Jones de Andrade wrote:
Hi all!
Ok, got what should be done. But now I have a (big) question: this code
compiles properly with gcc. Ok, maybe that means difference of tolerance
between different compilers. But the code also compiles with intel on
intel machines, and seems to work properly on older amd machines (not
quite sure if they need to be so old that there is no SSE even).
Is there any possibility the compiler is messing out with us somehow?
Cause the same machine, different compilers, would mean bogus or
something comiler, but same compiler, differente machines (or different
cpu manufacturer?), seems to mean evil economics practices. :(
Is there any chance this "suppositions" could be right? And so, it would
be useless to try to crack our heads on "debugging" for one specific
compiler the more optimized code of the world?
Thanks for everything in advance.
There may be a problem with arguments passing. The vararg mechanism is a
sleezy way of passing an arbitrary number of arguments to a function. It
is based on macros, and since arguments are passed as either ints,
doubles or strings, where ints may be 4 bytes and the others 8 bytes
there could be confusion in the compiler. We could probably make it
fool-proof, try attached file just for fun.
Jones
On 5/31/06, *David Mathog* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
> Program received signal SIGSEGV, Segmentation fault.
> 0x00002aaaab15a88c in __find_specmb () from /lib64/tls/libc.so.6
> (gdb) where
> #0 0x00002aaaab15a88c in __find_specmb () from /lib64/tls/libc.so.6
> #1 0x00002aaaab140e6f in vfprintf () from /lib64/tls/libc.so.6
> #2 0x00002aaaab15e2a9 in vsprintf () from /lib64/tls/libc.so.6
> #3 0x00002aaaab149568 in sprintf () from /lib64/tls/libc.so.6
> #4 0x000000000040248b in mknb_code (format=0x40cd2e "s") at
> mknb_metacode.c:282
This says that there's a call to sprintf() at mknb_metacode.c line
282. Just before that call check all the parameters that will
be passed to sprintf. You can do that in the debugger, but you
might find it easier to just put a bunch of printf's in at that point.
Looks like there's a a bad pointer in there somewhere. Once you
figure out which variable is bogus trace back up through the following
code with the debugger (or more printf's)
> #5 0x0000000000401aaf in mknb_declare_real (name=0x7fffffffd0d0
> "ix1,iy1,iz1,fix1,fiy1,fiz1") at mknb_metacode.c:104
> #6 0x0000000000403e62 in mknb_declare_variables () at
> mknb_declarations.c:258
> #7 0x0000000000400fef in mknb_write_function () at mknb.c:154
> #8 0x00000000004017cf in main (argc=1, argv=0x7fffffffd628) at
mknb.c:348
until you find out where things have gone wrong.
Regards,
David Mathog
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
Manager, Sequence Analysis Facility, Biology Division, Caltech
------------------------------------------------------------------------
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
/*
* $Id: mknb_metacode.c,v 1.2.2.1 2006/03/30 15:27:24 lindahl Exp $
*
* Gromacs 4.0 Copyright (c) 1991-2003
* David van der Spoel, Erik Lindahl, University of Groningen.
*
* 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.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org
*
* And Hey:
* Gnomes, ROck Monsters And Chili Sauce
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdarg.h>
#include <ctype.h>
#include <mknb_metacode.h>
/* This file is NOT threadsafe, but it is only used to create
* the nonbonded loops during the build process, so it will never be
* executed by multiple threads.
*/
/* Global variables: */
int mknb_fortran=0; /* 1 if fortran is used */
int mknb_double=0; /* 1 if double precision */
int mknb_keep_comments=0;
int mknb_indent_level=0;
FILE * mknb_output=NULL;
/* Return the current indentation as a string */
static char *
mknb_indent(void)
{
static char buf[255];
int i;
int indent;
if(mknb_fortran)
indent = 6 + MKNB_FORTRAN_INDENT_STEP * mknb_indent_level;
else
indent = MKNB_C_INDENT_STEP * (mknb_indent_level+1);
if(indent > 254)
indent = 254;
for(i=0; i<indent; i++)
buf[i] = ' ';
buf[i] = '\0';
return buf;
}
/* Write the provided string as a comment in the file */
void
mknb_comment(char *s)
{
if(mknb_keep_comments) {
if(mknb_fortran) {
mknb_indent_level--;
fprintf(mknb_output,"\nC%s%s\n",mknb_indent(),s);
mknb_indent_level++;
} else {
fprintf(mknb_output,"\n%s/* %s */\n",mknb_indent(),s);
}
}
}
/* We need to separate argument and variable declarations.
