[gmx-users] grompp error "Not enough space" on IBM AIX

[Marius Retegan]

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 <spoel at xray.bmc.uu.se> 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 at 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 gmx-users-request at gromacs.org.
> > 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
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080207/25a2f2f3/attachment.html>