[silo-llnl] 89/96: Add missing 4.9.1-3 changes
Alastair McKinstry
mckinstry at moszumanska.debian.org
Tue Jul 21 13:09:38 UTC 2015
This is an automated email from the git hooks/post-receive script.
mckinstry pushed a commit to branch debian/master
in repository silo-llnl.
commit 4685891253e85e31f2c33371250e797ee4853eaa
Author: Alastair McKinstry <mckinstry at debian.org>
Date: Fri Dec 12 16:39:35 2014 +0000
Add missing 4.9.1-3 changes
---
debian/changelog | 11 +++++++
debian/patches/python3.patch | 6 ++++
debian/patches/remove-mpiposix.patch | 40 +++++++++++++++++++++++
debian/patches/series | 2 +-
debian/patches/version-script.patch | 63 +++++++++++++++++++++++++++---------
debian/rules | 44 +++++++++++++++----------
6 files changed, 132 insertions(+), 34 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index b9f6d46..a647200 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -6,6 +6,17 @@ silo-llnl (4.10.2-1) UNRELEASED; urgency=medium
-- Alastair <mckinstry at debian.org> Fri, 12 Dec 2014 15:13:23 +0000
+silo-llnl (4.9.1-3) unstable; urgency=medium
+
+ * Remove unused qt-version.patch
+ * Add patch to remove H5*_fapl_mpiposix() calls, no longer present
+ in HDF5 1.8.13+
+ * Use new HDF5 layout in debian/rules.
+ * Update silo.ver version script with 4.9.1 changes.
+ * Fix --with-versioned-symbols patch to activate.
+
+ -- Alastair McKinstry <mckinstry at debian.org> Wed, 06 Aug 2014 17:08:11 +0100
+
silo-llnl (4.9.1-2) unstable; urgency=medium
* Undo dependencies on python3-*dev until we actually build python3-silo.
diff --git a/debian/patches/python3.patch b/debian/patches/python3.patch
index fc35791..3180c5c 100644
--- a/debian/patches/python3.patch
+++ b/debian/patches/python3.patch
@@ -1,3 +1,9 @@
+Author: Alastair McKinstry <mckinstry at debian.org>
+Description: Changes needed for Python3 support.
+ TODO: Changes to the C interface still needed.
+Last-Upated: 2014-05-02
+Forwarded: no
+
Index: silo-llnl-4.9.1/tests/test_error.py
===================================================================
--- silo-llnl-4.9.1.orig/tests/test_error.py 2014-03-04 14:26:08.992869807 +0000
diff --git a/debian/patches/remove-mpiposix.patch b/debian/patches/remove-mpiposix.patch
new file mode 100644
index 0000000..1c6449f
--- /dev/null
+++ b/debian/patches/remove-mpiposix.patch
@@ -0,0 +1,40 @@
+Index: silo-llnl-4.9.1/src/hdf5_drv/silo_hdf5.c
+===================================================================
+--- silo-llnl-4.9.1.orig/src/hdf5_drv/silo_hdf5.c
++++ silo-llnl-4.9.1/src/hdf5_drv/silo_hdf5.c
+@@ -4717,16 +4717,7 @@ db_hdf5_process_file_options(opts_set_id
+
+ /* default HDF5 mpi drivers */
+ case DB_FILE_OPTS_H5_DEFAULT_MPIP:
+- {
+-#ifdef H5_HAVE_PARALLEL
+- h5status |= H5Pset_fapl_mpiposix(retval, MPI_COMM_SELF, TRUE);
+-#else
+- H5Pclose(retval);
+- return db_perror("HDF5 MPI VFD", E_NOTENABLEDINBUILD, me);
+-#endif
+- break;
+- }
+-
++ /* FALLTHROUGH */
+ case DB_FILE_OPTS_H5_DEFAULT_MPIO:
+ {
+ #ifdef H5_HAVE_PARALLEL
+@@ -4963,15 +4954,8 @@ db_hdf5_process_file_options(opts_set_id
+ if (p = DBGetOption(opts, DBOPT_H5_MPIP_NO_GPFS_HINTS))
+ use_gpfs_hints = FALSE;
+
+- if (vfd == DB_H5VFD_MPIO)
+- {
+- h5status |= H5Pset_fapl_mpio(retval, mpi_comm, mpi_info);
+- if (created_info) MPI_Info_free(&mpi_info);
+- }
+- else
+- {
