debian/0000775000000000000000000000000012253675145007202 5ustar debian/rules0000775000000000000000000000435211767162054010265 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. # export DH_VERBOSE=1 # magic debhelper rule %: 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 ifeq ($(ARCH_DEFAULT_MPI_IMPL),lam) CC:=mpicc.lam else CC:=mpicc endif PYVERS:= `pyversions -s` DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH) override_dh_autoreconf: libtoolize -c -f dh_autoreconf --as-needed override_dh_auto_configure: LDFLAGS="$(LDFLAGS) -Wl,--as-needed" dh_auto_configure -- --enable-pythonmodule --enable-silex --with-qt=/usr --enable-pythonmodule --enable-silex --with-qt-bin=/usr/bin --with-qt-lib=/usr/lib --with-qt-include=/usr/include/qt4 --with-hdf5=/usr/include,/usr/lib CPPFLAGS=" -I$(MPI_INC) $(CPPFLAGS)" CC=$(CC) CFLAGS="$(CFLAGS)" override_dh_auto_build: dh_auto_build set -e ; for p in $(PYVERS) ; do \ LDFLAGS=" -Wl,--as-needed $(LDFLAGS)" dh_auto_configure -- \ --enable-pythonmodule --enable-silex \ --with-qt=/usr --with-qt-bin=/usr/bin --with-qt-lib=/usr/lib \ --with-qt-include=/usr/include/qt4 \ --with-hdf5=/usr/include,/usr/lib PYTHON=$$p CPPFLAGS=" -I$(MPI_INC) $(CPPFLAGS)" CC=$(CC) CFLAGS="$(CFLAGS)" ; \ $(MAKE) -C tools/browser CXX=$(CC) ; \ $(MAKE) -C tools/python ; \ mkdir -p debian/tmp/usr/lib/pyshared/$$p ; \ cp tools/python/.libs/Silo.so debian/Silo.so.$$p ; \ done override_dh_auto_install: dh_auto_install # move the python modules to where dh_pysupport will spot them ... set -e; for p in $(PYVERS); do \ mkdir -p debian/python-silo/usr/lib/$$p/site-packages ; \ chrpath -d debian/Silo.so.$$p ; \ cp debian/Silo.so.$$p debian/python-silo/usr/lib/$$p/site-packages/Silo.so ; \ done dh_link -p libsiloh5-0 /usr/lib/${DEB_HOST_MULTIARCH}/libsiloh5.so.0.0.0 /usr/lib/${DEB_HOST_MULTIARCH}/libsiloh5.so.0 dh_link -p libsilo-dev /usr/lib/${DEB_HOST_MULTIARCH}/libsiloh5.so.0.0.0 /usr/lib/${DEB_HOST_MULTIARCH}/libsiloh5.so mkdir -p debian/libsilo-dev/usr/lib/${DEB_HOST_MULTIARCH}/pkgconfig cp silo.pc debian/libsilo-dev/usr/lib/${DEB_HOST_MULTIARCH}/pkgconfig override_dh_auto_clean: dh_clean rm -f debian/Silo.so.* config.log -( [ -f Makefile ] && make distclean) debian/libsiloh5-0.links0000664000000000000000000000006611767162054012274 0ustar # /usr/lib/libsiloh5.so.0.0.0 /usr/lib/libsiloh5.so.0 debian/changelog0000664000000000000000000001045312253675142011054 0ustar silo-llnl (4.8-13build1) trusty; urgency=medium * No-change rebuild for libopenmpi1.3 -> libopenmpi1.6 transition. -- Logan Rosen Mon, 16 Dec 2013 17:10:29 -0500 silo-llnl (4.8-13) unstable; urgency=low * Enable QT version 4.8.2 as well. Closes: #671614. * Pass CPPFLAGS, CFLAGS, LDFLAGS in rules to enable hardening. -- Alastair McKinstry Sat, 16 Jun 2012 11:46:24 +0100 silo-llnl (4.8-12) unstable; urgency=low * Add support for QT version 4.8.1; add build-depends on it. Closes: #671614. * Standards-Version: 3.9.3; no changes required. -- Alastair McKinstry Thu, 07 Jun 2012 12:45:44 +0100 silo-llnl (4.8-11) unstable; urgency=low * ld-as-needed patch not robust. Use new dh_autoreconf --as-needed method. Closes: #652224 -- Alastair McKinstry Fri, 16 Dec 2011 13:50:16 +0000 silo-llnl (4.8-10) unstable; urgency=low * Don't delete config.status, it breaks 'make distclean' Closes: #642782. * Two fixes to fprintf() needed to compile with -Werror=format-security * Disable sh4-build patch as not needed now we do 'autoreconf'. Ditto, update qt-version.patch, add-lib-version.patch not to change files now autogenerated. -- Alastair McKinstry Mon, 03 Oct 2011 11:26:00 +0100 silo-llnl (4.8-9) unstable; urgency=low * Rename lib from libsilo0 -> libsiloh5-0 to match soname _before_ building visit, etc to depend on it. * Build with -Wl,--as-needed to remove unwanted dependencies. * Remove unnecessary ${shlibs:Depends} from libsilo-dev -- Alastair McKinstry Thu, 15 Sep 2011 07:27:03 +0100 silo-llnl (4.8-8) unstable; urgency=low * B-D on libtool too. -- Alastair McKinstry Sat, 10 Sep 2011 11:19:45 +0100 silo-llnl (4.8-7) unstable; urgency=low * Don't trust pdbuilder, even after pbuilder --clean. * B-D on autoconf, automake for autoreconf -- Alastair McKinstry Sat, 10 Sep 2011 09:43:46 +0100 silo-llnl (4.8-6) unstable; urgency=low * Fixes needed to make autoreconf -fiv work correctly. Closes: #619830. * B-D autoconf-archive to include AX_CHECK_COMPILE_FLAG needed now. * Build with mpicc.lam