add parallel solvers

.githelp

@@ -29,7 +29,7 @@ Working with remotes
   adding a remote: git remote add <shortname> <url>
 
 Pushing
-  pushing to remote ifsttar: git push ifsttar master
+  pushing to remote ifsttar: git push Universite-Gustave-Eiffel master
   pushing to remote dangla: git push dangla master
   adding a remote: git remote add <shortname> <url>
   Note: Github will no longer accept account passwords

BilConfig.h.in

@@ -0,0 +1,12 @@
+#ifndef BILCONFIG_H
+#define BILCONFIG_H
+
+#cmakedefine HAVE_OPENMP
+#cmakedefine HAVE_PTHREAD
+#cmakedefine HAVE_MPI
+
+//#define BIL_CONFIG_OPTIONS "${BIL_CONFIG_OPTIONS}"
+
+//${BIL_CONFIG_PRAGMAS}
+
+#endif

CMakeLists.txt

@@ -16,7 +16,11 @@ endif()
 
 
 # set the project name
-project(bil C CXX Fortran)
+project(bil LANGUAGES C CXX Fortran)
+
+
+option(ENABLE_OPENMP "Enable OpenMP parallelization" OFF)
+option(ENABLE_PTHREADS "Enable Pthreads parallelization" OFF)
 
 
 # Add the CMake directory for custon CMake modules
@@ -69,21 +73,12 @@ include(Extralibs)
 
 
 
-#[[
-# use, i.e. don't skip the full RPATH for the build tree
-set(CMAKE_SKIP_BUILD_RPATH FALSE)
-# when building, don't use the install RPATH already
-# (but later on when installing)
-set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
-set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
-# add the automatically determined parts of the RPATH
-# which point to directories outside the build tree to the install RPATH
-set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
-]]
-
+include(SetCompilerFlags)
 
 
-include(SetCompilerFlags)
+# Bil options
+# -----------
+include(SetBilConfig)
 
 
 # the executable and the library

EXTRALIBS

@@ -1,5 +1,12 @@
 # This is a comment. Put a # in the first column to comment the line.
-BLAS = /usr/lib/x86_64-linux-gnu/blas/libblas.so
-LAPACK = /usr/lib/x86_64-linux-gnu/lapack/liblapack.so
-SUPERLU = /usr/lib/x86_64-linux-gnu/libsuperlu.so
+#SUPERLU = /usr/lib/x86_64-linux-gnu/libsuperlu.so
+#SUPERLUMT = /home/dangla/Documents/Softwares/bil/bil-master/src/Libraries/superlu/superlu_mt-master/lib/libsuperlu_mt_OPENMP.so
+#SUPERLUMT = /home/dangla/Documents/Softwares/bil/bil-master/src/Libraries/superlu/superlu_mt-master/lib/libsuperlu_mt_PTHREAD.so
+SUPERLUDIST = /usr/local/lib/libsuperlu_dist.so
+#LAPACK = /usr/lib/x86_64-linux-gnu/liblapack.so
+#BLAS = /usr/lib/x86_64-linux-gnu/libblas.so
 #UEL = /home/dangla/Documents/Softwares/bil/Projects/IoannisStefanou/libUEL_64.so
+#GSL = /usr/lib/x86_64-linux-gnu/libgsl.so
+#GSLCBLAS = /usr/lib/x86_64-linux-gnu/libgslcblas.so
+#F2C = /usr/lib/x86_64-linux-gnu/libf2c.so
+

Makefile

@@ -83,6 +83,10 @@ BIL_LIBS += ${BIL_EXTRALIBS}
 include make.inc
 
 
+# Options file
+BILCONFIG_H := BilConfig.h
+
+
 #=======================================================================
 # Default target executed when no arguments are given to make.
 all: bin doc
@@ -92,12 +96,12 @@ all: bin doc
 # Target rules for binaries
 
