January 2011 - moab-dev - mailman3.cels.anl.gov

Q on initializing MOAB iMesh interface
by Tim Tautges 10 Jan '11

10 Jan '11

Hi all, Currently in MOAB's iMesh implementation, the class structure looks like: class MBiMesh : public Core {...} It's done this way because the iMesh implementation needs to keep some member data that Core doesn't need. However, it also makes it impossible to construct an iMesh object from an existing Core object. I'd like to change that. What I'd like to do is change MBiMesh from "isA" to "hasA", i.e. to make MBiMesh point to an Interface object. The MBiMesh object would keep track of whether it constructed MOAB or was passed one, so it would know whether it could destroy it in iMesh_dtor. I'd also like to enable the Interface::query_interface method to return an iMesh instance, consistent with other interfaces it already handles. The net effect of all this would that applications could gain access to an iMesh interface on a transient basis, e.g. if they wanted to call a service implemented in iMesh but not MOAB. Does anybody see any problem with this approach, or think I should do it differently? - tim -- ================================================================ "You will keep in perfect peace him whose mind is steadfast, because he trusts in you." Isaiah 26:3 Tim Tautges Argonne National Laboratory (tautges(a)mcs.anl.gov) (telecommuting from UW-Madison) phone: (608) 263-8485 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706

2 2

r4424 - MOAB/trunk/src/io
by kraftche＠cae.wisc.edu 07 Jan '11

07 Jan '11

Author: kraftche Date: 2011-01-07 12:33:20 -0600 (Fri, 07 Jan 2011) New Revision: 4424 Modified: MOAB/trunk/src/io/ReadHDF5.cpp Log: verify that filesystem is GPFS before prepending bglockless: to filenames Modified: MOAB/trunk/src/io/ReadHDF5.cpp =================================================================== --- MOAB/trunk/src/io/ReadHDF5.cpp 2011-01-06 21:36:08 UTC (rev 4423) +++ MOAB/trunk/src/io/ReadHDF5.cpp 2011-01-07 18:33:20 UTC (rev 4424) @@ -50,6 +50,12 @@ #include <limits> #include <functional> +#ifdef BLUEGENE +# include <sys/vfs.h> + // Magic number for GPFS file system (ASCII for 'G' 'P' 'F' 'S') +# define BG_LOCKLESS_GPFS 0x47504653 +#endif + #include "IODebugTrack.hpp" #include "ReadHDF5Dataset.hpp" #include "ReadHDF5VarLen.hpp" @@ -289,9 +295,15 @@ // lockless file IO on IBM BlueGene std::string pfilename(filename); #ifdef BLUEGENE - if (0 != pfilename.find("bglockless:")) - pfilename = std::string("bglockless:") + pfilename; - dbgOut.printf( 1, "Enabling lockless IO for BlueGene (filename: \"%s\")\n", pfilename.c_str() ); + if (0 != pfilename.find("bglockless:")) { + // check for GPFS file system + struct statfs fsdata; + statfs( filename, &fsdata ); + if (fsdata.f_type == BG_LOCKLESS_GPFS) { + pfilename = std::string("bglockless:") + pfilename; + dbgOut.printf( 1, "Enabling lockless IO for BlueGene (filename: \"%s\")\n", pfilename.c_str() ); + } + } #endif #ifndef HDF5_PARALLEL

1 0

r4423 - MOAB/trunk/src/io
by kraftche＠cae.wisc.edu 06 Jan '11

06 Jan '11

Author: kraftche Date: 2011-01-06 15:36:08 -0600 (Thu, 06 Jan 2011) New Revision: 4423 Modified: MOAB/trunk/src/io/ReadHDF5.cpp Log: re-enable single proc scan and bcast of hdf5 file summary Modified: MOAB/trunk/src/io/ReadHDF5.cpp =================================================================== --- MOAB/trunk/src/io/ReadHDF5.cpp 2011-01-06 20:55:51 UTC (rev 4422) +++ MOAB/trunk/src/io/ReadHDF5.cpp 2011-01-06 21:36:08 UTC (rev 4423) @@ -67,7 +67,7 @@ * which all nodes open file in parallel to read data. If undefined, * file is opened once in parallel and all nodes read summary data. */ -#undef BCAST_SUMMARY +#define BCAST_SUMMARY #define READ_HDF5_BUFFER_SIZE (128*1024*1024)

1 0

r4422 - in MOAB/trunk: . src/io src/io/mhdf/src
by kraftche＠cae.wisc.edu 06 Jan '11