+- h5status |= H5Pset_fapl_mpiposix(retval, mpi_comm, use_gpfs_hints);
+- }
++ h5status |= H5Pset_fapl_mpio(retval, mpi_comm, mpi_info);
++ if (created_info) MPI_Info_free(&mpi_info);
+ #else
+ H5Pclose(retval);
+ return db_perror("HDF5 MPI VFD", E_NOTENABLEDINBUILD, me);
diff --git a/debian/patches/series b/debian/patches/series
index ee1845a..6138d8f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,6 +1,5 @@
add-lib-version.patch
dist-undo.patch
-# qt-version.patch
testsuite-fix.patch
testsuite-python-write.patch
testsuite-skip-szip.patch
@@ -13,3 +12,4 @@ spell.patch
python3.patch
compile-fixes.patch
qt5.patch
+remove-mpiposix.patch
diff --git a/debian/patches/version-script.patch b/debian/patches/version-script.patch
index 4fcbcb3..4aeb6af 100644
--- a/debian/patches/version-script.patch
+++ b/debian/patches/version-script.patch
@@ -1,13 +1,13 @@
Author: Alastair McKinstry <mckinstry at debian.org>
Description: Add versioned symbols to SILO library
-Last-Updated: 2011-09-26
+Last-Updated: 2014-08-06
Forwarded: no
Index: silo-llnl-4.9.1/configure.ac
===================================================================
---- silo-llnl-4.9.1.orig/configure.ac 2014-03-04 14:25:59.744636511 +0000
-+++ silo-llnl-4.9.1/configure.ac 2014-03-04 14:25:59.736636309 +0000
-@@ -359,6 +359,9 @@
+--- silo-llnl-4.9.1.orig/configure.ac
++++ silo-llnl-4.9.1/configure.ac
+@@ -359,6 +359,9 @@ dnl
dnl Mark C. Miller, Wed Jul 21 09:31:24 PDT 2010
dnl Adjusted logic to support BSD releases which will NOT include
dnl hzip/fpzip compression features or source dirs.
@@ -17,14 +17,14 @@ Index: silo-llnl-4.9.1/configure.ac
dnl --------------------------------------------------------------------------
dnl
-@@ -447,6 +450,13 @@
+@@ -447,6 +450,13 @@ if test -n "$ORGANIZATION"; then
CONFIG_USER="$CONFIG_USER at $ORGANIZATION"
fi
+vsymldflags=
+AC_MSG_CHECKING([version script options])
-+AC_ARG_WITH([versioned-symbol],AC_HELP_STRING([--with-versioned-symbol],[Use versioned symbols]),[dnl
-+vsymldflags="-Wl,--version-script,silo.ver -Wl,-O1"
++AC_ARG_WITH([versioned-symbols],AC_HELP_STRING([--enable-versioned-symbols],[Use versioned symbols]),[dnl
++vsymldflags="-Wl,--version-script,`pwd`/silo.ver -Wl,-O1"
+])
+AC_SUBST(vsymldflags)
+AC_MSG_RESULT([${vsymldflags}])
@@ -33,9 +33,9 @@ Index: silo-llnl-4.9.1/configure.ac
Index: silo-llnl-4.9.1/src/Makefile.am
===================================================================
---- silo-llnl-4.9.1.orig/src/Makefile.am 2014-03-04 14:25:59.744636511 +0000
-+++ silo-llnl-4.9.1/src/Makefile.am 2014-03-04 14:25:59.736636309 +0000
-@@ -101,7 +101,7 @@
+--- silo-llnl-4.9.1.orig/src/Makefile.am
++++ silo-llnl-4.9.1/src/Makefile.am
+@@ -101,7 +101,7 @@ if HDF5_DRV_NEEDED
$(DRIVER_LIBS) \
unknown/libsilo_unknown.la \
filters/libsilo_filters.la
@@ -46,10 +46,10 @@ Index: silo-llnl-4.9.1/src/Makefile.am
lib_LTLIBRARIES = libsilo.la
Index: silo-llnl-4.9.1/silo.ver
===================================================================
---- /dev/null 1970-01-01 00:00:00.000000000 +0000
-+++ silo-llnl-4.9.1/silo.ver 2014-03-04 14:25:59.736636309 +0000
-@@ -0,0 +1,333 @@
-+SILOH5_0 {
+--- /dev/null
++++ silo-llnl-4.9.1/silo.ver
+@@ -0,0 +1,364 @@
++SILOH5_4_8 {
+ global:
+ DBOpenReal;
+ DBCreateReal;
@@ -378,7 +378,38 @@ Index: silo-llnl-4.9.1/silo.ver
+ lite_PD_cd;
+ lite_SC_alloc;
+ lite_SC_free;
++};
