Updated AutoTools files, began adding auto-making of Tecio and ParMet…

…is; Fixed Gmsh mesh reader to not require only 2 'tags' in '' section.

.gitignore

@@ -1,8 +1,20 @@
+# HiFiLES - High Fidelity Large Eddy Simulation
+# Aerospace Computing Lab, Stanford University
+#
+# .gitignore - files & folders to be ignored when commiting
+# to your local or web repository
+#
+# Note that you can still 'git add <file>' any ignored file
+# if desired
+
 # Compiled Object files
 *.slo
 *.lo
 *.o
 
+# External Libraries Folder (in order to compile in place)
+lib/
+
 # Compiled Dynamic libraries
 *.so
 *.dylib

Makefile.am

@@ -14,4 +14,4 @@
 
 ACLOCAL_AMFLAGS = ${ACLOCAL_FLAGS}
 
-SUBDIRS = obj/
+SUBDIRS = obj/ lib/

configure.ac

@@ -6,17 +6,54 @@
 #         - Current development: Aerospace Computing Laboratory (ACL) directed
 #                                by Prof. Jameson. (Aero/Astro Dept. Stanford University).
 # \version 1.0.0
-# \date Modified on 3/14/14
+# \date Created on 3/14/14
+#       Modified on 4/1/14
 #
 # HiFiLES (High Fidelity Large Eddy Simulation).
 # Copyright (C) 2013 Aerospace Computing Laboratory.
 #####################################################
 AC_INIT([HiFiLES], [1.0.0], [[email protected]],
         [HiFiLES], [http://hifiles.stanford.edu])
 AC_PREREQ([2.59])
+AC_CONFIG_MACRO_DIR([m4])
 AM_INIT_AUTOMAKE([foreign])
+m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES(yes)])
 