when using LAM. Closes: #639119. -- Alastair McKinstry Fri, 09 Sep 2011 11:11:02 +0100 silo-llnl (4.8-5) experimental; urgency=low * Add Multi-arch support. * Add pkgconfig file silo.pc * Add versioned symbols. -- Alastair McKinstry Fri, 26 Aug 2011 02:34:13 +0100 silo-llnl (4.8-4) unstable; urgency=low * Add dependency on python-all-dev for extensions. Closes: #628820. * Check for errors in debian/rules with 'set -e'. Closes: #628818. * Disable python-write test that fails on python2.7. forwrd upstream. (note: it appears the code didn't work as planned on 2.6; hence allow as exists rather than disable python2.7). * Python2.7 enables HDF5 tests: disable SZIP test, as Debian does not have SZIP for licensing reasons. * Disable HDF5 largefile test (test fails on rounding error using floats) -- Alastair McKinstry Sun, 03 Jul 2011 20:14:51 +0100 silo-llnl (4.8-3) unstable; urgency=low * Include patch by Nobuhiro Iwamatsu to build on SH4. Closes: #609074. -- Alastair McKinstry Wed, 13 Apr 2011 09:51:26 +0100 silo-llnl (4.8-2) unstable; urgency=low * Patch to allow silo-llnl build with Qt version 4.7.2. Closes: #621781. * Use python2 in debian/rules to add python dependencies. Closes: #619535. * Include full copy of BSD license in debian/copyright. Closes: #617912. * debian/rules clean: delete autogenerated log files. * Enable testsuite. Fix needed for one test (needs bash) * Now at Standards-Version: 3.9.2 -- Alastair McKinstry Sun, 10 Apr 2011 21:53:28 +0100 silo-llnl (4.8-1) unstable; urgency=low * Correct version number; non-native. * Build-conflict with qt3-dev-tools, or else qmake may give an obsolete version, and silex won't be built. -- Alastair McKinstry Sun, 02 Jan 2011 00:03:01 +0000 silo-llnl (4.8) unstable; urgency=low * Initial release. (Closes: #599747) -- Alastair McKinstry Fri, 08 Oct 2010 19:20:40 +0100 debian/compat0000664000000000000000000000000211767162054010377 0ustar 9 debian/libsilo-bin.install0000664000000000000000000000001311767162054012766 0ustar /usr/bin/* debian/copyright0000664000000000000000000000563711767162054011147 0ustar This package was debianized by Alastair McKinstry on Mon, 11 Oct 2010 19:19:54 +0100. It was downloaded from https://wci.llnl.gov/codes/silo/silo-4.8/silo-4.8-bsd.tar.gz Copyright: (C) Copyright 1994-2010, Lawrence Livermore National Security, LLC. This file is part of Silo. For details, see silo.llnl.gov. 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 disclaimer below. * 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 LLNS/LLNL 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 LAWRENCE LIVERMORE NATIONAL SECURITY, LLC, THE U.S. DEPARTMENT OF ENERGY 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. This work was produced at Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344 with the DOE. Neither the United States Government nor Lawrence Livermore National Security, 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. Any 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 Lawrence Livermore National Security, LLC. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or Lawrence Livermore National Security, LLC, and shall not be used for advertising or product endorsement purposes. debian/source/0000775000000000000000000000000011767162054010501 5ustar debian/source/format0000664000000000000000000000001411767162054011707 0ustar 3.0 (quilt) debian/python-silo.docs0000664000000000000000000000001211767162054012331 0ustar COPYRIGHT debian/libsilo-dev.docs0000664000000000000000000000004111767162054012257 0ustar COPYRIGHT FAQ docs/Silo.book.pdf debian/control0000664000000000000000000001112611767162054010605 0ustar Source: silo-llnl Section: science Priority: optional Maintainer: Alastair McKinstry Build-Depends: debhelper (>= 8.1.3~), libreadline-dev, libhdf5-mpi-dev | libhdf5-dev, zlib1g-dev, libqt4-dev (<< 4:4.9~), gfortran, python-dev, chrpath, python-all-dev, mpi-default-dev, autoconf-archive, autoconf, automake, libtool, dh-autoreconf (>= 4~) Build-Conflicts: qt3-dev-tools Standards-Version: 3.9.3 Homepage: https://wci.llnl.gov/codes/silo Package: libsilo-dev Section: libdevel Architecture: any Multi-Arch: same Depends: ${misc:Depends}, ${shlibs:Depends}, libsiloh5-0 (= ${binary:Version}) Description: Development files for SILO Scientific I/O library from LLNL Silo is a library for reading and writing a wide variety of scientific data to binary, disk files. The files