MPI IO. Timothy H. Kaiser, Ph.D. Friday, August 12, 11

Transcription

1 MPI IO Timothy H. Kaiser, Ph.D.

2 Purpose Introduce Parallel IO Introduce MPI-IO Not give an exhaustive survey Explain why you would want to use it Explain why you wouldn t want to use it Give a nontrivial and useful example

3 References 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 Lusk and Rajeev Thakur

4 What & Why of parallel IO

5 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 to move large amounts of data to/from disk quickly

6 What & Why of parallel IO Parallel implies that some number (or all) of your processors (simultaneously) participate in an IO operation Good parallel IO shows speedup as you add processors I write about 300 Mbytes/second, others faster

7 A Motivating Example Earthquake Model E3d Finite difference simulation with the grid distributed across N processors On BlueGene we run at sizes of 7509 x 7478 x 250 = 14,021,250,000 cells or 56 GBytes per volume, output 3 velocity volumes per dump For a restart file we write 14 volumes

8 Simple (nonmpi) Parallel IO Each processor dumps its portion of the grid to a separate unique file char* unique(char *name,int myid) { static char unique_str[40]; int i; for(i=0;i<40;i++) unique_str[i]=(char)0; sprintf(unique_str,"%s%5.5d",name,myid); return unique_str; }

9 Simple (nonmpi) Parallel module stuff contains function unique(name,myid) character (len=*) name character (len=20) unique character (len=80) temp write(temp,"(a,i5.5)")trim(name),myid unique=temp return end function unique end module

10 Why not just do this?

11 Why not just do this? Might write thousands of files Could be very slow Output is dependent on the number of processors We might want the data in a single file

12 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

13 Why not? Some functionality might not be available 3d data types

14 Why not? Some functionality might not be available 3d data types More likely to have/introduce bugs Memory leak File system overload Just hangs

15 Why not? More complex than normal output

16 Why not? More complex than normal output Need support from the file system for good performance Have seen 200 bytes/second NOT Megabytes Have run out of file locks

17 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 the same on each processor We are outputting some function of v, V=f(v) We do not Consider a spherical cow Each processor writes its values to a common file

18 Typical Small Case Grid size 472 x 250 x 242 on 16 processors Color shows processor number vista --raw minmax skip 36 \ -x 640 -y outformat png --swapbytes -r \ --fov 30 -g \ -a opacity 0.01 volume dsmpi

19 Special Considerations We are calculating our output on the fly Create a buffer Fill the buffer and write Different processors will have different number of writes

20 Special Considerations We want to use a collective write operation Each process must call the collective write the same number of times Each process must determine how many writes it needs to do The total number of writes is the max Some processors might call write with no data

21 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)

22 Procedure #2 Create a description of how the data is distributed Defined data type Hardest part of the whole process Set the view of the file to this description Determine how many writes are needed and AllReduce into do_call_max

23 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

24 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);

25 Synopsis: Opens a file MPI_File_open 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)

26 Synopsis: Sets the file view MPI_File_set_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)

27 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 file handle (handle) 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)

28 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 file handle (handle) 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)

29 MPI_File_close Synopsis: Closes a file int MPI_File_close(MPI_File *fh) Input Parameters fh file handle (handle)

30 The Data type Routines Our preferred routine creates a 3d description MPI_Type_create_subarray(3,gsizes,lsizes,istarts,MPI_ORDER_C,old_type,new_type); On some platforms we need to fake it MPI_Type_contiguous(sx,old_type,&VECT); MPI_Type_struct(sz,blocklens,indices,old_types,&TWOD); MPI_Type_commit(&TWOD);

31 MPI_Type_create_subarray Synopsis: Creates a datatype describing a subarray of an N dimensional array int 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)

32 MPI_Type_contiguous Synopsis: Creates a contiguous datatype int MPI_Type_contiguous( int count,mpi_datatype old_type,mpi_datatype *newtype) Input Parameters count replication count (nonnegative integer) oldtype old datatype (handle) Output Parameter newtype new datatype (handle)

33 MPI_Type_struct Synopsis: Creates a struct datatype int 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 blocklens number 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 new datatype (handle)

34 Our Program...! 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 ***********/!

35 /* the routine three takes the number of processors and returns a 3d decomposition or topology. this is simply a factoring of the number of processors into 3 integers stored in comp */! three(numprocs,comp);! /* the routine mpdecomposition takes the processor topology and the global grid dimensions and maps the grid to the topology. mpdecomposition returns the number of cells a processor holds and 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 ***********/!

