Update ParMETIS third party software (#132)

* Add gklib and copy over new code.

* Set int and real widths to 32, setting to 64 does not work.

* Add some READMEs.

Code/CMake/SimVascularInternals.cmake

@@ -1,6 +1,7 @@
 set(SV_LIBS
  THIRDPARTY_METIS_SVFSI
  THIRDPARTY_PARMETIS_SVFSI
+ THIRDPARTY_GKLIB_SVFSI
  THIRDPARTY_TETGEN
  THIRDPARTY_TINYXML
  THIRDPARTY_ZLIB

Code/CMake/SimVascularOptions.cmake

@@ -58,6 +58,7 @@ option(SV_USE_NOTIMER "Use notimer" ON)
 # Solver Build Options (Modules)
 option(SV_USE_EIGEN_SVFSI "Use Eigen headers" ON)
 option(SV_USE_METIS_SVFSI "Use metis_svfsi Library" ON)
+option(SV_USE_GKLIB_SVFSI "Use GKlib_svfsi Library" ON)
 option(SV_USE_PARMETIS_SVFSI "Use parmetis_svfsi Library" ON)
 option(SV_USE_TETGEN "Use tetgen Library" ON)
 

Code/CMake/SimVascularThirdParty.cmake

@@ -1,4 +1,12 @@
 #-----------------------------------------------------------------------------
+# GKLIB_SVFSI
+if(SV_USE_GKLIB_SVFSI)
+ set(USE_GKLIB_SVFSI ON)
+ simvascular_third_party(gklib_svfsi)
+ # require to be built here
+ set(GKLIB__SVFSI_LIBRARY ${SV_LIB_THIRDPARTY_GKLIB_SVFSI_NAME})
+endif()
+
 # METIS_SVFSI
 if(SV_USE_METIS_SVFSI)
  set(USE_METIS_SVFSI ON)

Code/Source/svFSI/SPLIT.c

@@ -40,20 +40,20 @@
 #include"parmetislib.h"
 
 int split_(int *nElptr, int *eNoNptr, int *eNoNbptr, int *IEN,
- int *nPartsPtr, idxtype *iElmdist, float *iWgt, idxtype *part)
+ int *nPartsPtr, idx_t *iElmdist, float *iWgt, idx_t *part)
 {
 
  int i, e, a, nEl=*nElptr, eNoN=*eNoNptr, eNoNb=*eNoNbptr,
  nparts, nTasks=*nPartsPtr, wgtflag, numflag, ncon, task,
  ncommonnodes, options[10], *exRanks, nExRanks, *map, edgecut;
 
  float ubvec[MAXNCON], *wgt;
- idxtype *eptr, *eind, *elmdist;
+ idx_t *eptr, *eind, *elmdist;
 
  map = (int *)malloc(nTasks*sizeof(int));
  exRanks = (int *)malloc(nTasks*sizeof(int));
  wgt = (float *)malloc(nTasks*sizeof(float));
- elmdist = (idxtype *)malloc((nTasks+1)*sizeof(idxtype));
+ elmdist = (idx_t *)malloc((nTasks+1)*sizeof(idx_t));
  MPI_Group newGrp, tmpGrp;
  MPI_Comm comm;
 
@@ -92,8 +92,8 @@ int split_(int *nElptr, int *eNoNptr, int *eNoNbptr, int *IEN,
  return -1;
  }
 
- eptr = (idxtype *)malloc((nEl+1)*sizeof(idxtype));
- eind = (idxtype *)malloc(nEl*eNoN*sizeof(idxtype));
+ eptr = (idx_t *)malloc((nEl+1)*sizeof(idx_t));
+ eind = (idx_t *)malloc(nEl*eNoN*sizeof(idx_t));
 
  for (e=0; e<=nEl; e++) {
  eptr[e] = e*eNoN;

Code/Source/svFSI/distribute.cpp

@@ -62,7 +62,7 @@ void distribute(Simulation* simulation)
  auto& com_mod = simulation->com_mod;
  auto& cm = com_mod.cm;
 
- #define n_debug_distribute
+ #define debug_distribute
  #ifdef debug_distribute
  DebugMsg dmsg(__func__, com_mod.cm.idcm());
  dmsg.banner();
@@ -1434,7 +1434,7 @@ void part_msh(Simulation* simulation, int iM, mshType& lM, Vector<int>& gmtl, in
  int num_proc = cm.np();
  int task_id = cm.idcm();
 
- #define n_dbg_part_msh
+ #define dbg_part_msh
  #ifdef dbg_part_msh
  DebugMsg dmsg(__func__, com_mod.cm.idcm());
  dmsg.banner();

