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Hi,<br><br>First of all, Gromacs is full of memory leaks, which by itself it not so nice,<br>but this is not a problem (unless we are eating up all the memory).<br><br>I guess you meant to say illegal memory access iso memory leaks.<br><br>The current valgrind warnings in the graph code are due to a bug in valgrind.<br>I have thoroughly checked this code, especially because of the valgrind warnings.<br><br>The sse2 warnings should be checked.<br><br>Berk<br><br><br>> Date: Thu, 28 Jan 2010 10:28:59 +0100<br>> From: jochen@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] valgrind warnigs with git mdrun<br>> <br>> Hi,<br>> <br>> I am implementing some addition stuff to mdrun, but my mdrun (in <br>> particle decomposition) stops with lincs warings after running fine for <br>> 10 to 50 ps or so. The same system with the git master does not crash <br>> (with -pd), which, of course, does not mean there is no memory leak as <br>> well. So I was running my system with the git master mdrun within <br>> valgrind --leak-check=yes, and got the following warnings (see below), <br>> which eventually stop in a fatal error:<br>> <br>> Program mdrun_debug, VERSION 4.0.99_development_20090927<br>> Source code file: mshift.c, line: 647<br>> <br>> Fatal error:<br>> No GREY nodes found while nG=4<br>> <br>> I am now wondering if that is a valgrind problem or if mdrun has a <br>> problem that shows up as crashes in my altered version of mdrun.<br>> <br>> Thanks for any hints,<br>> <br>> Jochen<br>> <br>> ps: I have compiled mdrun on a linux with an intel compiler via:<br>> export LDFLAGS="-L/opt/fftw/3.2/icc11/lib"<br>> export CPPFLAGS=-I/opt/fftw/3.2/icc11/include<br>> source /opt/intel/ictce/3.2.1.015/ictvars.sh<br>> export CC=icc<br>> export I_MPI_CC=icc<br>> export LD=icc<br>> export CFLAGS="-g -O0"<br>> make distclean<br>> ./configure --prefix=/home/jhub/src/git/gmx-master/build.debug <br>> --without-x --enable-mpi --program-suffix=_debug --disable-shared <br>> --without-xml<br>> <br>> During compilation, I get the following warnings. Don't know if they are <br>> a problem though:<br>> <br>> ../../../../include/gmx_sse2_single.h(251): warning #167: argument of <br>> type "__m128i" is incompatible with parameter of type<br>> "__m128"<br>> xmm2 = _mm_add_epi32(xmm2,gmx_mm_castps_si128(base));<br>> ^<br>> ../../../../include/gmx_sse2_single.h(251): warning #167: argument of <br>> type "__m128i" is incompatible with parameter of type<br>> "__m128"<br>> xmm2 = _mm_add_epi32(xmm2,gmx_mm_castps_si128(base));<br>> <br>> ../../include/gmx_sse2_single.h(251): warning #167: argument of type <br>> "__m128i" is incompatible with parameter of type "__m1<br>> 28"<br>> xmm2 = _mm_add_epi32(xmm2,gmx_mm_castps_si128(base));<br>> ^<br>> resall.c(488): warning #167: argument of type "const char *" is <br>> incompatible with parameter of type "char *"<br>> n=neq_str(key,rtp[i].resname);<br>> ^<br>> grompp.c(306): warning #592: variable "mbs" is used before its value is set<br>> mbs;<br>> ^<br>> <br><br> <br /><hr />New Windows 7: Simplify what you do everyday. <a href='http://windows.microsoft.com/shop' target='_new'>Find the right PC for you.</a></body>
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