Silo produces and the data within them can be easily shared and exchanged between wholly independently developed applications running on disparate computing platforms. Consequently, Silo facilitates the development of general purpose tools for processing scientific data. One of the more popular tools that process Silo data files is the VisIt visualization tool. . Silo supports gridless (point) meshes, structured meshes, unstructured-zoo and unstructured-arbitrary-polyhedral meshes, block structured AMR meshes, constructive solid geometry (CSG) meshes, piecewise-constant (e.g. zone-centered) and piecewise-linear (e.g. node-centered) variables defined on the node, edge, face or volume elements of meshes as well as the decomposition of meshes into arbitrary subset hierarchies including materials and mixing materials. In addition, Silo supports a wide variety of other useful objects to address various scientific computing application needs. Although the Silo library is a serial library, it has some key features which enable it to be applied quite effectively and scalable in parallel. . Architecturally, the library is divided into two main pieces; an upper-level application programming interface (API) and a lower-level I/O implementation called a driver. Silo supports multiple I/O drivers, the two most common of which are the HDF5 (Hierarchical Data Format 5) and PDB (Portable Data Base) drivers. Package: libsiloh5-0 Section: libs Architecture: any Pre-Depends: ${misc:Pre-Depends} Multi-Arch: same Depends: ${misc:Depends}, ${shlibs:Depends} Description: SILO Science I/O library from LLNL Silo is a library for reading and writing a wide variety of scientific data to binary, disk files. . Silo supports gridless (point) meshes, structured meshes, unstructured-zoo and unstructured-arbitrary-polyhedral meshes, block structured AMR meshes, constructive solid geometry (CSG) meshes, piecewise-constant (e.g. zone-centered) and piecewise-linear (e.g. node-centered) variables defined on the node, edge, face or volume elements of meshes as well as the decomposition of meshes into arbitrary subset hierarchies including materials and mixing materials. In addition, Silo supports a wide variety of other useful objects to address various scientific computing application needs. Although the Silo library is a serial library, it has some key features which enable it to be applied quite effectively and scalable in parallel. Package: libsilo-bin Architecture: any Multi-Arch: foreign Depends: libsiloh5-0 (= ${binary:Version}), ${misc:Depends}, ${shlibs:Depends} Description: Utilities to manipulate libsilo files This package contains a number of utilities for manipulating and viewing Silo files. Silo is a scientific data format library. . Silo supports gridless (point) meshes, structured meshes, unstructured-zoo and unstructured-arbitrary-polyhedral meshes, block structured AMR meshes, constructive solid geometry (CSG) meshes, piecewise-constant (e.g. zone-centered) and piecewise-linear (e.g. node-centered) variables defined on the node, edge, face or volume elements of meshes as well as the decomposition of meshes into arbitrary subset hierarchies including materials and mixing materials. In addition, Silo supports a wide variety of other useful objects to address various scientific computing application needs. Although the Silo library is a serial library, it has some key features which enable it to be applied quite effectively and scalable in parallel. Package: python-silo Section: python Architecture: any X-Python-Version: all Depends: ${python:Depends}, ${misc:Depends}, ${shlibs:Depends}, libsiloh5-0 (=${binary:Version}) Provides: ${python:Provides} Description: Python interface to the SILO Scientific I/O library This is a python interface to SILO, a scientific I/O library. debian/libsiloh5-0.docs0000664000000000000000000000001211767162054012073 0ustar COPYRIGHT debian/libsilo-dev.install0000664000000000000000000000004511767162054013001 0ustar usr/lib/*/libsiloh5.a usr/include/* debian/libsilo-bin.docs0000664000000000000000000000001311767162054012250 0ustar COPYRIGHT debian/patches/0000775000000000000000000000000011767162054010630 5ustar debian/patches/version-script.patch0000664000000000000000000001704511767162054014647 0ustar Author: Alastair McKinstry Description: Add versioned symbols to SILO library Last-Updated: 2011-09-26 Forwarded: no Index: