[gmx-users] gromacs 4.0 on CRAY-XT4

Tue Apr 6 17:14:46 CEST 2010

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 <zhngbn at 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 <zhngbn at 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.Abraham at 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
>>>>> --
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>>>>
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>>
>>
>>
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>
>
>
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> 865-241-1537, ORNL PO BOX 2008 MS6309
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-- 
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865-241-1537, ORNL PO BOX 2008 MS6309
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