-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
+ * Copyright (c) 2009,2010,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2012, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program 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 2
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
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*
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*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * Groningen Machine for Chemical Simulation
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+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <algorithm>
+#include "fft5d.h"
+#include <assert.h>
+#include <float.h>
+#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
+#include <algorithm>
+
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "config.h"
+
#ifdef NOGMX
#define GMX_PARALLEL_ENV_INITIALIZED 1
#else
#endif
#endif
-#include "gromacs/utility/gmxmpi.h"
-
#ifdef GMX_OPENMP
/* TODO: Do we still need this? Are we still planning ot use fftw + OpenMP? */
#define FFT5D_THREADS
/* #define FFT5D_FFTW_THREADS (now set by cmake) */
#endif
-#include "fft5d.h"
-#include <float.h>
-#include <math.h>
-#include <assert.h>
-#include "smalloc.h"
-
#ifndef __FLT_EPSILON__
#define __FLT_EPSILON__ FLT_EPSILON
#define __DBL_EPSILON__ DBL_EPSILON
FILE* debug = 0;
#endif
-#include "gmx_fatal.h"
-
-
#ifdef GMX_FFT_FFTW3
#include "thread_mpi/mutex.h"
+
#include "gromacs/utility/exceptions.h"
/* none of the fftw3 calls, except execute(), are thread-safe, so
we need to serialize them with this mutex. */
#define FFTW_UNLOCK try { big_fftw_mutex.unlock(); } GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
#endif /* GMX_FFT_FFTW3 */
+#ifdef GMX_MPI
/* largest factor smaller than sqrt */
static int lfactor(int z)
{
- int i;
- for (i = static_cast<int>(sqrt(static_cast<double>(z)));; i--)
+ int i = static_cast<int>(sqrt(static_cast<double>(z)));
+ while (z%i != 0)
{
- if (z%i == 0)
- {
- return i;
- }
+ i--;
}
- return 1;
+ return i;
}
+#endif
/* largest factor */
static int l2factor(int z)
int i;
if (z == 1)
{
- return 1;
+ i = 1;
}
- for (i = z/2;; i--)
+ else
{
- if (z%i == 0)
+ i = z/2;
+ while (z%i != 0)
{
- return i;
+ i--;
}
}
- return 1;
+ return i;
}
/* largest prime factor: WARNING: slow recursion, only use for small numbers */
if (debug)
{
- fprintf(debug, "FFT5D: Using %dx%d processor grid, rank %d,%d\n",
+ fprintf(debug, "FFT5D: Using %dx%d rank grid, rank %d,%d\n",
P[0], P[1], prank[0], prank[1]);
}
#ifdef GMX_MPI
if ((s == 0 && !(plan->flags&FFT5D_ORDER_YZ)) || (s == 1 && (plan->flags&FFT5D_ORDER_YZ)))
{
- MPI_Alltoall(lout2, N[s]*pM[s]*K[s]*sizeof(t_complex)/sizeof(real), GMX_MPI_REAL, lout3, N[s]*pM[s]*K[s]*sizeof(t_complex)/sizeof(real), GMX_MPI_REAL, cart[s]);
+ MPI_Alltoall((real *)lout2, N[s]*pM[s]*K[s]*sizeof(t_complex)/sizeof(real), GMX_MPI_REAL, (real *)lout3, N[s]*pM[s]*K[s]*sizeof(t_complex)/sizeof(real), GMX_MPI_REAL, cart[s]);
}
else
{
- MPI_Alltoall(lout2, N[s]*M[s]*pK[s]*sizeof(t_complex)/sizeof(real), GMX_MPI_REAL, lout3, N[s]*M[s]*pK[s]*sizeof(t_complex)/sizeof(real), GMX_MPI_REAL, cart[s]);
+ MPI_Alltoall((real *)lout2, N[s]*M[s]*pK[s]*sizeof(t_complex)/sizeof(real), GMX_MPI_REAL, (real *)lout3, N[s]*M[s]*pK[s]*sizeof(t_complex)/sizeof(real), GMX_MPI_REAL, cart[s]);
}
#else
gmx_incons("fft5d MPI call without MPI configuration");
{
if (prank == 0)
{
- printf("FFT5D: WARNING: Number of processors %d not evenly dividable by %d\n", size, P0);
+ printf("FFT5D: WARNING: Number of ranks %d not evenly divisible by %d\n", size, P0);
}
P0 = lfactor(size);
}
MPI_Cart_get(gcart, 2, P, wrap, coor);
MPI_Cart_sub(gcart, rdim1, &cart[0]);
MPI_Cart_sub(gcart, rdim2, &cart[1]);
+#else
+ (void)P0;
+ (void)comm;
#endif
return fft5d_plan_3d(NG, MG, KG, cart, flags, rlin, rlout, rlout2, rlout3, nthreads);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff