Dev

Examples/Parareal/ERK/bm1.nml

@@ -0,0 +1,22 @@
+!
+!  Test parameters for the nonlinear Schroedinger eq
+!
+
+&PARAMS
+
+    Tfin = 13.5
+    nx =   1024 1024
+
+    nsteps = 1
+    nsteps_rk =  1  1
+    rk_order = 4 4
+
+    eq_type = 3	
+    ic_type = 3	
+
+    split_damp=.true.   
+    split_rho=0.0245436926061703   !  pi/128
+    Lx=25.1327412287183      !  8 pi
+
+    pfasst_nml="parareal.nml"  !  Use the common input file for pfasst parameters    
+/

Examples/Parareal/ERK/bm1serial.nml

@@ -0,0 +1,23 @@
+!
+!  Test parameters for the nonlinear Schroedinger eq
+!
+
+&PARAMS
+
+    Tfin = 13.5
+    nx =   1024
+
+    nsteps = 4096
+    nsteps_rk =  128
+    rk_order = 4 
+
+    eq_type = 3	
+    ic_type = 3	
+
+    split_damp=.false.   
+    split_rho=0.0245436926061703   !  pi/128
+    Lx=25.1327412287183      !  8 pi
+
+    pfasst_nml="serial.nml"  !  Use the common input file for pfasst parameters
+!    pfasst_nml="parareal.nml"  !  Use the common input file for pfasst parameters    
+/

Examples/Parareal/ERK/serial.nml

@@ -0,0 +1,32 @@
+&PF_PARAMS
+   !  These are internal pfasst variables that must be set
+    nlevels  = 1
+
+    !  These are internal pfasst variables that can be reset
+    niters = 1   !  default is 5 - 0 leaves predictor on coarse level
+
+     !  optional variables to control termination  (defaults are 0.0)
+     abs_res_tol = 1.d-10
+     rel_res_tol = 1.d-10
+
+     nnodes =  2 2
+
+     !  Choices to run parareal instead of PFASST
+     use_rk_stepper=.true.
+     use_sdc_sweeper=.false.
+
+     !  These flags control the output.  For fastest timings, turn them off
+     save_residuals=.false.
+     save_delta_q0=.false.
+     save_errors=.false.
+
+     ! Flag for timings.  For fastest timing of only full algorithm, set to 1
+     save_timings = 1
+
+    ! Flag for saving solutions, needed for problems with no exact solution
+     save_solutions = 1
+
+     !  Directory name for output
+     outdir="serial"
+/
+

Examples/Parareal/ERK/src/stepper_include.f90

@@ -70,7 +70,7 @@ end subroutine destroy
 
 !F_EVAL: evaluates the nonlinear function f(t,y(t)) at y, t.
 subroutine f_eval(this, y, t, level_index, f)
-  use probin, only: eq_type,splitting
+  use probin, only: eq_type,split_damp
   ! arguments
   class(my_stepper_t), intent(inout) :: this
   class(pf_encap_t),   intent(in)    :: y
@@ -90,7 +90,7 @@ subroutine f_eval(this, y, t, level_index, f)
   call f_NL(this%yvec,this%fvec,this%fft_ops%opNL,this%tmp,fft)
 
   ! include damping
-  if (split_damping)  this%fvec=  this%fvec - this%fft_ops%opDamp*this%yvec
+  if (split_damp)  this%fvec=  this%fvec - this%fft_ops%opDamp*this%yvec
 end subroutine f_eval
 
   subroutine compA(this, dt, i, j, F, val)

Examples/Parareal/Make.package

@@ -9,6 +9,7 @@ endif
 FFLAGS  += -I$(LIBPFASST)/include  -I$(LIBNPY)/include 
 LDFLAGS  += -L$(LIBNPY)/libnpy_fortran_mod -lnpy
 
+
 build/main_rk.o : ../src/main_rk.f90 build/probin.o build/hooks_rk.o build/level_rk.o build/stepper_$(DIM)d.o build/utils_$(DIM)d.o $(LIBPFASST)/lib/libpfasst.a 
 build/probin.o :../src/probin.f90 build/dim_$(DIM)d.o $(LIBPFASST)/lib/libpfasst.a 
 build/utils_$(DIM)d.o : ../src/utils_$(DIM)d.f90 build/probin.o 