Code/ThirdParty/README.md

@@ -0,0 +1,18 @@
+This directory contains the source for external applications used by svFSIplus. The applications are compiled and liked with svFSIplus. 
+
+Each application has its own license agreement.
+
+Applications
+
+eigen - A header-only application for matrix objects.
+
+gklib_svfsi - A library used by METIS and ParMETIS applications.
+
+metis_svfsi - The METIS mesh partitioning application used by ParMETIS.
+
+parmetis_svfsi - The ParMETIS parallel mesh partitioning application.
+
+tetgen - A mesh generatin application.
+
+tinyxml - A header-only application used to read and write XML files.
+

Code/ThirdParty/gklib_svfsi/CMakeLists.txt

@@ -0,0 +1 @@
+simvascular_third_party(gklib_svfsi)

Code/ThirdParty/gklib_svfsi/README.md

@@ -0,0 +1,5 @@
+
+The GKlib library contains various helper routines used by METIS and ParMETIS. 
+
+The METIS-v5.1.1-DistDGL-0.5 version of the source was downloaded from https://github.com/KarypisLab/GKlib.
+

Code/ThirdParty/gklib_svfsi/simvascular_gklib_svfsi.h.in

@@ -0,0 +1,37 @@
+/*=========================================================================
+ *
+ * Copyright (c) 2014-2015 The Regents of the University of California.
+ * All Rights Reserved.
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining
+ * a copy of this software and associated documentation files (the
+ * "Software"), to deal in the Software without restriction, including
+ * without limitation the rights to use, copy, modify, merge, publish,
+ * distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject
+ * to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included
+ * in all copies or substantial portions of the Software.
+ *
+ * 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 THE COPYRIGHT OWNER
+ * 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.
+ *
+ *=========================================================================*/
+
+#ifndef __simvascular_GKlib_svfsi_svfsi_h
+#define __simvascular_GKlib_svfsi_svfsi_h
+
+# hardcoded to build, update if want to allow system version
+#include <simvascular_GKlib_svfsi/METISLib/metis.h>
+
+#endif

Code/ThirdParty/gklib_svfsi/simvascular_gklib_svfsi/CMakeLists.txt

@@ -0,0 +1,41 @@
+cmake_minimum_required(VERSION 2.8.8)
+
+project(GKLIB_SVFSI)
+
+#set default build type to relwithdebinfo, also sets flags O2 on linux
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+ message(STATUS "Setting build type to 'RelWithDebInfo' as none was specified.")
+ set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build." FORCE)
+ mark_as_advanced(CMAKE_BUILD_TYPE)
+ # Set the possible values of build type for cmake-gui
+ set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
+ "MinSizeRel" "RelWithDebInfo")
+endif()
+
+if(WIN32)
+ add_definitions("/Zi")
+ add_definitions("-DWINDOWS")
+endif()
+
+include_directories(./)
+include_directories(${MPI_C_INCLUDE_PATH})
+
+set(CSRCS b64.c blas.c cache.c csr.c error.c evaluate.c
+ fkvkselect.c fs.c getopt.c gk_util.c gkregex.c graph.c
+ htable.c io.c itemsets.c mcore.c memory.c pqueue.c
+ random.c rw.c seq.c sort.c string.c timers.c tokenizer.c
+)
+
+if(SV_USE_THIRDPARTY_SHARED_LIBRARIES)
+ add_library(${GKLIB_SVFSI_LIBRARY_NAME} SHARED ${CSRCS})
+else()
+ add_library(${GKLIB_SVFSI_LIBRARY_NAME} STATIC ${CSRCS})
+endif()
+
+if(SV_INSTALL_LIBS)
+ install(TARGETS ${GKLIB_SVFSI_LIBRARY_NAME}
+ RUNTIME DESTINATION ${SV_INSTALL_RUNTIME_DIR} COMPONENT ThirdPartyExecutables
+ LIBRARY DESTINATION ${SV_INSTALL_LIBRARY_DIR} COMPONENT ThirdPartyLibraries
+ ARCHIVE DESTINATION ${SV_INSTALL_ARCHIVE_DIR} COMPONENT ThirdPartyLibraries)
+endif()
+

