[petsc-users] Integrate PETSC with existing Fortran
Yaxiong Chen
chen2018 at purdue.edu
Wed Jan 23 12:27:12 CST 2019
Hi Matt,
I tried to modify the structure of present code and use KSP in the main program(optimal_mechanical_part). Now the makefile is as following :
#================================================================================
OUT_DIR := HiDACX/
## Define mode
ifndef MODE
.PHONY: debug release
debug: export MODE := debug
release: export MODE := release
debug release:
@$(MAKE) $@
clean:
rm -rf $(OUT_DIR)obj/ $(OUT_DIR)lib/ $(OUT_DIR)bin/
else
## SRCS = $(shell find ../../MyGit/Hidac_Fortran_Lib/ "*.f90")
SRCS_DIR := $(HOME)/Documents/HiDAC_Code_Git/HiDAC_Tao_NURBS_Petsc/Hidac_Fortran_Lib/
FSRCS := \
HiDAC_Utils/HiDAC_parameter.f90 \
HiDAC_Utils/HiDAC_dataStructure.f90 \
HiDAC_Utils/HiDAC_Math/HiDAC_mathFunction.f90 \
HiDAC_Utils/HiDAC_Math/HiDAC_mathType.f90 \
HiDAC_Utils/HiDAC_Math/HiDAC_tensor.f90 \
HiDAC_Utils/HiDAC_Math/HiDAC_Math.f90 \
HiDAC_Utils/HiDAC_Port/HiDAC_IGES.f90 \
HiDAC_Utils/HiDAC_Port/IR_Precision.f90 \
HiDAC_Utils/HiDAC_Port/Lib_Pack_Data.f90 \
HiDAC_Utils/HiDAC_Port/Lib_Base64.f90 \
HiDAC_Utils/HiDAC_Port/Lib_VTK_IO.f90 \
HiDAC_Utils/HiDAC_Port/HiDAC_VTK.f90 \
HiDAC_Utils/HiDAC_Port/HiDAC_Port.f90 \
HiDAC_Utils/HiDAC_DistanceField/HiDAC_QhullInterface_F.f90 \
HiDAC_Utils/HiDAC_DistanceField/HiDAC_BezierHull.f90 \
HiDAC_Utils/HiDAC_DistanceField/HiDAC_DistanceField.f90 \
HiDAC_Utils/HiDAC_Utils.f90 \
HiDAC_Material/HiDAC_baseMat.f90 \
HiDAC_Material/HiDAC_isoElasticMat.f90 \
HiDAC_Material/HiDAC_thermoMat.f90 \
HiDAC_Material/HiDAC_Material.f90 \
HiDAC_Approximation/HiDAC_node.f90 \
HiDAC_Approximation/HiDAC_nodeNet.f90 \
HiDAC_Approximation/HiDAC_baseApproximation.f90 \
HiDAC_Approximation/HiDAC_Approximation.f90 \
HiDAC_Approximation/HiDAC_Approximation_NURBS/HiDAC_knot.f90 \
HiDAC_Approximation/HiDAC_Approximation_NURBS/HiDAC_BezierApproximation.f90 \
HiDAC_Approximation/HiDAC_Approximation_NURBS/HiDAC_NURBSApproximation.f90 \
HiDAC_Approximation/HiDAC_Approximation_NURBS/HiDAC_THBApproximation.f90 \
HiDAC_Domain/HiDAC_primitive.f90 \
HiDAC_Domain/HiDAC_enrichment.f90 \
HiDAC_Domain/HiDAC_composedDomain.f90 \
HiDAC_Domain/HiDAC_Domain.f90 \
HiDAC_Quadrature/HiDAC_quadType.f90 \
HiDAC_Quadrature/HiDAC_directQuadrature.f90 \
HiDAC_Quadrature/HiDAC_adaptiveQuadrature.f90 \
HiDAC_Quadrature/HiDAC_Quadrature.f90 \
HiDAC_Analysis/HiDAC_BC.f90 \
HiDAC_Analysis/HiDAC_baseAnalysis.f90 \
HiDAC_Analysis/HiDAC_elastostatics.f90 \
HiDAC_Analysis/HiDAC_heatConduction.f90 \
HiDAC_Analysis/HiDAC_phaseTransition.f90 \
HiDAC_Analysis/HiDAC_fracture.f90 \
HiDAC_Analysis/HiDAC_lineenrich.f90 \
HiDAC_Analysis/HiDAC_sensitivityAnalysis.f90 \
HiDAC_Analysis/HiDAC_Analysis.f90 \
HiDAC_Solver/HiDAC_baseSolver.f90 \
HiDAC_Solver/HiDAC_LapackSolver.f90 \
HiDAC_Solver/HiDAC_MumpsSolver.f90 \
HiDAC_Solver/HiDAC_Solver.f90 \
IGES/read_iges_file.f90 \
IGES/nrb.f90 \
IGES/parse.f90 \
