Bin,<div><br></div><div>sorry I overlooked your email. I think this is a bug in the libtool distributed with gromacs. </div><div>See <a href="http://lists.gromacs.org/pipermail/gmx-developers/2010-March/004088.html">http://lists.gromacs.org/pipermail/gmx-developers/2010-March/004088.html</a></div>
<div><br></div><div>Roland<br><br><div class="gmail_quote">On Wed, Mar 17, 2010 at 3:31 PM, BIN ZHANG <span dir="ltr"><<a href="mailto:zhngbn@gmail.com" target="_blank">zhngbn@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div><div>Dear Roland:</div><div><br></div><div>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. </div>
<div><br></div><div>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. </div><div><br></div><div>Sincerely,</div><div>Bin</div><div>
<br></div><div>===============================================================</div><div><br></div><div>/opt/cray/xt-asyncpe/3.3/bin/cc: INFO: linux target is being used<br>/opt/cray/xt-asyncpe/3.3/bin/cc:
INFO: WARNING: gcc/4.2.3 does not support barcelona options.<br>/opt/cray/xt-asyncpe/3.3/bin/cc:
INFO: Swap gcc/4.2.3 for gcc/420quadcore or a post 4.3 gcc version.<br>/usr/bin/ld:
attempted static link of dynamic object
`/opt/fftw/3.2.2/lib/libfftw3f.so'<br>collect2: ld returned 1 exit
status<br>make[3]: *** [grompp] Error 1<br>make[3]: Leaving directory
`/global/u2/b/bingo/bin/gromacs-4.0.7/src/kernel'<br>make[2]: ***
[all-recursive] Error 1<br>make[2]: Leaving directory
`/global/u2/b/bingo/bin/gromacs-4.0.7/src'<br>make[1]: *** [all] Error 2<br>make[1]:
Leaving directory `/global/u2/b/bingo/bin/gromacs-4.0.7/src'<br>make:
*** [all-recursive] Error 1</div><div><div></div><div><div>On Mar 17, 2010, at 11:04 AM, Roland Schulz wrote:</div><br></div></div><blockquote type="cite"><div><div></div><div>Hi,<div><br></div><div>
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.</div><div><br></div><div>You are welcome to use the version I have installed there:</div>
<div>/global/homes/r/rschulz/software/gromacs (4.0.7)</div><div>/global/homes/r/rschulz/software/gromacs.head/ (GIT master)</div><div><br></div><div>You can also look at the config.log and env.sh in /global/homes/r/rschulz/download/ to look how it is compiled. </div>
<div><br></div><div>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.</div>
<div><br></div><div>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).</div><div><br></div><div>Roland</div>
<div>
<br><div class="gmail_quote">On Wed, Mar 17, 2010 at 1:27 PM, BIN ZHANG <span dir="ltr"><<a href="mailto:zhngbn@gmail.com" target="_blank">zhngbn@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Dear mark, and Roland:<div><br></div><div>Thanks for all the suggestions.</div><div>I was confused gromacs4 paper with another one by Erik Lindahl. (<a href="http://www.ncbi.nlm.nih.gov/pubmed/19229308" target="_blank">http://www.ncbi.nlm.nih.gov/pubmed/19229308</a>) 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: <a href="http://www.nersc.gov/nusers/systems/franklin/" target="_blank">http://www.nersc.gov/nusers/systems/franklin/</a></div>
<div><br></div><div>Bin. </div><div><br></div><div><br><div><div><div><div></div><div><div>On Mar 17, 2010, at 1:39 AM, Roland Schulz wrote:</div><br></div></div><blockquote type="cite"><div><div></div><div> <br><br><div class="gmail_quote">
On Wed, Mar 17, 2010 at 3:55 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>On 17/03/2010 6:19 PM, BIN ZHANG wrote:<br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Dear Mark:<br> <br> Thanks for your reply and sorry for my less info.<br>
</blockquote> <br></div> 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<div>
<br> <br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Here is the configuration line I used:<br> module load fftw/<a href="http://2.1.5.1" target="_blank">2.1.5.1</a><br>
module load libxml2<br> CXX=CC CC=cc F77=ftn MPICC=cc LIBS="$XML2_LIBDIR -L/usr/X11/lib64"<br> ./configure --enable-mpi --enable-double --enable-fortran<br> --prefix=$HOME/gmx/para --disable-nice --with-fft=fftw2<br>
--program-suffix=_mpi<br> </blockquote> <br></div> 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.</blockquote>
<div><br></div> <div>No. These are standard AMD CPUs and thus SSE2 works find.</div><div><br></div><div>I use </div><div><div>module swap PrgEnv-pgi PrgEnv-gnu</div><div>module swap gcc gcc/4.2.4</div></div><div>./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' </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><br> <br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Also, I searched the maillist and added ddorder in the mdrun line, but<br> that doesn't seem to help much.<br> aprun -n 128 $gmxdir/mdrun_mpi -deffnm npt_02 -g npt_02.log -ddorder<br> cartesian -npme 32<br> </blockquote>
<br></div> You will need to experiment with npme and ddorder to find what's best. Also consider g_tune_pme in the git codebase.<br> </blockquote><div><br></div><div>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)</div>
<div><br></div><div>Roland</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><font color="#888888"> <br> Mark</font><div><div></div><div><br> <br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
The system is a membrane protein and I'm using berger lipid/OPLS-AA<br> force filed.<br> <br> Thanks<br> Bin<br> <br> <br> On Mar 17, 2010, at 12:02 AM, Mark Abraham wrote:<br> <br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
On 17/03/2010 5:43 PM, BIN ZHANG wrote:<br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Dear all:<br> <br> I was trying to build gromacs 4.0 on a cray-xt4 machine, the same one as<br>
the benchmark in the gromacs4 paper (). However, my timing for a similar<br> system, ~100,000 atoms, is almost 3 times slower than in the paper. For<br> example, I only got ~25 ns/day with 128 cpus. So is there any special<br>
flags, or tricks I can use during the configuration for detailed tuning?<br> </blockquote> <br> Probably. You've made it hard to help you when you haven't provided<br> (at least) your configure command, compiler and version, mdrun command<br>
line and simulation system composition.<br> <br> Mark<br> --<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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