[gmx-users] Gromacs 5.0 compilation slower than 4.6.5. What went wrong ?

Carsten Kutzner ckutzne at gwdg.de
Fri Sep 5 15:58:49 CEST 2014 

Hi,

you might want to use g_tune_pme to find out the optimal number
of PME nodes for 4.6 and 5.0.

Carsten



On 05 Sep 2014, at 15:39, David McGiven <davidmcgivenn at gmail.com> wrote:

> What is even more strange is that I tried with 10 pme nodes (mdrun -ntmpi
> 48 -v -c TEST_md.gro -npme 16), got a 15,8% performance loss and ns/day are
> very similar : 33 ns/day
> 
> D.
> 
> 2014-09-05 14:54 GMT+02:00 David McGiven <davidmcgivenn at gmail.com>:
> 
>> Hi Abhi,
>> 
>> Yes I noticed that imbalance but I thought gromacs knew better than the
>> user how to split PP/PME!!
>> 
>> How is it possible that 4.6.5 guesses better than 5.0 ?
>> 
>> Anyway, I tried :
>> mdrun -nt 48 -v -c test.out
>> 
>> Exits with an error "You need to explicitly specify the number of MPI
>> threads (-ntmpi) when using separate PME ranks"
>> 
>> Then:
>> mdrun -ntmpi 48 -v -c TEST_md.gro -npme 12
>> 
>> Then again 35 ns/day with the warning :
>> NOTE: 8.5 % performance was lost because the PME ranks
>>      had less work to do than the PP ranks.
>>      You might want to decrease the number of PME ranks
>>      or decrease the cut-off and the grid spacing.
>> 
>> 
>> I don't know much about Gromacs so I am puzzled.
>> 
>> 
>> 
>> 
>> 2014-09-05 14:32 GMT+02:00 Abhi Acharya <abhi117acharya at gmail.com>:
>> 
>>> Hello,
>>> 
>>> From the log files it is clear that out of 48 cores, the 5.0 run had 8
>>> cores allocated to PME while the 4.6.5 run had 12 cores. This seems to
>>> have
>>> caused a greater load imbalance in case of the 5.0 run.
>>> 
>>> If you notice the last table in both .mdp files, you will notice that the
>>> PME spread/gather wall time values for 5.0 is more than double the wall
>>> time value in case of the 4.6.5.
>>> 
>>> Try running the simulation by explicitly setting the -npme flag as 12.
>>> 
>>> Regards,
>>> Abhishek Acharya
>>> 
>>> 
>>> On Fri, Sep 5, 2014 at 4:43 PM, David McGiven <davidmcgivenn at gmail.com>
>>> wrote:
>>> 
>>>> Thanks Szilard, here it goes! :
>>>> 
>>>> 4.6.5 : http://pastebin.com/nqBn3FKs
>>>> 5.0 : http://pastebin.com/kR4ntHtK
>>>> 
>>>> 2014-09-05 12:47 GMT+02:00 Szilárd Páll <pall.szilard at gmail.com>:
>>>> 
>>>>> mdrun writes a log file, named md.log by default, which contains among
>>>>> other things results of hardware detection and performance
>>>>> measurements. The list does not accept attachments, please upload it
>>>>> somewhere (dropbox, pastebin, etc.) and post a link.
>>>>> 
>>>>> Cheers,
>>>>> --
>>>>> Szilárd
>>>>> 
>>>>> 
>>>>> On Fri, Sep 5, 2014 at 12:37 PM, David McGiven <
>>> davidmcgivenn at gmail.com>
>>>>> wrote:
>>>>>> Command line in both cases is :
>>>>>> 1st :     grompp -f grompp.mdp -c conf.gro -n index.ndx
>>>>>> 2nd :    mdrun -nt 48 -v -c test.out
>>>>>> 
>>>>>> Log file you mean the standard output/error ? Attached to the email
>>> ?
>>>>>> 
>>>>>> Thanks
>>>>>> 
>>>>>> 2014-09-05 12:30 GMT+02:00 Szilárd Páll <pall.szilard at gmail.com>:
>>>>>> 
>>>>>>> Please post the command lines you used to invoke mdrun as well as
>>> the
>>>>>>> log files of the runs you are comparing.
>>>>>>> 
>>>>>>> Cheers,
>>>>>>> --
>>>>>>> Szilárd
>>>>>>> 
>>>>>>> 
>>>>>>> On Fri, Sep 5, 2014 at 12:10 PM, David McGiven <
>>>> davidmcgivenn at gmail.com
>>>>>> 
>>>>>>> wrote:
>>>>>>>> Dear Gromacs users,
>>>>>>>> 
>>>>>>>> I just compiled gromacs 5.0 with the same compiler (gcc 4.7.2),
>>> same
>>>>> OS
>>>>>>>> (RHEL 6) same configuration options and basically everything
>>> than my
>>>>>>>> previous gromacs 4.6.5 compilation and when doing one of our
>>> typical
>>>>>>>> simulations, I get worst performance.
>>>>>>>> 
>>>>>>>> 4.6.5 does 45 ns/day
>>>>>>>> 5.0 does 35 ns/day
>>>>>>>> 
>>>>>>>> Do you have any idea of what could be happening ?
>>>>>>>> 
>>>>>>>> Thanks.
>>>>>>>> 
>>>>>>>> Best Regards,
>>>>>>>> D.
>>>>>>>> --
>>>>>>>> Gromacs Users mailing list
>>>>>>>> 
>>>>>>>> * Please search the archive at
>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>> posting!
>>>>>>>> 
>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>> 
>>>>>>>> * For (un)subscribe requests visit
>>>>>>>> 
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>> or
>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>> --
>>>>>>> Gromacs Users mailing list
>>>>>>> 
>>>>>>> * Please search the archive at
>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>> posting!
>>>>>>> 
>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>> 
>>>>>>> * For (un)subscribe requests visit
>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>> or
>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>> 
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>> 
>>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
>>>>>> 
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>> 
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>> or
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>> --
>>>>> Gromacs Users mailing list
>>>>> 
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
>>>>> 
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>> 
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>> 
>>>> --
>>>> Gromacs Users mailing list
>>>> 
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>> 
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>> 
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>> 
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>> 
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> 
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>> 
>> 
>> 
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.


--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa

More information about the gromacs.org_gmx-users mailing list