IGES/map.f90 \
DXF/dxf_reader.f90 \
TSRCS_DIR := $(SRCS_DIR)HiDAC_Test/
CSRCS := \
HiDAC_Utils/HiDAC_DistanceField/HiDAC_QhullInterface_C.c \
SRCS := $(addprefix $(SRCS_DIR), $(FSRCS) $(CSRCS))
OBJS_DIR := $(OUT_DIR)obj/$(MODE)/
LIB_DIR := $(OUT_DIR)lib/$(MODE)/
EXE_DIR := $(OUT_DIR)bin/$(MODE)/
EXT_DIR := /usr/local/
#petsc lib
include ${PETSC_DIR}/lib/petsc/conf/variables
include ${PETSC_DIR}/lib/petsc/conf/rules
#========================
OBJS := $(addprefix $(OBJS_DIR), \
$(patsubst %.f90, %.o, $(notdir $(FSRCS))) \
$(patsubst %.c, %.o, $(notdir $(CSRCS))))
LIB = $(LIB_DIR)libhidac.a
VPATH := $(sort $(dir $(SRCS))) $(TSRCS_DIR)
FC := mpif90
CC := mpicc
AR := ar rcs
FCFLAGS := -cpp -J$(OBJS_DIR) # ${PETSC_KSP_LIB}# -fprofile-arcs -ftest-coverage
CCFLAGS := -Dqh_QHpointer -ansi
LFLAGS := -Wl,-rpath,$(EXT_DIR)lib, ${PETSC_KSP_LIB}
FIDIR := \
-I$(EXT_DIR)include \
-I$(PETSC_DIR)/include
CIDIR := \
-I$(EXT_DIR)include/libqhull
# sequence does matter
EXTLIBS := \
-L$(EXT_DIR)lib \
-ldmumps -lmumps_common \
-lparmetis -lmetis -lpord -lscalapack \
-llapack -lblas -lqhullstatic_p \
-lpetsc
.PHONY: debug release all clean
# Handle different mode using target-specific variable
debug: FCFLAGS += -Wall -fcheck=bounds
debug: CCFLAGS += -Wall
debug: LFLAGS += -Wall -fcheck=bounds
release: FCFLAGS += -O2
release: CCFLAGS += -O2
release: LFLAGS += -O2
debug release: $(EXE_DIR)optimal_mechanical_part.hdc
## Rules
.SUFFIXES: .hdc
# Note the sequence of $(OBJS_DIR)%.o $(LIB) and $(EXTLIBS) does matter! Lib later!
$(EXE_DIR)%.hdc: $(OBJS_DIR)%.o $(LIB)
@mkdir -p $(EXE_DIR)
echo $(OBJS_DIR)
$(FC) $(LFLAGS) -o $@ $^ $(EXTLIBS) ${PETSC_KSP_LIB}
$(LIB): $(OBJS)
echo $(OBJS)
@mkdir -p $(LIB_DIR)
$(AR) $@ $^
$(OBJS_DIR)%.o:
@mkdir -p $(OBJS_DIR)
@echo $@
$(if $(findstring .f90, $<), \
$(FC) $(FCFLAGS) $(FIDIR) -c $< -o $@, \
$(CC) $(CCFLAGS) $(CIDIR) -c $< -o $@)
## Dependencies of files
$(OBJS_DIR)optimal_mechanical_part.o: \
optimal_mechanical_part.f90 \
$(OBJS_DIR)read_iges_file.o \
$(OBJS_DIR)HiDAC_Approximation.o \
$(OBJS_DIR)HiDAC_Domain.o \
$(OBJS_DIR)HiDAC_Material.o \
$(OBJS_DIR)HiDAC_Quadrature.o \
$(OBJS_DIR)HiDAC_Analysis.o \
$(OBJS_DIR)HiDAC_Utils.o
$(OBJS_DIR)read_iges_file.o: \
read_iges_file.f90 \
$(OBJS_DIR)HiDAC_Approximation.o \
$(OBJS_DIR)HiDAC_Utils.o \
$(OBJS_DIR)nrb.o \
$(OBJS_DIR)parse.o \
$(OBJS_DIR)map.o \
$(OBJS_DIR)dxf_reader.o
$(OBJS_DIR)test_main.o: \
test_main.f90 \
$(OBJS_DIR)read_iges_file.o
$(OBJS_DIR)dxf_reader.o: \
dxf_reader.f90 \
$(OBJS_DIR)nrb.o
$(OBJS_DIR)parse.o: \
parse.f90 \
$(OBJS_DIR)nrb.o
$(OBJS_DIR)map.o: \
map.f90 \
$(OBJS_DIR)nrb.o
<Other dependencies >
