xml_write_byid_SOURCES = no_xml_write_byid.F90 no_xml_write_byid_LDADD = $(top_builddir)/src/libadiosf.a no_xml_write_byid_LDFLAGS = $(ADIOSLIB_LDFLAGS) -no_xml_write_byid_LDADD += $(ADIOSLIB_LDADD) +no_xml_write_byid_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) CLEANFILES = *.bp CC=$(MPICC) @@ -26,6 +26,6 @@ FCLINK = \ $(LIBTOOL) --mode=link --tag F77 $(FC) \ - $(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) -o $@ + $(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) $(NETCDF_LIBS) -o $@ EXTRA_DIST = adios_global.xml gread_temperature.fh gwrite_temperature.fh job.pbs Index: adios-1.5.0/examples/Fortran/scalars/Makefile.am =================================================================== --- adios-1.5.0.orig/examples/Fortran/scalars/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/examples/Fortran/scalars/Makefile.am 2014-01-27 23:51:02.573667936 -0500 @@ -8,12 +8,12 @@ scalars_write_SOURCES = scalars_write.F90 scalars_write_LDADD = $(top_builddir)/src/libadiosf.a scalars_write_LDFLAGS = $(ADIOSLIB_LDFLAGS) -scalars_write_LDADD += $(ADIOSLIB_LDADD) +scalars_write_LDADD += $(ADIOSLIB_LDADD) $(NETCDF_LIBS) scalars_read_SOURCES = scalars_read.F90 scalars_read_LDADD = $(top_builddir)/src/libadiosreadf.a scalars_read_LDFLAGS = $(ADIOSREADLIB_LDFLAGS) -scalars_read_LDADD += $(ADIOSREADLIB_LDADD) +scalars_read_LDADD += $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) CLEANFILES = *.bp CC=$(MPICC) @@ -23,4 +23,4 @@ FCLINK = \ $(LIBTOOL) --mode=link --tag F77 $(FC) \ - $(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) -o $@ + $(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) $(NETCDF_LIBS) -o $@ Index: adios-1.5.0/tests/suite/programs/Makefile.am =================================================================== --- adios-1.5.0.orig/tests/suite/programs/Makefile.am 2013-12-09 10:23:31.000000000 -0500 +++ adios-1.5.0/tests/suite/programs/Makefile.am 2014-01-28 00:01:55.195473693 -0500 @@ -45,68 +45,68 @@ # posix_method posix_method_SOURCES=posix_method.F90 -posix_method_LDADD = $(top_builddir)/src/libadiosf.a $(ADIOSLIB_LDADD) +posix_method_LDADD = $(top_builddir)/src/libadiosf.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) posix_method_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_LDFLAGS) posix_method.o: gwrite_posix_method.fh gwrite_posix_method.fh: posix_method.xml $(top_srcdir)/utils/gpp/gpp.py posix_method.xml local_array_time_SOURCES=local_array_time.c -local_array_time_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +local_array_time_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) local_array_time_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_LDFLAGS) adios_amr_write_SOURCES=adios_amr_write.c -adios_amr_write_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +adios_amr_write_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) adios_amr_write_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_LDFLAGS) adios_amr_write.o: adios_amr_write.c adios_amr_write_2vars_SOURCES=adios_amr_write_2vars.c -adios_amr_write_2vars_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +adios_amr_write_2vars_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) adios_amr_write_2vars_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_LDFLAGS) adios_amr_write_2vars.o: adios_amr_write_2vars.c adios_staged_read_SOURCES=adios_staged_read.c -adios_staged_read_LDADD = $(top_builddir)/src/libadiosread.a $(ADIOSREADLIB_LDADD) +adios_staged_read_LDADD = $(top_builddir)/src/libadiosread.a $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) adios_staged_read_LDFLAGS = $(AM_LDFLAGS) $(ADIOSREADLIB_LDFLAGS) adios_staged_read.o: adios_staged_read.c adios_staged_read_v2_SOURCES=adios_staged_read_v2.c -adios_staged_read_v2_LDADD = $(top_builddir)/src/libadiosread.a $(ADIOSREADLIB_LDADD) +adios_staged_read_v2_LDADD = $(top_builddir)/src/libadiosread.a $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) adios_staged_read_v2_LDFLAGS = $(AM_LDFLAGS) $(ADIOSREADLIB_LDFLAGS) adios_staged_read_v2.o: adios_staged_read_v2.c adios_staged_read_2vars_SOURCES=adios_staged_read_2vars.c -adios_staged_read_2vars_LDADD = $(top_builddir)/src/libadiosread.a $(ADIOSREADLIB_LDADD) +adios_staged_read_2vars_LDADD = $(top_builddir)/src/libadiosread.a $(ADIOSREADLIB_LDADD) $(NETCDF_LIBS) adios_staged_read_2vars_LDFLAGS = $(AM_LDFLAGS) $(ADIOSREADLIB_LDFLAGS) adios_staged_read_2vars.o: adios_staged_read_2vars.c write_read_SOURCES=write_read.c -write_read_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +write_read_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) write_read_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_LDFLAGS) write_read.o: write_read.c write_alternate_SOURCES=write_alternate.c -write_alternate_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +write_alternate_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) write_alternate_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_LDFLAGS) write_alternate.o: write_alternate.c two_groups_SOURCES=two_groups.c -two_groups_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +two_groups_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) two_groups_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_LDFLAGS) two_groups.o: two_groups.c many_vars_SOURCES=many_vars.c -many_vars_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +many_vars_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) many_vars_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_LDFLAGS) many_vars.o: many_vars.c selections_SOURCES=selections.c -selections_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +selections_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) selections_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_LDFLAGS) selections.o: selections.c connect_to_space_subset_SOURCES=connect_to_space_subset.c -connect_to_space_subset_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) +connect_to_space_subset_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD) $(NETCDF_LIBS) connect_to_space_subset_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_LDFLAGS) connect_to_space_subset.o: connect_to_space_subset.c @@ -121,4 +121,4 @@ FCLINK = \ $(LIBTOOL) --mode=link --tag F77 $(FC) \ - $(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) -o $@ + $(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) $(NETCDF_LIBS) -o $@ debian/libadios-dev.examples0000664000000000000000000000001312251427211013261 0ustar examples/* debian/watch0000664000000000000000000000015712251427211010221 0ustar version=3 http://www.olcf.ornl.gov/center-projects/adios/ .