I had similar memory related problems. Try compiling Gromacs with no optimization and rerun the grompp.
On Feb 7, 2008 7:45 AM, David van der Spoel <[EMAIL PROTECTED]> wrote: > Chris Neale wrote: > > I have a large system of 0.7 million atoms. This system runs fine on > > opterons with 4GB of ram. However, grompp gives me an error that it has > > run out of memory on a new IBM AIX system that we have with 46GB of ram. > > Smaller systems work fine on both processors. In both cases I am running > > on 4 processors. > > > > The IBM system is running AIX 5L 5.3, and it has eight CPU cores and > > 46GB of available memory to the OS. > > > > Here is the relevant error output from grompp > > > > Program grompp, VERSION 3.3.1 > > Source code file: smalloc.c, line: 137 > > > > Fatal error: > > realloc for dest->atom (28504800 bytes, file topcat.c, line 176, > > dest->atom=0x0x2aa231c8) > > Hard to say, you are not running with dmalloc or something like that? > Otherwise you can run grompp on another machine although that may be > slightly inconvenient of course. > Is this really a power 6? IBM machines always give problems when > compiling for another system then what you are running it on, in > particular the head node where you run grompp could be a different > processor. > > > ------------------------------------------------------- > > > > "I'm Not Gonna Die Here !" (Sphere) > > : Not enough space > > > > ### > > > > I realize that this is a pretty clear message that I don't have enough > > ram, but I am confused how a different architecture plus different > > compiler could cause such a tremendous increase in the amount of memory > > required since the AIX has 11times the available memory as the opterons > > (on which this grompp runs fine). > > > > Here is some simple memory test on the IBM AIX: > > > > -bash-3.00$ ulimit -a > > core file size (blocks, -c) 0 > > data seg size (kbytes, -d) unlimited > > file size (blocks, -f) unlimited > > max memory size (kbytes, -m) unlimited > > open files (-n) 2000 > > pipe size (512 bytes, -p) 64 > > stack size (kbytes, -s) hard > > cpu time (seconds, -t) unlimited > > max user processes (-u) 128 > > virtual memory (kbytes, -v) unlimited > > > > ### > > > > Here is the commands that I used to compile the source on the AIX, in > > case that helps. To be clear, the AIX compilation works fine for smaller > > systems. > > > > export > > > PATH=/usr/vac/bin:/usr/vacpp/bin:/opt/freeware:/usr/bin:/etc:/usr/sbin:/usr/ucb:/usr/bin/X11:/sbin:/usr/java14/jre/bin:/usr/java14/bin:.:/tools/local/bin > > > > export F77=xlf_r > > export CC=xlc_r > > export CXX=xlc++_r > > export FFLAGS="-O5 -qarch=pwr6 -qtune=pwr6" > > export CFLAGS="-O5 -qarch=pwr6 -qtune=pwr6" > > export CXXFLAGS="-O5 -qarch=pwr6 -qtune=pwr6" > > > > export FFTW_LOCATION=/hpf/data/pomes/cneale/exe/fftw-3.1.2_aix/exec > > export GROMACS_LOCATION=/hpf/data/pomes/cneale/exe/gromacs- > 3.3.1_aix/exec > > export CPPFLAGS=-I$FFTW_LOCATION/include > > export LDFLAGS=-L$FFTW_LOCATION/lib > > > > cd /hpf/data/pomes/cneale/exe/gromacs-3.3.1_aix > > mkdir exec > > > > ./configure --prefix=$GROMACS_LOCATION >output.configure 2>&1 > > make >output.make 2>&1 > > make install >output.make_install 2>&1 > > make distclean > > touch DONE_SERIAL > > > > echo "cn-r0-10" > ~/.rhosts > > echo localhost > ~/host.list > > for((i=2;i<=16;i++)); do > > echo localhost >> ~/host.list > > done > > export MP_HOSTFILE=~/host.list > > > > ./configure --prefix=$GROMACS_LOCATION --enable-mpi --disable-nice > > --program-suffix="_mpi" CC=mpcc_r F77=mpxlf_r > output.configure_mpi2>&1 > > make mdrun > output.make_mpi 2>&1 > > make install-mdrun > output.make_install_mpi 2>&1 > > make distclean > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > 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 > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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