Examples/Parareal/src/probin.f90

@@ -36,7 +36,8 @@ module probin
   real(pfdp), save :: gamma    
   !  parameters for split damping
   real(pfdp), save :: d0,d1,r0,r1  
-  logical,    save :: split_damping
+  logical,    save :: split_damp
+  real(pfdp), save :: split_rho
   character(len=32), save :: pfasst_nml
 
   character(len=64), save :: output ! directory name for output
@@ -46,7 +47,7 @@ module probin
   integer :: ios,iostat 
   namelist /params/  nx,ic_type, eq_type, nsteps,nsteps_rk,rk_order, dt, Tfin
   namelist /params/  pfasst_nml, lam1,lam2,a,b,c, nu, t00, sigma, beta, gamma, splitting
-  namelist /params/  kfreqx,kfreqy,kfreqz,Lx,Ly,Lz,d0,d1,r0,r1,split_damping  
+  namelist /params/  kfreqx,kfreqy,kfreqz,Lx,Ly,Lz,d0,d1,r0,r1,split_damp,split_rho  
 
 contains
 
@@ -87,7 +88,8 @@ subroutine probin_init(pf_fname)
     Ly      = two_pi
     Lz      = two_pi
     ! Default damping parameters are 0
-    split_damping=.true.
+    split_damp=.true.
+    split_rho=two_pi/256.0_pfdp
     d0=0.0_pfdp
     d1=0.0_pfdp
     r0=0.0_pfdp

Examples/Parareal/src/utils_1d.f90

@@ -250,6 +250,7 @@ subroutine f_NL(yvec,fvec,opNL,tmp,fft)
     case DEFAULT
        call pf_stop(__FILE__,__LINE__,'Bad case in SELECT',eq_type)
     end select
+
   end subroutine f_NL
 
 end module pf_mod_zutils
@@ -275,7 +276,7 @@ module pf_mod_fftops
   contains
 
     subroutine fftops_init(this,fft,nx)
-      use probin, only: d0,d1,r0,r1
+      use probin, only: d0,d1,r0,r1,split_damp,split_rho
       class(pf_fft_ops_t), intent(inout)    :: this
       type(pf_fft_t), pointer, intent(in) :: fft
       integer, intent(in) :: nx
@@ -289,8 +290,6 @@ subroutine fftops_init(this,fft,nx)
       if (istat .ne. 0)  call pf_stop(__FILE__,__LINE__,'Allocate failed ',istat)
       allocate(this%opNL(nx),STAT=istat)
       if (istat .ne. 0)  call pf_stop(__FILE__,__LINE__,'Allocate failed ',istat)
-      allocate(this%opDamp(nx),STAT=istat)
-      if (istat .ne. 0)  call pf_stop(__FILE__,__LINE__,'Allocate failed ',istat)
 
       call fft%make_deriv(this%ddx) !  First derivative
       call fft%make_lap(this%lap)  !  Second derivative
@@ -299,19 +298,29 @@ subroutine fftops_init(this,fft,nx)
       call set_ops(this%opL,this%opNL,this%ddx,this%lap)
 
       ! Create damping op
-      this%opDamp= d0*this%ddx**r0 + d1*abs(this%ddx)**r1
-      !  add damping to linear operator
-      this%opL=this%opL+this%opDamp
+      if (split_damp) then
+         allocate(this%opDamp(nx),STAT=istat)
+         if (istat .ne. 0)  call pf_stop(__FILE__,__LINE__,'Allocate failed ',istat)
+         !      this%opDamp= d0*this%ddx**r0 + d1*abs(this%ddx)**r1
+         this%opDamp= abs(this%ddx)**2/tan(two_pi/4.0_pfdp + split_rho)
+
+         !  add damping to linear operator
+         this%opL=this%opL+this%opDamp
+      end if
       deallocate(this%lap)
       deallocate(this%ddx)
     end subroutine fftops_init
 
     subroutine fftops_destroy(this)
+      use probin, only: split_damp
       class(pf_fft_ops_t), intent(inout)    :: this
 
       deallocate(this%opL)
       deallocate(this%opNL)
-      deallocate(this%opDamp)
+      if (split_damp) then
+         deallocate(this%opDamp)
+      end if
+
     end subroutine fftops_destroy
 
