hillclimber 0.1.5a8__cp314-cp314-macosx_15_0_x86_64.whl

plumed/_lib/include/plumed/molfile/fastio.h

@@ -0,0 +1,683 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+University of Illinois Open Source License
+Copyright 2003 Theoretical and Computational Biophysics Group, 
+All rights reserved.
+
+Developed by:		Theoretical and Computational Biophysics Group
+			University of Illinois at Urbana-Champaign
+			http://www.ks.uiuc.edu/
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the Software), to deal with 
+the Software without restriction, including without limitation the rights to 
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies 
+of the Software, and to permit persons to whom the Software is furnished to 
+do so, subject to the following conditions:
+
+Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimers.
+
+Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimers in the documentation 
+and/or other materials provided with the distribution.
+
+Neither the names of Theoretical and Computational Biophysics Group, 
+University of Illinois at Urbana-Champaign, nor the names of its contributors 
+may be used to endorse or promote products derived from this Software without 
+specific prior written permission.
+
+THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL 
+THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR 
+OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, 
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 
+OTHER DEALINGS WITH THE SOFTWARE.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_molfile_fastio_h
+#define __PLUMED_molfile_fastio_h
+/***************************************************************************
+ *cr
+ *cr            (C) Copyright 1995-2016 The Board of Trustees of the
+ *cr                        University of Illinois
+ *cr                         All Rights Reserved
+ *cr
+ ***************************************************************************/
+/***************************************************************************
+ * RCS INFORMATION:
+ *
+ *      $RCSfile: fastio.h,v $
+ *      $Author: johns $       $Locker:  $             $State: Exp $
+ *      $Revision: 1.34 $       $Date: 2016/11/28 05:01:53 $
+ *
+ ***************************************************************************
+ * DESCRIPTION:
+ *   This is a simple abstraction layer for system-dependent I/O calls
+ * that allow plugins to do binary I/O using the fastest possible method.
+ *
+ * This code is intended for use by binary trajectory reader plugins that
+ * work with multi-gigabyte data sets, reading only binary data.
+ *
+ ***************************************************************************/
+
+#define FIO_READ    0x01
+#define FIO_WRITE   0x02
+#define FIO_DIRECT  0x04 /* emulate Unix O_DIRECT flag */
+ 
+/* Compiling on windows */
+#if defined(_MSC_VER) || defined(__MINGW32__)
+
+#if 1 
+/* use native Windows I/O calls */
+#define FASTIO_NATIVEWIN32 1
+
+#include <stdio.h>
+#include <string.h>
+#include <windows.h>
+
+namespace PLMD{
+namespace molfile{
+
+typedef HANDLE fio_fd;
+typedef LONGLONG fio_size_t;
+typedef void * fio_caddr_t;
+
+typedef struct {
+  fio_caddr_t iov_base;
+  int iov_len;
+} fio_iovec;
+
+
+#define FIO_SEEK_CUR  FILE_CURRENT
+#define FIO_SEEK_SET  FILE_BEGIN
+#define FIO_SEEK_END  FILE_END
+
+static int fio_win32convertfilename(const char *filename, char *newfilename, int maxlen) {
+  int i;
+  int len=strlen(filename);
+ 
+  if ((len + 1) >= maxlen)
+    return -1;
+   
+  for (i=0; i<len; i++) {
+    if (filename[i] == '/')
+      newfilename[i] = '\\';