# $(OBJS_DIR)HiDAC_PetscSolver.o : HiDAC_PetscSolver.f90 $(OBJS_DIR)HiDAC_baseSolver.o $(OBJS_DIR)HiDAC_Utils.o
# mpif90 -cpp -JHiDACX/obj/debug/ -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -I/Users/yaxiong/Downloads/petsc-3.9.4/include \
# -I/Users/yaxiong/Downloads/petsc-3.9.4/arch-darwin-c-debug/include \
# -I/opt/X11/include -o $(OBJS_DIR)HiDAC_PetscSolver.o \
# /Users/yaxiong/Documents/HiDAC_Code_Git/HiDAC_Tao_NURBS_PETSC/Hidac_Fortran_Lib/HiDAC_Solver/HiDAC_PetscSolver.f90 \
# /Users/yaxiong/Documents/HiDAC_Code_Git/HiDAC_Tao_NURBS_PETSC/Hidac_Fortran_Lib/HiDACX/obj/debug/HiDAC_baseSolver.o \
# /Users/yaxiong/Documents/HiDAC_Code_Git/HiDAC_Tao_NURBS_PETSC/Hidac_Fortran_Lib/HiDACX/obj/debug/HiDAC_Utils.o \
# This part is removed
endif
#============================Makefile finished ===============================
and the main program starts like this:
!============================ Main program starts=========================
program main
!******************************************************!
! Import all HiDAC library
!******************************************************!
include 'mpif.h'
#include <petsc/finclude/petscksp.h>
use petscksp
use read_iges_file
use HiDAC_Approximation
use HiDAC_Domain
use HiDAC_Material
use HiDAC_Analysis
use HiDAC_Utils
use HiDAC_quadType
implicit none
!=================================================================
I have not call the function in PETSC yet. Just add the KSP library in my main program. But I received the following error when compiling:
HiDACX/obj/debug/optimal_mechanical_part.o
mpif90 -cpp -JHiDACX/obj/debug/ -Wall -fcheck=bounds -I/usr/local/include -I/Users/yaxiong/Downloads/petsc-3.9.4/include -c /Users/yaxiong/Documents/HiDAC_Code_Git/HiDAC_Tao_NURBS_Petsc/Hidac_Fortran_Lib/HiDAC_Test/optimal_mechanical_part.f90 -o HiDACX/obj/debug/optimal_mechanical_part.o
/Users/yaxiong/Downloads/petsc-3.9.4/include/petsc/finclude/petscsys.h:13:2:
#if defined (PETSC_HAVE_MPIUNI)
1~~~~~~~~~~~~
Fatal Error: petscconf.h: No such file or directory
compilation terminated.
make[1]: *** [HiDACX/obj/debug/optimal_mechanical_part.o] Error 1
make: *** [debug] Error 2
How can I solve this problem?
Thanks
Yaxiong Chen,
Ph.D. Student
School of Mechanical Engineering, 3171
585 Purdue Mall
West Lafayette, IN 47907
________________________________
From: Matthew Knepley <knepley at gmail.com>
Sent: Friday, January 18, 2019 2:21 PM
To: Yaxiong Chen; PETSc
Subject: Re: [petsc-users]Integrate PETSC with existing Fortran
On Fri, Jan 18, 2019 at 2:06 PM Yaxiong Chen <chen2018 at purdue.edu<mailto:chen2018 at purdue.edu>> wrote:
Hi Matt,
Do not drop the Cc.
I have hundreds .F90 files to compile as well as an .c file to compile in this project. The present makefile is more complex than the PETSC makefile. Do you mean I should use the PETSC makefile as a template and add all the dependencies in it?
If you want to do it by hand you can, its just more error prone and verbose.
My present Makefile is like the following(Red parts are news added related to Petsc). Is this the right direction? Since a static pattern is defined while the compiling for PetscSolver is a little different. I guess I should list it as a specific case instead of using the pattern.
I will comment inline.
