[adios] 05/18: refresh patches; python3 now upstream
Alastair McKinstry
mckinstry at moszumanska.debian.org
Fri Oct 28 11:18:25 UTC 2016
This is an automated email from the git hooks/post-receive script.
mckinstry pushed a commit to tag debian/1.10.1-1
in repository adios.
commit d024f49b5c40d031ead2834e3eef1350dabfa1ce
Author: Alastair McKinstry <mckinstry at debian.org>
Date: Mon Oct 3 17:14:35 2016 +0100
refresh patches; python3 now upstream
---
debian/patches/mpi_in_place.patch | 77 ++++++++++++++-------------------------
debian/patches/netcdf-fix.patch | 27 ++++----------
debian/patches/security.patch | 31 ----------------
debian/patches/series | 2 +-
debian/patches/sh4.patch | 13 -------
5 files changed, 37 insertions(+), 113 deletions(-)
diff --git a/debian/patches/mpi_in_place.patch b/debian/patches/mpi_in_place.patch
index 71d1d87..1c6300b 100644
--- a/debian/patches/mpi_in_place.patch
+++ b/debian/patches/mpi_in_place.patch
@@ -3,13 +3,13 @@ Author: Alastair McKinstry <mckinstry at debian.org>
Last-Updated: 2013-04-10
Forwarded: no
-Index: adios-1.6.0/src/write/adios_mpi_lustre.c
+Index: adios-1.10.1/src/write/adios_mpi_lustre.c
===================================================================
---- adios-1.6.0.orig/src/write/adios_mpi_lustre.c 2014-02-17 09:36:58.002897426 +0000
-+++ adios-1.6.0/src/write/adios_mpi_lustre.c 2014-02-17 09:36:57.998898475 +0000
-@@ -741,7 +741,11 @@
- ,fd->group->name, md->index
- );
+--- adios-1.10.1.orig/src/write/adios_mpi_lustre.c
++++ adios-1.10.1/src/write/adios_mpi_lustre.c
+@@ -709,7 +709,11 @@ int adios_mpi_lustre_open (struct adios_
+ ,fd->group->name, md->index
+ );
MPI_Scatter (offsets, 3, MPI_LONG_LONG
+#ifdef MPI_IN_PLACE
,MPI_IN_PLACE, 3, MPI_LONG_LONG
@@ -19,51 +19,30 @@ Index: adios-1.6.0/src/write/adios_mpi_lustre.c
,0, md->group_comm
);
md->b.read_pg_offset = offsets [0];
-@@ -835,7 +839,11 @@
- 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
- );
-@@ -858,7 +866,11 @@
- md->b.pg_index_offset = offsets [md->size - 1]
- + last_offset;
- MPI_Scatter (offsets, 1, MPI_LONG_LONG
+@@ -1091,8 +1095,11 @@ static void build_file_offsets (struct a
+ offsets [0] = (fd->bytes_written / LUSTRE_STRIPE_UNIT + 1) * LUSTRE_STRIPE_UNIT;
+ else
+ offsets [0] = fd->bytes_written;
+-
+#ifdef MPI_IN_PLACE
- ,MPI_IN_PLACE, 1, MPI_LONG_LONG
+ MPI_Gather (MPI_IN_PLACE, 1, MPI_LONG_LONG
+#else
-+ ,offsets, 1, MPI_LONG_LONG
-+#endif
- ,0, md->group_comm
- );
- fd->base_offset = offsets [0];
-@@ -1138,7 +1150,11 @@
- else
- offsets [0] = fd->write_size_bytes;
++ MPI_Gather (offsets, 1, MPI_LONG_LONG
++#endif
+ ,offsets, 1, MPI_LONG_LONG
+ ,0, md->group_comm
+ );
+@@ -1114,9 +1121,12 @@ static void build_file_offsets (struct a
+ md->b.pg_index_offset = offsets [md->size - 1]
+ + last_pgsize;
+-
+ MPI_Scatter (offsets, 1, MPI_LONG_LONG
+#ifdef MPI_IN_PLACE
- MPI_Gather (MPI_IN_PLACE, 1, MPI_LONG_LONG
+ ,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
- );
-@@ -1154,7 +1170,11 @@
- 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];
++ ,offsets, 1, MPI_LONG_LONG
++#endif
+ ,0, md->group_comm
+ );
+ fd->current_pg->pg_start_in_file = offsets[0];
diff --git a/debian/patches/netcdf-fix.patch b/debian/patches/netcdf-fix.patch
index 65e815d..e11c95c 100644
--- a/debian/patches/netcdf-fix.patch
+++ b/debian/patches/netcdf-fix.patch
@@ -4,31 +4,20 @@ Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=662995
Forwarded: no
Last-Updated: 2012-03-09
-Index: adios-1.9.0/utils/bp2ncd/Makefile.in
+Index: adios-1.10.1/utils/bp2ncd/Makefile.in
===================================================================
---- adios-1.9.0.orig/utils/bp2ncd/Makefile.in
