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CSCI-4320/6360: Parallel Programming & Computing Tues./Fri. 12-1:30 p.m. MPI File I/O

Prof. Chris Carothers Computer Science Department MRC 309a chrisc@cs.rpi.edu www.cs.rpi.edu/~chrisc/COURSES/PARALLEL/SPRING-2013 Adapted from: people.cs.uchicago.edu/~asiegel/courses/cspp51085/.../mpi-io.ppt.

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CSCI-4320/6360: Parallel Programming & Computing Tues./Fri. 12-1:30 p.m. MPI File I/O

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  1. PPC 2013 - MPI Parallel File I/O Prof. Chris Carothers Computer Science Department MRC 309a chrisc@cs.rpi.edu www.cs.rpi.edu/~chrisc/COURSES/PARALLEL/SPRING-2013 Adapted from: people.cs.uchicago.edu/~asiegel/courses/cspp51085/.../mpi-io.ppt CSCI-4320/6360: Parallel Programming & ComputingTues./Fri. 12-1:30 p.m.MPI File I/O

  2. PPC 2013 - MPI Parallel File I/O Common Ways of Doing I/O in Parallel Programs • Sequential I/O: • All processes send data to rank 0, and 0 writes it to the file

  3. PPC 2013 - MPI Parallel File I/O Pros and Cons of Sequential I/O • Pros: • parallel machine may support I/O from only one process (e.g., no common file system) • Some I/O libraries (e.g. HDF-4, NetCDF, PMPIO) not parallel • resulting single file is handy for ftp, mv • big blocks improve performance • short distance from original, serial code • Cons: • lack of parallelism limits scalability, performance (single node bottleneck)

  4. PPC 2013 - MPI Parallel File I/O Another Way • Each process writes to a separate file • Pros: • parallelism, high performance • Cons: • lots of small files to manage • LOTS OF METADATA – stress parallel filesystem • difficult to read back data from different number of processes

  5. PPC 2013 - MPI Parallel File I/O What is Parallel I/O? • Multiple processes of a parallel program accessing data (reading or writing) from a common file FILE P(n-1) P0 P1 P2

  6. PPC 2013 - MPI Parallel File I/O Why Parallel I/O? • Non-parallel I/O is simple but • Poor performance (single process writes to one file) or • Awkward and not interoperable with other tools (each process writes a separate file) • Parallel I/O • Provides high performance • Can provide a single file that can be used with other tools (such as visualization programs)

  7. PPC 2013 - MPI Parallel File I/O Why is MPI a Good Setting for Parallel I/O? • Writing is like sending a message and reading is like receiving. • Any parallel I/O system will need a mechanism to • define collective operations (MPI communicators) • define noncontiguous data layout in memory and file (MPI datatypes) • Test completion of nonblocking operations (MPI request objects) • i.e., lots of MPI-like machinery

  8. PPC 2013 - MPI Parallel File I/O MPI-IO Background • Marc Snir et al (IBM Watson) paper exploring MPI as context for parallel I/O (1994) • MPI-IO email discussion group led by J.-P. Prost (IBM) and Bill Nitzberg (NASA), 1994 • MPI-IO group joins MPI Forum in June 1996 • MPI-2 standard released in July 1997 • MPI-IO is Chapter 9 of MPI-2

  9. PPC 2013 - MPI Parallel File I/O FILE P(n-1) P0 P1 P2 Using MPI for Simple I/O Each process needs to read a chunk of data from a common file

  10. PPC 2013 - MPI Parallel File I/O Using Individual File Pointers #include<stdio.h> #include<stdlib.h> #include "mpi.h" #define FILESIZE 1000 int main(int argc, char **argv){ int rank, nprocs; MPI_File fh; MPI_Status status; int bufsize, nints; int buf[FILESIZE]; MPI_Init(&argc, &argv); MPI_Comm_rank(MPI_COMM_WORLD, &rank); MPI_Comm_size(MPI_COMM_WORLD, &nprocs); bufsize = FILESIZE/nprocs; nints = bufsize/sizeof(int); MPI_File_open(MPI_COMM_WORLD, "datafile", MPI_MODE_RDONLY, MPI_INFO_NULL, &fh); MPI_File_seek(fh, rank * bufsize, MPI_SEEK_SET); MPI_File_read(fh, buf, nints, MPI_INT, &status); MPI_File_close(&fh); }