06 Jan '11

Author: kraftche Date: 2011-01-06 14:55:51 -0600 (Thu, 06 Jan 2011) New Revision: 4422 Modified: MOAB/trunk/configure.ac MOAB/trunk/src/io/ReadHDF5.cpp MOAB/trunk/src/io/mhdf/src/file.c Log: always try to do lockless IO for HDF5 on BlueGene Modified: MOAB/trunk/configure.ac =================================================================== --- MOAB/trunk/configure.ac 2011-01-06 17:26:13 UTC (rev 4421) +++ MOAB/trunk/configure.ac 2011-01-06 20:55:51 UTC (rev 4422) @@ -40,13 +40,13 @@ fi ]) - # Check if platform is BlueGene AC_MSG_CHECKING([if platform is IBM BlueGene]) -FATHOM_TRY_COMPILER_DEFINE([__bg__],[BLUEGENE=yes],[BLUEGENE=no]) -AC_MSG_RESULT([$BLUEGENE]) +FATHOM_TRY_COMPILER_DEFINE([__bg__], + [AM_CPPFLAGS="$AM_CPPFLAGS -DBLUEGENE" + AC_MSG_RESULT([yes])], + [AC_MSG_RESULT([no])]) - AC_CHECK_PROG([ZCAT],[gunzip],[gunzip -c],[]) AC_CHECK_PROG([ZCAT],[gzip],[gzip -cd],[]) AC_CHECK_PROG([ZCAT],[zcat],[zcat],[]) Modified: MOAB/trunk/src/io/ReadHDF5.cpp =================================================================== --- MOAB/trunk/src/io/ReadHDF5.cpp 2011-01-06 17:26:13 UTC (rev 4421) +++ MOAB/trunk/src/io/ReadHDF5.cpp 2011-01-06 20:55:51 UTC (rev 4422) @@ -56,8 +56,19 @@ namespace moab { +/* If defined, coordinates are read in blocked format (all X values before + * Y values before Z values.) If undefined, then all coordinates for a + * given vertex are read at the same time. + */ #undef BLOCKED_COORD_IO +/* If defined, file is opened first by root node only to read summary, + * file is the closed and the summary is broadcast to all nodes, after + * which all nodes open file in parallel to read data. If undefined, + * file is opened once in parallel and all nodes read summary data. + */ +#undef BCAST_SUMMARY + #define READ_HDF5_BUFFER_SIZE (128*1024*1024) #define assert_range( PTR, CNT ) \ @@ -274,6 +285,15 @@ return error(MB_MEMORY_ALLOCATION_FAILED); if (use_mpio || nativeParallel) {

1 0

r4421 - MOAB/trunk/src/io
by jain＠mcs.anl.gov 06 Jan '11

06 Jan '11

Author: jain Date: 2011-01-06 11:26:13 -0600 (Thu, 06 Jan 2011) New Revision: 4421 Modified: MOAB/trunk/src/io/Tqdcfr.cpp Log: o Increasing array size to prevent **stack smashing** Modified: MOAB/trunk/src/io/Tqdcfr.cpp =================================================================== --- MOAB/trunk/src/io/Tqdcfr.cpp 2011-01-06 17:03:21 UTC (rev 4420) +++ MOAB/trunk/src/io/Tqdcfr.cpp 2011-01-06 17:26:13 UTC (rev 4421) @@ -2280,7 +2280,7 @@ { unsigned int num_read; std::vector<std::string> attrib_vec; - char temp_name[80]; + char temp_name[1024]; char name_tag_val[NAME_TAG_SIZE]; std::string name_tag; int id = -1;

1 0

size of temp_name in Tqdcfr
by Rajeev Jain 06 Jan '11

06 Jan '11

I was getting *** stack smashing detected ***: ../../coregen terminated error when reading a cub file. There is a char variable: char temp_name[80]; in routine: Tqdcfr::parse_acis_attribs (line: 2282). Increasing the size of temp_name solves the problem. Please let me know what should be the size of this variable. Rajeev

2 1

r4420 - MOAB/trunk/src/moab
by tautges＠mcs.anl.gov 06 Jan '11

06 Jan '11

Author: tautges Date: 2011-01-06 11:03:21 -0600 (Thu, 06 Jan 2011) New Revision: 4420 Modified: MOAB/trunk/src/moab/Interface.hpp Log: Forgot to remove the anchor/ref statement. Modified: MOAB/trunk/src/moab/Interface.hpp =================================================================== --- MOAB/trunk/src/moab/Interface.hpp 2011-01-06 16:34:26 UTC (rev 4419) +++ MOAB/trunk/src/moab/Interface.hpp 2011-01-06 17:03:21 UTC (rev 4420) @@ -74,7 +74,6 @@ /** * \class Interface Interface.hpp "moab/Interface.hpp" * \brief Main interface class to MOAB - * \brief \ref interfacefuncs * \nosubgrouping */ #if defined(XPCOM_MB) @@ -92,8 +91,6 @@ /** \name Interface */ /**@{*/ - /**\anchor interfacefuncs - */ //! constructor Interface() {}