+# --------------------------------------------------------------
+# Build up contributed packages that we will build from source
+# --------------------------------------------------------------
+hifiles_externals_INCLUDES=""
+hifiles_externals_LIBS=""
+
+Tecplot
+CONFIGURE_TECIO
+if (test $enabletecio = yes); then
+  hifiles_externals_INCLUDES="$TECIO_INCLUDE $hifiles_externals_INCLUDES"
+  hifiles_externals_LIBS="$TECIO_LIB $hifiles_externals_LIBS"
+else
+  hifiles_externals_INCLUDES="-DNO_TECIO $hifiles_externals_INCLUDES"
+fi
+AM_CONDITIONAL(BUILD_TECIO, test x$enabletecio = xyes)
+AC_CONFIG_FILES([externals/tecio/Makefile])
+
+# Metis
+# CONFIGURE_METIS
+# if (test $enablemetis = yes); then
+#   su2_externals_INCLUDES="$METIS_INCLUDE $su2_externals_INCLUDES"
+#   su2_externals_LIBS="$METIS_LIB $su2_externals_LIBS"
+# else
+#   su2_externals_INCLUDES="-DNO_METIS $su2_externals_INCLUDES"
+# fi
+# AM_CONDITIONAL(BUILD_METIS, test x$enablemetis = xyes)
+# AC_CONFIG_FILES([externals/metis/Makefile])
+# 
+# 
+AC_SUBST([hifiles_externals_INCLUDES])
+AC_SUBST([hifiles_externals_LIBS])
+
+# --------------------------------------------------------------
 # optional bindings
+# --------------------------------------------------------------
 AC_ARG_WITH(CUDA,
     AS_HELP_STRING([--with-CUDA[=ARG]], [Build GPU version with NVidia CUDA compiler, ARG = CUDA compiler]), 
     [with_CUDA=$withval], [with_CUDA="no"])
@@ -26,26 +63,32 @@ AC_ARG_WITH(CUDA-lib,
 AC_ARG_WITH(CUDA-include,
     AS_HELP_STRING([--with-CUDA-include[=ARG]], [CUDA include directory, ARG = path to cuda.h]), 
     [with_CUDA_include=$withval], [with_CUDA_include="no"])
+
 AC_ARG_WITH(MPI,
     AS_HELP_STRING([--with-MPI[=ARG]], [Build parallel version with MPI tools, ARG = MPI C++ compiler]), 
     [with_MPI=$withval], [with_MPI="no"])
+
 AC_ARG_WITH(Tecio-lib,
     AS_HELP_STRING([--with-Tecio-lib[=ARG]], [Tecio library directory, ARG = path to libtecio.a]), 
     [with_Tecio_lib=$withval], [with_Tecio_lib="no"])
 AC_ARG_WITH(Tecio-include,
     AS_HELP_STRING([--with-Tecio-include[=ARG]], [Tecio include directory, ARG = path to TECIO.h]), 
     [with_Tecio_include=$withval], [with_Tecio_include="no"])
+
 AC_ARG_WITH(ParMetis-lib,
    	AS_HELP_STRING([--with-ParMetis-lib[=ARG]], [ParMetis library directory, ARG = path to libparmetis.a]), 
     [with_ParMetis_lib=$withval], [with_ParMetis_lib="no"])
 AC_ARG_WITH(ParMetis-include,
    	AS_HELP_STRING([--with-ParMetis-include[=ARG]], [ParMetis include directory, ARG = path to parmetis.h]), 
     [with_ParMetis_include=$withval], [with_ParMetis_include="no"])
-AC_ARG_WITH(ParMetis-version,
-   	AS_HELP_STRING([--with-ParMetis-version[=ARG]], [ParMetis major version, ARG = 4 (default) or 5]), 
-    [with_ParMetis_version=$withval], [with_ParMetis_version="4"])
-AC_ARG_WITH(CXX,
-    AS_HELP_STRING([--with-CXX[=ARG]], [Optional: Specify C++ compiler, ARG = C++ compiler]), [with_CXX=$withval], [with_CXX="GCC"])
+
+AC_ARG_WITH(Metis-lib,
+   	AS_HELP_STRING([--with-Metis-lib[=ARG]], [Metis library directory, ARG = path to libmetis.a]), 
+    [with_Metis_lib=$withval], [with_Metis_lib="no"])
+AC_ARG_WITH(Metis-include,
+   	AS_HELP_STRING([--with-Metis-include[=ARG]], [Metis include directory, ARG = path to metis.h]), 
+    [with_Metis_include=$withval], [with_Metis_include="no"]) 
+
 AC_ARG_WITH(BLAS,
     AS_HELP_STRING([--with-BLAS[=ARG]], [Build using support for a BLAS variant, ARG = BLAS library to use]), 
     [with_BLAS=$withval], [with_BLAS="no"])
@@ -55,6 +98,9 @@ AC_ARG_WITH(BLAS-lib,
 AC_ARG_WITH(BLAS-include,
     AS_HELP_STRING([--with-BLAS-include[=ARG]], [BLAS include directory, ARG = path to cblas.h]), 
     [with_BLAS_include=$withval], [with_BLAS_include="no"])
+
+AC_ARG_WITH(CXX,
+    AS_HELP_STRING([--with-CXX[=ARG]], [Optional: Specify C++ compiler, ARG = C++ compiler]), [with_CXX=$withval], [with_CXX="GCC"])
 
 ########################### CUDA (GPU-Enabled)
 # check if we're building GPU or CPU version
@@ -118,44 +164,63 @@ AC_SUBST([NVCCFLAGS])
 # check for lib
 ParMETISlib=libparmetis.a
 ParMETISheader=parmetis.h
+METISlib=libmetis.a
 ParMETISversion=
 have_ParMetis="no"
 
 if test "$with_ParMetis_lib" != "no" 
 then
+    # Optional value for separate Metis library file location
+    if test "$with_Metis_lib" == "no"
+    then
+        with_Metis_lib=$with_ParMetis_lib
+    fi    
+
   	AC_CHECK_FILE([$with_ParMetis_lib/$ParMETISlib],[have_ParMetis="yes"],[have_ParMetis="no"])   
 	if test "$have_ParMetis" == "no"
 	then
 		AC_MSG_ERROR([ParMETIS requested but library file not found.])
 	fi
+
+	AC_CHECK_FILE([$with_Metis_lib/$METISlib],[have_ParMetis="yes"],[have_ParMetis="no"])   
+	if test "$have_ParMetis" == "no"
+	then
+		AC_MSG_ERROR([ParMETIS requested but METIS library file not found.])
+	fi
 fi
 
