paral_IO

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MPI IOTimothy H. Kaiser, [email protected]

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Purpose Introduce Parallel IO

Introduce MPI-IO Not give an exhaustive survey

Explain why you would want to use it

Explain why you wouldnt want to use it Give a nontrivial and useful example

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References http://www.nersc.gov/nusers/resources/

software/libs/io/mpiio.php

Parallel I/O for High Performance Computing.John May

Using MPI-2 Advanced Features of the Message

Passing Interface. William Gropp, Ewing Luskand Rajeev Thakur

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What & Why of parallel IO Same motivation of going parallel initially

You have lots of data You want to do things fast

Parallel IO will (hopefully) enable you tomove large amounts of data to/from diskquickly

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What & Why of parallel IO Parallel implies that some number (or all) of

your processors (simultaneously) participatein an IO operation

Good parallel IO shows speedup as you addprocessors

I write about 300 Mbytes/second, othersfaster

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A Motivating Example Earthquake Model E3d

Finite difference simulation with the griddistributed across N processors

On BlueGene we run at sizes of 7509 x 7478 x250 = 14,021,250,000 cells or 56 GBytes per

volume, output 3 velocity volumes per dump For a restart file we write 14 volumes

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Simple (nonMPI) Parallel IO Each processor dumps its portion of the grid

to a separate unique filechar* unique(char *name,int myid) {

static char unique_str[40];int i;for(i=0;i

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Simple (nonMPI) Parallelmodule stuffcontainsfunction unique(name,myid)

character (len=*) namecharacter (len=20) uniquecharacter (len=80) tempwrite(temp,"(a,i5.5)")trim(name),myidunique=temp

returnend function uniqueend module

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Why not just do this?

Might write thousands of files

Could be very slow

Output is dependent on the number ofprocessors

We might want the data in a single file

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MPI-IO to the rescue MPI has over 55 calls related to file input and

output

Available in most modern MPI libraries Can produce exceptional results

Support striping

A collection of distributed files look like one

We will look at outputs to a single file

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Why not? Some functionality might not be available

3d data types More likely to have/introduce bugs

Memory leak

File system overload Just hangs

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Why not?

More complex than normal output

Need support from the file system for goodperformance

Have seen 200 bytes/second NOT Megabytes

Have run out of file locks

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Our Real World Example We have a 3d volume of some data v

distributed across N processor

The size and distribution are input and not thesame on each processor

We are outputting some function of v , V=f(v)

Each processor writes its values to a commonfile

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Special Considerations

We are calculating our output on the fly

Create a buffer

Fill the buffer and write

Different processors will have differentnumber of writes

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Special Considerations We want to use a collective write operation

Each process must call the collective writethe same number of times

Each process must determine how manywrites it needs to do

The total number of writes is the max Some processors might call write with no

data

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Procedure # 1

Allocate a temporary output buffer

Open the file

Set the view of the file to the beginning

Process 0 writes the file header (36 bytes)

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Procedure #3 Loop over the grid Fill buffer

If buffer is full Write it

Adjust offset

do_call_max=do_call_max-1

Call write with no data until do_call_max=0

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The MPI-IO Routines

MPI_File_open(MPI_COMM_WORLD,fname,(MPI_MODE_RDWR|MPI_MODE_CREATE),MPI_INFO_NULL,&fh);

MPI_File_set_view(fh,disp,MPI_INT,filetype,"native",MPI_INFO_NULL);

MPI_File_write_at(fh, 0, header, hl, MPI_INT,&status);

MPI_File_write_at_all(fh, offset, ptr, i2, MPI_INT,&status);

MPI_File_close(&fh);

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Synopsis: Opens a file

int MPI_File_open(MPI_Comm comm, char *filename, int amode, MPI_Info info, MPI_File *fh)

Input Parameters

comm

communicator (handle)

filename

name of file to open (string)

amode

file access mode (integer)

info

info object (handle)

Output Parameters

fh

file handle (handle)

MPI_File_open

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MPI_File_set_view

Synopsis: Sets the file view

int MPI_File_set_view(MPI_File fh, MPI_Offset disp, MPI_Datatype etype,MPI_Datatype filetype, char *datarep, MPI_Info info)

Input Parameters

fh

file handle (handle)disp

displacement (nonnegative integer)

etype

elementary datatype (handle)

filetype

filetype (handle)

datarep

data representation (string)info

info object (handle)

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MPI_File_write_at

Synopsis: Write using explicit offset, not collective

int MPI_File_write_at(MPI_File fh, MPI_Offset offset, void *buf,int count, MPI_Datatype datatype, MPI_Status *status)

