First-cut at PLFS support, integrating Brett K's code.
Builds, but not running yet. Requires 'configure ... --with-plfs', so it seems okay to leave this in as an optional build, pending further work.master
Jeffrey Thornton Inman
parent
28c94f8875
commit
ca801fe0ec
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@ -26,16 +26,21 @@ if USE_HDF5_AIORI
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ior_SOURCES += aiori-HDF5.c
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ior_LDADD += -lhdf5 -lz
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endif
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if USE_MPIIO_AIORI
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ior_SOURCES += aiori-MPIIO.c
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endif
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if USE_NCMPI_AIORI
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ior_SOURCES += aiori-NCMPI.c
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ior_LDADD += -lpnetcdf
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endif
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if USE_PLFS_AIORI
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ior_SOURCES += aiori-PLFS.c
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ior_LDADD += -lplfs
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endif
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if USE_POSIX_AIORI
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ior_SOURCES += aiori-POSIX.c
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endif
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@ -0,0 +1,473 @@
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/* -*- mode: c; c-basic-offset: 8; indent-tabs-mode: nil; -*-
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* vim:expandtab:shiftwidth=8:tabstop=8:
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*/
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/*
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* Copyright (c) 2009, Los Alamos National Security, LLC All rights reserved.
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* Copyright 2009. Los Alamos National Security, LLC. This software was produced
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* under U.S. Government contract DE-AC52-06NA25396 for Los Alamos National
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* Laboratory (LANL), which is operated by Los Alamos National Security, LLC for
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* the U.S. Department of Energy. The U.S. Government has rights to use,
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* reproduce, and distribute this software. NEITHER THE GOVERNMENT NOR LOS
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* ALAMOS NATIONAL SECURITY, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR
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* ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE. If software is
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* modified to produce derivative works, such modified software should be
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* clearly marked, so as not to confuse it with the version available from
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* LANL.
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*
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* Additionally, redistribution and use in source and binary forms, with or
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* without modification, are permitted provided that the following conditions are
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* met:
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*
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* • Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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*
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* • Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* • Neither the name of Los Alamos National Security, LLC, Los Alamos National
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* Laboratory, LANL, the U.S. Government, nor the names of its contributors may be
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* used to endorse or promote products derived from this software without specific
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* prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY LOS ALAMOS NATIONAL SECURITY, LLC AND CONTRIBUTORS
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* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
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* THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL LOS ALAMOS NATIONAL SECURITY, LLC OR
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* CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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* EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
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* OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
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* IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
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* OF SUCH DAMAGE.
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*/
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/******************************************************************************\
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*
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* Implement of abstract I/O interface for PLFS.
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*
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\******************************************************************************/
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#ifdef HAVE_CONFIG_H
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#include "config.h"
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#endif
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#include <stdio.h>
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#include <stdlib.h>
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#ifdef __linux__
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#include <sys/ioctl.h> /* necessary for: */
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#define __USE_GNU /* O_DIRECT and */
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#include <fcntl.h> /* IO operations */
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#undef __USE_GNU
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#endif /* __linux__ */
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#include <errno.h>
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#include <fcntl.h> /* IO operations */
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#include <sys/stat.h>
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#include <assert.h>
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/*
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#ifdef HAVE_LUSTRE_LUSTRE_USER_H
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#include <lustre/lustre_user.h>
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#endif
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*/
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#include "ior.h"
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#include "aiori.h"
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#include "iordef.h"
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#ifndef open64 /* necessary for TRU64 -- */
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# define open64 open /* unlikely, but may pose */
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#endif /* not open64 */ /* conflicting prototypes */
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#ifndef lseek64 /* necessary for TRU64 -- */
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# define lseek64 lseek /* unlikely, but may pose */
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#endif /* not lseek64 */ /* conflicting prototypes */
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#ifndef O_BINARY /* Required on Windows */
