[gmx-users] GPU warnings

[Thomas Evangelidis]

Hi Szilárd,

This is the warning message I get this time:

WARNING: Oversubscribing the available -66 logical CPU cores with 1
thread-MPI threads.
         This will cause considerable performance loss!

I have also attached the md.log file.

thanks,
Thomas


On 14 November 2012 19:48, Szilárd Páll <szilard.pall at cbr.su.se> wrote:

> Hi Thomas,
>
> Could you please try applying the attached patch (git apply
> hardware_detect.patch in the 4.6 source root) and let me know what the
> output is?
>
> This should show which sysconf macro is used and what its return value is
> as well as indicate if none of the macros are in fact defined by your
> headers.
>
> Thanks,
>
> --
> Szilárd
>
>
>
> On Sat, Nov 10, 2012 at 5:24 PM, Thomas Evangelidis <tevang3 at gmail.com>wrote:
>
>>
>>
>> On 10 November 2012 03:21, Szilárd Páll <szilard.pall at cbr.su.se> wrote:
>>
>>> Hi,
>>>
>>> You must have an odd sysconf version! Could you please check what is the
>>> sysconf system variable's name in the sysconf man page (man sysconf) where
>>> it says something like:
>>>
>>>     _SC_NPROCESSORS_ONLN
>>>              The number of processors currently online.
>>>
>>> The first line should be one of the
>>> following: _SC_NPROCESSORS_ONLN, _SC_NPROC_ONLN,
>>> _SC_NPROCESSORS_CONF, _SC_NPROC_CONF, but I guess yours is something
>>> different.
>>>
>>
>> The following text is taken from man sysconf:
>>
>>        These values also exist, but may not be standard.
>>
>>         - _SC_PHYS_PAGES
>>               The number of pages of physical memory.  Note that it is
>> possible for the product of this value and the value of _SC_PAGE_SIZE to
>> overflow.
>>
>>         - _SC_AVPHYS_PAGES
>>               The number of currently available pages of physical memory.
>>
>>         - _SC_NPROCESSORS_CONF
>>               The number of processors configured.
>>
>>         - _SC_NPROCESSORS_ONLN
>>               The number of processors currently online (available).
>>
>>
>>
>>
>>> Can you also check what your glibc version is?
>>>
>>
>> $ yum list installed | grep glibc
>> glibc.i686                            2.15-57.fc17
>> @updates
>> glibc.x86_64                          2.15-57.fc17
>> @updates
>> glibc-common.x86_64                   2.15-57.fc17
>> @updates
>> glibc-devel.i686                      2.15-57.fc17
>> @updates
>> glibc-devel.x86_64                    2.15-57.fc17
>> @updates
>> glibc-headers.x86_64                  2.15-57.fc17               @updates
>>
>>
>>
>>>
>>>
>>> On Fri, Nov 9, 2012 at 5:51 PM, Thomas Evangelidis <tevang3 at gmail.com>wrote:
>>>
>>>>
>>>>
>>>>
>>>> > I get these two warnings when I run the dhfr/GPU/dhfr-solv-PME.bench
>>>>> > benchmark with the following command line:
>>>>> >
>>>>> > mdrun_intel_cuda5 -v -s topol.tpr -testverlet
>>>>> >
>>>>> > "WARNING: Oversubscribing the available 0 logical CPU cores with 1
>>>>> > thread-MPI threads."
>>>>> >
>>>>> > 0 logical CPU cores? Isn't this bizarre? My CPU is Intel Core
>>>>> i7-3610QM
>>>>> >
>>>>>
>>>>> That is bizzarre. Could you run with "-debug 1" and have a look at the
>>>>> mdrun.debug output which should contain a message like:
>>>>> "Detected N processors, will use this as the number of supported
>>>>> hardware
>>>>> threads."
>>>>>
>>>>> I'm wondering, is N=0 in your case!?
>>>>>
>>>>> It says "Detected 0 processors, will use this as the number of
>>>> supported hardware threads."
>>>>
>>>>
>>>>>
>>>>> > (2.3 GHz). Unlike Albert, I don't see any performance loss, I get
>>>>> 13.4
>>>>> > ns/day on a single core with 1 GPU and 13.2 ns/day with GROMACS
>>>>> v4.5.5 on 4
>>>>> > cores (8 threads) without the GPU. Yet, I don't see any performance
>>>>> gain
>>>>> > with more that 4 -nt threads.
>>>>> >
>>>>> > mdrun_intel_cuda5 -v -nt 2 -s topol.tpr -testverlet : 15.4 ns/day
>>>>> > mdrun_intel_cuda5 -v -nt 3 -s topol.tpr -testverlet : 16.0 ns/day
>>>>> > mdrun_intel_cuda5 -v -nt 4 -s topol.tpr -testverlet : 16.3 ns/day
>>>>> > mdrun_intel_cuda5 -v -nt 6 -s topol.tpr -testverlet : 16.2 ns/day
>>>>> > mdrun_intel_cuda5 -v -nt 8 -s topol.tpr -testverlet : 15.4 ns/day
>>>>> >
>>>>>
>>>>> I guess there is not much point in not using all cores, is it? Note
>>>>> that
>>>>> the performance drops after 4 threads because Hyper-Threading with
>>>>> OpenMP
>>>>> doesn't always help.
>>>>>
>>>>>
>>>>> >
>>>>> > I have also attached my log file (from "mdrun_intel_cuda5 -v -s
>>>>> topol.tpr
>>>>> > -testverlet") in case you find it helpful.
>>>>> >
>>>>>
>>>>> I don't see it attached.
>>>>>
>>>>>
>>>>>
>>>> I have attached both mdrun_intel_cuda5.debug and md.log files.  They
>>>> will possibly be filtered by the mailing list but will be delivered to your
>>>> email.
>>>>
>>>> thanksm
>>>> Thomas
>>>>
>>>
>>>
>>
>>
>> --
>>
>> ======================================================================
>>
>> Thomas Evangelidis
>>
>> PhD student
>> University of Athens
>> Faculty of Pharmacy
>> Department of Pharmaceutical Chemistry
>> Panepistimioupoli-Zografou
>> 157 71 Athens
>> GREECE
>>
>> email: tevang at pharm.uoa.gr
>>
>>           tevang3 at gmail.com
>>
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>
>>
>>
>>
>


-- 

======================================================================

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tevang at pharm.uoa.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/