*/adios-(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz)) debian/control0000664000000000000000000000356412271537703010612 0ustar Source: adios Section: science Priority: optional Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Alastair McKinstry Build-Depends: debhelper (>= 9), libnetcdf-dev, gfortran, libhdf5-mpi-dev | libhdf5-dev, libmxml-dev, python-dev, mpi-default-dev, dh-autoreconf, libcurl4-gnutls-dev, libldap2-dev, heimdal-multidev, libsqlite3-dev, libsasl2-dev, libkeyutils-dev, libffi-dev, pkg-config, python3-dev Standards-Version: 3.9.5 Homepage: http://www.olcf.ornl.gov/center-projects/adios/ Package: libadios-dev Section: libdevel Architecture: any Multi-Arch: same Depends: ${misc:Depends}, ${shlibs:Depends} Recommends: libadios-bin Description: ADIOS Adaptable IO system for simulations The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation. By providing an external to the code XML file describing the various elements, their types, and how you wish to process them this run, the routines in the host code (either Fortran or C) can transparently change how they process the data. Package: libadios-bin Depends: ${misc:Depends}, ${shlibs:Depends}, ${python:Depends} Architecture: any Multi-Arch: foreign Recommends: libadios-dev Description: ADIOS Adaptable IO system for simulations - binaries The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation. By providing an external to the code XML file describing the various elements, their types, and how you wish to process them this run, the routines in the host code (either Fortran or C) can transparently change how they process the data. . This package provides tools for use with ADIOS. debian/source/0000775000000000000000000000000012251427211010465 5ustar debian/source/format0000664000000000000000000000001412251427211011673 0ustar 3.0 (quilt) debian/compat0000664000000000000000000000000212251427211010363 0ustar 9 debian/rules0000775000000000000000000000341012271562233010251 0ustar #!/usr/bin/make -f #export DH_VERBOSE=1 # Cope with lam not providing mpicc. include /usr/share/mpi-default-dev/debian_defaults ifeq ($(ARCH_DEFAULT_MPI_IMPL),lam) CC:=mpicc.lam else CC:=mpicc endif ARCH:=$(shell dpkg --print-architecture) WITH_LUSTRE := #ifeq ($(ARCH), i386) # WITH_LUSTRE:= --with-lustre=/usr #endif #ifeq ($(ARCH), amd64) # WITH_LUSTRE:= --with-lustre=/usr #endif #ifeq ($(ARCH), powerpc) # WITH_LUSTRE:= --with-lustre=/usr #endif #ifeq ($(ARCH), ia64) # WITH_LUSTRE:= --with-lustre=/usr #endif DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed DESTDIR:=$(shell pwd)/debian/tmp DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH) NETCDF_LIBS ?= $(shell pkg-config --libs heimdal-gssapi netcdf libffi) LIBDIR:=/usr/lib/$(DEB_HOST_MULTIARCH) BINDIR:=$(DESTDIR)/usr/bin # magic debhelper rule %: dh $@ --with python2,python3,autoreconf override_dh_auto_clean: dh_clean find . -name '*.pyc' -delete override_dh_auto_configure: dh_auto_configure -- $(WITH_LUSTRE) --enable-shared --prefix=$(DESTDIR) MPIFC=mpif77 CC=$(CC)\ --with-netcdf-libs="-lm -lcurl $(NETCDF_LIBS) -lz -lidn -lrtmp -lgcrypt -lgnutls -lgssapi_krb5\ -llber -lldap_r -lgpg-error -ltasn1 -lp11-kit -lk5crypto -lkrb5support -lsasl2 -lkeyutils\ -lsqlite3" override_dh_auto_install: $(MAKE) install prefix=$(DESTDIR)/usr # remove due to it not working in multi-arch; rm -f $(BINDIR)/adios_config.flags # renamed as per Adios CCS issue #118716, Debbug #639257 mv $(BINDIR)/gpp.py $(BINDIR)/adiosxml2h mv $(BINDIR)/ad_config.py $(BINDIR)/ad_config mv $(BINDIR)/skel_cat.py $(BINDIR)/skel_cat mv $(BINDIR)/skel_extract.py $(BINDIR)/skel_extract cp debian/adios_config $(BINDIR)/adios_config # mv $(DESTDIR)/bin/xmlparser.py $(DESTDIR)/bin/xmlparser debian/adios_config0000775000000000000000000000667012251427211011550 0ustar #!