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# define O_BINARY 0
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#endif
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#include "plfs.h"
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#include "utilities.h"
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/**************************** P R O T O T Y P E S *****************************/
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static void *PLFS_Create(char *, IOR_param_t *);
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static void *PLFS_Open(char *, IOR_param_t *);
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static IOR_offset_t PLFS_Xfer(int, void *, IOR_size_t *,
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IOR_offset_t, IOR_param_t *);
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static void PLFS_Close(void *, IOR_param_t *);
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static void PLFS_Delete(char *, IOR_param_t *);
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static void PLFS_SetVersion(IOR_param_t *);
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static void PLFS_Fsync(void *, IOR_param_t *);
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static IOR_offset_t PLFS_GetFileSize(IOR_param_t *, MPI_Comm, char *);
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/************************** D E C L A R A T I O N S ***************************/
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ior_aiori_t plfs_aiori = {
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"PLFS",
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PLFS_Create,
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PLFS_Open,
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PLFS_Xfer,
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PLFS_Close,
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PLFS_Delete,
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PLFS_SetVersion,
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PLFS_Fsync,
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PLFS_GetFileSize
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};
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/***************************** F U N C T I O N S ******************************/
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/*
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* Create or open the file. Pass TRUE if creating and FALSE if opening an existing file.
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*/
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static void *PLFS_Create_Or_Open( char *testFileName, IOR_param_t *param, unsigned char createFile ) {
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Plfs_fd *plfs_fd = NULL;
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int fd_oflags = 0, plfs_return;
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/*
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* Check for unsupported flags.
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*
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* If they want RDWR, we don't know if they're going to try to do both, so we
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* can't default to either O_RDONLY or O_WRONLY. Thus, we error and exit.
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*
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* The other two, we just note that they are not supported and don't do them.
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*/
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if ( param->openFlags & IOR_RDWR ) {
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ERR( "Opening or creating a file in RDWR is not implemented in PLFS" );
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}
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if ( param->openFlags & IOR_EXCL ) {
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fprintf( stdout, "Opening or creating a file in Exclusive mode is not implemented in PLFS\n" );
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}
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if ( param->openFlags & IOR_APPEND ) {
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fprintf( stdout, "Opening or creating a file for appending is not implemented in PLFS\n" );
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}
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/*
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* Setup the flags to be used.
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*/
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if ( createFile == TRUE ) {
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fd_oflags = O_CREAT;
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}
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if ( param->openFlags & IOR_WRONLY ) {
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if ( !param->filePerProc ) {
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// in N-1 mode, only rank 0 truncates the file
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if ( rank != 0 ) {
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fd_oflags |= O_WRONLY;
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} else {
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fd_oflags |= O_TRUNC;
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fd_oflags |= O_WRONLY;
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}
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} else {
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// in N-N mode, everyone does truncate
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fd_oflags |= O_TRUNC;
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fd_oflags |= O_WRONLY;
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}
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} else {
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fd_oflags |= O_RDONLY;
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}
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/*
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* Now see if O_DIRECT is needed.
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*/
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if ( param->useO_DIRECT == TRUE ) {
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set_o_direct_flag( &fd_oflags );
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}
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/*
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* For N-1 write, All other ranks wait for Rank 0 to open the file.
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* this is bec 0 does truncate and rest don't
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* it would be dangerous for all to do truncate as they might
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* truncate each other's writes
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*/
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if (( param->openFlags & IOR_WRONLY ) &&
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( !param->filePerProc ) &&
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( rank != 0 )) {
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MPI_CHECK(MPI_Barrier(testComm), "barrier error");
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}
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/*
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* Now rank zero can open and truncate, if necessary.
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*/
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plfs_return = plfs_open( &( plfs_fd ), testFileName, fd_oflags, rank, 0666, NULL );
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if ( plfs_return != 0 ) {
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ERR( "Failed to open the file" );
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}
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/*
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* For N-1 write, Rank 0 waits for the other ranks to open the file after it has.
