r45936 - in /packages/trilinos/trunk/debian: changelog control patches/hardening.patch patches/series rules
trophime-guest at users.alioth.debian.org
trophime-guest at users.alioth.debian.org
Fri May 17 14:10:42 UTC 2013
Author: trophime-guest
Date: Fri May 17 14:10:41 2013
New Revision: 45936
URL: http://svn.debian.org/wsvn/debian-science/?sc=1&rev=45936
Log:
try adding more packages and tests - matio from experimental is needed
Modified:
packages/trilinos/trunk/debian/changelog
packages/trilinos/trunk/debian/control
packages/trilinos/trunk/debian/patches/hardening.patch
packages/trilinos/trunk/debian/patches/series
packages/trilinos/trunk/debian/rules
Modified: packages/trilinos/trunk/debian/changelog
URL: http://svn.debian.org/wsvn/debian-science/packages/trilinos/trunk/debian/changelog?rev=45936&op=diff
==============================================================================
--- packages/trilinos/trunk/debian/changelog (original)
+++ packages/trilinos/trunk/debian/changelog Fri May 17 14:10:41 2013
@@ -2,7 +2,9 @@
* New upstream release
* debian/rules:
- - update extrea-flags thans to Nico Schlömer
+ - update thanks to Nico Schlomer
+ * debian/control:
+ - remove trilinos-bin package
-- Christophe Trophime <christophe.trophime at lncmi.cnrs.fr> Thu, 16 May 2013 09:11:51 +0200
Modified: packages/trilinos/trunk/debian/control
URL: http://svn.debian.org/wsvn/debian-science/packages/trilinos/trunk/debian/control?rev=45936&op=diff
==============================================================================
--- packages/trilinos/trunk/debian/control (original)
+++ packages/trilinos/trunk/debian/control Fri May 17 14:10:41 2013
@@ -10,18 +10,24 @@
mpi-default-dev, mpi-default-bin, binutils-dev,
python-dev (>= 2.6.6-3~),
libblas-dev, liblapack-dev,
+ libblacs-mpi-dev, libscalapack-mpi-dev,
libboost-dev,
libeigen3-dev,
- libhdf5-openmpi-dev (>= 1.8.7),
- libmatio-dev (>= 1.3.4),
+ libmatio-dev (>= 1.5.0),
libmumps-dev (>= 4.7.3),
+ libhdf5-mpi-dev (>= 1.8.7), libxdmf-dev,
libnetcdf-dev (>= 4.1.3),
+ libexodusii-dev,
libptscotch-dev,
+ libsuitesparse-dev,
+ libglpk-dev, libcppunit-dev, libqd-dev, libyaml-cpp-dev, libthrust-dev, libadolc-dev, libhypre-dev,
+ libpetsc3.2-dev, qt4-qmake, libqt4-dev,
libtbb-dev,
python-mpi4py,
python-numpy,
swig,
- zlib1g-dev
+ zlib1g-dev,
+ chrpath
Standards-Version: 3.9.3
Vcs-Svn: svn://svn.debian.org/svn/debian-science/packages/trilinos/trunk
Vcs-Browser: http://svn.debian.org/wsvn/debian-science/packages/trilinos/trunk
@@ -101,16 +107,16 @@
Some pages point to header files provided in the corresponding -dev package,
so it is suggested to install the latter as well.
-Package: trilinos-bin
-Architecture: any
-Section: math
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Suggests: libtrilinos-doc
-Description: object-oriented framework for large-scale problems
- The Trilinos Project is an effort to develop algorithms and enabling
- technologies within an object-oriented software framework for the
- solution of large-scale, complex multi-physics engineering and
- scientific problems. A unique design feature of Trilinos is its
- focus on packages.
- .
- This package contains the executable binaries.
+#Package: trilinos-bin
+#Architecture: any
+#Section: math
+#Depends: ${shlibs:Depends}, ${misc:Depends}
+#Suggests: libtrilinos-doc
+#Description: object-oriented framework for large-scale problems
+# The Trilinos Project is an effort to develop algorithms and enabling
+# technologies within an object-oriented software framework for the
+# solution of large-scale, complex multi-physics engineering and
+# scientific problems. A unique design feature of Trilinos is its
+# focus on packages.
+# .
+# This package contains the executable binaries.