   !> Routine to return out put the solution to numpy (dimension dependent)

Makefile.defaults

@@ -12,7 +12,7 @@ USE_PETSC ?= FALSE
 USE_HYPRE ?= FALSE
 USE_SUNDIALS ?= FALSE
 USE_AMREX ?= FALSE
-USE_FFT ?= FALSE
+USE_FFT ?= TRUE
 
 
 #  File for compiler options

Makefile.examples/Makefile.local

@@ -7,10 +7,12 @@ AR=ar rcs
 
 FFLAGS = -Ibuild -Jinclude -cpp -ffree-line-length-none
 #  Use this flag on newer compilers with stricter bounds checking
-#FFLAGS = -fallow-argument-mismatch
+#  FFLAGS_EXTRA is used for F77 in building dfftpack
+#FFLAGS += -fallow-argument-mismatch
+#FFLAGS_EXTRA += fallow-argument-mismatch
 
 ifeq ($(DEBUG),TRUE)
 FFLAGS += -fcheck=all -fbacktrace -g -ffpe-trap=invalid,zero,overflow -fbounds-check -fimplicit-none -ffree-line-length-none
 else
 FFLAGS += -O3 
-endif
+endif

Makefile.examples/Makefile.local.cori

@@ -0,0 +1,27 @@
+#  Set some compiler flags
+
+AR = ar rcs
+ifeq ($(PE_ENV),INTEL)
+#FC = mpiifort
+#CC = mpiiCC
+FC = ftn
+LD = ftn -static
+CC = cc
+FFLAGS = -Ibuild -module include -cpp -static
+ifeq ($(DEBUG),TRUE)
+FFLAGS +=   -g -O0
+endif
+endif
+
+ifeq ($(PE_ENV),CRAY)
+#FC = mpiifort
+#CC = mpiiCC
+FC = ftn
+LD = ftn
+CC = cc
+FFLAGS = -Ibuild -Jinclude 
+LDLAGS = -Ibuild -Jinclude 
+ifeq ($(DEBUG),TRUE)
+FFLAGS +=   -g
+endif
+endif

README.md

@@ -6,6 +6,25 @@ Approximation Scheme in Space and Time (PFASST) algorithm.  It is
 written in Fortran (mostly F90, with some F03), but can be interfaced
 with C and C++ fairly easily.
 
+## References
+- Matthew Emmett, Michael Minion: Toward an efficient parallel in time method for partial differential equations, Commun. Appl. Math. Comput. Sci. 7(1), 105-132, 2012. [http://dx.doi.org/10.2140/camcos.2012.7.105](http://dx.doi.org/10.2140/camcos.2012.7.105)
+- Matthew Emmett, Michael Minion: Efficient Implementation of a Multi-Level Parallel in Time Algorithm. In: Erhel, J., Gander, M., Halpern, L., Pichot, G., Sassi, T., Widlund, O. (eds) Domain Decomposition Methods in Science and Engineering XXI. Lecture Notes in Computational Science and Engineering, vol 98. Springer, Cham, 2014. [https://doi.org/10.1007/978-3-319-05789-7_33](https://doi.org/10.1007/978-3-319-05789-7_33)
+
+##  Documentation
+We are currently writing better documentation, examples, and a tutorial, at [https://libpfasst.github.io/LibPFASST](https://libpfasst.github.io/LibPFASST).
+The documentation can be edited on the gh-pages branch of this repo.
+
+## Requirements
+- a Fortran compiler, for some external libraries like FFTW C/C++ compiler
+- an MPI library
+- makedepf90 for generating dependencies
+- python 3.12 for the test (including numpy, matplotlib, pandas, scipy, tqdm, pytest)
+
+## Quickstart
+- compile the library, see [https://libpfasst.github.io/LibPFASST/docs/build/html/compiling.html](https://libpfasst.github.io/LibPFASST/docs/build/html/compiling.html)
+- look through the tutorials, see [https://libpfasst.github.io/LibPFASST/docs/build/html/tutorial.html](https://libpfasst.github.io/LibPFASST/docs/build/html/tutorial.html)
+
+## License
 
 Libpfasst Copyright (c) 2018, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy) and Sebastian Goetschel.  All rights reserved.
 