Input Parameters

fh


offset

file offset (nonnegative integer)buf

initial address of buffer (choice)

count

number of elements in buffer (nonnegative integer)

datatype

datatype of each buffer element (handle)

Output Parameters

status

status object (Status)

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MPI_File_write_at_all

Synopsis: Collective write using explicit offset

int MPI_File_write_at_all(MPI_File fh, MPI_Offset offset, void *buf,int count, MPI_Datatype datatype, MPI_Status *status)

Input Parameters

fh


offset

file offset (nonnegative integer)

buf

initial address of buffer (choice)

count

number of elements in buffer (nonnegative integer)

datatype

datatype of each buffer element (handle)

Output Parameters

status

status object (Status)

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MPI_File_close

Synopsis: Closes a file

int MPI_File_close(MPI_File *fh)

Input Parameters

fh


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The Data type Routines MPI_Type_create_subarray(3,gsizes,lsizes,istarts,MPI_ORDER_C,old_type,new_type);

MPI_Type_contiguous(sx,old_type,&VECT);

MPI_Type_struct(sz,blocklens,indices,old_types,&TWOD);

MPI_Type_commit(&TWOD);

Our preferred routine creates a 3d description

On some platforms we need to fake it

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MPI_Type_create_subarray

Synopsis: Creates a datatype describing a subarray of an N dimensional arrayint MPI_Type_create_subarray(int ndims, int *array_of_sizes,

int *array_of_subsizes, int *array_of_starts, int order,MPI_Datatype oldtype, MPI_Datatype *newtype)

Input Parameters

ndims

number of array dimensions (positive integer)

array_of_sizes

number of elements of type oldtype in each dimension of the full array (array of positive integers)array_of_subsizes

number of elements of type oldtype in each dimension of the subarray (array of positive integers)

array_of_starts

starting coordinates of the subarray in each dimension (array of nonnegative integers)

order

array storage order flag (state)

oldtype

old datatype (handle)

Output Parameters

newtype

new datatype (handle)

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MPI_Type_contiguous

Synopsis: Creates a contiguous datatype

int MPI_Type_contiguous( int count,MPI_Datatype old_type,MPI_Datatype *newtype)

Input Parameters

countreplication count (nonnegative integer)

oldtype

old datatype (handle)

Output Parameter

newtype


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MPI_Type_struct

Synopsis: Creates a struct datatypeint MPI_Type_struct( int count, int blocklens[], MPI_Aint indices[],

MPI_Datatype old_types[], MPI_Datatype *newtype )

Input Parameters

count

number of blocks (integer) -- also number of entries in arrays array_of_types ,

array_of_displacements and array_of_blocklengths

blocklensnumber of elements in each block (array)

indices

byte displacement of each block (array)

old_types

type of elements in each block (array of handles to datatype objects)

Output Parameter

newtype


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MPI_Init(&argc,&argv); MPI_Comm_rank( MPI_COMM_WORLD, &myid); MPI_Comm_size( MPI_COMM_WORLD, &numprocs); MPI_Get_processor_name(name,&resultlen); printf("process %d running on %s\n",myid,name);/* we read and broadcast the global grid size (nx,ny,nz) */ if(myid == 0) { if(argc != 4){ printf("the grid size is not on the command line assuming 100 x 50 x 75\n"); gblsize[0]=100; gblsize[1]=50; gblsize[2]=75; } else { gblsize[0]=atoi(argv[1]); gblsize[1]=atoi(argv[2]); gblsize[2]=atoi(argv[3]); }

} MPI_Bcast(gblsize,3,MPI_INT,0,MPI_COMM_WORLD);/********** a ***********/

Our Program...

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/* the routine three takes the number of processors andreturns a 3d decomposition or topology. this is simplya factoring of the number of processors into 3 integersstored in comp */ three(numprocs,comp);

/* the routine mpDecomposition takes the processor topology andthe global grid dimensions and maps the grid to the topology.

mpDecomposition returns the number of cells a processor holdsand the starting coordinates for its portion of the grid */ if(myid == 0 ) {

printf("input mpDecomposition %5d%5d%5d%5d%5d%5d\n",gblsize[1],gblsize[2],gblsize[0], comp[1], comp[2], comp[0]);} mpDecomposition( gblsize[1],gblsize[2]gblsize[0],comp[1],comp[2],comp[0],myid,dist);printf(" out mpDecomposition %5d%5d%5d%5d%5d%5d%5d\n",myid,dist[0],dist[1],dist[2],

dist[3],dist[4],dist[5]);

/********** b ***********/

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Global size 50 x 200 x 100 on 8 processors

Example Distribution

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/* global grid size */nx=gblsize[0]; ny=gblsize[1]; nz=gblsize[2];

/* amount that i hold */ sx=dist[0]; sy=dist[1]; sz=dist[2];/* my grid starts here */ x0=dist[3]; y0=dist[4]; z0=dist[5];/********** c ***********/

Back to our program...