 # check for header
 if test "$have_ParMetis" != "no"
 then
 	if test "$with_ParMetis_include" != "no"
 	then
+	    # Optional value for separate Metis header file location
+	    if test "$with_Metis_include" == "no"
+        then
+            with_Metis_include=$with_ParMetis_include
+        fi  
+
 		AC_CHECK_FILE([$with_ParMetis_include/$ParMETISheader],[have_ParMetis="yes"],[have_ParMetis="no"]) 
 		if test "$have_ParMetis" == "no"
 		then
 			AC_MSG_ERROR([ParMETIS requested but header file not found.])
 		fi
+
+		AC_CHECK_FILE([$with_Metis_include/$METISheader],[have_ParMetis="yes"],[have_ParMetis="no"]) 
+		if test "$have_ParMetis" == "no"
+		then
+			AC_MSG_ERROR([ParMETIS requested but METIS header file not found.])
+		fi
 	else
 		have_ParMetis="no"
 	fi  
 fi
 
-# ParMETIS version check
-if test "$with_ParMetis_version" == "5"
-then
-	ParMETISversion=-DPARMETIS_5
-fi
-
 if test "$have_ParMetis" != "no"
 then
   	AM_CONDITIONAL(BUILD_PARMETIS,true)
-	PARMETIS_CXX="-I"$with_ParMetis_include $ParMETISversion
-	PARMETIS_LD=$with_ParMetis_lib"/"$ParMETISlib
+	PARMETIS_CXX="-I$with_ParMetis_include $ParMETISversion"
+	PARMETIS_LD="$with_ParMetis_lib/$ParMETISlib $with_Metis_lib/$METISlib"
 else
 	AM_CONDITIONAL(BUILD_PARMETIS,false)
 	PARMETIS_CXX=-DNO_PARMETIS
@@ -225,12 +290,12 @@ fi
 
 ########################### BLAS
 # *** still need to implement library & header-file checks ***
-if test "$with_BLAS" == "ACCELERATE_BLAS"
+if test "$with_BLAS" == "ACCELERATE"
 then
     BLAS_CXX=" -flax-vector-conversions -D_ACCELERATE_BLAS"
     BLAS_LDFLAGS=" -framework Accelerate"
     BLAS_LD=
-elif test "$with_BLAS" == "STANDARD_BLAS"
+elif test "$with_BLAS" == "STANDARD"
 then
     AC_CHECK_FILE([$with_BLAS_lib/libcblas.a],[have_BLAS="yes"],[have_BLAS="no"]) 
 	if test "$have_BLAS" != "no"
@@ -241,9 +306,9 @@ then
 	fi
 	if test "$have_BLAS" == "no"
 	then
-		AC_MSG_ERROR([BLAS linking requested but library file not found.])
+		AC_MSG_ERROR([BLAS linking requested but library file not found (libcblas.a).])
 	fi
-elif test "$with_BLAS" == "ATLAS_BLAS"
+elif test "$with_BLAS" == "ATLAS"
 then
     AC_CHECK_FILE([$with_BLAS_lib/libcblas.a],[have_BLAS="yes"],[have_BLAS="no"]) 
 	if test "$have_BLAS" != "no"
@@ -256,10 +321,10 @@ then
         BLAS_LD="$with_BLAS_lib/libcblas.a $with_BLAS_lib/libatlas.a"
         BLAS_LDFLAGS=
 	else
-		AC_MSG_ERROR([BLAS linking requested but library file not found.])
+		AC_MSG_ERROR([BLAS linking requested but library files not found (libcblas.a, libatlas.a).])
 	fi
 # needs more work here (not terribly familiar with our MKL usage)
-elif test "$with_BLAS" == "MKL_BLAS"
+elif test "$with_BLAS" == "MKL"
 then
     if test "$CXX" == "icpc"
     then
@@ -268,13 +333,7 @@ then
         BLAS_INCLUDE=
         BLAS_LDFLAGS=
     fi
-elif test "$with_BLAS" == "NO_BLAS"
-then
-    BLAS_CXX="-DNO_BLAS"
-    BLAS_LD=
-    BLAS_LDFLAGS=
-    have_BLAS="no"
-elif test "$with_BLAS" == "no"
+elif [test "$with_BLAS" == "NO"] || [test "$with_BLAS" == "no"]
 then
     BLAS_CXX="-DNO_BLAS"
     BLAS_LD=
@@ -292,7 +351,6 @@ AC_PROG_CXX
 AC_PROG_CC
 AM_PROG_CC_C_O
 AM_PROG_LIBTOOL
-#AC_PROG_RANLIB
 AC_OUTPUT(Makefile \
 	obj/Makefile)
 

