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

Chris Neale chris.neale at utoronto.ca
Wed Feb 6 23:46:54 CET 2008

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, 

"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 

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

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

echo "cn-r0-10" > ~/.rhosts
echo localhost > ~/host.list
for((i=2;i<=16;i++)); do
  echo localhost >> ~/host.list
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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