March 2010 - moab-dev - mailman3.cels.anl.gov

r3705 - MOAB/trunk/test
by smithrm＠mcs.anl.gov 06 Apr '10

06 Apr '10

Author: smithrm Date: 2010-03-24 14:31:21 -0500 (Wed, 24 Mar 2010) New Revision: 3705 Modified: MOAB/trunk/test/MBTest.cpp Log: o Commented out line 770 in mb_adjacencies_test(). This line caused this test to do nothing and return. Modified: MOAB/trunk/test/MBTest.cpp =================================================================== --- MOAB/trunk/test/MBTest.cpp 2010-03-24 18:29:26 UTC (rev 3704) +++ MOAB/trunk/test/MBTest.cpp 2010-03-24 19:31:21 UTC (rev 3705) @@ -767,7 +767,7 @@ //mb->delete_mesh(); //result = mb->load_mesh("mbtest2.g", 0); //if (MB_SUCCESS != result) - return result; + //return result; // lets create a skin of the hexes // this may be far from being the most efficient, but

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r3732 - MOAB/trunk/src
by kraftche＠cae.wisc.edu 31 Mar '10

31 Mar '10

Author: kraftche Date: 2010-03-31 10:31:42 -0500 (Wed, 31 Mar 2010) New Revision: 3732 Modified: MOAB/trunk/src/AdaptiveKDTree.cpp Log: uncomment commented-out tolerant ray-plane intersection in KDTree Modified: MOAB/trunk/src/AdaptiveKDTree.cpp =================================================================== --- MOAB/trunk/src/AdaptiveKDTree.cpp 2010-03-31 14:40:58 UTC (rev 3731) +++ MOAB/trunk/src/AdaptiveKDTree.cpp 2010-03-31 15:31:42 UTC (rev 3732) @@ -2047,38 +2047,41 @@ return rval; const double t = (plane.coord - ray_pt[plane.norm]) / ray_dir[plane.norm]; - if (!finite(t)) { // ray parallel to plane + // If ray is parallel to plane... + if (!finite(t)) { if (ray_pt[plane.norm] - tol <= plane.coord) list.push_back( NodeSeg( children[0], seg.beg, seg.end ) ); if (ray_pt[plane.norm] + tol >= plane.coord) list.push_back( NodeSeg( children[1], seg.beg, seg.end ) ); } + // If ray direction points towards left (below) plane else if (ray_dir[plane.norm] < 0.0) { if (seg.beg > t) { // segment left of plane list.push_back( NodeSeg( children[0], seg.beg, seg.end ) ); -// if (plane.coord - ray_pt[plane.norm] + ray_dir[plane.norm] * seg.beg < tol) -// list.push_back( NodeSeg( children[1], seg.beg, seg.end ) ); + if (plane.coord - ray_pt[plane.norm] + ray_dir[plane.norm] * seg.beg < tol) + list.push_back( NodeSeg( children[1], seg.beg, seg.end ) ); } else if (seg.end < t) { // segment right of plane list.push_back( NodeSeg( children[1], seg.beg, seg.end ) ); -// if (ray_pt[plane.norm] + ray_dir[plane.norm] * seg.end - plane.coord < tol) -// list.push_back( NodeSeg( children[0], seg.beg, seg.end ) ); + if (ray_pt[plane.norm] + ray_dir[plane.norm] * seg.end - plane.coord < tol) + list.push_back( NodeSeg( children[0], seg.beg, seg.end ) ); } else { // segment crosses plane list.push_back( NodeSeg( children[1], seg.beg, t ) ); list.push_back( NodeSeg( children[0], t, seg.end ) ); } } + // If ray direction points towards right (above) plane else { if (seg.beg > t) { // segment right of plane list.push_back( NodeSeg( children[1], seg.beg, seg.end ) ); -// if (ray_pt[plane.norm] + ray_dir[plane.norm] * seg.beg - plane.coord < tol) -// list.push_back( NodeSeg( children[0], seg.beg, seg.end ) ); + if (ray_pt[plane.norm] + ray_dir[plane.norm] * seg.beg - plane.coord < tol) + list.push_back( NodeSeg( children[0], seg.beg, seg.end ) ); } else if (seg.end < t) { // segment left of plane list.push_back( NodeSeg( children[0], seg.beg, seg.end ) ); -// if (plane.coord - ray_pt[plane.norm] + ray_dir[plane.norm] * seg.end < tol) -// list.push_back( NodeSeg( children[1], seg.beg, seg.end ) ); + if (plane.coord - ray_pt[plane.norm] + ray_dir[plane.norm] * seg.end < tol) + list.push_back( NodeSeg( children[1], seg.beg, seg.end ) ); } else { // segment crosses plane list.push_back( NodeSeg( children[0], seg.beg, t ) );

