vivek sharma wrote:
Hi Carsten and Justin,
I am interrupting here as I tried with the option u suggested..
I tried cut-off instead of PME as coulombtype option it is running well
for 24 processor, then I tried with 60 processor , following is the
result I am getting
Result1: When tried for 50 ps of run on 24 processors, with PME took
12:29 in comparison to 7:54 with cut-off
This looks reasonable to me.
Result2: When tried for 500 ps of run on 60 processors, with PME it is
giving same segmentation fault again and with cut-off it is giving LINCS
warning and exiting with writing the intermediate step.pdb
Don't run gromacs 3.3 on 60 processors with such a small system. You should
have at least 1000 particles per CPU with gmx 3. Try with gromacs 4, where
also your protein can be split among the processors.
Carsten
Can you suggest some more option that I can try for scaling experiment...
Also I tried with shuffle and sort option it didn't worked for me as my
system is simply one protein molecule in a ater box (around 45000 no. of
atoms)
connected Gromacs version I am using is 3.3.3 and the hardware is like
all nodes contain quad-core 3.0 GHz Intel Xeon processors connected via
infiniband.
With Thanks,
Vivek
2008/9/26 Carsten Kutzner <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
Hi Tiago,
if you swith off PME and suddenly your system scales, then the
problems are likely to result from bad MPI_Alltoall performance. Maybe
this is worth a check. If this is the case, there's a lot more
information
about this in the paper "Speeding up parallel GROMACS on high-
latency networks" from 2007 to which you will also find link on the
gromacs webpage.
What you can also do to track down the problem is to compile gromacs
with
MPE logging, for which you have to enable the #define USE_MPE macro
at the
begin of mpelogging.h (you will have to use gmx version 4, though). You
will get a logfile which you can view with jumpshot then. The MPE tools
come with the MPICH MPI distribution.
Carsten
Tiago Marques wrote:
We currently have no funds available to migrate to infiniband
but we will in the future.
I thought on doing interface bonding but I really think that
isn't really the problem here, there must be something I'm
missing, since most applications scale well to 32 cores on GbE.
I can't scale any application to more than 8 though.
Best regards,
Tiago Marques
On Tue, Sep 23, 2008 at 6:30 PM, Diego Enry
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> wrote:
Tiago you can try merging two network interfaces with "channel
bonding" it's native on all new (2.6.x) linux kernels. You
only need
two network adapters (most dual socket boards come with
then), two
network switches ( or two VPN on the same switch).
To tell you the truth, you will not much improvement even
with the
latest gromacs version (4beta). However other software that
may be
used by your group like NAMD, GAMESS, will benefit a lot from
this
approach. (it almost doubles network bandwidth)
The best solution for gromacs is to migrate to infiniband. Go
for it,
it is not super expensive anymore.
On Tue, Sep 23, 2008 at 1:48 PM, Jochen Hub <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> wrote:
> Tiago Marques wrote:
>> I don't know how large the system is. I'm the cluster's
system
administrator
>> and don't understand much of what's going on. The test
was given
to me by a
>> person who works with it. I can ask him or look at it, if you
can point me
>> how to do it.
>
> Hi,
>
> you can count the nr of atoms in the structure:
>
> grep -c ATOM protein.pdb
>
> Jochen
>
>>
>> Thanks, I will look at some of his posts.
>>
>> Best regards,
>>
>> Tiago Marques
>>
>>
>> On Tue, Sep 23, 2008 at 4:03 PM, Jochen Hub <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> wrote:
>> Tiago Marques wrote:
>>> Hi!
>>>
>>> I've been using Gromacs on dual-socket quad-core Xeons with
8GiB of RAM,
>>> connected with Gigabit Ethernet and I always seem to have
problems scaling
>>> to more than a node.
>>>
>>> When I run a test on 16 cores, it does run but the result is
often slower
>>> than when running on only 8 cores on the same machine.
The best
result
>> I've
>>> managed is not being slower than 8 cores on 16.
>>>
>>> What am I missing here, or are the tests inappropriate
to run
over more
>> than
>>> one machine?
>>
>> How large is your system? Which gromacs version are you
using?
>>
>> And have a look at the messages by Carsten Kutzner in
this list, he
>> wrote a lot on gromacs scaling.
>>
>> Jochen
>>
>>> Best regards,
>>>
>>> Tiago Marques
>>>
>>>
>>>
>>>
------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
>>> http://www.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
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>.
>>> Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
>>
>>
>> --
>> ************************************************
>> Dr. Jochen Hub
>> Max Planck Institute for Biophysical Chemistry
>> Computational biomolecular dynamics group
>> Am Fassberg 11
>> D-37077 Goettingen, Germany
>> Email: jhub[at]gwdg.de <http://gwdg.de> <http://gwdg.de>
>> Tel.: +49 (0)551 201-2312
>> ************************************************
>> _______________________________________________
>> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
>> http://www.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 [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>.
>> Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
>> http://www.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 [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>.
>> Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> ************************************************
> Dr. Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de <http://gwdg.de> <http://gwdg.de>
> Tel.: +49 (0)551 201-2312
> ************************************************
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
> http://www.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 [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>.
> Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
>
--
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
http://www.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 [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://www.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 [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
www.mpibpc.mpg.de/home/grubmueller/
<http://www.mpibpc.mpg.de/home/grubmueller/>
www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne/
<http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne/>
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://www.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 [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
www.mpibpc.mpg.de/home/grubmueller/
www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne/
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