 .PHONY: bin
-bin: make.inc path_init version_init info_init lib compile link
+bin: make.inc path_init version_init info_init config_init lib compile link
 
 compile: make.inc path_init version_init info_init lib
 	@echo "\nCompilation"
 	mkdir -p ${BIL_LIBDIR}
-	for i in ${BIL_DIRS}; do (cd $$i && ${MAKE}); done
+	for i in ${BIL_DIRS}; do ( ${MAKE} -C $$i ); done
 
 link: make.inc
 	@echo "\nLinking with embedded location of shared libraries (rpath method), if any"
@@ -141,15 +145,15 @@ install-liba:
 
 install-doc:
 	@echo "\nInstalling documentations"
-	cd doc && ${MAKE} install-doc
+	( ${MAKE} -C doc install-doc )
 
 
 #=======================================================================
 # Target rules for cleaning
 
 clean:
 	@echo "\nCleaning directories (removing binaries,...)"
-	for i in ${BIL_DIRS} doc examples base; do (cd $$i && ${MAKE} clean); done
+	for i in ${BIL_DIRS} doc examples base; do (${MAKE} -C $$i clean); done
 	rm -f make.log
 	@echo "\nRemoving libraries"
 	rm -f ${BIL_LIBDIR}/*.a
@@ -164,7 +168,8 @@ clean-all: clean
 	rm -f ${BILINFO_H} 
 	rm -f ${BILEXTRALIBS_H}
 	rm -f ${BILPATH_H}
-	cd doc && ${MAKE} clean-all
+	rm -f ${BILCONFIG_H}
+	( ${MAKE} -C doc clean-all )
 
 
 #=======================================================================
@@ -233,18 +238,45 @@ lib:
 	touch ${BILEXTRALIBS_H}
 	echo "#ifndef BILEXTRALIBS_H"    >>  ${BILEXTRALIBS_H}
 	echo "#define BILEXTRALIBS_H"    >>  ${BILEXTRALIBS_H}
-	@if [ -n "${SUPERLU_DIR}" ]; then \
-	  echo "#define SUPERLULIB  ${SUPERLU_DIR}" >> ${BILEXTRALIBS_H} ; \
+	if [ -n "${LAPACK_DIR}" ] ; then \
+	  echo "#define LAPACKLIB   ${LAPACK_DIR}"  >> ${BILEXTRALIBS_H} ; \
 	fi
-	@if [ -n "${BLAS_DIR}" ] ; then \
+	if [ -n "${BLAS_DIR}" ] ; then \
 	  echo "#define BLASLIB     ${BLAS_DIR}"    >> ${BILEXTRALIBS_H} ; \
 	fi
-	@if [ -n "${LAPACK_DIR}" ] ; then \
-	  echo "#define LAPACKLIB   ${LAPACK_DIR}"  >> ${BILEXTRALIBS_H} ; \
+	if [ -n "${GSLCBLAS_DIR}" ] ; then \
+	  echo "#define GSLCBLASLIB     ${GSLCBLAS_DIR}"    >> ${BILEXTRALIBS_H} ; \
+	fi
+	if [ -n "${SUPERLU_DIR}" ]; then \
+	  echo "#define SUPERLULIB  ${SUPERLU_DIR}" >> ${BILEXTRALIBS_H} ; \
+	fi
+	if [ -n "${SUPERLUMT_DIR}" ]; then \
+	  echo "#define SUPERLUMTLIB  ${SUPERLUMT_DIR}" >> ${BILEXTRALIBS_H} ; \
 	fi
 	echo "#endif"    >>  ${BILEXTRALIBS_H}
 
