Bin, sorry I overlooked your email. I think this is a bug in the libtool distributed with gromacs. See http://lists.gromacs.org/pipermail/gmx-developers/2010-March/004088.html
Roland On Wed, Mar 17, 2010 at 3:31 PM, BIN ZHANG <zhn...@gmail.com> wrote: > Dear Roland: > > Thank you very much for the reply. Since I'm planning to play with the > source code a little bit, I would prefer to compile my own version ;-) Aslo, > I don't think I have the permission to look at your config.log file. > > After using the configuration you suggested, I got some strange error as > attached. I will try to contact the help-desk for more compiler info. > > Sincerely, > Bin > > =============================================================== > > /opt/cray/xt-asyncpe/3.3/bin/cc: INFO: linux target is being used > /opt/cray/xt-asyncpe/3.3/bin/cc: INFO: WARNING: gcc/4.2.3 does not support > barcelona options. > /opt/cray/xt-asyncpe/3.3/bin/cc: INFO: Swap gcc/4.2.3 for gcc/420quadcore > or a post 4.3 gcc version. > /usr/bin/ld: attempted static link of dynamic object > `/opt/fftw/3.2.2/lib/libfftw3f.so' > collect2: ld returned 1 exit status > make[3]: *** [grompp] Error 1 > make[3]: Leaving directory > `/global/u2/b/bingo/bin/gromacs-4.0.7/src/kernel' > make[2]: *** [all-recursive] Error 1 > make[2]: Leaving directory `/global/u2/b/bingo/bin/gromacs-4.0.7/src' > make[1]: *** [all] Error 2 > make[1]: Leaving directory `/global/u2/b/bingo/bin/gromacs-4.0.7/src' > make: *** [all-recursive] Error 1 > On Mar 17, 2010, at 11:04 AM, Roland Schulz wrote: > > 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 > > > > -- > 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