* The arguments are written directly to the output file,
* while
*/
/* Define a new floating-point variable */
void
mknb_declare_real(char *name)
{
char type_name[255];
if(mknb_fortran)
sprintf(type_name, "%-13s", mknb_double ? "real*8" : "real*4");
else
sprintf(type_name, "%-13s", mknb_double ? "double" : "float");
mknb_code("%s %s%s",type_name,name, mknb_fortran ? "" : ";");
}
/* Declare a single-precision floating point var. */
void
mknb_declare_real4(char *name)
{
char type_name[255];
sprintf(type_name, "%-13s", mknb_fortran ? "real*4" : "float");
mknb_code("%s %s%s", type_name ,name, mknb_fortran ? "" : ";");
}
/* Declare a constant fp variable */
void
mknb_declare_const_real(char *name, double value)
{
char type_name[255];
if(mknb_fortran) {
sprintf(type_name, "%-13s", mknb_double ? "real*8" : "real*4");
mknb_code("%s %s",type_name,name);
mknb_code(" parameter (%s = %f)",name,value);
} else {
sprintf(type_name, "%-13s",
mknb_double ? "const double" : "const float");
mknb_code("%s %s = %.16f;",type_name,name,value);
}
}
/* Integer */
void
mknb_declare_int(char *name)
{
char type_name[255];
sprintf(type_name, "%-13s", mknb_fortran ? "integer*4" : "int");
mknb_code("%s %s%s", type_name ,name, mknb_fortran ? "" : ";");
}
/* integer constant */
void
mknb_declare_const_int(char *name, int value)
{
char type_name[255];
sprintf(type_name, "%-13s", mknb_fortran ? "integer*4" : "const int");
if(mknb_fortran) {
mknb_code("%s %s", type_name ,name);
mknb_code(" parameter (%s = %d)",name,&value);
} else
mknb_code("%s %s = %d;", type_name ,name, &value);
}
/* 4-byte Integer (same size as single precision fp) */
void
mknb_declare_int4(char *name)
{
char type_name[255];
sprintf(type_name, "%-13s", mknb_fortran ? "integer*4" : "int");
mknb_code("%s %s%s", type_name ,name, mknb_fortran ? "" : ";");
}
/* Arbitrary declaration */
void
mknb_declare_other(char *type_name,char *name)
{
char tmp[255];
sprintf(tmp,"%-13s", type_name);
mknb_code("%s %s%s", tmp, name, mknb_fortran ? "" : ";");
}
/* Reference an element in a list */
char *
mknb_array(char *a, char *idx)
{
static char buf[1024];
sprintf(buf,"%s%c%s%c",a, mknb_fortran ? '(' : '[',
idx, mknb_fortran ? ')' : ']');
return buf;
}
/* Split a line to adhere to the stupid 72 column limits of fortran,
* and write it to the output file
*/
static void
mknb_fortran_splitline(char *line)
{
char tmpbuf[4096];
int i,j,maxlen;
int indent;
maxlen=strlen(line);
i=0;
indent = MKNB_FORTRAN_INDENT_STEP*mknb_indent_level;
/* we can write 72-indentation characters on each line */
while(i+72-indent<maxlen) {
/* set j to the last position */
j=i+71-indent;
if (j>=maxlen)
j=maxlen;
while(j>(i+1)) {
if(line[j]=='+' ||
line[j]=='-' ||
line[j]=='/' ||
(line[j]=='*' && line[j-1]!='*') || /* dont split "**" */
line[j]==' ')
break;
j--;
}
if(j==i) {
printf("Error: Couldn't break this line:\n%s\n",line);
exit(1);
}
strncpy(tmpbuf,line+i,j-i+1);
tmpbuf[j-i]=0;
fprintf(mknb_output,tmpbuf);
fprintf(mknb_output,"\n");
fprintf(mknb_output," & ");
i=j;
}
fprintf(mknb_output,line+i);
}
/* Print a line of code to the output file.
* This routine does proper indentation, and also supports the
* same type of variable-argument lists as printf, apart from
* field widths.