  11. PPC 2013 - MPI Parallel File I/O Using Explicit Offsets #include<stdio.h> #include<stdlib.h> #include "mpi.h" #define FILESIZE 1000 int main(int argc, char **argv){ int rank, nprocs; MPI_File fh; MPI_Status status; int bufsize, nints; int buf[FILESIZE]; MPI_Init(&argc, &argv); MPI_Comm_rank(MPI_COMM_WORLD, &rank); MPI_Comm_size(MPI_COMM_WORLD, &nprocs); bufsize = FILESIZE/nprocs; nints = bufsize/sizeof(int); MPI_File_open(MPI_COMM_WORLD, "datafile", MPI_MODE_RDONLY, MPI_INFO_NULL, &fh); MPI_File_read_at(fh, rank*bufsize, buf, nints, MPI_INT, &status); MPI_File_close(&fh); }

  12. PPC 2013 - MPI Parallel File I/O Function Details MPI_File_open(MPI_Comm comm, char *file, int mode, MPI_Info info, MPI_File *fh) (note: mode = MPI_MODE_RDONLY, MPI_MODE_RDWR, MPI_MODE_WRONLY, MPI_MODE_CREATE, MPI_MODE_EXCL, MPI_MODE_DELETE_ON_CLOSE, MPI_MODE_UNIQUE_OPEN, MPI_MODE_SEQUENTIAL, MPI_MODE_APPEND) MPI_File_close(MPI_File *fh) MPI_File_read(MPI_File fh, void *buf, int count, MPI_Datatype type, MPI_Status *status) MPI_File_read_at(MPI_File fh, int offset, void *buf, int count, MPI_Datatype type, MPI_Status *status) MPI_File_seek(MPI_File fh, MPI_Offset offset, in whence); (note: whence = MPI_SEEK_SET, MPI_SEEK_CUR, or MPI_SEEK_END) MPI_File_write(MPI_File fh, void *buf, int count, MPI_Datatype datatype, MPI_Status *status) MPI_File_write_at( …same as read_at … ); (Note: Many other functions to get/set properties (see Gropp et al))

  13. PPC 2013 - MPI Parallel File I/O Writing to a File • Use MPI_File_write or MPI_File_write_at • Use MPI_MODE_WRONLY or MPI_MODE_RDWR as the flags to MPI_File_open • If the file doesn’t exist previously, the flag MPI_MODE_CREATE must also be passed to MPI_File_open • We can pass multiple flags by using bitwise-or ‘|’ in C, or addition ‘+” in Fortran

  14. PPC 2013 - MPI Parallel File I/O MPI Datatype Interlude • Datatypes in MPI • Elementary: MPI_INT, MPI_DOUBLE, etc • everything we’ve used to this point • Contiguous • Next easiest: sequences of elementary types • Vector • Sequences separated by a constant “stride”

  15. PPC 2013 - MPI Parallel File I/O MPI Datatypes, cont • Indexed: more general • does not assume a constant stride • Struct • General mixed types (like C structs)

  16. PPC 2013 - MPI Parallel File I/O Creating simple datatypes • Let’s just look at the simplest types: contiguous and vector datatypes. • Contiguous example • Let’s create a new datatype which is two ints side by side. The calling sequence is MPI_Type_contiguous(int count, MPI_Datatype oldtype, MPI_Datatype *newtype); MPI_Datatype newtype; MPI_Type_contiguous(2, MPI_INT, &newtype); MPI_Type_commit(newtype); /* required */

  17. PPC 2013 - MPI Parallel File I/O Using File Views • Processes write to shared file • MPI_File_set_view assigns regions of the file to separate processes

  18. PPC 2013 - MPI Parallel File I/O File Views • Specified by a triplet (displacement, etype, and filetype) passed to MPI_File_set_view • displacement = number of bytes to be skipped from the start of the file • etype = basic unit of data access (can be any basic or derived datatype) • filetype = specifies which portion of the file is visible to the process • This is a collective operation and so all processors/ranks must use the same data rep, etypes in the group determined when the file was open..

  19. PPC 2013 - MPI Parallel File I/O File Interoperability • Users can optionally create files with a portable binary data representation • “datarep” parameter to MPI_File_set_view • native -default, same as in memory, not portable • internal - impl. defined representation providing an impl. defined level of portability • external32 - a specific representation defined in MPI, (basically 32-bit big-endian IEEE format), portable across machines and MPI implementations

  20. PPC 2013 - MPI Parallel File I/O File View Example MPI_File thefile; for (i=0; i<BUFSIZE; i++) buf[i] = myrank * BUFSIZE + i; MPI_File_open(MPI_COMM_WORLD, "testfile", MPI_MODE_CREATE | MPI_MODE_WRONLY, MPI_INFO_NULL, &thefile); MPI_File_set_view(thefile, myrank * BUFSIZE, MPI_INT, MPI_INT, "native", MPI_INFO_NULL); MPI_File_write(thefile, buf, BUFSIZE, MPI_INT, MPI_STATUS_IGNORE); MPI_File_close(&thefile);