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/* allocate memory for our volume */vol=getArrayF3D((long)sy,(long)0,(long)0,(long)sz,(long)0,(long)0,

(long)sx,(long)0,(long)0);

/* fill the volume with numbers 1 to global grid size *//* the program from which this example was derived, e3d,

holds its data as a collection of vertical planes.plane number increases with y. that is why we loopon y with the outer most loop. */ k=1+(x0+nx*z0+(nx*nz)*y0);

for (ltmp=0;ltmp

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/* create a file name based on the grid size */ for(j=1;j

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/* we create a description of the layout of the data *//* more on this later */ printf("mysubgrid0 %5d%5d%5d%5d%5d%5d%5d%5d%5d%5d\n",myid,nx,ny,nz,sx,sy,sz,x0,y0,z0);

mysubgrid0(nx, ny, nz,sx, sy, sz, x0, y0, z0, MPI_INT,&disp,&filetype);

/* length of the header */ disp=disp+(4*hl);/* every processor "moves" past the header */

ierr=MPI_File_set_view(fh, disp, MPI_INT, filetype, "native",MPI_INFO_NULL);/********** 02 ***********/

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/* we are going to create the data on the fly *//* so we allocate a buffer for it */

t3=MPI_Wtime();isize=sx*sy*sz;buf_size=NUM_VALS*sizeof(FLT);if( isize < NUM_VALS) {buf_size=isize*sizeof(FLT);

}else {buf_size=NUM_VALS*sizeof(FLT);

}ptr=(FLT*)malloc(buf_size);offset=0;

/* find the max and min number of isize of each processors buffer */ierr=MPI_Allreduce ( &isize, &max_size, 1, MPI_INT, MPI_MAX, MPI_COMM_WORLD);ierr=MPI_Allreduce ( &isize, &min_size, 1, MPI_INT, MPI_MIN, MPI_COMM_WORLD);

/********** 03 ***********/

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/* find out how many times each processor will dump its buffer */i=0;i2=0;do_call=0;sample=1;grid_l=y0+sy;grid_m=z0+sz;grid_n=x0+sx;

/* could just do division but that would be too easy */

for(l = y0; l < grid_l; l = l + sample) {for(m = z0; m < grid_m; m = m + sample) {for(n = x0; n < grid_n; n = n + sample) {i++;i2++;if(i == isize || i2 == NUM_VALS){do_call++;i2=0;

} } } }

/* get the maximum number of many times a processor will dump its buffer */ierr= MPI_Allreduce ( &do_call, &do_call_max, 1, MPI_INT, MPI_MAX, MPI_COMM_WORLD);/********** 04 ***********/

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/* finally we start to write the data */i=0;i2=0;

/* we loop over our grid filling the output buffer */

for(l = y0; l < grid_l; l = l + sample) {for(m = z0; m < grid_m; m = m + sample) {for(n = x0; n < grid_n; n = n + sample) {ptr[i2] = getS3D(vol,l, m, n,y0,z0,x0);i++;i2++;

/********** 05 ***********/

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/* when we have all our data or the buffer is full we write */if(i == isize || i2 == NUM_VALS){t5=MPI_Wtime();t7++;if((isize == max_size) && (max_size == min_size)) {

/* as long as every processor has data to write we use the collective version *//* the collective version of the write is MPI_File_write_at_all */

ierr=MPI_File_write_at_all(fh, offset, ptr, i2, MPI_INT,&status);do_call_max=do_call_max-1;

}else {

/* if only I have data to write then we use MPI_File_write_at *//*ierr=MPI_File_write_at(fh, offset, ptr, i2, MPI_INT,&status);*/

/* Wait! Why was that line commented out? Why are we using MPI_File_write_at_all? *//* Answer: Some versions of MPI work better using MPI_File_write_at_all *//* What happens if some processors are done writing and don't call this? *//* Answer: See below. */

ierr=MPI_File_write_at_all(fh, offset, ptr, i2, MPI_INT,&status);do_call_max=do_call_max-1;

