hisat-3n/shmem.h

/*
 * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
 *
 * This file is part of Bowtie 2.
 *
 * Bowtie 2 is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * Bowtie 2 is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with Bowtie 2.  If not, see <http://www.gnu.org/licenses/>.
 */

#ifndef SHMEM_H_
#define SHMEM_H_

#ifdef BOWTIE_SHARED_MEM

#include <string>
#include <sys/shm.h>
#include <unistd.h>
#include <sys/shm.h>
#include <errno.h>
#include <stdint.h>
#include <stdexcept>
#include "str_util.h"
#include "btypes.h"

extern void notifySharedMem(void *mem, size_t len);

extern void waitSharedMem(void *mem, size_t len);

#define ALLOC_SHARED_U allocSharedMem<TIndexOffU>
#define ALLOC_SHARED_U8 allocSharedMem<uint8_t>
#define ALLOC_SHARED_U32 allocSharedMem<uint32_t>
#define FREE_SHARED shmdt
#define NOTIFY_SHARED notifySharedMem
#define WAIT_SHARED waitSharedMem

#define SHMEM_UNINIT  0xafba4242
#define SHMEM_INIT    0xffaa6161

/**
 * Tries to allocate a shared-memory chunk for a given file of a given size.
 */
template <typename T>
bool allocSharedMem(std::string fname,
                    size_t len,
                    T ** dst,
                    const char *memName,
                    bool verbose)
{
	using namespace std;
	int shmid = -1;
	// Calculate key given string
	key_t key = (key_t)hash_string(fname);
	shmid_ds ds;
	int ret;
	// Reserve 4 bytes at the end for silly synchronization
	size_t shmemLen = len + 4;
	if(verbose) {
		cerr << "Reading " << len << "+4 bytes into shared memory for " << memName << endl;
	}
	T *ptr = NULL;
	while(true) {
		// Create the shrared-memory block
		if((shmid = shmget(key, shmemLen, IPC_CREAT | 0666)) < 0) {
			if(errno == ENOMEM) {
				cerr << "Out of memory allocating shared area " << memName << endl;
			} else if(errno == EACCES) {
				cerr << "EACCES" << endl;
			} else if(errno == EEXIST) {
				cerr << "EEXIST" << endl;
			} else if(errno == EINVAL) {
				cerr << "Warning: shared-memory chunk's segment size doesn't match expected size (" << (shmemLen) << ")" << endl
					 << "Deleteing old shared memory block and trying again." << endl;
				shmid = shmget(key, 0, 0);
				if((ret = shmctl(shmid, IPC_RMID, &ds)) < 0) {
					cerr << "shmctl returned " << ret
						 << " for IPC_RMID, errno is " << errno
						 << ", shmid is " << shmid << endl;
					throw 1;
				} else {
					cerr << "Deleted shared mem chunk with shmid " << shmid << endl;
				}
				continue;
			} else if(errno == ENOENT) {
				cerr << "ENOENT" << endl;
			} else if(errno == ENOSPC) {
				cerr << "ENOSPC" << endl;
			} else {
				cerr << "shmget returned " << shmid << " for and errno is " << errno << endl;
			}
			throw 1;
		}
		ptr = (T*)shmat(shmid, 0, 0);
		if(ptr == (void*)-1) {
			cerr << "Failed to attach " << memName << " to shared memory with shmat()." << endl;
			throw 1;
		}
		if(ptr == NULL) {
			cerr << memName << " pointer returned by shmat() was NULL." << endl;
			throw 1;
		}
		// Did I create it, or did I just attach to one created by
		// another process?
		if((ret = shmctl(shmid, IPC_STAT, &ds)) < 0) {
			cerr << "shmctl returned " << ret << " for IPC_STAT and errno is " << errno << endl;
			throw 1;
		}
		if(ds.shm_segsz != shmemLen) {
			cerr << "Warning: shared-memory chunk's segment size (" << ds.shm_segsz
				 << ") doesn't match expected size (" << shmemLen << ")" << endl
				 << "Deleteing old shared memory block and trying again." << endl;
			if((ret = shmctl(shmid, IPC_RMID, &ds)) < 0) {
				cerr << "shmctl returned " << ret << " for IPC_RMID and errno is " << errno << endl;
				throw 1;
			}
		} else {
			break;
		}
	} // while(true)
	*dst = ptr;
	bool initid = (((volatile uint32_t*)((char*)ptr + len))[0] == SHMEM_INIT);
	if(ds.shm_cpid == getpid() && !initid) {
		if(verbose) {
			cerr << "  I (pid = " << getpid() << ") created the "
			     << "shared memory for " << memName << endl;
		}
		// Set this value just off the end of the chunk to
		// indicate that the data hasn't been read yet.
		((volatile uint32_t*)((char*)ptr + len))[0] = SHMEM_UNINIT;
		return true;
	} else {
		if(verbose) {
			cerr << "  I (pid = " << getpid()
			     << ") did not create the shared memory for "
			     << memName << ".  Pid " << ds.shm_cpid << " did." << endl;
		}
		return false;
	}
}

#else

#define ALLOC_SHARED_U(...) 0
#define ALLOC_SHARED_U8(...) 0
#define ALLOC_SHARED_U32(...) 0
#define FREE_SHARED(...)
#define NOTIFY_SHARED(...)
#define WAIT_SHARED(...)

#endif /*BOWTIE_SHARED_MEM*/

#endif /* SHMEM_H_ */