  21. PPC 2013 - MPI Parallel File I/O Ways to Write to a Shared File like Unix seek • MPI_File_seek • MPI_File_read_at • MPI_File_write_at • MPI_File_read_shared • MPI_File_write_shared • Collective operations combine seek and I/O for thread safety use shared file pointer good when order doesn’t matter

  22. PPC 2013 - MPI Parallel File I/O Collective I/O in MPI • A critical optimization in parallel I/O • Allows communication of “big picture” to file system • Framework for 2-phase I/O, in which communication precedes I/O (can use MPI machinery) • Basic idea: build large blocks, so that reads/writes in I/O system will be large Small individual requests Large collective access

  23. PPC 2013 - MPI Parallel File I/O Collective I/O • MPI_File_read_all, MPI_File_read_at_all, etc • _all indicates that all processes in the group specified by the communicator passed to MPI_File_open will call this function • Each process specifies only its own access information -- the argument list is the same as for the non-collective functions

  24. PPC 2013 - MPI Parallel File I/O Collective I/O • By calling the collective I/O functions, the user allows an implementation to optimize the request based on the combined request of all processes • The implementation can merge the requests of different processes and service the merged request efficiently • Particularly effective when the accesses of different processes are noncontiguous and interleaved

  25. PPC 2013 - MPI Parallel File I/O Collective non-contiguousMPI-IO examples #define “mpi.h” #define FILESIZE 1048576 #define INTS_PER_BLK 16 int main(int argc, char **argv){ int *buf, rank, nprocs, nints, bufsize; MPI_File fh; MPI_Datatype filetype; MPI_Init(&argc, &argv); MPI_Comm_rank(MPI_COMM_WORLD, &rank); MPI_Comm_size(MPI_COMM_WORLD, &nprocs); bufsize = FILESIZE/nprocs; buf = (int *) malloc(bufsize); nints = bufsize/sizeof(int); MPI_File_open(MPI_COMM_WORLD, “filename”, MPI_MODE_RD_ONLY, MPI_INFO_NULL, &fh); MPI_Type_vector(nints/INTS_PER_BLK, INTS_PER_BLK, INTS_PER_BLK*nprocs, MPI_INT, &filetype); MPI_Type_commit(&filetype); MPI_File_set_view(fh, INTS_PER_BLK*sizeof(int)*rank, MPI_INT, filetype, “native”, MPI_INFO_NULL); MPI_File_read_all(fh, buf, nints, MPI_INT, MPI_STATUS_IGNORE); MPI_Type_free(&filetype); free(buf) MPI_Finalize(); return(0); }

  26. PPC 2013 - MPI Parallel File I/O More on MPI_Read_all • Note that the _all version has the same argument list • Difference is that all processes involved in MPI_Open must call this the read • Contrast with the non-all version where any subset may or may not call it • Allows for many optimizations

  27. PPC 2013 - MPI Parallel File I/O Split Collective I/O • A restricted form of nonblocking collective I/O • Only one active nonblocking collective operation allowed at a time on a file handle • Therefore, no request object necessary MPI_File_write_all_begin(fh, buf, count, datatype); // available on Blue Gene/L, but may not improve // performance for (i=0; i<1000; i++) { /* perform computation */ } MPI_File_write_all_end(fh, buf, &status);

  28. PPC 2013 - MPI Parallel File I/O Passing Hints to the Implementation MPI_Info info; MPI_Info_create(&info); /* no. of I/O devices to be used for file striping */ MPI_Info_set(info, "striping_factor", "4"); /* the striping unit in bytes */ MPI_Info_set(info, "striping_unit", "65536"); MPI_File_open(MPI_COMM_WORLD, "/pfs/datafile", MPI_MODE_CREATE | MPI_MODE_RDWR, info, &fh); MPI_Info_free(&info);

  29. PPC 2013 - MPI Parallel File I/O Examples of Hints (used in ROMIO) • striping_unit • striping_factor • cb_buffer_size • cb_nodes • ind_rd_buffer_size • ind_wr_buffer_size • start_iodevice • pfs_svr_buf • direct_read • direct_write MPI-2 predefined hints New Algorithm Parameters Platform-specific hints

  30. PPC 2013 - MPI Parallel File I/O I/O Consistency Semantics • The consistency semantics specify the results when multiple processes access a common file and one or more processes write to the file • MPI guarantees stronger consistency semantics if the communicator used to open the file accurately specifies all the processes that are accessing the file, and weaker semantics if not • The user can take steps to ensure consistency when MPI does not automatically do so

  31. PPC 2013 - MPI Parallel File I/O Process 0 Process 1 MPI_File_open(MPI_COMM_WORLD,…) MPI_File_write_at(off=0,cnt=100) MPI_File_read_at(off=0,cnt=100) MPI_File_open(MPI_COMM_WORLD,…) MPI_File_write_at(off=100,cnt=100) MPI_File_read_at(off=100,cnt=100) Example 1 • File opened with MPI_COMM_WORLD. Each process writes to a separate region of the file and reads back only what it wrote. • MPI guarantees that the data will be read correctly

  32. PPC 2013 - MPI Parallel File I/O Example 2 • Same as example 1, except that each process wants to read what the other process wrote (overlapping accesses) • In this case, MPI does not guarantee that the data will automatically be read correctly Process 0 Process 1 /* incorrect program */ MPI_File_open(MPI_COMM_WORLD,…) MPI_File_write_at(off=0,cnt=100) MPI_Barrier MPI_File_read_at(off=100,cnt=100) /* incorrect program */ MPI_File_open(MPI_COMM_WORLD,…) MPI_File_write_at(off=100,cnt=100) MPI_Barrier MPI_File_read_at(off=0,cnt=100) • In the above program, the read on each process is not guaranteed to get the data written by the other process!

  33. PPC 2013 - MPI Parallel File I/O Example 2 contd. • The user must take extra steps to ensure correctness • There are three choices: • set atomicity to true • close the file and reopen it • ensure that no write sequence on any process is concurrent with any sequence (read or write) on another process/MPI rank • Can hurt performance….

  34. PPC 2013 - MPI Parallel File I/O Process 0 Process 1 MPI_File_open(MPI_COMM_WORLD,…) MPI_File_set_atomicity(fh1,1) MPI_File_write_at(off=0,cnt=100) MPI_Barrier MPI_File_read_at(off=100,cnt=100) MPI_File_open(MPI_COMM_WORLD,…) MPI_File_set_atomicity(fh2,1) MPI_File_write_at(off=100,cnt=100) MPI_Barrier MPI_File_read_at(off=0,cnt=100) Example 2, Option 1Set atomicity to true

  35. PPC 2013 - MPI Parallel File I/O Example 2, Option 2Close and reopen file Process 0 Process 1 MPI_File_open(MPI_COMM_WORLD,…) MPI_File_write_at(off=0,cnt=100) MPI_File_close MPI_Barrier MPI_File_open(MPI_COMM_WORLD,…) MPI_File_read_at(off=100,cnt=100) MPI_File_open(MPI_COMM_WORLD,…) MPI_File_write_at(off=100,cnt=100) MPI_File_close MPI_Barrier MPI_File_open(MPI_COMM_WORLD,…) MPI_File_read_at(off=0,cnt=100)

  36. PPC 2013 - MPI Parallel File I/O Example 2, Option 3 • Ensure that no write sequence on any process is concurrent with any sequence (read or write) on another process • a sequence is a set of operations between any pair of open, close, or file_sync functions • a write sequence is a sequence in which any of the functions is a write operation

  37. PPC 2013 - MPI Parallel File I/O Process 0 Process 1 MPI_File_open(MPI_COMM_WORLD,…) MPI_File_write_at(off=0,cnt=100) MPI_File_sync MPI_Barrier MPI_File_sync /*collective*/ MPI_File_sync /*collective*/ MPI_Barrier MPI_File_sync MPI_File_read_at(off=100,cnt=100) MPI_File_close MPI_File_open(MPI_COMM_WORLD,…) MPI_File_sync /*collective*/ MPI_Barrier MPI_File_sync MPI_File_write_at(off=100,cnt=100) MPI_File_sync MPI_Barrier MPI_File_sync /*collective*/ MPI_File_read_at(off=0,cnt=100) MPI_File_close Example 2, Option 3

  38. PPC 2013 - MPI Parallel File I/O General Guidelines for Achieving High I/O Performance • Buy sufficient I/O hardware for the machine • Use fast file systems, not NFS-mounted home directories • Do not perform I/O from one process only • Make large requests wherever possible • For noncontiguous requests, use derived datatypes and a single collective I/O call

  39. PPC 2013 - MPI Parallel File I/O Optimizations • Given complete access information, an implementation can perform optimizations such as: • Data Sieving: Read large chunks and extract what is really needed • Collective I/O: Merge requests of different processes into larger requests • Improved prefetching and caching

  40. PPC 2013 - MPI Parallel File I/O Summary • MPI-IO has many features that can help users achieve high performance • The most important of these features are the ability to specify noncontiguous accesses, the collective I/O functions, and the ability to pass hints to the implementation • Users must use the above features! • In particular, when accesses are noncontiguous, users must create derived datatypes, define file views, and use the collective I/O functions

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