Compilation of Fortran 90 code that uses PETSc

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• Makefile with Objects in Seperare Directory Tree

  I have been trying to devise a makefile example which can build object files to a different directory structure than the associated source. The directory tree, both with source and targets, is as follows:

  /repo-root
  |-- /build
      |-- /example_lib
          |-- makefile
          |-- /Release*
              |-- libexample_lib.a*
              |-- /obj*
                  |-- example_lib.o*
                  |-- example_lib.d*
  |-- /source
      |-- /example_lib
          |-- /inc
              |-- example_lib.h
          |-- /src
              |-- example_lib.cpp
  

  The asterisk folders/files are those the makefile should be generating.

  I have seen other questions and answers (Makefile : Build in a separate directory tree), (Makefile with directory for object files), etc., but if I understand their source-to-object rules correctly these appear to create a subdirectory tree within the output directory matching that of the source.

  The current makefile I am using is as follows, run using GNU Make 3.82:

  SHELL = /bin/sh
  
  .SUFFIXES:
  .SUFFIXES: .cpp .o
  
  # @todo Variables passed to make.
  BUILD_CONFIG=Release
  
  # Makefile specific variables
  REPO_ROOT=../..
  LIBRARY_NAME=example_lib
  
  #-------------------------------------------------------------------
  # Derived variables
  #-------------------------------------------------------------------
  
  LIBRARY_FILENAME=lib$(LIBRARY_NAME).a
  LIBRARY_FILEPATH=$(BUILD_CONFIG)/$(LIBRARY_FILENAME)
  
  # Source directories
  CPP_SRC_DIRS=$(REPO_ROOT)/source/example_lib/src
  
  # Source files
  vpath %.cpp $(CPP_SRC_DIRS)
  CPP_SRCS=$(foreach cpp_src_dir, $(CPP_SRC_DIRS), $(wildcard $(cpp_src_dir)/*.cpp))
  
  # Object/dependencies directory
  OBJ_DEPS_DIR=./$(BUILD_CONFIG)/obj
  
  # Object files
  OBJS=$(CPP_SRCS:%.cpp=$(OBJ_DEPS_DIR)/%.o)
  
  # Dependency files (built with objects)
  DEPS=$(CPP_SRCS:%.cpp=$(OBJ_DEPS_DIR)/%.d)
  
  #-------------------------------------------------------------------
  # C++ compiler settings
  #-------------------------------------------------------------------
  
  CPP_COMMAND=g++
  CPP_OPTIONS_INC_PATHS=-I"$(REPO_ROOT)/source/example_lib/inc"
  CPP_OPTIONS_OPTIM=-O3
  CPP_OPTIONS_WARN=-Wall
  CPP_OPTIONS_MISC=-c -fmessage-length=0
  CPP_OPTIONS=$(CPP_OPTIONS_INC_PATHS) $(CPP_OPTIONS_OPTIM) $(CPP_OPTIONS_WARN) $(CPP_OPTIONS_MISC)
  
  #-------------------------------------------------------------------
  # Archiver settings
  #-------------------------------------------------------------------
  
  AR_COMMAND=ar
  AR_OPTIONS=-r
  
  #-------------------------------------------------------------------
  # Targets
  #-------------------------------------------------------------------
  
  # Object/dependency directory target
  $(OBJS): | $(OBJ_DEPS_DIR)
  $(OBJ_DEPS_DIR):
      mkdir -p $(OBJ_DEPS_DIR)
  
  # Object targets
  $(OBJ_DEPS_DIR)/%.o: %.cpp
      @echo 'Building file: $<'
      @echo 'Invoking: GCC C++ Compiler'
      $(CPP_COMMAND) $(CPP_OPTIONS) -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@)" -o "$@" "$<"
      @echo 'Finished building: $<'
      @echo ' '
  
  # 'all' target
  all: $(LIBRARY_FILEPATH)
  
  # Output library target
  $(LIBRARY_FILEPATH): $(OBJS)
      @echo 'Building target: $@'
      @echo 'Invoking: GCC Archiver'
      $(AR_COMMAND) $(AR_OPTIONS)  "$@" $(OBJS)
      @echo 'Finished building target: $@'
      @echo ' '
  
  # 'clean' target
  clean:
      @echo 'Cleaning targets'
      rm -rf $(OBJS) $(DEPS) $(LIBRARY_FILENAME)
      @echo ' '
  
  # 'PHONY' target
  .PHONY: all clean
  

  What 'make' outputs, which makes sense, is:

  make all 
  Building file: ../../source/example_lib/src/example_lib.cpp
  Invoking: GCC C++ Compiler
  g++ -I"../../source/example_lib/inc" -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"Release/obj/../../source/example_lib/src/example_lib.d" -MT"Release/obj/../../source/example_lib/src/example_lib.o" -o "Release/obj/../../source/example_lib/src/example_lib.o" "../../source/example_lib/src/example_lib.cpp"
  ../../source/example_lib/src/example_lib.cpp:6:1: fatal error: opening dependency file Release/obj/../../source/example_lib/src/example_lib.d: No such file or directory
   }
   ^
  compilation terminated.
  make: *** [Release/obj/../../source/example_lib/src/example_lib.o] Error 1
  