configure_run.sh

@@ -19,7 +19,7 @@ HIFILES_RUN=$PWD/bin
 # Basic User-Modifiable Build Settings [Change these as desired]
 NODE="CPU"              # CPU or GPU
 CODE="DEBUG"            # DEBUG or RELEASE
-BLAS="ATLAS_BLAS"       # *_BLAS: ATLAS, STANDARD, ACCLERATE, MKL, or NO
+BLAS="ATLAS"            # ATLAS, STANDARD, ACCLERATE, MKL, or NO
 PARALLEL="no"           # MPI or NO
 TECIO="no"              # YES or NO
 # ---------------------------------------------------------------
@@ -29,18 +29,20 @@ NVCC="nvcc"             # NVidia CUDA compiler
 MPICC="mpicxx"          # MPI compiler
 # ---------------------------------------------------------------
 # Library Locations [Change filepaths as needed]
-#BLAS_LIB="/usr/local/atlas/lib"
+BLAS_LIB="/usr/local/atlas/lib"
 BLAS_INCLUDE="/usr/local/atlas/include"
-BLAS_LIB="/usr/lib/atlas-base"
 
 PARMETIS_LIB="/usr/local/lib"
 PARMETIS_INCLUDE="/usr/local/include"
 
+METIS_LIB="/usr/local/lib"
+METIS_INCLUDE="/usr/local/include"
+
 TECIO_LIB="lib/tecio-2008/lib"
 TECIO_INCLUDE="lib/tecio-2008/include"
 
 CUDA_LIB="/usr/local/cuda/lib64"
-CUDA_INCLUE="/usr/local/cuda/include"
+CUDA_INCLUDE="/usr/local/cuda/include"
 # ---------------------------------------------------------------
 # Run configure using the chosen options [Should not change this]
 if [[ "$NODE" == "GPU" ]]

lib/Makefile.am

@@ -0,0 +1,9 @@
+SUBDIRS =
+
+if BUILD_TECIO
+  SUBDIRS += tecio-2008
+endif
+
+if BUILD_METIS
+  SUBDIRS += parmetis-4.0.2
+endif

lib/parmetis-4.0.2/Makefile.am

@@ -0,0 +1,60 @@
+pkg_cppflags  = @HIFILES_METIS_CPPFLAGS@
+pkg_cppflags += -I$(srcdir)/include  -I$(srcdir)/GKlib -I$(srcdir)/libmetis
+pkg_sources = \
+    akwayfm.c \
+    ametis.c \
+    balancemylink.c \
+    comm.c \
+    csrmatch.c \
+    ctrl.c \
+    debug.c \
+    diffutil.c \
+    frename.c \
+    gkmetis.c \
+    gkmpi.c \
+    graph.c \
+    initbalance.c \
+    initmsection.c \
+    initpart.c \
+    kmetic.c \
+    kwayrefine.c \
+    match.c \
+    mdiffusion.c \
+    mesh.c \
+    mmetis.c \
+    move.c \
+    msetup.c \
+    node_refine.c \
+    ometis.c \
+    pspases.c \
+    redomylink.c \
+    remap.c \
+    renumber.c \
+    rmetis.c \
+    selectq.c \
+    serial.c \
+    stat.c \
+    timer.c \
+    util.c \
+    wave.c \
+    weird.c \
+    wspace.c \
+    xyapart.c
+
+
+
+
+######################################################################
+AUTOMAKE_OPTIONS = subdir-objects
+
+AM_CPPFLAGS  = $(pkg_cppflags) # any defined package-specific include paths
+AM_CFLAGS    =
+AM_CXXFLAGS  =
+AM_LDFLAGS   = $(srcdir)/metis/libmetis/libmetis.a
+
+noinst_LIBRARIES = libparmetis.a
+
+libparmetis_a_SOURCES  = $(pkg_sources)
+libparmetis_a_CPPFLAGS = $(CPPFLAGS_DBG) $(AM_CPPFLAGS)
+libparmetis_a_CXXFLAGS = $(CXXFLAGS_DBG)
+libparmetis_a_CFLAGS   = $(CFLAGS_DBG)