Adding HDF5 Archive

CMakeLists.txt

@@ -102,6 +102,7 @@ option(ENABLE_LIBUNWIND
 option(ENABLE_PAPI "Enables use of PAPI" OFF)
 option(ENABLE_LIBXC "Enables use of the libxc library of density functionals" ON)
 option(ENABLE_PCM "Enables use of the polarizable continuum model library" ON)
+option(ENABLE_HDF5 "Enables use of the HDF5 library support" OFF)
 
 ####### preferred task backend
 set(MADNESS_TASK_VALID_BACKENDS Pthreads TBB PaRSEC)
@@ -632,6 +633,7 @@ include(external/gperftools.cmake)
 include(external/tbb.cmake)
 include(external/parsec.cmake)
 include(external/boost.cmake)
+include(external/hdf5.cmake)
 if (NOT MADNESS_BUILD_MADWORLD_ONLY)
   include(external/lapack.cmake)
   include(external/libxc.cmake)
@@ -642,6 +644,7 @@ if (DEFINED ELEMENTAL_TAG)
   include(external/elemental.cmake)
 endif (DEFINED ELEMENTAL_TAG)
 
+
 # Add project subdirectories ===================================================
 
 # predefine targets

external/hdf5.cmake

@@ -0,0 +1,17 @@
+
+#Find HDF5 support
+if (ENABLE_HDF5)
+  set(HDF5_PREFER_PARALLEL FALSE)
+  find_package(HDF5 COMPONENTS C)
+
+  if (HDF5_FOUND)
+    message(STATUS "Found HDF5: ${HDF5_LIBRARIES}")
+    set(HAVE_HDF5 ON CACHE INTERNAL "Have HDF5" FORCE)
+  endif ()
+#  if (HDF5_IS_PARALLEL)
+#    set(HAVE_HDF5 0)
+#    message(STATUS "Found HDF5 Parallel -  Disable")
+#    list(REMOVE_ITEM HDF5_C_LIBRARY_NAMES)
+#  endif ()
+
+endif ()

src/madness/world/CMakeLists.txt

@@ -12,14 +12,14 @@ set(MADWORLD_HEADERS
     text_fstream_archive.h worlddc.h mem_func_wrapper.h taskfn.h group.h 
     dist_cache.h distributed_id.h type_traits.h function_traits.h stubmpi.h 
     bgq_atomics.h binsorter.h parsec.h meta.h worldinit.h thread_info.h
-    cloud.h test_utilities.h timing_utilities.h)
+    cloud.h test_utilities.h timing_utilities.h h5_archive.h )
 set(MADWORLD_SOURCES
     madness_exception.cc world.cc timers.cc future.cc redirectio.cc
     archive_type_names.cc info.cc debug.cc print.cc worldmem.cc worldrmi.cc
     safempi.cc worldpapi.cc worldref.cc worldam.cc worldprofile.cc thread.cc 
     world_task_queue.cc worldgop.cc deferred_cleanup.cc worldmutex.cc
     binary_fstream_archive.cc text_fstream_archive.cc lookup3.c worldmpi.cc 
-    group.cc parsec.cc archive.cc)
+    group.cc parsec.cc archive.cc h5_archive.cc )
 
 if(MADNESS_ENABLE_CEREAL)
     set(MADWORLD_HEADERS ${MADWORLD_HEADERS} "cereal_archive.h")