  The source-to-object rule is substituting the full path of the %.cpp file into the %.o target, which results in an object path of:

  Release/obj/../../source/example_lib/src/example_lib.o
  

  What I don't understand is how to get the implicit rules for a source and object file to match when they are in different trees. I used vpath for this to help with source resolution, but the object (target) portion doesn't match up. I also tried changing the source-to-object rule to:

  $(OBJ_DEPS_DIR)/$(notdir %.o): %.cpp
  

  But this resulted in the same path (it appears commands like $(notdir ...) aren't supported for wildcard matching?). I also realize that dropping all object files from potentially different source directories could result in a name collision if the two source directories happen to have a file with the same name - this isn't a problem for the code I am working with.

  Any help is appreciated, and thanks in advance!
• Include in Makefile another Makefile with relative path

  I have a directory tree like this with some "shared targets" in the file rules.Makefile:

  ├── Makefile
  ├── rules.Makefile
  └── my_subdir
      └── Makefile
  

  I would like to invoke these "shared targets" in both the Makefile(s) in the parent directory and the child directory.

  Also the "custom targets" in the Makefile in the child directory should be callable from the Makefile in the parent directory.

  For some reason I am able to call the targets in rules.Makefile only from the sibling Makefile (the one in the parent directory). When using relative paths in the Makefile in the child directory trying to access the rules.Makefile in the parent directory I get some errors.

  The content of the Makefile in the parent directory:

  RULES_MAKEFILE_PATH=$(PWD)/rules.Makefile
  include $(RULES_MAKEFILE_PATH)
  
  foo-parent:
      @echo $(RULES_MAKEFILE_PATH)
  

  The content of the Makefile in the child directory (please note that double dot ..):

  RULES_MAKEFILE_PATH=$(PWD)/../rules.Makefile
  include "$(RULES_MAKEFILE_PATH)"
  
  foo-child:
      @echo $(RULES_MAKEFILE_PATH)
  

  When calling from the parent directory make foo-parent then I see the expected path.

  When calling from the child directyr make foo-child then I see this error:

  $ make foo-child 
  Makefile:9: "/<PARENT_PATH>/my_subdir/../rules.Makefile": No such file or directory
  make: *** No rule to make target '"/<PARENT_PATH>/my_subdir/../rules.Makefile"'. Stop.
  

  • How can I make the relative paths work in the "child directory"?
  • Also how can I call the targets defined in the Makefile in child directory (e.g. foo-child) from the Makefile in the parent directory?
• change directory in makefile for python

  My instructor wrote a script for test cases. The test cases are located in "input" directory. I need to change from "input" to the directory where my "*.py" files are located. In the makefile, I tried the following :

  DIR = $(PWD)
  All : 
      cd $(DIR) ;
      echo "python main.py" > run
  

  But it still says that python : can't find main.py. However, I added pwd in the "All", it shows the correct directory.
• Fortran Subroutine not returning value

  i run into a strange problem. I am using the locate subroutine from the Fortran-Recipe book. The goal is to find a random number in a CDF-table and return the index of the arrax, such that i can look in another table for the value this would correspond. However i cannot ge it to pass the value of j (jlo in the encompassing function) back. It just stays 0. The subroutine locate changes the value of j to the correct one, but then does not pass it back.

        SUBROUTINE locate(xx,n,x,j)
        INTEGER, INTENT(out) :: j
        REAL*8 x,xx(n)
        INTEGER jl,jm,ju,n
        jl=0
        ju=n+1
  
  10    if(ju-jl.gt.1)then
          jm=(ju+jl)/2
          if((xx(n).ge.xx(1)).eqv.(x.ge.xx(jm)))then
            jl=jm
          else
            ju=jm
          endif
        goto 10
        endif
  
        if(x.eq.xx(1))then
          j=1
        else if(x.eq.xx(n))then
          j=n-1
        else
          j=jl
        endif
        return
        END
  

  This is the design of the subroutine

  and this is how it is included:

  function CDF() result(xyz)
  implicit none
  real(BW) :: rand
  integer(I2B) :: jlo, N_points_table
  real(BW), allocatable :: CDFtable(:)
  
  
  N_points_table= 1000
  jlo=0
  CALL RANDOM_NUMBER(rand)
  
  allocate(CDFtable(N_points_table))
  ...
  !setting the content of CDFtable to a CDF of some kind
  ...
  call locate(CDFtable,N_points_table,rand,jlo)
  ....
  ....
  