/bin/bash # # Print compiler/linker flags to use ADIOS # Version based on pkg-config, works with Multiarch. # - Alastair McKinstry, # function Usage () { echo "`basename $0` [-d | -c | -l] [-f] [-r] [-s] [-v] Arguments -d Print base directory for ADIOS install -c Print compiler flags for C/C++, using ADIOS write/read methods -l Print linker flags for C/C++, using ADIOS write/read methods -f Print above flags for Fortran90 -r Print above flags for using ADIOS read library only. -s Print above flags for using ADIOS in a sequential code (no MPI). -v Print version of the installed package Notes - Multiple options of d,c,l are enabled. In such a case, the output is a list of FLAG=flags, where FLAG is one of (DIR, CFLAGS, LDFLAGS) - If none of d,c,l are given, all of them is printed - If none of f,r,s are given, flags for C/C++, using ADIOS write/read methods are printed " } # default PRINT_DIR=no PRINT_CFLAGS=no PRINT_LDFLAGS=no OPT_FORTRAN=no OPT_READ=no OPT_SEQ=no NFLAGS_ASKED=0 while getopts ":dclfrsvh" Option do case $Option in d) PRINT_DIR=yes; let "NFLAGS_ASKED=NFLAGS_ASKED+1";; c) PRINT_CFLAGS=yes; let "NFLAGS_ASKED=NFLAGS_ASKED+1";; l) PRINT_LDFLAGS=yes; let "NFLAGS_ASKED=NFLAGS_ASKED+1";; f) OPT_FORTRAN=yes;; r) OPT_READ=yes;; s) OPT_SEQ=yes;; v) echo "$VERSIONSTRING"; exit 0;; h) Usage; exit 0;; *) echo "Invalid option -$Option."; Usage; exit 255;; # DEFAULT esac done shift $(($OPTIND - 1)) if [ $NFLAGS_ASKED == 0 ]; then NFLAGS_ASKED=3; PRINT_DIR=yes PRINT_CFLAGS=yes PRINT_LDFLAGS=yes fi #if [ "$OPT_SEQ" == "yes" ]; then # OPT_READ=yes #fi # Print requested values if [ "$PRINT_DIR" == "yes" ]; then if [ $NFLAGS_ASKED -gt 1 ]; then echo -n "DIR=" fi echo $ADIOS_DIR fi if [ "$PRINT_CFLAGS" == "yes" ]; then if [ "$OPT_READ" == "yes" ]; then if [ "$OPT_SEQ" == "yes" ]; then CFLAGS="$ADIOSREAD_SEQ_INC" else CFLAGS="$ADIOSREAD_INC" fi else if [ "$OPT_SEQ" == "yes" ]; then CFLAGS="$ADIOS_SEQ_INC" else CFLAGS="$ADIOS_INC" fi fi if [ $NFLAGS_ASKED -gt 1 ]; then echo -n "CFLAGS=" fi echo $CFLAGS fi if [ "$PRINT_LDFLAGS" == "yes" ]; then if [ "$OPT_SEQ" == "yes" ]; then if [ "$OPT_READ" == "yes" ]; then # ADIOSREAD + SEQ if [ "$OPT_FORTRAN" == "yes" ]; then LDFLAGS="$ADIOSREAD_SEQ_FLIB" else LDFLAGS="$ADIOSREAD_SEQ_CLIB" fi else # ADIOS + SEQ if [ "$OPT_FORTRAN" == "yes" ]; then #LDFLAGS="$ADIOS_SEQ_FLIB" LDFLAGS="There is no Fortran library of ADIOS for sequential codes" else LDFLAGS="$ADIOS_SEQ_CLIB" fi fi elif [ "$OPT_READ" == "yes" ]; then # ADIOSREAD + parallel code if [ "$OPT_FORTRAN" == "yes" ]; then LDFLAGS="$ADIOSREAD_FLIB" else LDFLAGS="$ADIOSREAD_CLIB" fi else # ADIOS + parallel code if [ "$OPT_FORTRAN" == "yes" ]; then LDFLAGS="$ADIOS_FLIB" else LDFLAGS="$ADIOS_CLIB" fi fi if [ $NFLAGS_ASKED -gt 1 ]; then echo -n "LDFLAGS=" fi echo $LDFLAGS fi debian/libadios-bin.install0000664000000000000000000000044012251427211013107 0ustar usr/bin/ad_config usr/bin/adios_config usr/bin/adios_lint usr/bin/bp2bp usr/bin/bp2h5 usr/bin/bp2ncd usr/bin/bpappend usr/bin/bpdump usr/bin/bpgettime usr/bin/bpls usr/bin/bpsplit usr/bin/skel_cat usr/bin/skel_extract usr/bin/type_mapper.py /usr/shared/pyshared etc/skel /etc/adios/skel