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

[David van der Spoel]

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_mpi 2>&1
> make mdrun > output.make_mpi 2>&1
> make install-mdrun > output.make_install_mpi 2>&1
> make distclean
> 
> 
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-- 
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
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