Modified: packages/trilinos/trunk/debian/patches/hardening.patch
URL: http://svn.debian.org/wsvn/debian-science/packages/trilinos/trunk/debian/patches/hardening.patch?rev=45936&op=diff
==============================================================================
--- packages/trilinos/trunk/debian/patches/hardening.patch (original)
+++ packages/trilinos/trunk/debian/patches/hardening.patch Fri May 17 14:10:41 2013
@@ -1,60 +1,11 @@
-Index: trilinos-10.8.5.dfsg/packages/galeri/src/iohb.cpp
-===================================================================
---- trilinos-10.8.5.dfsg.orig/packages/galeri/src/iohb.cpp 2012-07-03 12:08:45.000000000 +0200
-+++ trilinos-10.8.5.dfsg/packages/galeri/src/iohb.cpp 2012-07-03 12:59:17.000000000 +0200
-@@ -1611,7 +1611,7 @@
+--- a/packages/isorropia/example/order_example.cpp 2013-05-17 11:28:58.000000000 +0200
++++ b/packages/isorropia/example/order_example.cpp 2013-05-17 11:30:14.000000000 +0200
+@@ -115,7 +115,7 @@
+ cout << "Matrix market file name: " << MMFileName << endl;
+ }
- void IOHBTerminate(char* message)
- {
-- fprintf(stderr,message);
-+ fprintf(stderr,"%s",message);
- exit(1);
- }
+- sprintf(file_name, MMFileName.c_str());
++ sprintf(file_name, "%s", MMFileName.c_str());
-Index: trilinos-10.8.5.dfsg/packages/triutils/src/iohb.cpp
-===================================================================
---- trilinos-10.8.5.dfsg.orig/packages/triutils/src/iohb.cpp 2012-07-03 12:08:45.000000000 +0200
-+++ trilinos-10.8.5.dfsg/packages/triutils/src/iohb.cpp 2012-07-03 12:59:17.000000000 +0200
-@@ -1617,7 +1617,7 @@
-
- void IOHBTerminate(const char* message)
- {
-- std::fprintf(stderr,message);
-+ std::fprintf(stderr,"%s",message);
- std::exit(1);
- }
-
-Index: trilinos-10.8.5.dfsg/packages/ml/src/Coarsen/ml_agg_min_energy.cpp
-===================================================================
---- trilinos-10.8.5.dfsg.orig/packages/ml/src/Coarsen/ml_agg_min_energy.cpp 2012-07-03 12:08:45.000000000 +0200
-+++ trilinos-10.8.5.dfsg/packages/ml/src/Coarsen/ml_agg_min_energy.cpp 2012-07-03 12:59:17.000000000 +0200
-@@ -1256,7 +1256,7 @@
- for(int i = 0; i < rows; i++)
- {
- sprintf(str, "%d %d %1.16e \n", i+1, j+1, mat[counter]);
-- fprintf(fid, str);
-+ fprintf(fid, "%s", str);
- counter++;
- }
- }
-Index: trilinos-10.8.5.dfsg/packages/fei/support-Trilinos/fei_Aztec_LinSysCore.cpp
-===================================================================
---- trilinos-10.8.5.dfsg.orig/packages/fei/support-Trilinos/fei_Aztec_LinSysCore.cpp 2012-01-09 18:07:59.000000000 +0100
-+++ trilinos-10.8.5.dfsg/packages/fei/support-Trilinos/fei_Aztec_LinSysCore.cpp 2012-07-03 12:59:50.000000000 +0200
-@@ -2999,14 +2999,14 @@
- if (path != debugPath_) {
- delete [] debugPath_;
- debugPath_ = new char[pathLength + 1];
-- sprintf(debugPath_, path);
-+ sprintf(debugPath_, "%s", path);
- }
-
- int nameLength = strlen(name);
- if (name != debugFileName_) {
- delete [] debugFileName_;
- debugFileName_ = new char[nameLength + 1];
-- sprintf(debugFileName_,name);
-+ sprintf(debugFileName_,"%s", name);
- }
-