1 0

r4419 - MOAB/trunk/src/moab
by tautges＠mcs.anl.gov 06 Jan '11

06 Jan '11

Author: tautges Date: 2011-01-06 10:34:26 -0600 (Thu, 06 Jan 2011) New Revision: 4419 Modified: MOAB/trunk/src/moab/Interface.hpp Log: Adding doxygen fields for better layout in the doxygenized documentation. Modified: MOAB/trunk/src/moab/Interface.hpp =================================================================== --- MOAB/trunk/src/moab/Interface.hpp 2011-01-05 19:42:02 UTC (rev 4418) +++ MOAB/trunk/src/moab/Interface.hpp 2011-01-06 16:34:26 UTC (rev 4419) @@ -72,11 +72,10 @@ /** + * \class Interface Interface.hpp "moab/Interface.hpp" * \brief Main interface class to MOAB - * \author Tim Tautges, Karl Merkley, Ray Meyers, Corey Ernst, Clinton Stimpson, - * \author Hong-Jun Kim, Jason Kraftcheck - * \version 1.00 - * \date April, 2004 + * \brief \ref interfacefuncs + * \nosubgrouping */ #if defined(XPCOM_MB) class NS_NO_VTABLE Interface : public nsISupports { @@ -90,9 +89,11 @@ NS_DEFINE_STATIC_IID_ACCESSOR(MBINTERFACE_IID) #endif - //! \name Interface-level functions + /** \name Interface */ - //@{ + /**@{*/ + /**\anchor interfacefuncs + */ //! constructor Interface() {} @@ -123,11 +124,11 @@ */ virtual float impl_version(std::string *version_string = NULL)=0; - //@} + /**@}*/ - //! \name Type and id utility functions + /** \name Type and id */ - //@{ + /**@{*/ //! Returns the entity type of an EntityHandle. /** Returns the EntityType (ie, MeshVertex, MeshQuad, MeshHex ) of <em>handle</em>. @@ -177,11 +178,11 @@ const EntityID, EntityHandle& handle) const =0;

1 0

r4418 - MOAB/trunk/src
by kraftche＠cae.wisc.edu 05 Jan '11

05 Jan '11

Author: kraftche Date: 2011-01-05 13:42:02 -0600 (Wed, 05 Jan 2011) New Revision: 4418 Modified: MOAB/trunk/src/SparseTag.cpp MOAB/trunk/src/VarLenDenseTag.cpp MOAB/trunk/src/VarLenSparseTag.cpp Log: fix build issues on BGP Modified: MOAB/trunk/src/SparseTag.cpp =================================================================== --- MOAB/trunk/src/SparseTag.cpp 2011-01-05 16:07:07 UTC (rev 4417) +++ MOAB/trunk/src/SparseTag.cpp 2011-01-05 19:42:02 UTC (rev 4418) @@ -383,12 +383,12 @@ { if (!intersect) - get_tagged( mData, type, entities ); + get_tagged<Container>( mData, type, entities ); else if (MBMAXTYPE == type) - get_tagged( mData, intersect->begin(), intersect->end(), entities ); + get_tagged<Container>( mData, intersect->begin(), intersect->end(), entities ); else { std::pair<Range::iterator,Range::iterator> r = intersect->equal_range(type); - get_tagged( mData, r.first, r.second, entities ); + get_tagged<Container>( mData, r.first, r.second, entities ); } } Modified: MOAB/trunk/src/VarLenDenseTag.cpp =================================================================== --- MOAB/trunk/src/VarLenDenseTag.cpp 2011-01-05 16:07:07 UTC (rev 4417) +++ MOAB/trunk/src/VarLenDenseTag.cpp 2011-01-05 19:42:02 UTC (rev 4418) @@ -491,12 +491,12 @@ const Range* intersect ) { if (!intersect) - return get_tagged( seqman, mySequenceArray, type, entities ); + return get_tagged<Container>( seqman, mySequenceArray, type, entities ); else if (MBMAXTYPE == type) - return get_tagged( seqman, mySequenceArray, intersect->begin(), intersect->end(), entities ); + return get_tagged<Container>( seqman, mySequenceArray, intersect->begin(), intersect->end(), entities ); else { std::pair<Range::iterator,Range::iterator> r = intersect->equal_range(type); - return get_tagged( seqman, mySequenceArray, r.first, r.second, entities ); + return get_tagged<Container>( seqman, mySequenceArray, r.first, r.second, entities ); } } Modified: MOAB/trunk/src/VarLenSparseTag.cpp =================================================================== --- MOAB/trunk/src/VarLenSparseTag.cpp 2011-01-05 16:07:07 UTC (rev 4417) +++ MOAB/trunk/src/VarLenSparseTag.cpp 2011-01-05 19:42:02 UTC (rev 4418) @@ -317,12 +317,12 @@ { if (!intersect) - get_tagged( mData, type, entities );

1 0

r4417 - MOAB/trunk
by kraftche＠cae.wisc.edu 05 Jan '11

05 Jan '11

Author: kraftche Date: 2011-01-05 10:07:07 -0600 (Wed, 05 Jan 2011) New Revision: 4417 Modified: MOAB/trunk/ Log: remove svn ignore specs on top directory for files that were moved to config/ subdir Property changes on: MOAB/trunk ___________________________________________________________________ Modified: svn:ignore - configure config.guess config.sub libtool ltmain.sh aclocal.m4 depcomp config.log config.h config.h.in config.status autom4te.cache Makefile.in Makefile moab.make moab.config stamp-* missing install-sh + configure libtool ltmain.sh aclocal.m4 config.log config.h config.h.in config.status autom4te.cache Makefile.in Makefile moab.make moab.config stamp-*

1 0