@@ -23,9 +42,7 @@ You are under no obligation whatsoever to provide any bug fixes, patches, or upg
 
 
 
-#  Documentation
-We are currently writing better documentation, examples, and a tutorial, at https://libpfasst.github.io/LibPFASST.
-The documentation can be edited on the gh-pages branch of this repo.
+
 
 
 

pf/__init__.py

@@ -1,5 +1,5 @@
-import io
-import convergence
-import speedup
-import pfasst
-import nwc
+import pf.io
+import pf.convergence
+import pf.speedup
+import pf.pfasst
+import pf.nwc

pf/convergence.py

@@ -2,7 +2,8 @@
 from itertools import product
 
 import numpy as np
-import pylab
+#import pylab
+import matplotlib.pyplot as plt
 import pf.io
 
 
@@ -57,7 +58,7 @@ def errors(reference, approximate, **kwargs):
       err = abs(ref - app).max()
       errors[step, aiter, alev] = err
     except:
-      print 'WARNING: size mismatch:', step, aiter, alev
+      print('WARNING: size mismatch:', step, aiter, alev)
 
   return errors, steps, iters, levels
 
@@ -84,19 +85,19 @@ def plot(errs, steps, iters, levels, **kwargs):
   # if not isinstance(ax, list):
   #   ax = [ ax ]
 
-  pylab.figure()
+  plt.figure()
 
   for l, level in enumerate(levels):
     for i, iter in enumerate(iters):
 
       x = steps
       y = [ errs[step,iter,level] for step in steps ]
 
-      pylab.subplot(1, len(levels), l+1)
+      plt.subplot(1, len(levels), l+1)
 
-      pylab.semilogy(x, y, **kwargs)
-      pylab.title('level %d' % level)
-      pylab.xlabel('step/processor')
-      pylab.ylabel('max abs. error')
+      plt.semilogy(x, y, **kwargs)
+      plt.title('level %d' % level)
+      plt.xlabel('step/processor')
+      plt.ylabel('max abs. error')
 
   # return fig, ax

pf/nwc.py

@@ -2,7 +2,7 @@
 from os import getcwd, chdir, makedirs, devnull
 from subprocess import call
 from scipy.io import FortranFile
-from pfasst import PFASST
+from pf.pfasst import PFASST
 import numpy as np
 
 class NWC(PFASST):
@@ -11,7 +11,7 @@ def __init__(self, home, params=None, **kwargs):
         if params is None:
             params = Params()
         PFASST.__init__(self, home, params, **kwargs)
-        print 'Setting up NWC'
+        print('Setting up NWC')
         self.nwc = self.home + '/nwc.sh'
         self.cwd = getcwd() + '/'
         self.nwc_base_string = 'echo\nscratch_dir ./scratch\npermanent_dir ./perm\n\n'\
@@ -33,7 +33,7 @@ def __init__(self, home, params=None, **kwargs):
             except:
                 raise Exception('unsuccessful NWC run, check input!')
         else:
-            print 'exact dirs already exist'
+            print('exact dirs already exist')
 
         self.xtrans, self.ytrans = self._parse_transforms()
         self.initial = self._get_nwc_dmat('initial_condition')
@@ -68,7 +68,7 @@ def _create_nwc_inp(self):
     def _run_nwc(self):
         FNULL = open(devnull, 'w')
         chdir(self.p.exact_dir)
-        print '---- running nwc ----'
+        print('---- running nwc ----')
         call([self.nwc, 'nw'], stdout=FNULL)
         chdir(self.cwd)
         FNULL.close()