Hi, gromacs is installed on Franklin. (module load gromacs). But I don't recommend the installed version. It is compiled only in double precision and with FFTW2 and PGI.
You are welcome to use the version I have installed there: /global/homes/r/rschulz/software/gromacs (4.0.7) /global/homes/r/rschulz/software/gromacs.head/ (GIT master) You can also look at the config.log and env.sh in /global/homes/r/rschulz/download/ to look how it is compiled. Of course if you do you do that on your own risk and I don't support it there. Also I recompile it there frequently so you probably want to make a copy if you want to keep the same binary during your simulation. It is probably better to ask the help-desk to compile with single precision, fftw3 (to make it faster) and gcc (there were problems with Gromacs and PGI before). Roland On Wed, Mar 17, 2010 at 1:27 PM, BIN ZHANG <zhn...@gmail.com> wrote: > Dear mark, and Roland: > > Thanks for all the suggestions. > I was confused gromacs4 paper with another one by Erik Lindahl. ( > http://www.ncbi.nlm.nih.gov/pubmed/19229308) Since there they studied the > same system (Kv1.2 voltage-gated ion channel), and they mentioned about the > same speed as the benckmark, on a cray-xt4 machine. Here is also a link for > the machine I'm working on: http://www.nersc.gov/nusers/systems/franklin/ > > Bin. > > > On Mar 17, 2010, at 1:39 AM, Roland Schulz wrote: > > > > On Wed, Mar 17, 2010 at 3:55 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > >> On 17/03/2010 6:19 PM, BIN ZHANG wrote: >> >>> Dear Mark: >>> >>> Thanks for your reply and sorry for my less info. >>> >> >> I'm confused about your statement "I was trying to build gromacs 4.0 on a >> cray-xt4 machine, the same one as the benchmark in the gromacs4 paper" >> because I can't see any mention of results on such a machine in J. Chem. >> Theory Comput. 2008, 4, 435-447 >> >> >> Here is the configuration line I used: >>> module load fftw/2.1.5.1 >>> module load libxml2 >>> CXX=CC CC=cc F77=ftn MPICC=cc LIBS="$XML2_LIBDIR -L/usr/X11/lib64" >>> ./configure --enable-mpi --enable-double --enable-fortran >>> --prefix=$HOME/gmx/para --disable-nice --with-fft=fftw2 >>> --program-suffix=_mpi >>> >> >> The use of double precision and the absence of hardware-optimized inner >> loops (--enable-fortran, since AFAIK there's no alternative on XT4) will >> slow things down compared to an Intel machine. > > > No. These are standard AMD CPUs and thus SSE2 works find. > > I use > module swap PrgEnv-pgi PrgEnv-gnu > module swap gcc gcc/4.2.4 > ./configure '--enable-mpi' '--without-x' 'CC=cc' 'CPP=cpp' 'CXXCPP=cpp' > 'CXX=CC' '--without-xml' > 'CPPFLAGS=-I/sw/xt5/fftw/3.1.2/sles10.1_gnu4.2.4/include' > 'LDFLAGS=-L/sw/xt5/fftw/3.1.2/sles10.1_gnu4.2.4/lib -lfftw3f' 'CFLAGS=-O3 > -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 > -funroll-all-loops -std=gnu99' > >> >> >> Also, I searched the maillist and added ddorder in the mdrun line, but >>> that doesn't seem to help much. >>> aprun -n 128 $gmxdir/mdrun_mpi -deffnm npt_02 -g npt_02.log -ddorder >>> cartesian -npme 32 >>> >> >> You will need to experiment with npme and ddorder to find what's best. >> Also consider g_tune_pme in the git codebase. >> > > If you want to scale to larger number of CPUs you probably need 2D PME. It > is available in the 2dpme git branch. (That it is in a branch means it is at > the moment considered experimental - even more than mast that is) > > Roland > > >> >> Mark >> >> >> The system is a membrane protein and I'm using berger lipid/OPLS-AA >>> force filed. >>> >>> Thanks >>> Bin >>> >>> >>> On Mar 17, 2010, at 12:02 AM, Mark Abraham wrote: >>> >>> On 17/03/2010 5:43 PM, BIN ZHANG wrote: >>>> >>>>> Dear all: >>>>> >>>>> I was trying to build gromacs 4.0 on a cray-xt4 machine, the same one >>>>> as >>>>> the benchmark in the gromacs4 paper (). However, my timing for a >>>>> similar >>>>> system, ~100,000 atoms, is almost 3 times slower than in the paper. For >>>>> example, I only got ~25 ns/day with 128 cpus. So is there any special >>>>> flags, or tricks I can use during the configuration for detailed >>>>> tuning? >>>>> >>>> >>>> Probably. You've made it hard to help you when you haven't provided >>>> (at least) your configure command, compiler and version, mdrun command >>>> line and simulation system composition. >>>> >>>> Mark >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.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-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>> >>> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov > 865-241-1537, ORNL PO BOX 2008 MS6309 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
-- gmx-users mailing list gmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