+
++SILOH5_4_9_1 {
++ global:
++ DBAllocPointvar;
++ DBFreePointvar;
++ DBGetAllowEmptyObjects;
++ DBIsEmptyCSGZonelist;
++ DBIsEmptyCsgmesh;
++ DBIsEmptyCsgvar;
++ DBIsEmptyCurve;
++ DBIsEmptyFacelist;
++ DBIsEmptyMaterial;
++ DBIsEmptyMatspecies;
++ DBIsEmptyMeshvar;
++ DBIsEmptyPHZonelist;
++ DBIsEmptyPointmesh;
++ DBIsEmptyPointvar;
++ DBIsEmptyQuadmesh;
++ DBIsEmptyQuadvar;
++ DBIsEmptyUcdmesh;
++ DBIsEmptyUcdvar;
++ DBIsEmptyZonelist;
++ DBSetAllowEmptyObjects;
++ db_hdf5_WriteCKZ;
++ db_num_registered_files;
++ dbaddiaopt_;
++ lite_PD_DEF_CREATM;
++ lite_PD_append;
++ lite_PD_append_as;
++ lite_PD_append_as_alt;
++ lite_PD_defent;
+ local:
-+ *;
-+};
++ *;
++} SILOH5_4_8;
diff --git a/debian/rules b/debian/rules
index b209b68..cec114d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -8,10 +8,10 @@ export DH_VERBOSE=1
dh $@ --with python2,autoreconf
include /usr/share/mpi-default-dev/debian_defaults
-#ARCH_DEFAULT_MPI_IMPL=lam
-MPI_INC=/usr/lib/$(ARCH_DEFAULT_MPI_IMPL)/include
+MPI:=$(ARCH_DEFAULT_MPI_IMPL)
+MPI_INC:=/usr/lib/$(MPI)/include
-ifeq ($(ARCH_DEFAULT_MPI_IMPL),lam)
+ifeq ($(MPI),lam)
CC:=mpicc.lam
CXX:=mpic++.lam
else
@@ -19,16 +19,25 @@ else
CC:=mpicc
endif
-# QT version 4 or 5
-QT:=qt5
-QT_INCLUDES:=-I/usr/include/$(QT) -I/usr/include/$(QT)/QtGui -I/usr/include/$(QT)/QtCore -I/usr/include/$(QT)/QtWidgets
-
-DEFAULT_PYTHON:=`pyversions -d`
-PYVERS:= `pyversions -s`
-PY3VERS:=
+DEFAULT_PYTHON=$(shell pyversions -d)
+PYVERS= $(shell pyversions -s)
DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
+LIBDIR:=/usr/lib/$(DEB_HOST_MULTIARCH)
+
+# QT version 4 or 5
+QT:=5
+QT_INC:=/usr/include/$(DEB_HOST_MULTIARCH)/$(QT)
QT_BINDIR=/usr/lib/$(DEB_HOST_MULTIARCH)/bin
-LIBDIR=/usr/lib/$(DEB_HOST_MULTIARCH)
+QT_INCLUDES:=-I$(QT_INC) -I$(QT_INC)/QtGui -I$(QT_INC)/QtCore -I$(QT_INC)/QtWidgets
+
+# Work with either old or new-style (co-installable) HDF5 layouts
+ifneq ($(wildcard $(LIBDIR)/hdf5/$(MPI)/libhdf5.so),)
+HDF5_INC:=/usr/include/hdf5/$(MPI)
+HDF5_LIB:=$(LIBDIR)/hdf5/$(MPI)
+else
+HDF5_INC:=/usr/include
+HDF5_LIB:=/usr/lib
+endif
override_dh_autoreconf:
libtoolize -c -f
@@ -39,12 +48,13 @@ override_dh_autoreconf:
override_dh_auto_configure:
dh_auto_configure -- \
- --enable-versioned-symbol --enable-pythonmodule \
- --with-hdf5=/usr/include,/usr/lib \
- --with-Qt-bin=$(QT_BINDIR) --with-Qt-include-dir=/usr/include/$(QT) -with-Qt-lib=Qt5Widgets \
+ --with-versioned-symbols \
+ --enable-pythonmodule \
+ --with-hdf5=$(HDF5_INC),$(HDF5_DIR) \
+ --with-Qt-bin-dir=$(QT_BINDIR) --with-Qt-include-dir=$(QT_INC) -with-Qt-lib=Qt5Widgets \
CC=$(CXX) CXX=$(CXX) CFLAGS="$(CFLAGS) -fPIC " CXXFLAGS="$(CXXFLAGS) -fPIC " \
- LIBS=" -lQt5Core " LDFLAGS="$(LDFLAGS) " \
- CPPFLAGS=" $(QT_INCLUDES) -I$(MPI_INC) $(CPPFLAGS)"
+ LIBS=" -lQt5Core " LDFLAGS="$(LDFLAGS) -L$(HDF5_LIB) " \
+ CPPFLAGS=" $(QT_INCLUDES) -I$(MPI_INC) $(CPPFLAGS)"
# Iterate over some directories to avoid stepping into tools/silex, which doesn't build.
override_dh_auto_build:
@@ -60,7 +70,7 @@ override_dh_auto_build:
override_dh_auto_test:
for d in src tools/browser tools/silock ; do \
$(MAKE) -C $$d check; done
-
+
override_dh_auto_install:
# move the python modules to where dh_python* will spot them ...
set -e; for p in $(PYVERS) $(PY3VERS); do \
--
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