+    else
+      newfilename[i] = filename[i];
+  }
+  newfilename[len] = '\0'; /* NUL terminate the string */
+
+  return 0;
+}
+
+static int fio_open(const char *filename, int mode, fio_fd *fd) {
+  HANDLE fp;
+  char winfilename[8192];
+  DWORD access;
+  DWORD sharing;
+  LPSECURITY_ATTRIBUTES security;
+  DWORD createmode;
+  DWORD flags;
+
+  if (fio_win32convertfilename(filename, winfilename, sizeof(winfilename)))
+    return -1;  
+
+  access = 0;
+  if (mode & FIO_READ)
+    access |= GENERIC_READ;
+  if (mode & FIO_WRITE)
+    access |= GENERIC_WRITE;
+#if 0
+  access = FILE_ALL_ACCESS; /* XXX hack if above modes fail */
+#endif
+#if 1
+  if (mode & FIO_DIRECT)
+    flags = FILE_FLAG_NO_BUFFERING;
+  else
+    flags = FILE_ATTRIBUTE_NORMAL;
+#else
+  if (mode & FIO_DIRECT)
+    return -1; /* not supported yet */
+#endif
+
+  sharing = 0;       /* disallow sharing with other processes  */
+  security = NULL;   /* child processes don't inherit anything */
+
+  /* since we never append, blow away anything that's already there */
+  if (mode & FIO_WRITE)
+    createmode = CREATE_ALWAYS;
+  else 
+    createmode = OPEN_EXISTING;
+
+  fp = CreateFile(winfilename, access, sharing, security, 
+                  createmode, flags, NULL);
+
+  if (fp == NULL) {
+    return -1;
+  } else {
+    *fd = fp;
+    return 0;
+  }
+}
+
+
+static int fio_fclose(fio_fd fd) {
+  BOOL rc;
+  rc = CloseHandle(fd);
+  if (rc) 
+    return 0;
+  else 
+    return -1;
+}
+
+static fio_size_t fio_fread(void *ptr, fio_size_t size, 
+                            fio_size_t nitems, fio_fd fd) {
+  BOOL rc;
+  DWORD len;
+  DWORD readlen;
+
+  len = size * nitems;
+
+  rc = ReadFile(fd, ptr, len, &readlen, NULL);
+  if (rc) {
+    if (readlen == len)
+      return nitems;
+    else 
+      return 0;
+  } else {
+    return 0;
+  }
+}
+
+static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) {
+  int i;
+  fio_size_t len = 0; 
+
+  for (i=0; i<iovcnt; i++) {
+    fio_size_t rc = fio_fread(iov[i].iov_base, iov[i].iov_len, 1, fd);
+    if (rc != 1)
+      break;
+    len += iov[i].iov_len;
+  }
+
+  return len;
+}
+
+static fio_size_t fio_fwrite(void *ptr, fio_size_t size, 
+                             fio_size_t nitems, fio_fd fd) {
+  BOOL rc;
+  DWORD len;
+  DWORD writelen;
+
+  len = size * nitems; 
+ 
+  rc = WriteFile(fd, ptr, len, &writelen, NULL);
+  if (rc) {
+    if (writelen == len)
+      return nitems;
+    else
+      return 0;
+  } else {
+    return 0;
+  }
+}
+
+static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) {
+#if 1
+  /* code that works with older MSVC6 compilers */
+  LONGLONG finaloffset;
+  LARGE_INTEGER bigint;
+  LARGE_INTEGER finalint;
+
+  bigint.QuadPart = offset;
+  finalint = bigint;      /* set the high part, which will be overwritten */
+  finalint.LowPart = SetFilePointer(fd, bigint.LowPart, &finalint.HighPart, whence);
+  if (finalint.LowPart == -1) {
+    /* if (finalint.LowPart == INVALID_SET_FILE_POINTER) { */
+    /* INVALID_SET_FILE_POINTER is a possible "ok" low order result when */
+    /* working with 64-bit offsets, so we have to also check the system  */
+    /* error value for this thread to be sure */
+    if (GetLastError() != ERROR_SUCCESS) {
+      return -1;
+    }
+  } 
+
+  finaloffset = finalint.QuadPart;
+  return 0;
+#else
+  BOOL rc;
+  LONGLONG finaloffset;
+
+  /* SetFilePointerEx() only exists with new .NET compilers */
+  rc = SetFilePointerEx(fd, offset, &finaloffset, whence);
+
+  if (rc) 
+    return 0;
+  else
+    return -1;
+#endif
+}
+
+static fio_size_t fio_ftell(fio_fd fd) {