 
+#=======================================================================
+# Target rules for config file
+
+config:
+	rm -f ${BILCONFIG_H}
+	touch ${BILCONFIG_H}
+	echo "#ifndef BILCONFIG_H"    >>  ${BILCONFIG_H}
+	echo "#define BILCONFIG_H"    >>  ${BILCONFIG_H}
+	if [ ${ENABLE_OPENMP} = ON ]; then \
+	  echo "#define HAVE_OPENMP" >> ${BILCONFIG_H} ; \
+	fi
+	if [ ${ENABLE_PTHREAD} = ON ]; then \
+	  echo "#define HAVE_PTHREAD" >> ${BILCONFIG_H} ; \
+	fi
+	echo "#endif"    >>  ${BILCONFIG_H}
+
+config_init:
+	@if [ ! -r ${BILCONFIG_H} ]; then ${MAKE} config ; fi
+
+
+
 #=======================================================================
 # Target rules for documentations
 
@@ -284,7 +316,7 @@ githelp:
 # Target rules for tests
 
 test:
-	@( cd base; pwd )
+	@( echo "base:"; cd base; pwd )
 	@( echo "BIL_PATH = ${BIL_PATH}" )
 	@( echo "Last part of BIL_PATH = ${notdir ${BIL_PATH}}" )
 	@( echo "BIL_COPYRIGHT = ${BIL_COPYRIGHT}" )
@@ -293,6 +325,7 @@ test:
 	@( echo "BLAS_DIR = ${BLAS_DIR}" )
 	@( echo "LAPACK_DIR = ${LAPACK_DIR}" )
 	@( echo "UEL_DIR = ${UEL_DIR}" )
+	@( echo "CFLAGS = ${CFLAGS}" )
 
 
 #=======================================================================

OPTIONS

@@ -0,0 +1,4 @@
+# This is a comment. Put a # in the first column to comment the line.
+ENABLE_OPENMP   = OFF
+ENABLE_PTHREAD  = OFF
+ENABLE_MPI      = OFF

README.md

@@ -24,7 +24,7 @@ Building the documentation from source requires:
 and optionally
 
   - Doxygen (<http://www.stack.nl/~dimitri/doxygen>)
-
+  
 
 List of folders
 ===============
@@ -44,9 +44,9 @@ Building and Installation
 
 There are two methods to build Bil from the command line:
 
-  1. from make (native method suited for linux-based OS)
-  2. from cmake (suited for any OS like Windows or MacOS)
-
+  - from make (native method suited for linux-based OS)
+  - from cmake (suited for any OS like Windows or MacOS)
+  
 
 1. Build Bil from make (native method)
 --------------------------------------
@@ -77,8 +77,8 @@ Once the installation is completed, running
         make clean  
 
 will delete all the local files previously created.
-
-
+  
+  
 2. Build Bil from cmake (command line)
 --------------------------------------
 
@@ -162,16 +162,17 @@ Some functionalities (like solvers ma38 and superlu) require the use of the foll
 
   - **LAPACK**: you can obtain the latest LAPACK from http://www.netlib.org/lapack  
 
-  - **SUPERLU**: you can obtain the relevant C functions by visiting the following
-            URL: https://github.com/xiaoyeli/superlu  
+  - **SuperLU, SuperLU_MT, SuperLU_DIST**: you can obtain the relevant C functions by visiting the following
+            URL: https://portal.nersc.gov/project/sparse/superlu/.
+            Note that these three libraries cannot be mixed, only one can be loaded per build target. SuperMU_MT needs either "omp" or "pthread" library. SuperLU_DIST needs "mpi" library.
 
 These librairies are not included in this package. You need to explicitly specify their location in the file "EXTRALIBS". You can also choose to disable the use of these libraries and the associated functionalities by deleting or commenting the locations.
 
 
 External software
 =================
 
-This package contains some fortran routines provided by HSL: "HSL, a collection of Fortran codes for large-scale scientific computation. See http://www.hsl.rl.ac.uk/"
+This package contains some fortran routines provided by HSL: "HSL, a collection of Fortran codes for large-scale scientific computation". See http://www.hsl.rl.ac.uk/.
 