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*/
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if (( param->openFlags & IOR_WRONLY ) &&
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( !param->filePerProc ) &&
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( rank == 0 )) {
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MPI_CHECK(MPI_Barrier(testComm), "barrier error");
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}
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return ((void *) plfs_fd );
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}
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/*
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* Create and open a file through the PLFS interface.
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*/
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static void *PLFS_Create( char *testFileName, IOR_param_t * param ) {
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return PLFS_Create_Or_Open( testFileName, param, TRUE );
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}
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/*
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* Open a file through the PLFS interface.
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*/
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static void *PLFS_Open( char *testFileName, IOR_param_t * param ) {
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if ( param->openFlags & IOR_CREAT ) {
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return PLFS_Create_Or_Open( testFileName, param, TRUE );
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} else {
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return PLFS_Create_Or_Open( testFileName, param, FALSE );
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}
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}
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/*
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* Write or read access to file using the PLFS interface.
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*/
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static IOR_offset_t PLFS_Xfer(int access, void *file, IOR_size_t * buffer,
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IOR_offset_t length, IOR_param_t * param) {
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int xferRetries = 0;
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long long remaining = (long long)length;
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char * ptr = (char *)buffer;
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long long rc;
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off_t offset = param->offset;
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Plfs_fd * plfs_fd = (Plfs_fd *)file;
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while ( remaining > 0 ) {
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/* write/read file */
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if (access == WRITE) { /* WRITE */
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if (verbose >= VERBOSE_4) {
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fprintf( stdout, "task %d writing to offset %lld\n",
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rank,
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param->offset + length - remaining);
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}
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#if 0
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rc = plfs_write( plfs_fd, ptr, remaining, offset, rank ); /* PLFS 2.4 */
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#else
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ssize_t bytes_written = 0;
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rc = plfs_write( plfs_fd, ptr, remaining, offset, rank, &bytes_written ); /* PLFS 2.5 */
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#endif
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if ( rc < 0 ) {
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ERR( "plfs_write() failed" );
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}
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offset += rc;
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if ( param->fsyncPerWrite == TRUE ) {
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PLFS_Fsync( plfs_fd, param );
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}
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} else { /* READ or CHECK */
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if (verbose >= VERBOSE_4) {
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fprintf( stdout, "task %d reading from offset %lld\n",
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rank,
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param->offset + length - remaining );
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}
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#if 0
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rc = plfs_read( plfs_fd, ptr, remaining, param->offset ); /* PLFS 2.4 */
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#else
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ssize_t bytes_read = 0;
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rc = plfs_read( plfs_fd, ptr, remaining, param->offset, &bytes_read ); /* PLFS 2.5 */
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#endif
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if ( rc == 0 ) {
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ERR( "plfs_read() returned EOF prematurely" );
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}
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if ( rc < 0 ) {
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ERR( "plfs_read() failed" );
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}
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offset += rc;
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}
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if ( rc < remaining ) {
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fprintf(stdout, "WARNING: Task %d, partial %s, %lld of %lld bytes at offset %lld\n",
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rank,
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access == WRITE ? "plfs_write()" : "plfs_read()",
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rc, remaining,
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param->offset + length - remaining );
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if ( param->singleXferAttempt == TRUE ) {
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MPI_CHECK( MPI_Abort( MPI_COMM_WORLD, -1 ), "barrier error" );
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}
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if ( xferRetries > MAX_RETRY ) {
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ERR( "too many retries -- aborting" );
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}
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}
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assert( rc >= 0 );
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assert( rc <= remaining );
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remaining -= rc;
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ptr += rc;
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xferRetries++;
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}
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return ( length );
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}
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/*
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* Perform plfs_sync().
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*/
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static void PLFS_Fsync( void *fd, IOR_param_t * param ) {
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Plfs_fd *plfs_fd = (Plfs_fd *)fd;
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if ( plfs_sync( plfs_fd ) != 0 ) {
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EWARN( "plfs_sync() failed" );
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}
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}
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/*
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* Close a file through the PLFS interface.