# ============================================================================
# Name : Makefile
# Author : Tao Song
# Version : 2.1
# Copyright : GNU 2.1
# Description : Makefile for HiDACX
# ============================================================================
OUT_DIR := HiDACX/
## Define mode
ifndef MODE
.PHONY: debug release
debug: export MODE := debug
release: export MODE := release
debug release:
@$(MAKE) $@
clean:
rm -rf $(OUT_DIR)obj/ $(OUT_DIR)lib/ $(OUT_DIR)bin/
else
## SRCS = $(shell find ../../MyGit/Hidac_Fortran_Lib/ "*.f90")
SRCS_DIR := $(HOME)/Documents/HiDAC_Code_Git/HiDAC_Tao_NURBS_Petsc/Hidac_Fortran_Lib/
FSRCS := \
HiDAC_Utils/HiDAC_parameter.f90 \
HiDAC_Utils/HiDAC_dataStructure.f90 \
......
<other .f90 files>
HiDAC_Domain/HiDAC_primitive.f90 \
HiDAC_Solver/HiDAC_PetscSolver.F90 \
HiDAC_Solver/HiDAC_Solver.f90 \
IGES/read_iges_file.f90 \
IGES/nrb.f90 \
IGES/parse.f90 \
IGES/map.f90 \
DXF/dxf_reader.f90 \
TSRCS_DIR := $(SRCS_DIR)HiDAC_Test/
CSRCS := \
HiDAC_Utils/HiDAC_DistanceField/HiDAC_QhullInterface_C.c \
SRCS := $(addprefix $(SRCS_DIR), $(FSRCS) $(CSRCS))
OBJS_DIR := $(OUT_DIR)obj/$(MODE)/
LIB_DIR := $(OUT_DIR)lib/$(MODE)/
EXE_DIR := $(OUT_DIR)bin/$(MODE)/
EXT_DIR := /usr/local/
#petsc lib
include ${PETSC_DIR}/lib/petsc/conf/variables
include ${PETSC_DIR}/lib/petsc/conf/rules
You do not need 'rules' if you are doing things by hand. Although it is easier to just use the builtin rule for building source.
#========================
OBJS := $(addprefix $(OBJS_DIR), \
$(patsubst %.f90, %.o, $(notdir $(FSRCS))) \
$(patsubst %.c, %.o, $(notdir $(CSRCS))))
LIB = $(LIB_DIR)libhidac.a
VPATH := $(sort $(dir $(SRCS))) $(TSRCS_DIR)