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r3731 - MOAB/trunk/src
by kraftche＠cae.wisc.edu 31 Mar '10

31 Mar '10

Author: kraftche Date: 2010-03-31 09:40:58 -0500 (Wed, 31 Mar 2010) New Revision: 3731 Modified: MOAB/trunk/src/MBEntityType.h Log: o Do not try to define increment/decrement operators for MBEntityType if included in C (not C++) code. o Document the slightly confusing preprocessor logic that makes the moab::EntityType/MBEntityType stuff work. Modified: MOAB/trunk/src/MBEntityType.h =================================================================== --- MOAB/trunk/src/MBEntityType.h 2010-03-31 14:20:00 UTC (rev 3730) +++ MOAB/trunk/src/MBEntityType.h 2010-03-31 14:40:58 UTC (rev 3731) @@ -22,6 +22,43 @@ * grouped together. */ +/* This file can be used to define several different things. + * + * A) If included in C code (not C++), it defines: + * 1) An enum named MBEntityType, guarded by the MB_ENTITY_TYPE_H + * include guards and + * 2) a typedef MBEntityType guarded by MOAB_ENTITY_TYPE_C include guards. + * + * B) If included in C++ code, it defines: + * 1) An enum named EntiyType in the MOAB namespace, guarded + * by the MB_ENTITY_TYPE include guards + * 2) Increment and decrement oeprators for the moab::EntityType enum, + * also guarded by the MB_ENTITY_TYPE include guards + * 3) A typedef for moab::EntityType in the global namespace + * named MBEntityType, guarded by the MOAB_ENTITY_TYPE_NS_ONLY + * include guards + * + * The C and C++ code should be entirely independent. They are defined + * in the same file only to avoid code duplication and inconsistent enum + * values. OTOH, the C++ definitions must be in the same file because + * the compiler must treat both the namespaced and non-namespaced names + * as the same type. + * + * The C++ code must be able to provide: + * a) An enum in the moab namespace + * b) An enum in the global namespace that is the *same type* + * as a) as far as the compiler is concerned. + * c) Nothing in the global namespace unless requested + * d) No breakage if both namespaced and non-namespaced headers + * are both included. + * + * This is acheived with the somewhat complicated set of multiple + * included guards described above, where moab/EntityType.hpp will + * include this file with MOAB_ENTITY_TYPE_NS_OLNY temporarily defined + * so as to pull in only the namespaced version at that time, without + * prohibiting the non-namespaced version from being pulled in previously + * or later. + */ #ifdef __cplusplus namespace moab { # define MOAB_ENTITY_TYPE_NAME EntityType @@ -46,6 +83,7 @@ /**< dimensioning purposes */ }; +#ifdef __cplusplus /** prefix increment operator for MBEntityType */ inline MOAB_ENTITY_TYPE_NAME & operator++(MOAB_ENTITY_TYPE_NAME &type) { @@ -74,7 +112,6 @@ return oldval; } -#ifdef __cplusplus } /* namespace moab*/ #endif /* __cplusplus */

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r3730 - MOAB/trunk
by kraftche＠cae.wisc.edu 31 Mar '10