 
 Usage

TODO

@@ -1,3 +1,6 @@
+Request(21/10/2022)  - Rename all files using the prefix "bil_".
+To avoid confusion rename also "Bil.[c,h]" as "BilEntry.[c,h]"
+
 Request(21/09/2019)  - Improve solver "ludcmp" by pivoting rows and columns.
 
 Request(22/04/2019)  - Introduce a pointer to char in structures having to be initialized by data to be read in the datafile. This pointer should point to the beginning of the data in the file content.

base/BBM/BBM

@@ -0,0 +1,74 @@
+Geometry       # dimension (1, 2, 3) et symétrie (axis, plan) du pb
+2 axis
+
+Mesh                # maillage considéré (généré avec GMSH)
+carre.msh
+
+Material            # liste des matériaux (modèles et param. associés)
+Model = BBM         # nom du modèle
+gravity = 0         # gravité
+rho_s = 2000        # masse volumique des particules solides
+slope_of_swelling_line = 0.004       # indice de gonflement elastique
+slope_of_virgin_consolidation_line = 0.037      # pente de la NCL dans le plan (ln p', e)
+shear_modulus = 1.e8# module de cisaillement
+slope_of_critical_state_line = 1.2             # pente de la CSL dans le plan (p', q)
+initial_pre-consolidation_pressure = 20e3         # preconsolidation
+reference_consolidation_pressure = 0.01e6         # reference consolidation pressure
+kappa_s = 0.008
+initial_stress_11 = -1000        # contrainte initiale (isotrope)
+initial_stress_22 = -1000        # contrainte initiale (isotrope)
+initial_stress_33 = -1000        # contrainte initiale (isotrope)
+initial_porosity = 0.25          # porosite initiale
+rho_l = 1000        # masse volumique du fluide
+k_int = 1e-20       # permeabilite intrinseque
+mu_l = 0.001        # viscosite du liquide
+suction_cohesion_coefficient = 0.8
+#Curves = wrc        # nom du fichier contenant p_c S_l k_rl LC
+Curves = wrc2   pc = Range{x1 = 0 , x2 = 30.e6, n = 171}  sl = Expressions(1){p0 = 1.e6 ; m = 0.6 ; sl = (1 + (pc/p0)**(1/(1-m)))**(-m)} kl = Expressions(1){kl = 1} kg = Expressions(1){kg = 1} lc = Expressions(1){l0 = 0.037 ; k = 0.004 ; beta = 20.e-6 ; r = 0.75 ; lc = (l0 - k)/(l0*((1-r)*exp(-beta*pc) + r) - k)}
+
+
+
+Fields                # champs constants ou linéaires dans l'espace
+2
+Value = 0.e3 Gradient = 0 0 Point = 0 0
+Value = 1.e3 Gradient = 0 0 Point = 0 0
+
+Initialization                # initialisation des variables
+0
+
+Functions                # fonctions temporelles, pour les CL
+1
+N = 3 F(0) = 1 F(1) = 250 F(2) = 1
+
+Boundary Conditions                # conditions aux limites (Dirichlet)
+3
+Region = 14 Unknown = u_1 Field = 0 Function = 0
+Region = 11 Unknown = u_2 Field = 0 Function = 0
+Region = 100 Unknown = p_l Field = 1 Function = 0
+
+Loads                # conditions aux limites (Neumann)
+2
+Region = 13 Equation = meca_1 Type = pressure Field = 2 Function = 1
+Region = 12 Equation = meca_1 Type = pressure Field = 2 Function = 1
+
+Points                # points de l'espace pour le stockage des variables
+1
+0.5 0.5
+
+Dates                # dates pour le stockage des données
+2
+0 1 2
+
+Objective Variations                # variables objectives (une par ddl)
+u_1 = 1.e-4
+u_2 = 1.e-4
+p_l = 1000
+
+Iterative Process                # param. num. pour le contrôle de la convergence
+Iteration = 100
+Tolerance = 1e-06
+Repetition = 0
+
+Time Steps
+Dtini = 1.e-4
+Dtmax = 1e-3