FC := mpif90
CC := mpicc
AR := ar rcs
FCFLAGS := -cpp -J$(OBJS_DIR) # ${PETSC_KSP_LIB}# -fprofile-arcs -ftest-coverage
CCFLAGS := -Dqh_QHpointer -ansi
LFLAGS := -Wl,-rpath,$(EXT_DIR)lib, ${PETSC_KSP_LIB}
FIDIR := \
-I$(EXT_DIR)include \
-I$(PETSC_DIR)/include
CIDIR := \
-I$(EXT_DIR)include/libqhull
# sequence does matter
EXTLIBS := \
-L$(EXT_DIR)lib \
-ldmumps -lmumps_common \
-lparmetis -lmetis -lpord -lscalapack \
-llapack -lblas -lqhullstatic_p \
-lpetsc
.PHONY: debug release all clean
# Handle different mode using target-specific variable
debug: FCFLAGS += -Wall -fcheck=bounds
debug: CCFLAGS += -Wall
debug: LFLAGS += -Wall -fcheck=bounds
release: FCFLAGS += -O2
release: CCFLAGS += -O2
release: LFLAGS += -O2
debug release: $(EXE_DIR)optimal_mechanical_part.hdc
## Rules
.SUFFIXES: .hdc
# Note the sequence of $(OBJS_DIR)%.o $(LIB) and $(EXTLIBS) does matter! Lib later!
$(EXE_DIR)%.hdc: $(OBJS_DIR)%.o $(LIB)
@mkdir -p $(EXE_DIR)
echo $OBJS_DIR
$(FC) $(LFLAGS) -o $@ $^ $(EXTLIBS)
$(LIB): $(OBJS)
echo $OBJS
@mkdir -p $(LIB_DIR)
$(AR) $@ $^
$(OBJS_DIR)%.o:
@mkdir -p $(OBJS_DIR)
@echo $@
$(if $(findstring .f90, $<), \
$(FC) $(FCFLAGS) $(FIDIR) -c $< -o $@, \
$(CC) $(CCFLAGS) $(CIDIR) -c $< -o $@)
## Dependencies of files
$(OBJS_DIR)read_iges_file.o: \
read_iges_file.f90 \
$(OBJS_DIR)HiDAC_Approximation.o \
$(OBJS_DIR)HiDAC_Utils.o \
$(OBJS_DIR)nrb.o \
$(OBJS_DIR)parse.o \
$(OBJS_DIR)map.o \
$(OBJS_DIR)dxf_reader.o
$(OBJS_DIR)test_main.o: \
test_main.f90 \
$(OBJS_DIR)read_iges_file.o
<.... Other dependencies>
$ (OBJS_DIR)HiDAC_PetscSolver.o : HiDAC_PetscSolver.F90 $(OBJS_DIR)HiDAC_baseSolver.o $(OBJS_DIR)HiDAC_Utils.o
mpif90 -cpp -JHiDACX/obj/debug/ -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -I/Users/yaxiong/Downloads/petsc-3.9.4/include \
-I/Users/yaxiong/Downloads/petsc-3.9.4/arch-darwin-c-debug/include \
-I/opt/X11/include -o $(OBJS_DIR)HiDAC_PetscSolver.o \
/Users/yaxiong/Documents/HiDAC_Code_Git/HiDAC_Tao_NURBS_PETSC/Hidac_Fortran_Lib/HiDAC_Solver/HiDAC_PetscSolver.F90 \
/Users/yaxiong/Documents/HiDAC_Code_Git/HiDAC_Tao_NURBS_PETSC/Hidac_Fortran_Lib/HiDACX/obj/debug/HiDAC_baseSolver.o \
/Users/yaxiong/Documents/HiDAC_Code_Git/HiDAC_Tao_NURBS_PETSC/Hidac_Fortran_Lib/HiDACX/obj/debug/HiDAC_Utils.o \
${PETSC_KSP_LIB}
You can do this, but to be certain you should should use
${FC} -c ${FC_FLAGS} ${FFLAGS} ${FCPPFLAGS}
along with your flags (-J, etc.). Notice that you do not need the *.o files here since you are only compiling.
You can simplify this by includeing 'rules' and just putting the $ (OBJS_DIR)HiDAC_PetscSolver.o as a
dependence for your link.
Thanks,
Matt
endif
Yaxiong Chen,
Ph.D. Student
School of Mechanical Engineering, 3171
585 Purdue Mall
West Lafayette, IN 47907
________________________________
From: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>
Sent: Friday, January 18, 2019 11:57 AM
To: Yaxiong Chen; PETSc
Subject: Re: [petsc-users]Integrate PETSC with existing Fortran
On Fri, Jan 18, 2019 at 11:37 AM Yaxiong Chen <chen2018 at purdue.edu<mailto:chen2018 at purdue.edu>> wrote:
Hi Matt,
Now I have some problem with makefile.I want to integrate PETSC with a previous FEM Fortran code. To do that, I add a module named PetscSolver. It starts as the following:
It needs to have suffix .F or .F90 so the preprocessor is invoked. Use the PETSc makefiles to avoid problems.
Matt
!===================================================================
module HiDAC_PetscSolver
#include <petsc/finclude/petscksp.h>
use petscksp
use HiDAC_Utils
use HiDAC_baseSolver
implicit none
private
type, extends(Solver), public :: PetscSolver
private
Vec xvec,bvec,uvec
Mat Amat
KSP ksp
contains
procedure :: initialize => initialize_PetscSolver
procedure :: assemble => assemble_PetscSolver
procedure :: solve => solve_PetscSolver
procedure :: postprocess => postprocess_PetscSolver
procedure :: finalize => finalize_PetscSolver
procedure :: getID
end type PetscSolver
......
<Functions>
end module HiDAC_PetscSolver
!===================================================================
However, it did not compile successfully. It gave me the error:
#include <petsc/finclude/petscksp.h>
1
Warning: Illegal preprocessor directive
/Users/yaxiong/Documents/HiDAC_Code_Git/HiDAC_Tao_NURBS_PETSC/Hidac_Fortran_Lib/HiDAC_Solver/HiDAC_PetscSolver.f90:23:5:
Vec xvec,bvec,uvec
1
Error: Unclassifiable statement at (1)
/Users/yaxiong/Documents/HiDAC_Code_Git/HiDAC_Tao_NURBS_PETSC/Hidac_Fortran_Lib/HiDAC_Solver/HiDAC_PetscSolver.f90:24:5:
Mat Amat
All function and type related to Petsc are not defined.
I must have made a very silly mistake. Can you show me how to fix it?
Thanks
Yaxiong Chen,
Ph.D. Student
School of Mechanical Engineering, 3171
585 Purdue Mall
West Lafayette, IN 47907
--
What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
-- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/<http://www.cse.buffalo.edu/~knepley/>
--
What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
-- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/<http://www.cse.buffalo.edu/~knepley/>
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