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 wrote:
> Dear Roland:
>
> Thank you very much for the reply. Since
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 st
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/rsc
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 benck
On Wed, Mar 17, 2010 at 3:55 AM, Mark Abraham 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
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
Dear Mark:
Thanks for your reply and sorry for my less info.
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/par
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/d
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
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