[gmx-users] fix for range checking errors in parallel double precision mdrun
Berk Hess
gmx3 at hotmail.com
Thu Oct 4 16:06:05 CEST 2007
Hi,
A user reported a problem and fix for crashes of parallel double precision
simulations which manifest themselves with "range checking error:..."
during neighbor searching.
When writing xtc in double precision the box was converted to single
precision,
which in parallel can give inconsistent neighbor search grids on the master
and other nodes.
This bug seems to have plagued simulations of several people.
Unfortunately this fix came just after the 3.3.2 release.
For the people who need to run parallel double precision simulations,
below there is a corrected version of src/gmxlib/xtcio.c
Berk.
/*
* $Id: xtcio.c,v 1.19.2.7 2007/10/04 13:52:12 hess Exp $
*
* This source code is part of
*
* G R O M A C S
*
* GROningen MAchine for Chemical Simulations
*
* VERSION 3.3.2
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2007, 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
* of the License, or (at your option) any later version.
*
* If you want to redistribute modifications, 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 www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
*
* For more info, check our website at http://www.gromacs.org
*
* And Hey:
* Groningen Machine for Chemical Simulation
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <string.h>
#include "typedefs.h"
#include "xdrf.h"
#include "gmxfio.h"
#include "xtcio.h"
#include "smalloc.h"
#include "vec.h"
#include "futil.h"
#include "gmx_fatal.h"
#define XTC_MAGIC 1995
static int xdr_r2f(XDR *xdrs,real *r,bool bRead)
{
#ifdef GMX_DOUBLE
float f;
int ret;
if (!bRead)
f = *r;
ret = xdr_float(xdrs,&f);
if (bRead)
*r = f;
return ret;
#else
return xdr_float(xdrs,(float *)r);
#endif
}
int open_xtc(char *fn,char *mode)
{
return fio_open(fn,mode);
}
void close_xtc(int fp)
{
fio_close(fp);
}
static void check_xtc_magic(int magic)
{
if (magic != XTC_MAGIC)
gmx_fatal(FARGS,"Magic Number Error in XTC file (read %d, should be
%d)",
magic,XTC_MAGIC);
}
int xtc_check(char *str,bool bResult,char *file,int line)
{
if (!bResult) {
if (debug)
fprintf(debug,"\nXTC error: read/write of %s failed, "
"source file %s, line %d\n",str,file,line);
return 0;
}
return 1;
}
void xtc_check_fat_err(char *str,bool bResult,char *file,int line)
{
if (!bResult) {
gmx_fatal(FARGS,"XTC read/write of %s failed, "
"source file %s, line %d\n",str,file,line);
}
}
static int xtc_header(XDR *xd,int *magic,int *natoms,int *step,real *time,
bool bRead,bool *bOK)
{
int result;
if (xdr_int(xd,magic) == 0)
return 0;
result=XTC_CHECK("natoms", xdr_int(xd,natoms)); /* number of atoms */
if (result)
result=XTC_CHECK("step", xdr_int(xd,step)); /* frame number */
if (result)
result=XTC_CHECK("time", xdr_r2f(xd,time,bRead)); /* time */
*bOK=(result!=0);
return result;
}
static int xtc_coord(XDR *xd,int *natoms,matrix box,rvec *x,real *prec, bool
bRead)
{
int i,j,result;
#ifdef GMX_DOUBLE
float *ftmp;
float fprec;
#endif
/* box */
result=1;
for(i=0; ((i<DIM) && result); i++)
for(j=0; ((j<DIM) && result); j++)
result=XTC_CHECK("box",xdr_r2f(xd,&(box[i][j]),bRead));
if (!result)
return result;
#ifdef GMX_DOUBLE
/* allocate temp. single-precision array */
snew(ftmp,(*natoms)*DIM);
/* Copy data to temp. array if writing */
if(!bRead)
{
for(i=0; (i<*natoms); i++)
{
ftmp[DIM*i+XX]=x[i][XX];
ftmp[DIM*i+YY]=x[i][YY];
ftmp[DIM*i+ZZ]=x[i][ZZ];
}
fprec = *prec;
}
result=XTC_CHECK("x",xdr3dfcoord(xd,ftmp,natoms,&fprec));
/* Copy from temp. array if reading */
if(bRead)
{
for(i=0; (i<*natoms); i++)
{
x[i][XX] = ftmp[DIM*i+XX];
x[i][YY] = ftmp[DIM*i+YY];
x[i][ZZ] = ftmp[DIM*i+ZZ];
}
*prec = fprec;
}
sfree(ftmp);
#else
result=XTC_CHECK("x",xdr3dfcoord(xd,x[0],natoms,prec));
#endif
return result;
}
int write_xtc(int fp,
int natoms,int step,real time,
matrix box,rvec *x,real prec)
{
int magic_number = XTC_MAGIC;
XDR *xd;
bool bDum;
xd = fio_getxdr(fp);
/* write magic number and xtc identidier */
if (!xtc_header(xd,&magic_number,&natoms,&step,&time,FALSE,&bDum))
return 0;
/* write data */
return xtc_coord(xd,&natoms,box,x,&prec,FALSE);
}
int read_first_xtc(int fp,int *natoms,int *step,real *time,
matrix box,rvec **x,real *prec,bool *bOK)
{
int magic;
XDR *xd;
*bOK=TRUE;
xd = fio_getxdr(fp);
/* read header and malloc x */
if ( !xtc_header(xd,&magic,natoms,step,time,TRUE,bOK))
return 0;
/* Check magic number */
check_xtc_magic(magic);
snew(*x,*natoms);
*bOK=xtc_coord(xd,natoms,box,*x,prec,TRUE);
return *bOK;
}
int read_next_xtc(int fp,
int natoms,int *step,real *time,
matrix box,rvec *x,real *prec,bool *bOK)
{
int magic;
int n;
XDR *xd;
*bOK=TRUE;
xd = fio_getxdr(fp);
/* read header */
if (!xtc_header(xd,&magic,&n,step,time,TRUE,bOK))
return 0;
if (n>natoms)
gmx_fatal(FARGS, "Frame contains more atoms (%d) than expected (%d)",
n, natoms);
/* Check magic number */
check_xtc_magic(magic);
*bOK=xtc_coord(xd,&natoms,box,x,prec,TRUE);
return *bOK;
}
_________________________________________________________________
Play online games with your friends with Messenger
http://www.join.msn.com/messenger/overview
More information about the gromacs.org_gmx-users
mailing list