31 Mar '10

Author: kraftche Date: 2010-03-31 09:20:00 -0500 (Wed, 31 Mar 2010) New Revision: 3730 Modified: MOAB/trunk/configure.ac Log: make --disable-fortran work with libtool 2.2.6b Modified: MOAB/trunk/configure.ac =================================================================== --- MOAB/trunk/configure.ac 2010-03-30 19:47:59 UTC (rev 3729) +++ MOAB/trunk/configure.ac 2010-03-31 14:20:00 UTC (rev 3730) @@ -43,7 +43,7 @@ FATHOM_TEMPLATE_FUNC_SPECIALIZATION AM_CPPFLAGS="$AM_CPPFLAGS $TEMPLATE_SPECIALIZATION $TEMPLATE_FUNC_SPECIALIZATION" -if test "x" != "x$FC"; then +if test "xyes" = "x$ENABLE_FORTRAN" && test "x" != "x$FC"; then AC_FC_WRAPPERS fi

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disable-fortran [Was: Re: AdaptiveKDTree.cpp: need to move mpi include out of moab namespace]
by Jason Kraftcheck 30 Mar '10

30 Mar '10

I think the problem is with the version of libtool that you have installed. Which version are you using? It seems to be running the configure tests for Fortran regardless of what we ask for in the configure script. If this is the problem, then the attached patch should work around the problem. It will disable FORTRAN name mangling regardless of whether or not a FORTRAN compiler is configured. Please let me know if this works. - jason

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Nightly docs
by James Porter 30 Mar '10

30 Mar '10

Nightly Doxygen documentation for MOAB is up now: <http://gnep.mcs.anl.gov:8010/moab-docs/>. Hopefully this won't cause the Buildbot to burst into flames (I really don't know how well it performs as a regular webserver). There are also nightly tarballs for MOAB and CGM: http://gnep.mcs.anl.gov:8010/moab-nightly.tar.gz http://gnep.mcs.anl.gov:8010/cgm-nightly.tar.gz At some point, we should probably move these somewhere else, but this is good enough for now, I think. - Jim

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MBCN bug with Fortran
by Wollaber, Allan B. 30 Mar '10

30 Mar '10

To Whom it May Concern: I have just updated our installed version of MOAB to match what's in the repo and I got a linking error (object not found) for the FORTRAN interface of the MBCN functions (such as MBCN_VerticesPerEntity). I traced this to the following macro definition error in moab/src/MBCN_protos.h: the preprocessor macro MBCN_FC_FUNC_ never gets defined, so the interfaces in moab/src/MBCN.h never get exposed. After replacing MBCN_FC_FUNC_ with MOAB_FC_FUNC_ , everything works fine. Since it looks like these files are generated in the configure process, it's possible that this is a simple fix (just add MBCN_FC_FUNC_ to wherever MOAB_FC_FUNC_ is getting set). Thanks, - Allan

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r3728 - MOAB/trunk/src
by kraftche＠cae.wisc.edu 30 Mar '10

30 Mar '10

Author: kraftche Date: 2010-03-30 14:05:48 -0500 (Tue, 30 Mar 2010) New Revision: 3728 Modified: MOAB/trunk/src/Makefile.am Log: fix MBCN Fortran API Modified: MOAB/trunk/src/Makefile.am =================================================================== --- MOAB/trunk/src/Makefile.am 2010-03-30 15:49:23 UTC (rev 3727) +++ MOAB/trunk/src/Makefile.am 2010-03-30 19:05:48 UTC (rev 3728) @@ -151,7 +151,7 @@ MBCN_protos.h MBCN_protos.h: MBCN.h $(top_srcdir)/itaps/mkprotos.sh - $(top_srcdir)/itaps/mkprotos.sh MBCN MBCN $< $@ MOAB_FCDefs.h + $(top_srcdir)/itaps/mkprotos.sh MBCN MOAB $< $@ MOAB_FCDefs.h MOAB_FCDefs.h: FCDefs.h

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r3727 - MOAB/trunk/itaps/imesh
by kraftche＠cae.wisc.edu 30 Mar '10