+  /* code that works with older MSVC6 compilers */
+  LONGLONG finaloffset;
+  LARGE_INTEGER bigint;
+  LARGE_INTEGER finalint;
+
+  bigint.QuadPart = 0;
+  finalint = bigint;      /* set the high part, which will be overwritten */
+
+  finalint.LowPart = SetFilePointer(fd, bigint.LowPart, &finalint.HighPart, FILE_CURRENT);
+  if (finalint.LowPart == -1) {
+    /* if (finalint.LowPart == INVALID_SET_FILE_POINTER) { */
+    /* INVALID_SET_FILE_POINTER is a possible "ok" low order result when */
+    /* working with 64-bit offsets, so we have to also check the system  */
+    /* error value for this thread to be sure */
+    if (GetLastError() != ERROR_SUCCESS) {
+      return -1;
+    }
+  }
+
+  finaloffset = finalint.QuadPart;
+
+  return finaloffset;
+}
+
+
+#else
+
+/* Version for machines with plain old ANSI C  */
+
+#include <stdio.h>
+#include <string.h>
+
+typedef FILE * fio_fd;
+typedef size_t fio_size_t;  /* MSVC doesn't uinversally support ssize_t */
+typedef void * fio_caddr_t; /* MSVC doesn't universally support caddr_t */
+
+typedef struct {
+  fio_caddr_t iov_base;
+  int iov_len;
+} fio_iovec;
+
+#define FIO_SEEK_CUR SEEK_CUR
+#define FIO_SEEK_SET SEEK_SET
+#define FIO_SEEK_END SEEK_END
+
+static int fio_open(const char *filename, int mode, fio_fd *fd) {
+  char * modestr;
+  FILE *fp;
+
+  if (mode & FIO_READ) 
+    modestr = "rb";
+
+  if (mode & FIO_WRITE) 
+    modestr = "wb";
+
+  if (mode & FIO_DIRECT)
+    return -1; /* not supported yet */
+ 
+  fp = fopen(filename, modestr);
+  if (fp == NULL) {
+    return -1;
+  } else {
+    *fd = fp;
+    return 0;
+  }
+}
+
+static int fio_fclose(fio_fd fd) {
+  return fclose(fd);
+}
+
+static fio_size_t fio_fread(void *ptr, fio_size_t size, 
+                            fio_size_t nitems, fio_fd fd) {
+  return fread(ptr, size, nitems, fd);
+}
+
+static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) {
+  int i;
+  fio_size_t len = 0; 
+
+  for (i=0; i<iovcnt; i++) {
+    fio_size_t rc = fread(iov[i].iov_base, iov[i].iov_len, 1, fd);
+    if (rc != 1)
+      break;
+    len += iov[i].iov_len;
+  }
+
+  return len;
+}
+
+static fio_size_t fio_fwrite(void *ptr, fio_size_t size, 
+                             fio_size_t nitems, fio_fd fd) {
+  return fwrite(ptr, size, nitems, fd);
+}
+
+static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) {
+  return fseek(fd, offset, whence);
+}
+
+static fio_size_t fio_ftell(fio_fd fd) {
+  return ftell(fd);
+}
+#endif /* plain ANSI C */
+
+}
+}
+
+#else 
+
+/* Version for UNIX machines */
+#if defined(__linux)
+#ifndef _GNU_SOURCE
+#define _GNU_SOURCE            /* required for O_DIRECT */
+#endif
+#endif
+#include <unistd.h>
+#include <stdio.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+#include <string.h>
+
+namespace PLMD{
+namespace molfile{
+
+typedef int fio_fd;
+typedef off_t fio_size_t;      /* off_t is 64-bits with LFS builds */
+
+/*
+ * Enable use of kernel readv() if available and reliable
+ *
+ * Note: Some Linux implementations incorporate readv() code in libc 
+ * that does userspace copying of I/O vectors to internal temporary
+ * buffers in order to meet the atomicity requirements of the POSIX standard.
+ * Such copies make the use of vectorized I/O APIs much less useful for
+ * large trajectory files because the internal buffer allocations can fail
+ * badly when performing large aggregate I/O operations.  It may be that
+ * other implementations of vector I/O have similar problems, and in these
+ * cases it is probably best not to use it at all, and to fall back to 
+ * non-vectorized I/O APIs to avoid such extra copies.