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*/
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static void PLFS_Close( void *fd, IOR_param_t * param ) {
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Plfs_fd * plfs_fd = (Plfs_fd *)fd;
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int open_flags;
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long long rc;
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if ( param->openFlags & IOR_WRONLY ) {
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open_flags = O_CREAT | O_WRONLY;
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} else {
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open_flags = O_RDONLY;
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}
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#if 0
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rc = plfs_close( plfs_fd, rank, param->id, open_flags, NULL ); /* PLFS 2.4 */
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#else
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int ref_count = 0;
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rc = plfs_close( plfs_fd, rank, param->id, open_flags, NULL, &ref_count ); /* PLFS 2.5 */
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#endif
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if ( rc != 0 ) {
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ERR( "plfs_close() failed" );
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}
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free( fd );
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}
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/*
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* Delete a file through the POSIX interface.
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*/
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static void PLFS_Delete( char *testFileName, IOR_param_t * param ) {
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char errmsg[256];
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if ( plfs_unlink( testFileName ) != 0 ) {
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sprintf(
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errmsg,
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"[RANK %03d]: plfs_unlink() of file \"%s\" failed\n",
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rank, testFileName);
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EWARN( errmsg );
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}
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}
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/*
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* Determine api version.
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*/
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static void PLFS_SetVersion( IOR_param_t * test ) {
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strcpy( test->apiVersion, test->api );
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}
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/*
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* Use plfs_getattr to return aggregate file size.
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*/
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static IOR_offset_t PLFS_GetFileSize(
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IOR_param_t * test, MPI_Comm testComm, char *testFileName) {
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int plfs_return;
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Plfs_fd * plfs_fd = NULL;
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struct stat stat_buf;
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IOR_offset_t aggFileSizeFromStat, tmpMin, tmpMax, tmpSum;
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long long rc;
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plfs_return = plfs_open( &( plfs_fd ), testFileName, O_RDONLY, rank, 0666, NULL );
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if ( plfs_return != 0 ) {
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ERR( "plfs_open() failed before reading the file size attribute" );
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}
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if ( plfs_getattr( plfs_fd, testFileName, &stat_buf, 1 ) != 0 ) {