-+++ adios-1.9.0/utils/bp2ncd/Makefile.in
-@@ -115,12 +115,12 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCE
+--- adios-1.10.1.orig/utils/bp2ncd/Makefile.in
++++ adios-1.10.1/utils/bp2ncd/Makefile.in
+@@ -203,11 +203,10 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCE
ACLOCAL = @ACLOCAL@
ADIOSLIB_CFLAGS = @ADIOSLIB_CFLAGS@
ADIOSLIB_CPPFLAGS = @ADIOSLIB_CPPFLAGS@
-ADIOSLIB_EXTRA_CPPFLAGS = @ADIOSLIB_EXTRA_CPPFLAGS@
-+
+ ADIOSLIB_EXTRA_LDFLAGS = @ADIOSLIB_EXTRA_LDFLAGS@
ADIOSLIB_INT_CFLAGS = @ADIOSLIB_INT_CFLAGS@
ADIOSLIB_INT_CPPFLAGS = @ADIOSLIB_INT_CPPFLAGS@
- ADIOSLIB_INT_LDADD = @ADIOSLIB_INT_LDADD@
+-ADIOSLIB_INT_LDADD = @ADIOSLIB_INT_LDADD@
++ADIOSLIB_INT_LDADD = @ADIOSLIB_INT_LDADD@ @NETCDF_LIBS@
ADIOSLIB_INT_LDFLAGS = @ADIOSLIB_INT_LDFLAGS@
--ADIOSLIB_LDADD = @ADIOSLIB_LDADD@
-+ADIOSLIB_LDADD = @ADIOSLIB_LDADD@ @NETCDF_LIBS@
+ ADIOSLIB_LDADD = @ADIOSLIB_LDADD@
ADIOSLIB_LDFLAGS = @ADIOSLIB_LDFLAGS@
- ADIOSLIB_SEQ_CFLAGS = @ADIOSLIB_SEQ_CFLAGS@
- ADIOSLIB_SEQ_CPPFLAGS = @ADIOSLIB_SEQ_CPPFLAGS@
-@@ -384,7 +384,7 @@ bp2ncd_SOURCES = bp2ncd.c
- @USE_PARALLEL_COMPILER_TRUE at bp2ncd_LDFLAGS = $(ADIOSLIB_LDFLAGS) -static-libtool-libs
- @USE_PARALLEL_COMPILER_FALSE at bp2ncd_LDADD = $(top_builddir)/src/libadios_internal_nompi.a \
- @USE_PARALLEL_COMPILER_FALSE@ $(ADIOSLIB_INT_LDADD)
-- at USE_PARALLEL_COMPILER_TRUE@bp2ncd_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
-+ at USE_PARALLEL_COMPILER_TRUE@bp2ncd_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
- EXTRA_DIST = bp2ncd.h
- all: all-am
-
diff --git a/debian/patches/security.patch b/debian/patches/security.patch
index 7f6f60d..5699f06 100644
--- a/debian/patches/security.patch
+++ b/debian/patches/security.patch
@@ -3,34 +3,3 @@ Description: Silence spurious warnings when building with security flags
Last-Updated: 2015-05-11
Forwarded: no
-Index: adios-1.7.0/utils/skeldump/skeldump.c
-===================================================================
---- adios-1.7.0.orig/utils/skeldump/skeldump.c
-+++ adios-1.7.0/utils/skeldump/skeldump.c
-@@ -919,7 +919,7 @@ int print_data_hist(ADIOS_VARINFO * vi,
- strcat(xtics, ")\n");
-
- fprintf(out_plot, "start = -0.5\npos(x) = start + x * 1\nset boxwidth 1\nset style fill solid border 5#5lt6#6\n");
-- fprintf(out_plot, xtics);
-+ fprintf(out_plot, "%s",xtics);
- fprintf(out_plot, "plot '%s' using 3 smooth frequency w boxes\n", hist_file);
- fprintf(out_plot, "pause -1 'Press Enter to quit'\n");
- }
-@@ -1498,7 +1498,7 @@ int print_data_characteristics(void * mi
-
- case adios_long_double:
- //fprintf(outf,(f ? format : "%g "), ((double *) data)[item]);
-- fprintf(outf,(f ? format : "????????"));
-+ fprintf(outf,"%s", (f ? format : "????????"));
- break;
-
- // TO DO
-@@ -1566,7 +1566,7 @@ int print_data(void *data, int item, enu
-
- case adios_long_double:
- //fprintf(outf,(f ? format : "%g "), ((double *) data)[item]);
-- fprintf(outf,(f ? format : "????????"));
-+ fprintf(outf,"%s", (f ? format : "????????"));
- break;
-
-
diff --git a/debian/patches/series b/debian/patches/series
index e36c299..ab7fc5f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,7 +2,7 @@ sh4.patch
mpi_in_place.patch
security.patch
netcdf-fix.patch
-python3.patch
+#python3.patch
debian_paths.patch
mpi4py_fix.patch
pkgconfig.patch
diff --git a/debian/patches/sh4.patch b/debian/patches/sh4.patch
index e966ba2..69104ca 100644
--- a/debian/patches/sh4.patch
+++ b/debian/patches/sh4.patch
@@ -5,16 +5,3 @@ Forwarded: not-needed
Author: Nobuhiro Iwamatsu <iwamatsu at nigauri.org>
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"
--
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