30 Mar '10

Author: kraftche Date: 2010-03-30 10:49:23 -0500 (Tue, 30 Mar 2010) New Revision: 3727 Modified: MOAB/trunk/itaps/imesh/Makefile.am Log: fix 'make dist' issue Modified: MOAB/trunk/itaps/imesh/Makefile.am =================================================================== --- MOAB/trunk/itaps/imesh/Makefile.am 2010-03-29 21:07:33 UTC (rev 3726) +++ MOAB/trunk/itaps/imesh/Makefile.am 2010-03-30 15:49:23 UTC (rev 3727) @@ -39,8 +39,8 @@ testc_cbind_DEPENDENCIES = $(TESTDEPS) partest_SOURCES = partest.cpp partest_DEPENDENCIES = $(TESTDEPS) -# iMeshP_unit_tests_SOURCES = iMeshP_unit_tests.cpp -# iMeshP_unit_tests_DEPENDENCIES = $(TESTDEPS) +iMeshP_unit_tests_SOURCES = iMeshP_unit_tests.cpp +iMeshP_unit_tests_DEPENDENCIES = $(TESTDEPS) lib_LTLIBRARIES = libiMesh.la

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buildbot failure in Fathom on moab-distcheck
by moab-dev＠mcs.anl.gov 30 Mar '10

30 Mar '10

The Fathomatic has detected a failed build of moab-distcheck on Fathom. Full details are available at: http://gnep.mcs.anl.gov:8010/builders/moab-distcheck/builds/103 Buildbot URL: http://gnep.mcs.anl.gov:8010/ Buildslave for this Build: gnep Build Reason: The Nightly scheduler named 'nightly' triggered this build Build Source Stamp: None Blamelist: BUILD FAILED: failed compile LOG EXCERPT: fi; \ done make[4]: Entering directory `/nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/src/io/mhdf' ... make[3]: Entering directory `/nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/src/oldinc' ... make[2]: Entering directory `/nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/test' list='. io dual obb perf h5file parallel oldinc'; for subdir in $list; do \ if test "$subdir" = .; then :; else \ test -d "/nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/moab-3.99/test/$subdir" \ || /bin/mkdir -p "/nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/moab-3.99/test/$subdir" \ || exit 1; \ distdir=`CDPATH="${ZSH_VERSION+.}:" && cd /nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/moab-3.99/test && pwd`; \ top_distdir=`CDPATH="${ZSH_VERSION+.}:" && cd /nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/moab-3.99 && pwd`; \ (cd $subdir && \ make \ top_distdir="$top_distdir" \ distdir="$distdir/$subdir" \ am__remove_distdir=: \ am__skip_length_check=: \ distdir) \ || exit 1; \ fi; \ done make[3]: Entering directory `/nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/test/io' ... make[3]: Entering directory `/nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/test/dual' ... make[3]: Entering directory `/nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/test/obb' ... make[3]: Entering directory `/nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/test/perf' ... make[3]: Entering directory `/nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/test/h5file' ... make[3]: Entering directory `/nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/test/parallel' ... make[3]: Entering directory `/nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/test/oldinc' ... make[2]: Entering directory `/nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/itaps' list='imesh igeom'; for subdir in $list; do \ if test "$subdir" = .; then :; else \ test -d "/nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/moab-3.99/itaps/$subdir" \ || /bin/mkdir -p "/nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/moab-3.99/itaps/$subdir" \ || exit 1; \ distdir=`CDPATH="${ZSH_VERSION+.}:" && cd /nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/moab-3.99/itaps && pwd`; \ top_distdir=`CDPATH="${ZSH_VERSION+.}:" && cd /nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/moab-3.99 && pwd`; \ (cd $subdir && \ make \ top_distdir="$top_distdir" \ distdir="$distdir/$subdir" \ am__remove_distdir=: \ am__skip_length_check=: \ distdir) \ || exit 1; \ fi; \ done make[3]: Entering directory `/nfs/mcs-homes15/jvporter/buildslave1/moab-distcheck/build/itaps/imesh' ./../mkprotos.sh iMesh MOAB iMesh.h iMesh_protos.h MOAB_FCDefs.h make[3]: *** No rule to make target `iMeshP_unit_tests.c', needed by `distdir'. Stop. sincerely, -The Fathomatic

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