silo-llnl-4.8/configure.ac =================================================================== --- silo-llnl-4.8.orig/configure.ac 2011-08-28 16:16:32.000000000 +0100 +++ silo-llnl-4.8/configure.ac 2011-08-28 16:16:32.000000000 +0100 @@ -359,6 +359,9 @@ dnl Mark C. Miller, Wed Jul 21 09:31:24 PDT 2010 dnl Adjusted logic to support BSD releases which will NOT include dnl hzip/fpzip compression features or source dirs. +dnl +dnl Alastair McKinstry, Fri Aug 25 17:24:00 BST 2011 +dnl Add version script support. dnl -------------------------------------------------------------------------- dnl @@ -447,6 +450,13 @@ CONFIG_USER="$CONFIG_USER at $ORGANIZATION" fi +vsymldflags= +AC_MSG_CHECKING([version script options]) +AC_ARG_WITH([versioned-symbol],AC_HELP_STRING([--with-versioned-symbol],[Use versioned symbols]),[dnl +vsymldflags="-Wl,--version-script,silo.ver -Wl,-O1" +]) +AC_SUBST(vsymldflags) +AC_MSG_RESULT([${vsymldflags}]) dnl ---------------------------------------------------------------------- Index: silo-llnl-4.8/src/Makefile.am =================================================================== --- silo-llnl-4.8.orig/src/Makefile.am 2011-08-28 16:16:32.000000000 +0100 +++ silo-llnl-4.8/src/Makefile.am 2011-08-28 16:16:32.000000000 +0100 @@ -101,7 +101,7 @@ $(DRIVER_LIBS) \ unknown/libsilo_unknown.la \ filters/libsilo_filters.la - libsiloh5_la_LDFLAGS = + libsiloh5_la_LDFLAGS = -export-dynamic @vsymldflags@ else SETTINGSFILE=libsilo.settings lib_LTLIBRARIES = libsilo.la Index: silo-llnl-4.8/silo.ver =================================================================== --- /dev/null 1970-01-01 00:00:00.000000000 +0000 +++ silo-llnl-4.8/silo.ver 2011-08-28 16:53:01.000000000 +0100 @@ -0,0 +1,333 @@ +SILOH5_0 { + global: + DBOpenReal; + DBCreateReal; + DBInqFileReal; + DBAllocCompoundarray; + DBAllocCurve; + DBAllocDefvars; + DBAllocMultimesh; + DBAllocMultimeshadj; + DBAllocMultivar; + DBAllocMultimat; + DBAllocMultimatspecies; + DBAllocCsgmesh; + DBAllocQuadmesh; + DBAllocPointmesh; + DBAllocMeshvar; + DBAllocUcdmesh; + DBAllocCsgvar; + DBAllocQuadvar; + DBAllocUcdvar; + DBAllocZonelist; + DBAllocPHZonelist; + DBAllocCSGZonelist; + DBAllocEdgelist; + DBAllocFacelist; + DBAllocMaterial; + DBAllocMatspecies; + DBAllocNamescheme; + DBAllocGroupelmap; + DBFreeMatspecies; + DBFreeMaterial; + DBFreeFacelist; + DBFreeEdgelist; + DBFreeZonelist; + DBFreePHZonelist; + DBFreeCSGZonelist; + DBResetUcdvar; + DBFreeUcdvar; + DBResetQuadvar; + DBFreeCsgvar; + DBFreeQuadvar; + DBFreeUcdmesh; + DBFreeMeshvar; + DBFreePointmesh; + DBFreeQuadmesh; + DBFreeCsgmesh; + DBFreeDefvars; + DBFreeMultimesh; + DBFreeMultimeshadj; + DBFreeMultivar; + DBFreeMultimat; + DBFreeMultimatspecies; + DBFreeCompoundarray; + DBFreeCurve; + DBFreeNamescheme; + DBSetDataReadMask; + DBGetDataReadMask; + DBSetAllowOverwrites; + DBGetAllowOverwrites; + DBSetEnableChecksums; + DBGetEnableChecksums; + DBSetCompression; + DBGetCompression; + DBSetFriendlyHDF5Names; + DBGetFriendlyHDF5Names; + DBGuessHasFriendlyHDF5Names; + DBSetDeprecateWarnings; + DBGetDeprecateWarnings; + DBSetUnknownDriverPriorities; + DBGetUnknownDriverPriorities; + DBRegisterFileOptionsSet; + DBUnregisterFileOptionsSet; + DBUnregisterAllFileOptionsSets; + DBGrabDriver; + DBUngrabDriver; + DBGetDriverType; + DBGetDriverTypeFromPath; + DBJoinPath; + DBVersion; + DBVersionGE; + DBFileVersion; + DBFileVersionGE; + DBShowErrors; + DBErrString; + DBErrFunc; + DBErrFuncname; + DBErrfunc; + DBErrno; + DBErrlvl; + DBClose; + DBPause; + DBContinue; + DBInqVarExists; + DBForceSingle; + DBUninstall; + DBMakeOptlist; + DBClearOptlist; + DBFreeOptlist; + DBAddOption; + DBGetOption; + DBClearOption; + DBGetToc; + DBNewToc; + DBSortObjectsByOffset; + DBFilters; + DBFilterRegistration; + DBGetAtt; + DBGetObject; + DBChangeObject; + DBWriteObject; + DBGetComponent; + DBGetComponentType; + DBWriteComponent; + DBWriteSlice; + DBWrite; + DBCalcExternalFacelist; + DBCalcExternalFacelist2; + DBGetDir; + DBSetDir; + DBSetDirID; + DBListDir; + DBMkDir; + DBCpDir; + DBReadAtt; + DBRead; + DBReadVar; + DBReadVar1; + DBReadVarSlice; + DBMakeObject; + DBFreeObject; + DBClearObject; + DBAddVarComponent; + DBAddIntComponent; + DBAddFltComponent; + DBAddDblComponent; + DBAddStrComponent; + DBGetComponentNames; + DBGetCompoundarray; + DBGetCurve; + DBGetDefvars; + DBGetMaterial; + DBGetMatspecies; + DBGetMultimesh; + DBGetMultimeshadj; + DBGetMultivar; + DBGetMultimat; + DBGetMultimatspecies; + DBGetPointmesh; + DBGetPointvar; + DBGetQuadmesh; + DBGetQuadvar; + DBGetQuadvar1; + DBAnnotateUcdmesh; + DBGetUcdmesh; + DBGetUcdvar; + DBGetCsgmesh; + DBGetCsgvar; + DBGetCSGZonelist; + DBGetFacelist; + DBGetZonelist; + DBGetPHZonelist; + DBGetVar; + DBGetVarByteLength; + DBGetVarLength; + DBGetVarDims; + DBGetVarType; + DBInqFileHasObjects; + DBInqMeshname; + DBInqMeshtype; + DBInqCompoundarray; + DBInqVarType; + DBPutCompoundarray; + DBPutCurve; + DBPutDefvars; + DBPutFacelist; + DBPutMaterial; + DBPutMatspecies; + DBPutMultimesh; + DBPutMultimeshadj; + DBPutMultivar; + DBPutMultimat; + DBPutMultimatspecies; + DBPutPointmesh; + DBPutPointvar; + DBPutPointvar1; + DBPutQuadmesh; + DBPutQuadvar; + DBPutQuadvar1; + DBPutUcdmesh; + DBPutUcdsubmesh; + DBPutUcdvar; + DBPutUcdvar1; + DBPutZonelist; + DBPutZonelist2; + DBPutPHZonelist; + DBPutCsgmesh; + DBPutCSGZonelist; + DBPutCsgvar; + DBFreeMrgtree; + DBPrintMrgtree; + DBLinearizeMrgtree; + DBWalkMrgtree; + DBMakeMrgtree; + DBAddRegion; + DBAddRegionArray; + DBSetCwr; + DBGetCwr; + DBPutMrgtree; + DBGetMrgtree; + DBPutMrgvar; + DBGetMrgvar; + DBFreeMrgvar; + DBPutGroupelmap; + DBGetGroupelmap; + DBFreeGroupelmap; + DBFortranAccessPointer; + DBFortranAllocPointer; + DBFortranRemovePointer; + DBVariableNameValid; + DBFreeCompressionResources; + DBMakeNamescheme; + DBGetName; + DBStringArrayToStringList; + DBStringListToStringArray; + DBOpenCB; + DBCreateCB; + DBFSingleCB; + dbsetdirid_; + dbgethdfnms_; + dbsethdfnms_; + dbregfopts_; + dbclose_; + dbwrite_; + dbputgrplmap_; + dbaddrcmp_; + dbmkmrgtree_; + dbputzl_; + dbcreate_; + dbputmat_; + dbsetcwr_; + dbpmrgv_; + dbmkdir_; + dbaddiopt_; + dbgetqv1_; + dbgetdepwarn_; + dbputmmat_; + dbgetovrwrt_; + dbsetovrwrt_; + dbgetca_; + dbputpm_; + dbsetcksums_; + dbinqca_; + dbputfl_; + dbinqfile_; + dbcalcfl_; + dbputca_; + dbaddropt_; + dbfreemrgtree_; + dbputcsgv_; + dbputqm_; + dbfreeobject_; + dbfgetca_; + dbwriteslice_; + dberrno_; + dbputmsp_; + dbaddccmp_; + dbinqlen_; + dbaddregion_; + dbgetcksums_; + dbputmmesh_; + db_get_used_file_options_; + dbaddcaopt_; + dbsetcompress_; + dbputuv1_; + dbputcsgzl_; + dbputzl2_; + dbsetdepwarn_; + dbmkobject_; + dbputqv1_; + dbgetcurve_; + dbputpv1_; + dbset2dstrlen_; + dbmkoptlist_; + dbputum_; + dbaddcopt_; + dbputmrgtree_; + dbputcsgm_; + dbgetcompress_; + dbopen_; + dbrdvarslice_; + dbsetdir_; + dbputmvar_; + dbmkptr_; + dbaddregiona_; + dbputqv_; + dbaddicmp_; + dbrdvar_; + dbrmptr_; + dbfreeoptlist_; + dbunregafopts_; + dbget2dstrlen_; + dbadddopt_; + dbputdefvars_; + dbwrtfl_; + dbunregfopts_; + dbshowerrors_; + dbputcurve_; + DBDebugAPI; + db_errno; + db_errfunc; + safe_strdup; /* Should this really be here? its neede by browser, etc. */ + Silo_version*; + + /* filters */ + f_debug_Open; + f_ale3d_Open; + + lite_PD_close; + lite_PD_create; + lite_PD_defstr; + lite_PD_open; + lite_PD_read; + lite_PD_write; + lite_PD_write_alt; + lite_PD_mkdir; + lite_PD_cd; + lite_SC_alloc; + lite_SC_free; + + local: + *; +}; debian/patches/autoreconf.patch0000664000000000000000000000674511767162054014032 0ustar Author: Alastair McKinstry Description: Fixes needed for autoreconf to work on Debian When autoreconf is run, VL_LIB_READLINE is lost from aclocal, so included in config/ Also include AX_CHECK_COMPLER_FLAG() which is not in autoconf (just autoconf-archive) AX_CHECK_COMPILER_FLAGS() is obsolete Last-Updated: 2011-09-05 Forwarded: no Index: silo-llnl-4.8/configure.ac =================================================================== --- silo-llnl-4.8.orig/configure.ac 2011-09-09 20:02:41.000000000 +0100 +++ silo-llnl-4.8/configure.ac 2011-09-09 21:14:41.000000000 +0100 @@ -362,6 +362,9 @@ dnl dnl Alastair McKinstry, Fri Aug 25 17:24:00 BST 2011 dnl Add version script support. +dnl +dnl Alastair McKinstry Mon Sep 5 09:55:00 IST 2011 +dnl Add AC_PROG_F77 needed for autoreconf to work. dnl -------------------------------------------------------------------------- dnl @@ -409,6 +412,8 @@ dnl This allows multiple src-dir builds within one host. AC_PREFIX_DEFAULT("SILO_TOP_SRC_DIR") +AC_PROG_F77 + dnl dnl Handle the python module right away to determine if we need shared libs. dnl Ordinarily, we default to static libs @@ -772,10 +777,10 @@ # it is an argument to the -D argument. So, I think this is # just totally bogus! # Default to large file support -AX_CHECK_COMPILER_FLAGS("-D_LARGEFILE_SOURCE",CFLAGS="$CFLAGS -D_LARGEFILE_SOURCE";) -AX_CHECK_COMPILER_FLAGS("-D_LARGEFILE64_SOURCE",CFLAGS="$CFLAGS -D_LARGEFILE64_SOURCE";) -AX_CHECK_COMPILER_FLAGS("-D_FILE_OFFSET_BITS=64",CFLAGS="$CFLAGS -D_FILE_OFFSET_BITS=64";) -AX_CHECK_COMPILER_FLAGS("-Wdeclaration-after-statement",CFLAGS="$CFLAGS -Wdeclaration-after-statement";) +AX_CHECK_COMPILE_FLAG("-D_LARGEFILE_SOURCE",CFLAGS="$CFLAGS -D_LARGEFILE_SOURCE";) +AX_CHECK_COMPILE_FLAG("-D_LARGEFILE64_SOURCE",CFLAGS="$CFLAGS -D_LARGEFILE64_SOURCE";) +AX_CHECK_COMPILE_FLAG("-D_FILE_OFFSET_BITS=64",CFLAGS="$CFLAGS -D_FILE_OFFSET_BITS=64";) +AX_CHECK_COMPILE_FLAG("-Wdeclaration-after-statement",CFLAGS="$CFLAGS -Wdeclaration-after-statement";) # # Note: regardless of what the stuff above regarding large file support @@ -1463,12 +1468,12 @@ tools/silex/Makefile tools/silock/Makefile silo.pc]) -if test -n "$HZIP"; then - AC_CONFIG_FILES([src/hzip/Makefile]) -fi -if test -n "$FPZIP"; then - AC_CONFIG_FILES([src/fpzip/Makefile]) -fi +#if test -n "$HZIP"; then +# AC_CONFIG_FILES([src/hzip/Makefile]) +#fi +#if test -n "$FPZIP"; then +# AC_CONFIG_FILES([src/fpzip/Makefile]) +#fi if test -n "$HDF5_DRV"; then AC_CONFIG_FILES([src/libsiloh5.settings]) else Index: silo-llnl-4.8/src/Makefile.am =================================================================== --- silo-llnl-4.8.orig/src/Makefile.am 2011-09-09 20:02:41.000000000 +0100 +++ silo-llnl-4.8/src/Makefile.am 2011-09-09 20:02:41.000000000 +0100 @@ -75,17 +75,17 @@ DRIVER_DIRS += taurus DRIVER_LIBS += taurus/libsilo_taurus.la endif -if HZIP_NEEDED -DRIVER_DIRS += hzip -DRIVER_LIBS += hzip/libsilo_hzip.la -endif -if FPZIP_NEEDED -DRIVER_DIRS += fpzip -DRIVER_LIBS += fpzip/libsilo_fpzip.la -endif +#if HZIP_NEEDED +#DRIVER_DIRS += hzip +#DRIVER_LIBS += hzip/libsilo_hzip.la +#endif +#if FPZIP_NEEDED +#DRIVER_DIRS += fpzip +#DRIVER_LIBS += fpzip/libsilo_fpzip.la +#endif SUBDIRS = score pdb silo debug \ $(DRIVER_DIRS) unknown filters . -DIST_SUBDIRS = . debug filters hdf5_drv hzip netcdf \ +DIST_SUBDIRS = . debug filters hdf5_drv netcdf \ pdb pdb_drv pdbp_drv score silo taurus unknown MAKESETTINGS = make.settings debian/patches/testsuite-fix.patch0000664000000000000000000000104311767162054014464 0ustar Author: Alastair McKinstry Description: bash is needed to execute this testscript for test 62. Last-Updated: 2011-04-11 Forwarded: no Index: silo-llnl-4.8/tests/testdtypes =================================================================== --- silo-llnl-4.8.orig/tests/testdtypes 2011-04-10 23:53:36.000000000 +0100 +++ silo-llnl-4.8/tests/testdtypes 2011-04-10 23:53:40.000000000 +0100 @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Copyright (c) 1994 - 2010, Lawrence Livermore National Security, LLC. # LLNL-CODE-425250. debian/patches/test-disable-largefile.patch0000664000000000000000000000161211767162054016161 0ustar Author: Alastair McKinstry Description: Disable largefile test. Seems to fail on rounding error Forwarded: yes Last-Updated: 2011-06-09 Index: silo-llnl-4.8/tests/testsuite.at =================================================================== --- silo-llnl-4.8.orig/tests/testsuite.at 2011-06-09 10:28:17.000000000 +0100 +++ silo-llnl-4.8/tests/testsuite.at 2011-06-09 10:28:40.000000000 +0100 @@ -273,10 +273,10 @@ AT_SETUP(xversion) AT_CHECK(test -z "$BROWSER" -o "$STARGS" != DB_HDF5 && exit 77 || $VALGRIND testxvers `pwd`,,ignore,ignore) AT_CLEANUP -AT_SETUP(largefile) -AT_KEYWORDS(large) -AT_CHECK(test "$STARGS" != DB_HDF5 && exit 77 || $VALGRIND largefile,,ignore,ignore) -AT_CLEANUP +#AT_SETUP(largefile) +#AT_KEYWORDS(large) +#AT_CHECK(test "$STARGS" != DB_HDF5 && exit 77 || $VALGRIND largefile,,ignore,ignore) +#AT_CLEANUP AT_BANNER(Fortran) AT_SETUP(arrayf77) debian/patches/series0000664000000000000000000000035011767162054012043 0ustar add-lib-version.patch dist-undo.patch qt-version.patch testsuite-fix.patch testsuite-python-write.patch testsuite-skip-szip.patch test-disable-largefile.patch pkgconfig.patch version-script.patch autoreconf.patch security-fix.patch debian/patches/pkgconfig.patch0000664000000000000000000000226411767162054013624 0ustar Author: Alastair McKinstry Description: Add a pkgconfig file for the SILO library Last-Updated: 2011-08-25 Forwarded: no Index: silo-llnl-4.8/silo.pc.in =================================================================== --- /dev/null 1970-01-01 00:00:00.000000000 +0000 +++ silo-llnl-4.8/silo.pc.in 2011-09-09 13:26:19.000000000 +0100 @@ -0,0 +1,12 @@ +prefix=@prefix@ +exec_prefix=${prefix} +libdir=@libdir@ +includedir=@includedir@ + +Name: silo +Description: A mesh and field I/O library and scientific database +URL: https://wci.llnl.gov/codes/silo/ +Version: @VERSION@ +Libs: -L${libdir} -lsiloh5 +Libs.private: @LIBS@ +Cflags: -I${includedir} Index: silo-llnl-4.8/configure.ac =================================================================== --- silo-llnl-4.8.orig/configure.ac 2011-09-09 20:01:23.000000000 +0100 +++ silo-llnl-4.8/configure.ac 2011-09-09 20:01:36.000000000 +0100 @@ -1451,7 +1451,8 @@ tools/browser/Makefile tools/python/Makefile tools/silex/Makefile - tools/silock/Makefile]) + tools/silock/Makefile + silo.pc]) if test -n "$HZIP"; then AC_CONFIG_FILES([src/hzip/Makefile]) fi debian/patches/add-lib-version.patch0000664000000000000000000000154311767162054014633 0ustar Author: Alastair McKinstry Description: Add version numbers to libsilo*; we need them in Debian. Last-Updated: 2011-10-03 Forwarded: no Index: silo-llnl-4.8/src/Makefile.am =================================================================== --- silo-llnl-4.8.orig/src/Makefile.am 2010-10-16 14:44:11.000000000 +0100 +++ silo-llnl-4.8/src/Makefile.am 2010-10-16 14:44:21.000000000 +0100 @@ -101,7 +101,7 @@ $(DRIVER_LIBS) \ unknown/libsilo_unknown.la \ filters/libsilo_filters.la - libsiloh5_la_LDFLAGS = -avoid-version + libsiloh5_la_LDFLAGS = else SETTINGSFILE=libsilo.settings lib_LTLIBRARIES = libsilo.la @@ -114,7 +114,7 @@ $(DRIVER_LIBS) \ unknown/libsilo_unknown.la \ filters/libsilo_filters.la - libsilo_la_LDFLAGS = -avoid-version + libsilo_la_LDFLAGS = endif BUILT_SOURCES = $(MAKESETTINGS) debian/patches/testsuite-skip-szip.patch0000664000000000000000000000256111767162054015635 0ustar Author: Alastair McKinstry Description: Disable szip tests, as SZIP not available on Debian for licensing reasons. Last-Updated: 2011-06-09 Forwarded: no Index: silo-llnl-4.8/tests/testsuite.at =================================================================== --- silo-llnl-4.8.orig/tests/testsuite.at 2011-06-08 22:38:52.000000000 +0100 +++ silo-llnl-4.8/tests/testsuite.at 2011-06-08 22:44:16.000000000 +0100 @@ -244,11 +244,11 @@ AT_CHECK(test "$STARGS" != DB_HDF5 && exit 77 || $VALGRIND compression gzip,,ignore,ignore) AT_CHECK(test "$STARGS" != DB_HDF5 && exit 77 || $VALGRIND compression readonly,,ignore,ignore) AT_CLEANUP -AT_SETUP(compression szip) -AT_KEYWORDS(compression) -AT_CHECK(test "$STARGS" != DB_HDF5 && exit 77 || $VALGRIND compression szip,,ignore,ignore) -AT_CHECK(test "$STARGS" != DB_HDF5 && exit 77 || $VALGRIND compression readonly,,ignore,ignore) -AT_CLEANUP +#AT_SETUP(compression szip) +#AT_KEYWORDS(compression) +#AT_CHECK(test "$STARGS" != DB_HDF5 && exit 77 || $VALGRIND compression szip,,ignore,ignore) +#AT_CHECK(test "$STARGS" != DB_HDF5 && exit 77 || $VALGRIND compression readonly,,ignore,ignore) +#AT_CLEANUP AT_SETUP(compression fpzip) AT_KEYWORDS(compression) AT_CHECK(test ! \( -e ../src/fpzip/read.o -o -e ../../../src/fpzip/read.o \) -o "$STARGS" != DB_HDF5 && exit 77 || $VALGRIND compression fpzip,,ignore,ignore) debian/patches/security-fix.patch0000664000000000000000000000216311767162054014306 0ustar Author: Alastair McKinstry Description: Allow code to compile with -Werror=format-security enabled. Relies on the code DBfile_as_string() being safe. Last-Updated: 2011-09-25 Forwarded: no Index: silo-llnl-4.8/tools/python/pydbfile.cpp =================================================================== --- silo-llnl-4.8.orig/tools/python/pydbfile.cpp 2011-09-26 13:58:24.000000000 +0100 +++ silo-llnl-4.8/tools/python/pydbfile.cpp 2011-09-26 14:09:43.000000000 +0100 @@ -548,7 +548,7 @@ { char str[1000]; DBfile_as_string(self, str); - fprintf(fp, str); + fprintf(fp, "%s", str); return 0; } Index: silo-llnl-4.8/tools/python/pydbtoc.cpp =================================================================== --- silo-llnl-4.8.orig/tools/python/pydbtoc.cpp 2011-09-26 13:58:24.000000000 +0100 +++ silo-llnl-4.8/tools/python/pydbtoc.cpp 2011-09-26 14:12:12.000000000 +0100 @@ -178,7 +178,7 @@ int len = DBtoc_as_string(self, 0); char *str = new char[len]; DBtoc_as_string(self, str); - fprintf(fp, str); + fprintf(fp, "%s", str); delete [] str; return 0; } debian/patches/qt-version.patch0000664000000000000000000000166411767162054013767 0ustar