如何解决Fortran流访问效率与MPI-IO的对比
我有一段代码的并行部分,其中我在多个块中写出n个大数组(表示一个数字网格),然后在不同大小的块中读取它们。为此,我使用了流访问,因此每个处理器都独立地写入其块,但是在本节的2个处理器组测试中,我看到不一致的时序花费了0.5-4秒的时间。
我知道您可以使用MPI-IO做类似的事情,但是我不确定会有什么好处,因为没有必要进行同步。我想知道是否有一种方法可以提高写入性能,或者是否有理由将MPI-IO作为本节的更好选择。
这是代码部分的示例,在该部分中,我创建文件以使用两个组(norb
= 0或1]来写mygroup
数组:
do irbsic=1,norb
[various operations]
blocksize=int(nmsh_tot/ngroups)
OPEN(unit=iunit,FILE='ZPOT',STATUS='UNKNOWN',ACCESS='STREAM')
mypos = 1 + (IRBSIC-1)*nmsh_tot*8 ! starting point for writing IRBSIC
mypos = mypos + mygroup*(8*blocksize) ! starting point for mesh group
WRITE(iunit,POS=mypos) POT(1:nmsh)
CLOSE(iunit)
OPEN(unit=iunit,FILE='RHOI',POS=mypos) RHOG(1:nmsh,1,1)
CLOSE(iunit)
[various operations]
end do
解决方法
(如评论中所述),我强烈建议不要为此使用Fortran流访问。只有在单个进程正在访问文件的情况下,才能保证标准Fortran I / O正常工作。在我自己的工作中,即使多个进程试图一次写入文件,我也看到了多个进程试图一次写入文件时文件的随机损坏。到文件的不同部分。 MPI-I / O或使用MPI-I / O的库(例如HDF5或NetCDF)是实现此目的的唯一明智方法。下面是一个简单的程序,说明了mpi_file_write_at_all
ian@eris:~/work/stack$ cat at.f90
Program write_at
Use mpi
Implicit None
Integer,Parameter :: n = 4
Real,Dimension( 1:n ) :: a
Real,Dimension( : ),Allocatable :: all_of_a
Integer :: me,nproc
Integer :: handle
Integer :: i
Integer :: error
! Set up MPI
Call mpi_init( error )
Call mpi_comm_size( mpi_comm_world,nproc,error )
Call mpi_comm_rank( mpi_comm_world,me,error )
! Provide some data
a = [ ( i,i = n * me,n * ( me + 1 ) - 1 ) ]
! Open the file
Call mpi_file_open( mpi_comm_world,'stuff.dat',&
mpi_mode_create + mpi_mode_wronly,mpi_info_null,handle,error )
! Describe how the processes will view the file - in this case
! simply a stream of mpi_real
Call mpi_file_set_view( handle,0_mpi_offset_kind,&
mpi_real,mpi_real,'native',&
mpi_info_null,error )
! Write the data using a collective routine - generally the most efficent
! but as collective all processes within the communicator must call the routine
Call mpi_file_write_at_all( handle,Int( me * n,mpi_offset_kind ),&
a,Size( a ),mpi_status_ignore,error )
! Close the file
Call mpi_file_close( handle,error )
! Read the file on rank zero using Fortran to check the data
If( me == 0 ) Then
Open( 10,file = 'stuff.dat',access = 'stream' )
Allocate( all_of_a( 1:n * nproc ) )
Read( 10,pos = 1 ) all_of_a
Write( *,* ) all_of_a
End If
! Shut down MPI
Call mpi_finalize( error )
End Program write_at
ian@eris:~/work/stack$ mpif90 --version
GNU Fortran (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0
Copyright (C) 2017 Free Software Foundation,Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
ian@eris:~/work/stack$ mpif90 -Wall -Wextra -fcheck=all -std=f2008 at.f90
ian@eris:~/work/stack$ mpirun -np 2 ./a.out
0.00000000 1.00000000 2.00000000 3.00000000 4.00000000 5.00000000 6.00000000 7.00000000
ian@eris:~/work/stack$ mpirun -np 5 ./a.out
0.00000000 1.00000000 2.00000000 3.00000000 4.00000000 5.00000000 6.00000000 7.00000000 8.00000000 9.00000000 10.0000000 11.0000000 12.0000000 13.0000000 14.0000000 15.0000000 16.0000000 17.0000000 18.0000000 19.0000000
ian@eris:~/work/stack$
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