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ERR( "plfs_getattr() failed" );
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}
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#if 0
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rc = plfs_close( plfs_fd, rank, test->id, O_RDONLY, NULL ); /* PLFS 2.4 */
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#else
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int ref_count = 0;
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rc = plfs_close( plfs_fd, rank, test->id, O_RDONLY, NULL, &ref_count ); /* PLFS 2.5 */
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#endif
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if ( rc != 0 ) {
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ERR( "plfs_close() failed after reading the file size attribute" );
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}
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aggFileSizeFromStat = stat_buf.st_size;
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if ( test->filePerProc == TRUE ) {
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MPI_CHECK(
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MPI_Allreduce(
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&aggFileSizeFromStat, &tmpSum, 1, MPI_LONG_LONG_INT, MPI_SUM, testComm ),
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"cannot total data moved" );
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aggFileSizeFromStat = tmpSum;
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} else {
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MPI_CHECK(
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MPI_Allreduce(
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&aggFileSizeFromStat, &tmpMin, 1, MPI_LONG_LONG_INT, MPI_MIN, testComm ),
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"cannot total data moved" );
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MPI_CHECK(
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MPI_Allreduce(
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&aggFileSizeFromStat, &tmpMax, 1, MPI_LONG_LONG_INT, MPI_MAX, testComm ),
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"cannot total data moved" );
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if ( tmpMin != tmpMax ) {
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if ( rank == 0 ) {
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WARN( "inconsistent file size by different tasks" );
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}
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/* incorrect, but now consistent across tasks */
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aggFileSizeFromStat = tmpMin;
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}
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}
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return ( aggFileSizeFromStat );
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}
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@ -13,46 +13,49 @@
|
|||
\******************************************************************************/
|
||||
|
||||
#ifdef HAVE_CONFIG_H
|
||||
#include "config.h"
|
||||
# include "config.h"
|
||||
#endif
|
||||
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
#ifdef __linux__
|
||||
#include <sys/ioctl.h> /* necessary for: */
|
||||
#define __USE_GNU /* O_DIRECT and */
|
||||
#include <fcntl.h> /* IO operations */
|
||||
#undef __USE_GNU
|
||||
# include <sys/ioctl.h> /* necessary for: */
|
||||
# define __USE_GNU /* O_DIRECT and */
|
||||
# include <fcntl.h> /* IO operations */
|
||||
# undef __USE_GNU
|
||||
#endif /* __linux__ */
|
||||
|
||||
#include <errno.h>
|
||||
#include <fcntl.h> /* IO operations */
|
||||
#include <sys/stat.h>
|
||||
#include <assert.h>
|
||||
#ifdef HAVE_LUSTRE_LUSTRE_USER_H
|
||||
#include <lustre/lustre_user.h>
|
||||
#endif
|
||||
|
||||
#ifdef HAVE_LUSTRE_LUSTRE_USER_H
|
||||
# include <lustre/lustre_user.h>
|
||||
#endif
|
||||
#ifdef HAVE_GPFS_H
|
||||
#include <gpfs.h>
|
||||
# include <gpfs.h>
|
||||
#endif
|
||||
#ifdef HAVE_GPFS_FCNTL_H
|
||||
#include <gpfs_fcntl.h>
|
||||
# include <gpfs_fcntl.h>
|
||||
#endif
|
||||
|
||||
#include "ior.h"
|
||||
#include "aiori.h"
