[gmx-users] valgrind warnigs with git mdrun

[Berk Hess]

Hi,

First of all, Gromacs is full of memory leaks, which by itself it not so nice,
but this is not a problem (unless we are eating up all the memory).

I guess you meant to say illegal memory access iso memory leaks.

The current valgrind warnings in the graph code are due to a bug in valgrind.
I have thoroughly checked this code, especially because of the valgrind warnings.

The sse2 warnings should be checked.

Berk


> Date: Thu, 28 Jan 2010 10:28:59 +0100
> From: jochen at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: [gmx-users] valgrind warnigs with git mdrun
> 
> Hi,
> 
> I am implementing some addition stuff to mdrun, but my mdrun (in 
> particle decomposition) stops with lincs warings after running fine for 
> 10 to 50 ps or so. The same system with the git master does not crash 
> (with -pd), which, of course, does not mean there is no memory leak as 
> well. So I was running my system with the git master mdrun within 
> valgrind --leak-check=yes, and got the following warnings (see below), 
> which eventually stop in a fatal error:
> 
> Program mdrun_debug, VERSION 4.0.99_development_20090927
> Source code file: mshift.c, line: 647
> 
> Fatal error:
> No GREY nodes found while nG=4
> 
> I am now wondering if that is a valgrind problem or if mdrun has a 
> problem that shows up as crashes in my altered version of mdrun.
> 
> Thanks for any hints,
> 
> Jochen
> 
> ps: I have compiled mdrun on a linux with an intel compiler via:
> export LDFLAGS="-L/opt/fftw/3.2/icc11/lib"
> export CPPFLAGS=-I/opt/fftw/3.2/icc11/include
> source /opt/intel/ictce/3.2.1.015/ictvars.sh
> export CC=icc
> export I_MPI_CC=icc
> export LD=icc
> export CFLAGS="-g -O0"
> make distclean
> ./configure --prefix=/home/jhub/src/git/gmx-master/build.debug 
> --without-x --enable-mpi --program-suffix=_debug --disable-shared 
> --without-xml
> 
> During compilation, I get the following warnings. Don't know if they are 
> a problem though:
> 
> ../../../../include/gmx_sse2_single.h(251): warning #167: argument of 
> type "__m128i" is incompatible with parameter of type
>  "__m128"
>         xmm2 = _mm_add_epi32(xmm2,gmx_mm_castps_si128(base));
>                                   ^
> ../../../../include/gmx_sse2_single.h(251): warning #167: argument of 
> type "__m128i" is incompatible with parameter of type
>  "__m128"
>         xmm2 = _mm_add_epi32(xmm2,gmx_mm_castps_si128(base));
> 
> ../../include/gmx_sse2_single.h(251): warning #167: argument of type 
> "__m128i" is incompatible with parameter of type "__m1
> 28"
>         xmm2 = _mm_add_epi32(xmm2,gmx_mm_castps_si128(base));
>                                   ^
> resall.c(488): warning #167: argument of type "const char *" is 
> incompatible with parameter of type "char *"
>       n=neq_str(key,rtp[i].resname);
>                 ^
> grompp.c(306): warning #592: variable "mbs" is used before its value is set
>     mbs;
>     ^
> 

 		 	   		  
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