I had similar memory related problems. Try compiling Gromacs with no optimization and rerun the grompp.<br><br><div class="gmail_quote">On Feb 7, 2008 7:45 AM, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">Chris Neale wrote:<br>> I have a large system of 0.7 million atoms. This system runs fine on<br>
> opterons with 4GB of ram. However, grompp gives me an error that it has<br>> run out of memory on a new IBM AIX system that we have with 46GB of ram.<br>> Smaller systems work fine on both processors. In both cases I am running<br>
> on 4 processors.<br>><br>> The IBM system is running AIX 5L 5.3, and it has eight CPU cores and<br>> 46GB of available memory to the OS.<br>><br>> Here is the relevant error output from grompp<br>><br>
> Program grompp, VERSION 3.3.1<br>> Source code file: smalloc.c, line: 137<br>><br>> Fatal error:<br>> realloc for dest->atom (28504800 bytes, file topcat.c, line 176,<br>> dest->atom=0x0x2aa231c8)<br>
<br></div>Hard to say, you are not running with dmalloc or something like that?<br>Otherwise you can run grompp on another machine although that may be<br>slightly inconvenient of course.<br>Is this really a power 6? IBM machines always give problems when<br>
compiling for another system then what you are running it on, in<br>particular the head node where you run grompp could be a different<br>processor.<br><div><div></div><div class="Wj3C7c"><br>> -------------------------------------------------------<br>
><br>> "I'm Not Gonna Die Here !" (Sphere)<br>> : Not enough space<br>><br>> ###<br>><br>> I realize that this is a pretty clear message that I don't have enough<br>> ram, but I am confused how a different architecture plus different<br>
> compiler could cause such a tremendous increase in the amount of memory<br>> required since the AIX has 11times the available memory as the opterons<br>> (on which this grompp runs fine).<br>><br>> Here is some simple memory test on the IBM AIX:<br>
><br>> -bash-3.00$ ulimit -a<br>> core file size (blocks, -c) 0<br>> data seg size (kbytes, -d) unlimited<br>> file size (blocks, -f) unlimited<br>> max memory size (kbytes, -m) unlimited<br>
> open files (-n) 2000<br>> pipe size (512 bytes, -p) 64<br>> stack size (kbytes, -s) hard<br>> cpu time (seconds, -t) unlimited<br>> max user processes (-u) 128<br>
> virtual memory (kbytes, -v) unlimited<br>><br>> ###<br>><br>> Here is the commands that I used to compile the source on the AIX, in<br>> case that helps. To be clear, the AIX compilation works fine for smaller<br>
> systems.<br>><br>> export<br>> 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<br>><br>> export F77=xlf_r<br>
> export CC=xlc_r<br>> export CXX=xlc++_r<br>> export FFLAGS="-O5 -qarch=pwr6 -qtune=pwr6"<br>> export CFLAGS="-O5 -qarch=pwr6 -qtune=pwr6"<br>> export CXXFLAGS="-O5 -qarch=pwr6 -qtune=pwr6"<br>
><br>> export FFTW_LOCATION=/hpf/data/pomes/cneale/exe/fftw-3.1.2_aix/exec<br>> export GROMACS_LOCATION=/hpf/data/pomes/cneale/exe/gromacs-3.3.1_aix/exec<br>> export CPPFLAGS=-I$FFTW_LOCATION/include<br>> export LDFLAGS=-L$FFTW_LOCATION/lib<br>
><br>> cd /hpf/data/pomes/cneale/exe/gromacs-3.3.1_aix<br>> mkdir exec<br>><br>> ./configure --prefix=$GROMACS_LOCATION >output.configure 2>&1<br>> make >output.make 2>&1<br>> make install >output.make_install 2>&1<br>
> make distclean<br>> touch DONE_SERIAL<br>><br>> echo "cn-r0-10" > ~/.rhosts<br>> echo localhost > ~/host.list<br>> for((i=2;i<=16;i++)); do<br>> echo localhost >> ~/host.list<br>
> done<br>> export MP_HOSTFILE=~/host.list<br>><br>> ./configure --prefix=$GROMACS_LOCATION --enable-mpi --disable-nice<br>> --program-suffix="_mpi" CC=mpcc_r F77=mpxlf_r > output.configure_mpi 2>&1<br>
> make mdrun > output.make_mpi 2>&1<br>> make install-mdrun > output.make_install_mpi 2>&1<br>> make distclean<br>><br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
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<br><br></div></div>--<br>David.<br>________________________________________________________________________<br><font color="#888888">David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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</div></div></blockquote></div><br>