Code/ThirdParty/gklib_svfsi/simvascular_gklib_svfsi/GKlib.h

@@ -0,0 +1,85 @@
+/*
+ * GKlib.h
+ * 
+ * George's library of most frequently used routines
+ *
+ * $Id: GKlib.h 14866 2013-08-03 16:40:04Z karypis $
+ *
+ */
+
+#ifndef _GKLIB_H_
+#define _GKLIB_H_ 1
+
+#define GKMSPACE
+
+#if defined(_MSC_VER)
+#define __MSC__
+#endif
+#if defined(__ICC)
+#define __ICC__
+#endif
+
+
+#include "gk_arch.h" /*!< This should be here, prior to the includes */
+
+
+/*************************************************************************
+* Header file inclusion section
+**************************************************************************/
+#include <stddef.h>
+#include <stdlib.h>
+#include <stdarg.h>
+#include <stdio.h>
+#include <memory.h>
+#include <errno.h>
+#include <ctype.h>
+#include <math.h>
+#include <float.h>
+#include <time.h>
+#include <string.h>
+#include <limits.h>
+#include <signal.h>
+#include <setjmp.h>
+#include <assert.h>
+#include <sys/stat.h>
+
+#if defined(__WITHPCRE__)
+ #include <pcreposix.h>
+#else
+ #if defined(USE_GKREGEX)
+ #include "gkregex.h"
+ #else
+ #include <regex.h>
+ #endif /* defined(USE_GKREGEX) */
+#endif /* defined(__WITHPCRE__) */
+
+
+
+#if defined(__OPENMP__) 
+#include <omp.h>
+#endif
+
+
+
+
+#include <gk_types.h>
+#include <gk_struct.h>
+#include <gk_externs.h>
+#include <gk_defs.h>
+#include <gk_macros.h>
+#include <gk_getopt.h>
+
+#include <gk_mksort.h>
+#include <gk_mkblas.h>
+#include <gk_mkmemory.h>
+#include <gk_mkpqueue.h>
+#include <gk_mkpqueue2.h>
+#include <gk_mkrandom.h>
+#include <gk_mkutils.h>
+
+#include <gk_proto.h>
+
+
+#endif /* GKlib.h */
+
+

Code/ThirdParty/gklib_svfsi/simvascular_gklib_svfsi/b64.c

@@ -0,0 +1,95 @@
+/*! 
+\file b64.c
+\brief This file contains some simple 8bit-to-6bit encoding/deconding routines
+
+Most of these routines are outdated and should be converted using glibc's equivalent
+routines.
+
+\date Started 2/22/05
+\author George
+\version\verbatim $Id: b64.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim
+
+\verbatim 
+$Copyright$ 
+$License$
+\endverbatim
+
+*/
+
+
+#include "GKlib.h"
+
+#define B64OFFSET 48 /* This is the '0' number */
+
+
+/******************************************************************************
+* Encode 3 '8-bit' binary bytes as 4 '6-bit' characters
+*******************************************************************************/
+void encodeblock(unsigned char *in, unsigned char *out)
+{
+ out[0] = (in[0] >> 2);
+ out[1] = (((in[0] & 0x03) << 4) | (in[1] >> 4));
+ out[2] = (((in[1] & 0x0f) << 2) | (in[2] >> 6));
+ out[3] = (in[2] & 0x3f);
+
+ out[0] += B64OFFSET;
+ out[1] += B64OFFSET;
+ out[2] += B64OFFSET;
+ out[3] += B64OFFSET;
+
+// printf("%c %c %c %c %2x %2x %2x %2x %2x %2x %2x\n", out[0], out[1], out[2], out[3], out[0], out[1], out[2], out[3], in[0], in[1], in[2]);
+}
+
+/******************************************************************************
+* Decode 4 '6-bit' characters into 3 '8-bit' binary bytes
+*******************************************************************************/
+void decodeblock(unsigned char *in, unsigned char *out)
+{ 
+ in[0] -= B64OFFSET;
+ in[1] -= B64OFFSET;
+ in[2] -= B64OFFSET;
+ in[3] -= B64OFFSET;
+
+ out[0] = (in[0] << 2 | in[1] >> 4);
+ out[1] = (in[1] << 4 | in[2] >> 2);
+ out[2] = (in[2] << 6 | in[3]);
+}
+
+
+/******************************************************************************
+* This function encodes an input array of bytes into a base64 encoding. Memory
+* for the output array is assumed to have been allocated by the calling program
+* and be sufficiently large. The output string is NULL terminated.
+*******************************************************************************/
+void GKEncodeBase64(int nbytes, unsigned char *inbuffer, unsigned char *outbuffer)
+{
+ int i, j;
+
+ if (nbytes%3 != 0)
+ gk_errexit(SIGERR, "GKEncodeBase64: Input buffer size should be a multiple of 3! (%d)\n", nbytes);
+
+ for (j=0, i=0; i<nbytes; i+=3, j+=4) 
+ encodeblock(inbuffer+i, outbuffer+j);
+
+//printf("%d %d\n", nbytes, j);
+ outbuffer[j] = '\0';
+}
+
+
+
+/******************************************************************************
+* This function decodes an input array of base64 characters into their actual
+* 8-bit codes. Memory * for the output array is assumed to have been allocated 
+* by the calling program and be sufficiently large. The padding is discarded.
+*******************************************************************************/
+void GKDecodeBase64(int nbytes, unsigned char *inbuffer, unsigned char *outbuffer)
+{
+ int i, j;
+
+ if (nbytes%4 != 0)
+ gk_errexit(SIGERR, "GKDecodeBase64: Input buffer size should be a multiple of 4! (%d)\n", nbytes);
+
+ for (j=0, i=0; i<nbytes; i+=4, j+=3) 
+ decodeblock(inbuffer+i, outbuffer+j);
+}
+