+ */
+#if defined(__sun) || defined(__APPLE_CC__) || defined(__linux)
+#define USE_KERNEL_READV 1
+#endif
+
+typedef void * fio_caddr_t;
+
+}
+}
+
+#if defined(USE_KERNEL_READV)
+#include <errno.h>
+#include <sys/uio.h>
+namespace PLMD{
+namespace molfile{
+typedef struct iovec fio_iovec;
+}
+}
+#else
+
+namespace PLMD{
+namespace molfile{
+typedef struct {
+  fio_caddr_t iov_base;
+  int iov_len;
+} fio_iovec;
+}
+}
+#endif
+
+#define FIO_SEEK_CUR SEEK_CUR
+#define FIO_SEEK_SET SEEK_SET
+#define FIO_SEEK_END SEEK_END
+
+namespace PLMD{
+namespace molfile{
+
+static int fio_open(const char *filename, int mode, fio_fd *fd) {
+  int nfd;
+  int oflag = 0;
+  
+  if (mode & FIO_READ) 
+    oflag = O_RDONLY;
+
+  if (mode & FIO_WRITE) 
+    oflag = O_WRONLY | O_CREAT | O_TRUNC;
+
+#if defined(__linux)
+  /* enable direct I/O, requires block-aligned buffers and I/O sizes */
+  if (mode & FIO_DIRECT)
+    oflag |= O_DIRECT;
+#else
+  if (mode & FIO_DIRECT)
+    return -1; /* not supported yet */
+#endif
+
+  nfd = open(filename, oflag, 0666);
+  if (nfd < 0) {
+    return -1;
+  } else {
+    *fd = nfd;
+    return 0;
+  }
+}
+
+static int fio_fclose(fio_fd fd) {
+  return close(fd);
+}
+
+static fio_size_t fio_fread(void *ptr, fio_size_t size, 
+                            fio_size_t nitems, fio_fd fd) {
+  fio_size_t i;
+  fio_size_t len = 0; 
+  fio_size_t cnt = 0;
+
+#if 1
+  /*
+   * On Linux individual calls to read() can end up doing short reads when
+   * reading more than 2GB in a single read call, even on 64-bit machines.  
+   * For large structures, e.g. 240M-atoms or larger, we have to use a loop
+   * to continue reading into the memory buffer until completion.
+   */ 
+  for (i=0; i<nitems; i++) {
+    fio_size_t szleft = size;
+    fio_size_t rc = 0;
+    for (szleft=size; szleft > 0; szleft -= rc) {
+      rc = read(fd, ((char*) ptr) + (cnt*size) + (size-szleft), szleft);
+       if (rc == 0) {
+          return cnt;  /* end of file scenario */
+       }
+//      if (rc != szleft) {
+//        printf("fio_fread(): rc %ld  sz: %ld\n", rc, szleft);
+//      }
+      if (rc < 0) {
+        printf("fio_fread(): rc %ld  sz: %ld\n", rc, size);
+        perror("  perror fio_fread(): ");
+        break;
+      }
+    }
+    len += rc;
+    cnt++;
+  }
+#else
+  for (i=0; i<nitems; i++) {
+    fio_size_t rc = read(fd, (void*) (((char *) ptr) + (cnt * size)), size);
+    if (rc != size) {
+//      printf("fio_fread(): rc %ld  sz: %ld\n", rc, size);
+//      perror("  perror fio_fread(): ");
+      break;
+    }
+    len += rc;
+    cnt++;
+  }
+#endif
+
+  return cnt;
+}
+
+static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) {
+  fio_size_t len;
+  int i;
+
+#if 0
+  fio_size_t tlen;
+  for (tlen=0,i=0; i<iovcnt; i++) {
+    tlen += iov[i].iov_len;
+  }
+
+#if defined(USE_KERNEL_READV)
+  len = readv(fd, iov, iovcnt);
+  if (len != tlen) {
+    printf("fio_readv(): readv() rc: %ld  sz: %ld\n", len, tlen);
+    printf("fio_readv(): readv() errno %d\n", errno);
+  }
+
+  if ((len < 0 && errno == ENOSYS) ||
+      (len != tlen && errno == EINVAL)) 
+#endif
+  {
+    /* XXX this loop doesn't meet the atomicity requirements of
+     *     real POSIX readv(), since we don't need that feature 
+     */
+    len = 0; 
+    for (i=0; i<iovcnt; i++) {
+      void *ptr = iov[i].iov_base;
+      fio_size_t sz = iov[i].iov_len;
+      fio_size_t szleft = sz;
+      fio_size_t rc=0;