- char* dbFileName = new char[pathLength + nameLength + 3];
+ // ==================== Read input Matrix ==============================
+ Epetra_CrsMatrix *A;
Modified: packages/trilinos/trunk/debian/patches/series
URL: http://svn.debian.org/wsvn/debian-science/packages/trilinos/trunk/debian/patches/series?rev=45936&op=diff
==============================================================================
--- packages/trilinos/trunk/debian/patches/series (original)
+++ packages/trilinos/trunk/debian/patches/series Fri May 17 14:10:41 2013
@@ -1,3 +1,4 @@
dist-packages.patch
sharedlibs.patch
install.patch
+hardening.patch
Modified: packages/trilinos/trunk/debian/rules
URL: http://svn.debian.org/wsvn/debian-science/packages/trilinos/trunk/debian/rules?rev=45936&op=diff
==============================================================================
--- packages/trilinos/trunk/debian/rules (original)
+++ packages/trilinos/trunk/debian/rules Fri May 17 14:10:41 2013
@@ -17,6 +17,9 @@
%:
dh $@ --buildsystem=cmake --with python2 --parallel
+
+export OMPI_MCA_plm_rsh_agent=/bin/false #workaround to start MPI-applications in chroot
+export LD_LIBRARY_PATH := $(CURDIR)/debian/tmp/usr/lib:$(LD_LIBRARY_PATH);
# Note that, since this is a compat=9 package, the CPPFLAGS
# don't have to be manually added to CFLAGS, CXXFLAGS;
@@ -51,23 +54,35 @@
# Disabling the Trilinos_ENABLE_DEVELOPMENT_MODE results in
# cleaner compile flags. The same goes for CMAKE_BUILD_TYPE=None.
+#extra_flags += \
+# -DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON \
+# -DTrilinos_ENABLE_SECONDARY_STABLE_CODE=OFF \
+# -DTrilinos_ENABLE_PyTrilinos:BOOL=ON \
+# -DTrilinos_ENABLE_TriKota:BOOL=OFF \
+# -DTrilinos_ENABLE_TESTS:BOOL=ON \
+# -DTrilinos_ENABLE_EXAMPLES:BOOL=OFF \
+# -DTPL_ENABLE_Eigen:BOOL=ON \
+# -DTPL_Eigen_INCLUDE_DIRS:PATH=/usr/include/eigen3/ \
+# -DTPL_ENABLE_MPI:BOOL=ON \
+# -DTPL_ENABLE_MATLAB:BOOL=OFF \
+# -DTrilinos_ENABLE_TriKota:BOOL=OFF \
+# -DSEACASExodus_ENABLE_MPI:BOOL=OFF \
+# -DNOX_ENABLE_LAPACK:BOOL=ON \
+# -DBUILD_SHARED_LIBS:BOOL=ON \
+# -DCMAKE_BUILD_TYPE:STRING=DEBUG \
+# -DTrilinos_ASSERT_MISSING_PACKAGES:BOOL=OFF
+
extra_flags += \
-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON \
- -DTrilinos_ENABLE_SECONDARY_STABLE_CODE=OFF \
- -DTrilinos_ENABLE_PyTrilinos:BOOL=ON \
- -DTrilinos_ENABLE_TriKota:BOOL=OFF \
- -DTrilinos_ENABLE_TESTS:BOOL=OFF \
- -DTrilinos_ENABLE_EXAMPLES:BOOL=OFF \
- -DTPL_ENABLE_Eigen:BOOL=ON \
+ -DTrilinos_ENABLE_SECONDARY_STABLE_CODE=ON \
+ -DTrilinos_ENABLE_TESTS:BOOL=ON \
+ -DTPL_ENABLE_Eigen:BOOL=ON \
-DTPL_Eigen_INCLUDE_DIRS:PATH=/usr/include/eigen3/ \
-DTPL_ENABLE_MPI:BOOL=ON \
-DTPL_ENABLE_MATLAB:BOOL=OFF \
- -DTrilinos_ENABLE_TriKota:BOOL=OFF \
- -DSEACASExodus_ENABLE_MPI:BOOL=OFF \
- -DNOX_ENABLE_LAPACK:BOOL=ON \
+ -DSEACASExodus_ENABLE_MPI:BOOL=OFF \
-DBUILD_SHARED_LIBS:BOOL=ON \
- -DCMAKE_BUILD_TYPE:STRING=DEBUG \
- -DTrilinos_ASSERT_MISSING_PACKAGES:BOOL=OFF
+ -DCMAKE_BUILD_TYPE:STRING=DEBUG
override_dh_auto_clean:
for v in $(PYVERS); do \
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