}offset=offset+i2;

i2=0;t6=MPI_Wtime();dt[5]=dt[5]+(t6-t5);

}}}}

/********** 06 ***********/

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/* Here is where we fix the problem of unmatched calls to MPI_File_write_at_all*//* If a processor is done with its writes and others still have *//* data to write the the done processor just calls *//* MPI_File_write_at_all but this 0 values to write *//* All processors call MPI_File_write_at_all the same number of *//* times so everyone is happy */

while(do_call_max > 0) {ierr=MPI_File_write_at_all(fh, (MPI_Offset)0, (void *)0, 0, MPI_INT,&status);do_call_max=do_call_max-1;

}/* We finally close the file */

ierr=MPI_File_close(&fh);/*********

ierr=MPI_Info_free(&fileinfo);*********/

MPI_Finalize();exit(0);

/********** 07 ***********/

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vista --rawtype int --minmax 0 1000000 --skip 12 -x 640 -y480 --outformat png --fov 30 bonk --raw 100 50 200 -r .5 .251.0 -g 0.9 0.9 0.9 1.0 -a 0.002 --opacity 0.01

Our output:

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http://peloton.sdsc.edu/~tkaiser/mpiio/mpiio.cSource

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void mpDecomposition(int l, int m, int n, int nx, int ny, int nz, int node, int *dist){

int nnode, mnode, rnode; int grid_n,grid_n0,grid_m,grid_m0,grid_l,grid_l0;/* x decomposition */ rnode = node%nx; mnode = (n%nx); nnode = (n/nx); grid_n = (rnode < mnode) ? (nnode + 1) : (nnode); grid_n0 = rnode*nnode; grid_n0 += (rnode < mnode) ? (rnode) : (mnode);/* z decomposition */ rnode = (node%(nx*nz))/nx; mnode = (m%nz); nnode = (m/nz); grid_m = (rnode < mnode) ? (nnode + 1) : (nnode); grid_m0 = rnode*nnode; grid_m0 += (rnode < mnode) ? (rnode) : (mnode);/* y decomposition */ rnode = node/(nx*nz); mnode = (l%ny); nnode = (l/ny); grid_l = (rnode < mnode) ? (nnode + 1) : (nnode); grid_l0 = rnode*nnode; grid_l0 += (rnode < mnode) ? (rnode) : (mnode); dist[0]=grid_n; dist[1]=grid_l; dist[2]=grid_m; dist[3]=grid_n0; dist[4]=grid_l0; dist[5]=grid_m0;}

/* the routine mpDecomposition takes theprocessor topology (nx, ny,nz) and theglobal grid dimensions (l,m,n) and mapsthe grid to the topology.

mpDecomposition returns the number ofcells a processor holds, dist[0:2], andthe starting coordinates for its portionof the grid dist[3:5] */

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void mysubgrid0(int nx, int ny, int nz, int sx, int sy, int sz, int x0, int y0, int z0,MPI_Datatype old_type, MPI_Offset *location,MPI_Datatype *new_type)

{

MPI_Datatype VECT;#define BSIZE 5000 int blocklens[BSIZE]; MPI_Aint indices[BSIZE]; MPI_Datatype old_types[BSIZE]; MPI_Datatype TWOD; int i; if(myid == 0)printf("using mysubgrid version 1\n"); if(sz > BSIZE)mpi_check(-1,"sz > BSIZE, increase BSIZE and recompile"); ierr=MPI_Type_contiguous(sx,old_type,&VECT);ierr=MPI_Type_commit(&VECT);

for (i=0;i

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void mysubgrid0(int nx, int ny, int nz,int sx, int sy, int sz,int x0, int y0, int z0,

MPI_Datatype old_type, MPI_Offset *location, MPI_Datatype *new_type){ int gsizes[3],lsizes[3],istarts[3]; gsizes[2]=nx; gsizes[1]=nz; gsizes[0]=ny; lsizes[2]=sx; lsizes[1]=sz; lsizes[0]=sy; istarts[2]=x0; istarts[1]=z0; istarts[0]=y0; if(myid == 0)printf("using mysubgrid version 2\n"); ierr=MPI_Type_create_subarray(3,gsizes,lsizes,istarts,MPI_ORDER_C,old_type,new_type); ierr=MPI_Type_commit(new_type);

*location=0;}

/* This one is actually perfered. it uses a singlecall to the mpi routine MPI_Type_create_subarray withthe the grid description as input. what we get back isa data type that is a 3d strided volume. Unfortunately,MPI_Type_create_subarray does not work for 3d arraysfor some versions of MPI, in particular LAM. */

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