Author: Alastair McKinstry Description: Allow for Qt 4.7.2+ Last-Updated: 2012-06-15 Bug-Debian: #621781 Forwarded: no Index: silo-llnl-4.8/configure.ac =================================================================== --- silo-llnl-4.8.orig/configure.ac 2011-04-10 21:32:02.000000000 +0100 +++ silo-llnl-4.8/configure.ac 2011-04-11 00:22:20.000000000 +0100 @@ -1310,11 +1310,12 @@ consumeCount=$((consumeCount-1)) fi done - + AC_MSG_RESULT([Qt $QtVersion in $QT_INCUDE]) ## Check for supported versions of Qt. for ver in 4.4.0 4.4.1 4.4.2 4.4.3 4.4.4 4.4.5 \ 4.5.0 4.5.1 4.5.2 4.5.3 4.5.4 4.5.5 \ - 4.6.0 4.6.1 4.6.2 4.6.3 4.6.4 4.6.5 ; do + 4.6.0 4.6.1 4.6.2 4.6.3 4.6.4 4.6.5 \ + 4.7.0 4.7.1 4.7.2 4.7.3 4.7.4 4.8.1 4.8.2 ; do if test "$QtVersion2" == "$ver"; then QtVersion=$ver break debian/patches/sh4-build.patch0000664000000000000000000000134311767162054013445 0ustar Author: Nobuhiro Iwamatsu Description: Fix to enable build on SH4 Bug-Debian: 609074. Forwarded: no Last-Updated: 2011-04-13 Index: silo-llnl-4.8/configure =================================================================== --- silo-llnl-4.8.orig/configure 2011-04-13 09:49:50.000000000 +0100 +++ silo-llnl-4.8/configure 2011-04-13 09:50:06.000000000 +0100 @@ -5134,7 +5134,7 @@ ;; # Ignore these flags. - -lang* | -lcrt*.o | -lc | -lgcc* | -lSystem | -libmil | -LANG:=* | -LIST:* | -LNO:*) + -lang* | -lcrt*.o | -lc | -lgcc* | -lSystem | -libmil | -LANG:=* | -little | -LIST:* | -LNO:*) ;; -lkernel32) test x"$CYGWIN" != xyes && ac_cv_fc_libs="$ac_cv_fc_libs $ac_arg" debian/patches/testsuite-python-write.patch0000664000000000000000000000363011767162054016353 0ustar Author: Alastair McKinstry Description: Python code seems to be broken. Disable test and inform upstream. Last-Updated: 2011-06-09 Forwarded: yes Index: silo-llnl-4.8/tests/test_write.py =================================================================== --- silo-llnl-4.8.orig/tests/test_write.py 2011-07-04 06:39:26.000000000 +0100 +++ silo-llnl-4.8/tests/test_write.py 2011-07-04 06:39:43.000000000 +0100 @@ -52,11 +52,13 @@ db = Silo.Create("foo.silo", "test file") db.Write("t1", 12) db.Write("t2", "hello") -db.Write("t3", (13,)) -db.Write("t4", 14.5) -db.Write("t5", (1.2, 10)) -db.Write("t6", (1.2, 10.2)) -db.Write("t7", (10, 1.2)) +# Disable writes with floating point. Seem to break on python2.7 +# --amck, 2011-06-09 +#db.Write("t3", (13,)) +#db.Write("t4", 14.5) +#db.Write("t5", (1.2, 10)) +#db.Write("t6", (1.2, 10.2)) +#db.Write("t7", (10, 1.2)) db.Write("t8", "a") db.MkDir("a") db.Write("a/t8", "x2") @@ -70,9 +72,9 @@ db2=Silo.Open("foo.silo") print "toc=%s"%db2.GetToc() print "t2='%s'"%db2.GetVar("t2") -print "t6=",db2.GetVar("t6") +print "#t6= (1.2, 10.199999999999999)" print "a/t8='%s'"%db2.GetVar("a/t8") db2.SetDir("a") print "t9=%s"%db2.GetVar("t9") -print "/t5=",db2.GetVar("../t5") +print "#/t5= (1.2, 10.0)" db2.Close() Index: silo-llnl-4.8/tests/testsuite =================================================================== --- silo-llnl-4.8.orig/tests/testsuite 2011-07-04 06:39:26.000000000 +0100 +++ silo-llnl-4.8/tests/testsuite 2011-07-04 06:46:36.000000000 +0100 @@ -3850,16 +3850,16 @@ cat >expout <<'_ATEOF' -toc=nvar = 12 -var_names = (_fileinfo, _silolibinfo, t1, t10, t11, t2, t3, t4, t5, t6, t7, t8) +toc=nvar = 7 +var_names = (_fileinfo, _silolibinfo, t1, t10, t11, t2, t8) ndir = 1 dir_names = (a) t2='hello' -t6= (1.2, 10.199999999999999) +#t6= (1.2, 10.199999999999999) a/t8='x2' t9=x3 -/t5= (1.2, 10.0) +#/t5= (1.2, 10.0) _ATEOF $at_traceoff debian/patches/dist-undo.patch0000664000000000000000000000131611767162054013560 0ustar Author: Alastair McKinstry Description: remove directories that will fail due to missing sources (non-free licensed). Last-Updated: 2010-12-01 Forwarded: no Index: silo-4.8-bsd/src/Makefile.am =================================================================== --- silo-4.8-bsd.orig/src/Makefile.am 2010-10-11 13:12:06.000000000 +0100 +++ silo-4.8-bsd/src/Makefile.am 2010-10-11 13:12:15.000000000 +0100 @@ -85,7 +85,7 @@ endif SUBDIRS = score pdb silo debug \ $(DRIVER_DIRS) unknown filters . -DIST_SUBDIRS = . debug filters hdf5_drv hzip fpzip netcdf \ +DIST_SUBDIRS = . debug filters hdf5_drv hzip netcdf \ pdb pdb_drv pdbp_drv score silo taurus unknown MAKESETTINGS = make.settings debian/libsiloh5-0.install0000664000000000000000000000003611767162054012617 0ustar /usr/lib/*/libsiloh5.so.0.0.0