  However after the subroutine ran, jlo is still 0 as it was initiated. Any help is greatly appreciated
• Fortran code returns 0 for every calculation in the loop

  Can anyone help me to find where I am going wrong about writing this code

      program time_period
      ! This program calculates time period of an SHM given length of the chord
      implicit none
      integer, parameter:: length=10
      real, parameter :: g=9.81, pi=3.1415926535897932384
      integer, dimension(1:length)::chordlength
      integer :: l
      real :: time
      do l= 1,length
      time = 2*pi*(chordlength(l)/(g))**.5
      print *, l, time
      enddo
      end program
  

  Result:

  1 0.00000000E+00
  2 0.00000000E+00
  3 0.00000000E+00
  4 0.00000000E+00
  5 0.00000000E+00
  6 0.00000000E+00
  7 0.00000000E+00
  8 0.00000000E+00
  9 0.00000000E+00
  10 0.00000000E+00
  

  
• Fortran - Sorting an array in random order

  Went through the Numerical Recipes but couldn't find an applicable solution. Does anyone have an example for sorting an array in random order? Thank you

  UPDATE: I have a large array and need to list it in random order.

  Here's the initial approach below (pardon the format- first time Fortran user).

  Instead of using the random number function and then pulling the numbers from array based on it I was looking for something like a Shuffle function?

  program Module3
  
  real, dimension(10,2) :: exceedancearray
  real, dimension(10000) ::  new
  integer :: positivetotal, rannumber,counter,i
  
  REAL :: num
  
  do i=1,10
  exceedancearray (i,1)=i*10
  exceedancearray (i,2)=1000
  end do
  
  positivetotal=0
  counter=1
  
  DO i=1,10
  positivetotal=exceedancearray(i,2)+positivetotal
  END DO
  
  PRINT *, positivetotal
  
  
  1 CALL RANDOM_SEED  
  DO WHILE (positivetotal>0)
  CALL RANDOM_NUMBER(num)     
  rannumber=nint(num*10)
  
  
  if (rannumber==0) then
  goto 1
  end if
  
          if (exceedancearray (rannumber,2)>0) then
          new(counter)=exceedancearray(rannumber,1)
           PRINT *, new(counter)
          counter=counter+1
          positivetotal=positivetotal-1
          exceedancearray(rannumber,2)=exceedancearray(rannumber,2)-1
  
          end if
  END DO 
  
  
  end program Module3
  
• How to call PetscFinalize from the root processor only?

  In my Fortran program, I call an external function only at the root processor. I have a few checks to ensure that the function worked. If it doesn't work, then I stopthe program and call PetscFinalize. For example:

  if(rank==0) then
     call_status = external_function(x)
  
     ! function failed
     if (call_status/=1) then
        write(6,*) "external_function failed"
        call PetscFinalize(ierr)
        stop
     end if
  end if
  

  However, I noticed that during runtime, if there is an error with external_function, the program hangs and is not finalized properly.

  My question is: what is the appropriate way to terminate the program at the root processor?
• Very simple PETSc Mat construction gives SEGV 11 error - C++

  I want to create a very simple 2x2 identity matrix in C++ using PETSc library. I have searched various tutorials on the internet and found that all of them indicate one way of doing this. However I get a "Caught signal number 11 SEGV: Segmentation Violation" error. This code is part of a much larger program where I need to create some matrices used in conjunction with other elements of it. Moreover, this code is a mere test, in which I am trying to find out how exactly does PETSc work with matrices. I could say I am still in the learning phase.

  The code is the following:

  Mat Y11;
  
   MatCreate(MPI_COMM_WORLD, &Y11);
   MatSetSizes(Y11, PETSC_DECIDE, PETSC_DECIDE, 2, 2);
   std::cout << "set mat type" << std::endl;
   MatSetType(Y11, MATSEQMAIJ);
  
   MatSetFromOptions(Y11);
  
   PetscScalar temp22[] = {std::complex<double>(1.0,0), std::complex<double>(0.0,0), std::complex<double>(0.0,0.0), std::complex<double>(1.0,0.0)};
   PetscInt tempis[] = {0, 1};
   std::cout << "MatSetValues" << std::endl;
   MatSetValues(Y11, 1, &tempis[0], 1, &tempis[0], &temp22[0], INSERT_VALUES);
   MatSetValues(Y11, 1, &tempis[0], 1, &tempis[1], &temp22[1], INSERT_VALUES);
   MatSetValues(Y11, 1, &tempis[1], 1, &tempis[0], &temp22[2], INSERT_VALUES);
   MatSetValues(Y11, 1, &tempis[1], 1, &tempis[1], &temp22[3], INSERT_VALUES);
  
   MatAssemblyBegin(Y11,MAT_FINAL_ASSEMBLY);
   MatAssemblyEnd(Y11,MAT_FINAL_ASSEMBLY);
  
   std::cout << std::endl << "Y11 block:" << std::endl;
   MatView(Y11,PETSC_VIEWER_STDOUT_WORLD);
  

  The error stems from MatSetValues function.

  Could anyone please tell me what could probably be wrong with this code? There are no simple examples like this on the internet (at least of what I can search, in C++). Thank you in advance!