+
+      for (szleft=sz; szleft > 0; szleft -= rc) {
+        rc = read(fd, ((char*) ptr)+(sz-szleft), szleft);
+        if (rc == 0) {
+          return len;  /* end of file scenario */
+        }
+        if (rc != szleft) {
+          printf("fio_readv(): read() rc %ld  sz: %ld\n", rc, szleft);
+        }
+        if (rc < 0) {
+          printf("fio_readv(): read() rc %ld  sz: %ld\n", rc, szleft);
+          perror("  perror fio_readv(): ");
+          break;
+        }
+      }
+      len += iov[i].iov_len;
+    }
+  }
+#else
+#if defined(USE_KERNEL_READV)
+  len = readv(fd, iov, iovcnt);
+  if (len < 0 && errno == ENOSYS)
+#endif
+  {
+    /* XXX this loop doesn't meet the atomicity requirements of
+     *     real POSIX readv(), since we don't need that feature 
+     */
+    len = 0; 
+    for (i=0; i<iovcnt; i++) {
+      fio_size_t rc = read(fd, iov[i].iov_base, iov[i].iov_len);
+      if (rc != iov[i].iov_len)
+        break;
+      len += iov[i].iov_len;
+    }
+  }
+#endif
+
+  return len;
+}
+
+static fio_size_t fio_fwrite(void *ptr, fio_size_t size, 
+                             fio_size_t nitems, fio_fd fd) {
+  fio_size_t i;
+  fio_size_t len = 0; 
+  fio_size_t cnt = 0;
+
+#if 1
+  /*
+   * On Linux individual calls to write() can end up doing short writes when
+   * writing more than 2GB in a single write call, even on 64-bit machines.  
+   * For large structures, e.g. 240M-atoms or larger, we have to use a loop
+   * to continue writing the memory buffer until completion.
+   */ 
+  int writecalls=0;
+  for (i=0; i<nitems; i++) {
+    fio_size_t szleft = size;
+    fio_size_t rc = 0;
+    for (szleft=size; szleft > 0; szleft -= rc) {
+      fio_size_t writesz = szleft;
+
+#if 0
+      /* On some kernel versions write calls beyond 2GB may not do */
+      /* a partial write and may just return an error immediately. */
+      /* Clamp maximum write size to 1GB per write call.           */
+      if (writesz > (1024L * 1024L * 1024L))
+        writesz = (1024L * 1024L * 1024L);
+#endif
+
+      writecalls++;
+      rc = write(fd, ((char*) ptr)+(size-szleft), writesz);
+      if (rc < 0) {
+        printf("fio_fwrite(): rc %ld  sz: %ld  szleft: %ld  calls: %d\n", 
+               rc, size, szleft, writecalls);
+        perror("  perror fio_fwrite(): ");
+        return cnt;
+      }
+    }
+    len += rc;
+    cnt++;
+  }
+#else
+  for (i=0; i<nitems; i++) {
+    fio_size_t rc = write(fd, ptr, size);
+    if (rc != size) {
+      printf("fio_fwrite(): rc %ld  sz: %ld\n", rc, size);
+      perror("  perror fio_fwrite(): ");
+      break;
+    }
+    len += rc;
+    cnt++;
+  }
+#endif
+
+  return cnt;
+}
+
+static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) {
+ if (lseek(fd, offset, whence) >= 0)
+   return 0;  /* success (emulate behavior of fseek) */
+ else 
+   return -1; /* failure (emulate behavior of fseek) */
+}
+
+static fio_size_t fio_ftell(fio_fd fd) {
+  return lseek(fd, 0, SEEK_CUR);
+}
+
+}
+}
+
+#endif
+
+namespace PLMD{
+namespace molfile{
+
+
+/* higher level routines that are OS independent */
+
+static int fio_write_int32(fio_fd fd, int i) {
+  return (fio_fwrite(&i, 4, 1, fd) != 1);
+}
+
+static int fio_read_int32(fio_fd fd, int *i) {
+  return (fio_fread(i, 4, 1, fd) != 1);
+}
+
+static int fio_write_str(fio_fd fd, const char *str) {
+  int len = strlen(str);
+  return (fio_fwrite((void *) str, len, 1, fd) != 1);
+}
+
+}
+}
+#endif