36 Example Distribution Processor Size X Size Y Size Z Start X Start Y Start Z Global size 50 x 200 x 100 on 8 processors

37 Back to our program... /* 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 ***********/!

38 /* 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 loop on y with the outer most loop. */! k=1+(x0+nx*z0+(nx*nz)*y0);! for (ltmp=0;ltmp<sy;ltmp++) {!! for (mtmp=0;mtmp<sz;mtmp++) {!!! for (ntmp=0;ntmp<sx;ntmp++) {!!!! val=k+ntmp+ mtmp*nx! + ltmp*nx*nz;!!!! if(val > (long)int_max)val=(long)int_max;!!!! vol[ltmp][mtmp][ntmp]=(int)val;!!! }!! }! } /********** d ***********/!

39 /* create a file name based on the grid size */! for(j=1;j<80;j++) {!! fname[j]=(char)0;! } sprintf(fname,"%s_%3.3d_%4.4d_%4.4d_%4.4d","mpiio_dat", numprocs,gblsize[0],gblsize[1],gblsize[2]); /* we open the file fname for output, info is NULL */ ierr=mpi_file_open(mpi_comm_world, fname,(mpi_mode_rdwr MPI_MODE_CREATE), MPI_INFO_NULL, &fh); /* we write a 9 integer header */ hl=3; /* set the view to the beginning of the file */ ierr=mpi_file_set_view(fh, 0, MPI_INT, MPI_INT, "native",mpi_info_null); /* process 0 writes the header */ if(myid == 0) { header[0]=nx; header[1]=ny; header[2]=nz; /* MPI_File_write_at is not a collective so only 0 calls it */ ierr=mpi_file_write_at(fh, 0, header, hl, MPI_INT,&status); } /********** 01 ***********/

40 /* 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 ***********/

41 /* 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 ***********/

42 /* 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 ***********/

43 /* 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 ***********/

44 /* 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 ***********/

45 /* 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 ***********/

46 Our output: vista --rawtype int --minmax skip 12 -x 640 -y outformat png --fov 30 bonk --raw r g a opacity 0.01

47 Source

48 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 the processor topology (nx, ny,nz) and the global grid dimensions (l,m,n) and maps the grid to the topology. mpdecomposition returns the number of cells a processor holds, dist[0:2], and the starting coordinates for its portion of the grid dist[3:5] */

49 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<sz;i++) {!blocklens[i]=1;!old_types[i]=vect;!indices[i]=i*nx*4; }! ierr=mpi_type_struct(sz,blocklens,indices,old_types,&twod); ierr=mpi_type_commit(&twod); for (i=0;i<sy;i++) {!blocklens[i]=1;!old_types[i]=twod;!indices[i]=i*nx*nz*4; }! ierr=mpi_type_struct(sy,blocklens,indices,old_types,new_type); ierr=mpi_type_commit(new_type); *location=4*(x0+nx*z0+(nx*nz)*y0); } /* we have two versions of mysubgrid0, the routine that creates the description of the data layout. /* /* This version of mysubgrid0 builds up the description from primatives. we start with x, then create VECT which is a vector of x values. we then take a collection of VECTs and create a vertical slice, TWOD. note that the distance between each VECT in TWOD is given in indices[i]. we next take a collection of vertical slices and create our volume. again we have the distances between the slices given in indices[i] */

50 /* This one is actually preferred. it uses a single call to the mpi routine MPI_Type_create_subarray with the the grid description as input. what we get back is a data type that is a 3d strided volume. Unfortunately, MPI_Type_create_subarray does not work for 3d arrays for some versions of MPI, in particular LAM. */ 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; }