[gmx-users] GPU warnings
Szilárd Páll
szilard.pall at cbr.su.se
Fri Nov 16 16:30:42 CET 2012
Hi Thomas,
The output you get means that you don't have any of the macros we try to
use although your man pages seem to be referring to them. Hence, I'm really
clueless why is this happening. Could you please file a bug report on
redmine.gromacs.org and add both the initial output as well as my patch and
the resulting output. Don't forget to specify version of software you were
using.
Thanks,
--
Szilárd
On Thu, Nov 15, 2012 at 3:53 PM, Thomas Evangelidis <tevang3 at gmail.com>wrote:
> 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/
>
>
>
>
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