我不能在特定情况下将 fortran-
readifortf2py我怀疑
ifortopen!rur/readr.f90
module readr
use omp_lib
implicit none
real(kind=8), dimension(:,:), allocatable :: real_table
integer(kind=4), dimension(:,:), allocatable :: integer_table
integer(kind=8), dimension(:,:), allocatable :: long_table
integer(kind=1), dimension(:,:), allocatable :: byte_table
integer :: nhvar
real(kind=8) :: aexp
contains
!#####################################################################
subroutine read_part(repo, iout, cpu_list, mode, verbose, longint, nthread)
!#####################################################################
implicit none
integer :: i, j, icpu, idim, ipart
integer :: ncpu, ndim
integer :: npart, nstar_int, nsink, ncursor
integer(kind=8) :: npart_tot, nstar, npart_c
integer :: part_n, nreal, nint, nbyte, nlong, nchem, nthread
integer :: pint
logical :: ok
character(len=128) :: file_path
character(len=128), intent(in) :: repo
integer, intent(in) :: iout
integer, dimension(:), intent(in) :: cpu_list
character(len=10), intent(in) :: mode
logical, intent(in) :: verbose
logical, intent(in) :: longint
integer(kind=4), dimension(:), allocatable :: cursors_temp, cursors
part_n = 30
file_path = part_filename(repo, iout, cpu_list(1), mode)
! Step 1: Verify there is file
inquire(file=file_path, exist=ok)
if ( .not. ok ) then
print *, file_path, ' not found.'
stop
endif
! Step 2: Count the total number of particles.
open(unit=part_n, file=file_path, status='old', form='unformatted')
read(part_n) ncpu
read(part_n) ndim
call skip_read(part_n, 2)
if(longint) then
read(part_n) nstar
else
read(part_n) nstar_int
nstar = nstar_int
end if
call skip_read(part_n, 2)
read(part_n) nsink
close(part_n)
npart_tot = 0
allocate(cursors(1:SIZE(cpu_list)))
allocate(cursors_temp(1:SIZE(cpu_list)))
cursors_temp = 0
!$OMP PARALLEL DO SHARED(npart_tot, cursors_temp) PRIVATE(i, icpu, npart, part_n) NUM_THREADS(nthread)
do i = 1, SIZE(cpu_list)
icpu = cpu_list(i)
part_n = 30 + omp_get_thread_num()
call get_npart(part_n, part_filename(repo, iout, icpu, mode), npart)
!$OMP ATOMIC
npart_tot = npart_tot + npart
cursors_temp(i) = npart
end do
!$OMP END PARALLEL DO
ncursor = 1
do i = 1, SIZE(cpu_list)
cursors(i) = ncursor
ncursor = ncursor + cursors_temp(i)
end do
deallocate(cursors_temp)
! Set coulum spaces of each datatype for different versions of RAMSES
if(nstar > 0 .or. nsink > 0) then
nreal = 2*ndim + 3
else
nreal = 2*ndim + 1
end if
nint = 3
nbyte = 0
if(longint) then
nint = nint-1
nlong = 1
else
nlong = 0
end if
call close()
! Allocate space for particle data
allocate(real_table(1:nreal, 1:npart_tot))
allocate(integer_table(1:nint, 1:npart_tot))
allocate(byte_table(1:nbyte, 1:npart_tot))
if(longint)allocate(long_table(1:nlong, 1:npart_tot))
! Step 3: Read the actual particle data
! Current position for particle
if(verbose)write(6, '(a)', advance='no') 'Progress: '
!$OMP PARALLEL DO &
!$OMP SHARED(integer_table, long_table, real_table, byte_table,ndim,nstar,nsink,nchem) &
!$OMP PRIVATE(i,j, icpu,npart,part_n,npart_c,idim,pint) &
!$OMP NUM_THREADS(nthread)
do i = 1, SIZE(cpu_list)
!$OMP CRITICAL
if(verbose)call progress_bar(i, SIZE(cpu_list))
!$OMP END CRITICAL
icpu = cpu_list(i)
part_n = 30 + omp_get_thread_num()
npart_c = cursors(i)
open(unit=part_n, file=part_filename(repo, iout, icpu, mode), status='old', form='unformatted')
! Skip headers
call skip_read(part_n, 2)
read(part_n) npart
call skip_read(part_n, 5)
! Read position(3), velocity(3), mass
do idim = 1, 2*ndim+1
read(part_n) real_table(idim, npart_c:npart_c+npart-1) ! <---- ERROR
end do
(...)
close(part_n)
end do
!$OMP END PARALLEL DO
deallocate(cursors)
end subroutine read_part
f2pygfortranifort#!/bin/bash
F2PY=f2py
f='readr.f90'
bn=$(basename "$f" .f90)
# (gfortran case)
FORT=gfortran
$F2PY -c -lgomp --f90exec=$FORT --f77exec=$FORT $f -m $bn --opt='-O3 -x f95-cpp-input'
# (ifort case)
FORT=ifort
$F2PY -m $bn -liomp5 --f90exec=$FORT --f77exec=$FORT --opt='-O3 -fpp -m64 -free' -c $f
#test.ipynb
...
from rur.readr import readr
readr.read_part(...)
read(part_n) real_table(idim, npart_c:npart_c+npart-1)我检查了这些：
gfortranifort如果我运行 python，而不是 jupyter，那么它运行良好
打开小文件就可以了
设置
ulimit -s unlimitedexport OMP_STACKSIZE='1G'我在setting.json中增加了max_buffer_size： “jupyter.jupyterCommandLineArguments”：[
"--NotebookApp.iopub_msg_rate_limit=1000000000",
"--NotebookApp.max_buffer_size=10240000000"
]
它在
read(part_n) real_table(idim, naprt_c:npart_c+npart-1)read(part_n) real_table1D(naprt_c:npart_c+npart-1)这里是版本：
$ ifort --version
ifort (IFORT) 19.0.4.243 20190416
Copyright (C) 1985-2019 Intel Corporation. All rights reserved.
$ f2py -h
...
Version: 1.22.4
numpy Version: 1.22.4
Requires: Python 3.5 or higher.
License: NumPy license (see LICENSE.txt in the NumPy source code)
Copyright 1999 - 2011 Pearu Peterson all rights reserved.
$ python3 --version
Python 3.10.4
$ conda list
...
ipython 8.11.0 pypi_0 pypi
ipython_genutils 0.2.0 pyhd3eb1b0_1
ipywidgets 8.0.4 pypi_0 pypi
...
jupyter 1.0.0 pypi_0 pypi
jupyter-client 8.0.3 pypi_0 pypi
jupyter-console 6.4.4 pypi_0 pypi
jupyter-core 5.2.0 pypi_0 pypi
jupyter-events 0.6.3 pypi_0 pypi
jupyter-server 1.23.4 pypi_0 pypi
jupyter-server-terminals 0.4.4 pypi_0 pypi
jupyter_client 7.2.2 py310h06a4308_0
jupyter_console 6.4.4 py310h06a4308_0
jupyter_core 4.10.0 py310hff52083_0 conda-forge
jupyter_server 1.23.4 py310h06a4308_0
jupyterlab 3.5.3 pypi_0 pypi
jupyterlab-pygments 0.2.2 pypi_0 pypi
jupyterlab-server 2.19.0 pypi_0 pypi
jupyterlab-widgets 3.0.5 pypi_0 pypi
jupyterlab_pygments 0.1.2 py_0
jupyterlab_server 2.19.0 py310h06a4308_0
jupyterlab_widgets 1.0.0 pyhd3eb1b0_1