src/madness/world/h5_archive.cc

@@ -0,0 +1,162 @@
+/*
+  This file is part of MADNESS.
+
+  Copyright (C) 2007,2010 Oak Ridge National Laboratory
+
+  This program is free software; you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation; either version 2 of the License, or
+  (at your option) any later version.
+
+  This program is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+  GNU General Public License for more details.
+
+  You should have received a copy of the GNU General Public License
+  along with this program; if not, write to the Free Software
+  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+  For more information please contact:
+
+  Robert J. Harrison
+  Oak Ridge National Laboratory
+  One Bethel Valley Road
+  P.O. Box 2008, MS-6367
+
+  email: [email protected]
+  tel:   865-241-3937
+  fax:   865-572-0680
+*/
+
+/**
+ \file text_fstream_archive.cc
+ \brief Implements an archive wrapping text filestream.
+ \ingroup serialization
+*/
+
+#include <madness/world/h5_archive.h>
+
+
+namespace madness {
+    namespace archive {
+
+//vama        void TextFstreamOutputArchive::store(const char* t, long /*n*/) const {
+//vama            // store character string, escaping &, < and > along the way
+//vama            while (*t) {
+//vama                char c = *t++;
+//vama                if (c == '\\') {
+//vama                    os.put('\\');
+//vama                    os.put('\\');
+//vama                }
+//vama                else if (c == '<') {
+//vama                    os.put('\\');
+//vama                    os.put('l');
+//vama                }
+//vama                else if (c == '>') {
+//vama                    os.put('\\');
+//vama                    os.put('r');
+//vama                }
+//vama                else {
+//vama                    os.put(c);
+//vama                }
+//vama            }
+//vama            os << std::endl;
+//vama        }
+//vama
+//vama        void TextFstreamOutputArchive::open(const char* filename,
+//vama                  std::ios_base::openmode mode)
+//vama        {
+//vama            os.open(filename, mode);
+//vama            os.setf(std::ios::scientific);
+//vama            os.precision(17);
+//vama            char tag[256];
+//vama            os << "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>" << std::endl;
+//vama            sprintf(tag,"<archive major_version=\"%d\" minor_version=\"%d\">",
+//vama                    ARCHIVE_MAJOR_VERSION, ARCHIVE_MINOR_VERSION);
+//vama            os << tag << std::endl;
+//vama            os << "<typemap>" << std::endl;
+//vama            for (int i=0; i<256; ++i) {
+//vama                sprintf(tag,"%d \"%s\"",i,archive_type_names[i]);
+//vama                store(tag,strlen(tag)); // Must use store to escape characters
+//vama            }
+//vama            os << "</typemap>" << std::endl;
+//vama        }
+//vama
+//vama
+//vama        void TextFstreamOutputArchive::close() {
+//vama            if (os.is_open()) {
+//vama                os << "</archive>" << std::endl;
+//vama                os.close();
+//vama            }
+//vama        }
+//vama
+//vama
+//vama        // Eat EOL after each entry to enable char-by-char read of strings
+//vama        void TextFstreamInputArchive::eat_eol() const {
+//vama            char eol;
+//vama            is.get(eol);
+//vama            if (eol != '\n')
+//vama                MADNESS_EXCEPTION("TextFstreamInputArchive: eat_eol: indigestion", static_cast<int>(eol));
+//vama        }
+//vama
+//vama
+//vama        void TextFstreamInputArchive::load(unsigned char* t, long n) const {
+//vama            for (long i=0; i<n; ++i) {
+//vama                unsigned int x;
+//vama                is >> x;
+//vama                t[i] = (unsigned char) x;
+//vama            }
+//vama            eat_eol();
+//vama        }
+//vama
+//vama        void TextFstreamInputArchive::load(char* t, long n) const {
+//vama            for (long i=0; i<n; ++i) {
+//vama                char c0;
+//vama                is.get(c0);
+//vama                if (c0 == '\\') {
+//vama                    char c1;
+//vama                    is.get(c1);
+//vama                    if (c1 == '\\') {
+//vama                        t[i] = '\\';
+//vama                    }
+//vama                    else if (c1 == 'l') {
+//vama                        t[i] = '<';
+//vama                    }
+//vama                    else if (c1 == 'r') {
+//vama                        t[i] = '>';
+//vama                    }
+//vama                    else {
+//vama                      MADNESS_EXCEPTION("TextFstreamInputArchive: malformed string?",
+//vama                              static_cast<int>(c1));
+//vama                    }
+//vama                }
+//vama                else {
+//vama                    t[i] = c0;
+//vama                }
+//vama            }
+//vama            eat_eol();
+//vama        }
+//vama
+//vama        void TextFstreamInputArchive::open(const char* filename, std::ios_base::openmode mode) {
+//vama            is.open(filename, mode);
+//vama            char buf[256];
+//vama            is.getline(buf,256);        // skip xml header
+//vama            is.getline(buf,256);
+//vama
+//vama            char tag[256];
+//vama            sprintf(tag,"<archive major_version=\"%d\" minor_version=\"%d\">",
+//vama                    ARCHIVE_MAJOR_VERSION, ARCHIVE_MINOR_VERSION);
+//vama            if (strcmp(buf,tag)) {
+//vama                std::cout << "TextFstreamInputArchive: not an archive/bad version?" << std::endl;
+//vama                std::cout << "Found this: " << buf;
+//vama                std::cout << "Expected  : " << tag;
+//vama                MADNESS_EXCEPTION("TextFstreamInputArchive: not an archive/bad version?", 1);
+//vama            }
+//vama
+//vama            // For now just skip over typemap
+//vama            for (int i=0; i<258; ++i) is.getline(buf,256);
+//vama        }
+//vama
+    }
+}