[gmx-developers] May be bug in 64-bit !

Utkal Ranjan Pradhan urpradhan at gmail.com
Wed May 30 12:12:16 CEST 2007

Hi Friends


I was trying to buid Gromacs 3.3.1 64-bit on NATIVE Windows 2003 Server RC2
(AMD 64 Bit Optron) with VS 2005.

The projects are getting build perfectly w/o any error.

But I have some RUN TIME ERROR while testing the binaries (*.exe) with the
demo.pl file




1.         The program "genbox" does generates the "temp.top" file and tries
to rename it "cpeptide.top". But it is not able to rename the file as the
folder contains another "cpeptide.top" file. But this behaviour is NOT seen
in 32-bit of UNIX. 


# The source files are: gmx_genbox.c (Line: 557) and gmx_genion.c (Line:

# Code snipset...



fclose(fpout);/* use ffopen to generate backup of topinout */



remove(topinout);//My Change




# Then I have added the line before these as: remove(topinout); So that the
updated "temp.top" file will be renamed to "cpeptide.top"





2.         The second problem is due to invalid range value (ci) in file:
nsgrid.c (Line: 225 & Line: 277)


# The out put is like ....


"Program mdrun, VERSION 3.3.1

Source code file: ..\..\..\src\mdlib\nsgrid.c, line: 228


Range checking error:

Explanation: During neighborsearching, we assign each particle to a grid

based on its coordinates. If your system contains collisions or parameter

errors that give particles very high velocities you might end up with some

coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot

put these on a grid, so this is usually where we detect those errors.

Make sure your system is properly energy-minimized and that the potential

energy seems reasonable before trying again.


Variable ci has value -2147483648. It should have been within [ 0 .. 96 ]

Please report this to the mailing list (gmx-users at gromacs.org)



# This may be due to pointer assignment at line: 213 and the int variable ci
is not able to initialize properly.

# Code snipset is ....



int    *cell_index=grid->cell_index;


for(i=CG0[m]; (i<CG1[m]); i++) {

ci = cell_index[i];           // Hear ci is not properly assigned to valid
integer value







So, can anybody plz help me to solve this problems for native 64-bit Windows
platform using VS 2005 ?


Thank you


Thank You;

URPradhan At Gmail Dot Com


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