|
||||
#include "iordef.h"
|
||||
#include "utilities.h"
|
||||
|
||||
#ifndef open64 /* necessary for TRU64 -- */
|
||||
#define open64 open /* unlikely, but may pose */
|
||||
# define open64 open /* unlikely, but may pose */
|
||||
#endif /* not open64 */ /* conflicting prototypes */
|
||||
|
||||
#ifndef lseek64 /* necessary for TRU64 -- */
|
||||
#define lseek64 lseek /* unlikely, but may pose */
|
||||
# define lseek64 lseek /* unlikely, but may pose */
|
||||
#endif /* not lseek64 */ /* conflicting prototypes */
|
||||
|
||||
#ifndef O_BINARY /* Required on Windows */
|
||||
#define O_BINARY 0
|
||||
# define O_BINARY 0
|
||||
#endif
|
||||
|
||||
/**************************** P R O T O T Y P E S *****************************/
|
||||
|
|
@ -82,21 +85,6 @@ ior_aiori_t posix_aiori = {
|
|||
|
||||
/***************************** F U N C T I O N S ******************************/
|
||||
|
||||
void set_o_direct_flag(int *fd)
|
||||
{
|
||||
/* note that TRU64 needs O_DIRECTIO, SunOS uses directio(),
|
||||
and everyone else needs O_DIRECT */
|
||||
#ifndef O_DIRECT
|
||||
#ifndef O_DIRECTIO
|
||||
WARN("cannot use O_DIRECT");
|
||||
#define O_DIRECT 000000
|
||||
#else /* O_DIRECTIO */
|
||||
#define O_DIRECT O_DIRECTIO
|
||||
#endif /* not O_DIRECTIO */
|
||||
#endif /* not O_DIRECT */
|
||||
|
||||
*fd |= O_DIRECT;
|
||||
}
|
||||
|
||||
#ifdef HAVE_GPFS_FCNTL_H
|
||||
void gpfs_free_all_locks(int fd)
|
||||
|
|
|
|||
|
|
@ -68,6 +68,7 @@ ior_aiori_t hdfs_aiori;
|
|||
ior_aiori_t mpiio_aiori;
|
||||
ior_aiori_t ncmpi_aiori;
|
||||
ior_aiori_t posix_aiori;
|
||||
ior_aiori_t plfs_aiori;
|
||||
|
||||
IOR_offset_t MPIIO_GetFileSize(IOR_param_t * test, MPI_Comm testComm,
|
||||
char *testFileName);
|
||||
|
|
|
|||
|
|
@ -66,6 +66,9 @@ ior_aiori_t *available_aiori[] = {
|
|||
#endif
|
||||
#ifdef USE_POSIX_AIORI
|
||||
&posix_aiori,
|
||||
#endif
|
||||
#ifdef USE_PLFS_AIORI
|
||||
&plfs_aiori,
|
||||
#endif
|
||||
NULL
|
||||
};
|
||||
|
|
@ -145,7 +148,7 @@ int main(int argc, char **argv)
|
|||
if (rank == 0 && verbose >= VERBOSE_3) {
|
||||
ShowTest(&tptr->params);
|
||||
}
|
||||
#if 0
|
||||
#if 1
|
||||
// This is useful for trapping a running MPI process. While
|
||||
// this is sleeping, run the script 'testing/hdfs/gdb.attach'
|
||||
printf("\tsleeping ...");
|
||||
|
|
|
|||
|
|
@ -14,8 +14,13 @@
|
|||
#ifdef HAVE_CONFIG_H
|
||||
# include "config.h"
|
||||
#endif
|
||||
|
||||
#ifdef USE_HDFS_AIORI
|
||||
# include <hdfs.h> /* hdfsFS */
|
||||
#else
|
||||
# include <stdint.h>
|
||||
typedef uint16_t tPort; /* unused, but needs a type */
|
||||
typedef void* hdfsFS; /* unused, but needs a type */
|
||||
#endif
|
||||
|
||||
#include "iordef.h"
|
||||
|
|
@ -123,7 +128,6 @@ typedef struct
|
|||
char hdfs_user[MAX_STR]; /* copied from ENV, for now */
|
||||
const char* hdfs_name_node;
|
||||
tPort hdfs_name_node_port; /* (uint16_t) */
|
||||
|
||||
hdfsFS hdfs_fs; /* file-system handle */
|
||||
int hdfs_replicas; /* n block replicas. (0 gets default) */
|
||||
int hdfs_block_size; /* internal blk-size. (0 gets default) */
|
||||
|
|
|
|||
|
|
@ -53,6 +53,27 @@ extern int verbose;
|
|||
|
||||
/***************************** F U N C T I O N S ******************************/
|
||||
|
||||
|
||||
/* Used in aiori-POSIX.c and aiori-PLFS.c
|
||||
*/
|
||||
|
||||
void set_o_direct_flag(int *fd)
|
||||
{
|
||||
/* note that TRU64 needs O_DIRECTIO, SunOS uses directio(),
|
||||
and everyone else needs O_DIRECT */
|
||||
#ifndef O_DIRECT
|
||||
# ifndef O_DIRECTIO
|
||||
WARN("cannot use O_DIRECT");
|
||||
# define O_DIRECT 000000
|
||||
# else /* O_DIRECTIO */
|
||||
# define O_DIRECT O_DIRECTIO
|
||||
# endif /* not O_DIRECTIO */
|
||||
#endif /* not O_DIRECT */
|
||||
|
||||
*fd |= O_DIRECT;
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
* Returns string containing the current time.
|
||||
*
|
||||
|
|
|
|||
|
|
@ -12,13 +12,14 @@
|
|||
#define _UTILITIES_H
|
||||
|
||||
#ifdef HAVE_CONFIG_H
|
||||
#include "config.h"
|
||||
# include "config.h"
|
||||
#endif
|
||||
|
||||
#include <mpi.h>
|
||||
|
||||
#include "ior.h"
|
||||
|
||||
void set_o_direct_flag(int *fd);
|
||||
|
||||
char *CurrentTimeString(void);
|
||||
void OutputToRoot(int, MPI_Comm, char *);
|
||||
int Regex(char *, char *);
|
||||
|
|
|
|||
Loading…
Reference in New Issue