*/
void
mknb_code(char *format, ...)
{
va_list ap;
int *d;
double f;
char *s;
char tmp[4096];
char outbuf[4096];
sprintf(outbuf,"%s",mknb_indent());
va_start(ap,format);
while(*format) {
if(*format!='%')
sprintf(tmp,"%c",*format);
else {
switch(*(++format)) {
case 'd': /* read an integer */
d = va_arg(ap, int *);
sprintf(tmp,"%d",*d);
break;
case 'f': /* read a (double precision) floating point number */
f = va_arg(ap, double);
sprintf(tmp,"%.16f",f);
break;
case 's': /* read a string */
s = va_arg(ap, char *);
sprintf(tmp,s);
break;
default:
fprintf(stderr,
"Error, unsupported format supplied to mknb_code():\nn");
exit(-1);
break;
}
}
format++;
strcat(outbuf,tmp);
}
va_end(ap);
if(mknb_fortran)
mknb_fortran_splitline(outbuf);
else
fprintf(mknb_output,outbuf);
fprintf(mknb_output,"\n");
}
/* Prints an assignment.
* This routine does proper indentation, and also supports the
* same type of variable-argument lists as printf (both in
* the left and right-hand side buffers), apart from field widths.
*
* a statement like mknb_assign("atom%d","data%d",3,5) will give
*
* atom3 = data5;
*
*
* In contrast to mknb_code(), mknb_assign() appends a semicolon when the
* language is not set to fortran.
*
*/
void
mknb_assign(char *left, char *right, ...)
{
int i;
char *format;
char buf[4096],tmp[4096];
char outbuf[4096];
va_list ap;
int d;
double f;
char *s;
sprintf(outbuf,"%s",mknb_indent());
va_start(ap,right);
for(i=0;i<=1;i++) {
/* first we do the left buffer, then repeat everything for the right. */
if(i==0)
format=left;
else
format=right;
buf[0]='\0';
while(*format) {
if(*format!='%')
sprintf(tmp,"%c",*format);
else {
switch(*(++format)) {
case 'd': /* read an integer */
d = va_arg(ap, int);
sprintf(tmp,"%d",d);
break;
case 'f': /* read a (double precision) floating point number */
f = va_arg(ap, double);
sprintf(tmp,"%.16f",f);
break;
case 's': /* read a string */
s = va_arg(ap, char *);
sprintf(tmp,s);
break;
default:
fprintf(stderr,
"Error, unsupported format supplied to mknb_assign()\n");
exit(-1);
break;
}
}
strcat(buf,tmp);
format++;
}
if(i==1 && !mknb_fortran)
strcat(buf,";");
sprintf(tmp,"%-16s",buf);
strcat(outbuf,tmp);
if(i==0)
strcat(outbuf," = ");
}
va_end(ap);
if(mknb_fortran)
mknb_fortran_splitline(outbuf);
else
fprintf(mknb_output,outbuf);
fprintf(mknb_output,"\n");
}
/* Start a for loop and increase indentation.*/
void
mknb_start_loop(char *lvar,char *from,char *to)
{
mknb_code("");
if(mknb_fortran)
{
mknb_code("do %s=%s,%s",lvar,from,to);
}
else
{
mknb_code("for(%s=%s; (%s<%s); %s++)", lvar,from,lvar,to,lvar);
mknb_code("{");
}
mknb_indent_level++;
}
/* decrease indentation and close for loop */
void
mknb_end_loop(void)
{
mknb_indent_level--;
if(mknb_fortran)
mknb_code("end do");
else
mknb_code("}");
mknb_code("");
}
void
mknb_start_if(char *cond)
{
mknb_code("");
if(mknb_fortran)
mknb_code("if (%s) then",cond);
else
{
mknb_code("if(%s)", cond);
mknb_code("{");
}
mknb_indent_level++;
}
void
mknb_do_else()
{
mknb_indent_level--;
if(mknb_fortran)
mknb_code("else");
else
{
mknb_code("}");
mknb_code("else");
mknb_code("{");
}
mknb_indent_level++;
}
void
mknb_end_if(void)
{
mknb_indent_level--;
if (mknb_fortran)
mknb_code("endif");
else
mknb_code("}");
mknb_code("");
}
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