[gmx-users] GPU warnings

[Szilárd Páll]

On Mon, Nov 19, 2012 at 6:25 PM, Szilárd Páll <szilard.pall at cbr.su.se>wrote:

> On Mon, Nov 19, 2012 at 4:09 PM, Thomas Evangelidis <tevang3 at gmail.com>wrote:
>
>> Hi Szilárd,
>>
>> I compiled with the Intel compilers, not gcc. In case I am missing
>> something, these are the versions I have:
>>
>
> Indeed, I see it now in the log file. Let me try with icc 13 and will get
> back to you.
>

I was able to run code compiled with icc 13 on Fedora 17, but as I don't
have Intel Compiler v13 on this machine I can't check it now.

Please check if it works for you with gcc 4.7.2 (which is the default) and
let me know if you succeed. The performance difference between icc and gcc
on your processor should be negligible with GPU runs and at most 5-10% with
CPU-only runs.

As the issue is quite annoying, I'll try to have a look later, probably
after the beta is out.

Cheers,
Sz.


>
>> 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
>>
>> gcc.x86_64                            4.7.2-2.fc17
>> @updates
>> gcc-c++.x86_64                        4.7.2-2.fc17
>> @updates
>> gcc-gfortran.x86_64                   4.7.2-2.fc17
>> @updates
>> libgcc.i686                           4.7.2-2.fc17
>> @updates
>> libgcc.x86_64                         4.7.2-2.fc17               @updates
>>
>>
>> Thomas
>>
>>
>>
>> On 19 November 2012 16:57, Szilárd Páll <szilard.pall at cbr.su.se> wrote:
>>
>> > Thomas & Albert,
>> >
>> > We are unable to reproduce the issue on FC 17 with glibc 2.15-58 and gcc
>> > 4.7.2.
>> >
>> > Please try to update your packages (you should have updates available
>> for
>> > glibc), try recompiling with the latest 4.6 code and report back whether
>> > you succeed.
>> >
>> > Cheers,
>> >
>> > --
>> > Szilárd
>> >
>> >
>> > On Fri, Nov 16, 2012 at 4:31 PM, Szilárd Páll <szilard.pall at cbr.su.se
>> > >wrote:
>> >
>> > > Hi Albert,
>> > >
>> > > Apologies for hijacking your thread. Do you happen to have Fedora 17
>> as
>> > > well?
>> > >
>> > > --
>> > > Szilárd
>> > >
>> > >
>> > >
>> > > On Sun, Nov 4, 2012 at 10:55 AM, Albert <mailmd2011 at gmail.com> wrote:
>> > >
>> > >> hello:
>> > >>
>> > >>  I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti
>> (2 x
>> > >> 1344 CUDA cores), and I got the following warnings:
>> > >>
>> > >> thank you very much.
>> > >>
>> > >> ---------------------------**messages----------------------**
>> > >> -------------
>> > >>
>> > >> WARNING: On node 0: oversubscribing the available 0 logical CPU cores
>> > per
>> > >> node with 2 MPI processes.
>> > >>          This will cause considerable performance loss!
>> > >>
>> > >> 2 GPUs detected on host boreas:
>> > >>   #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
>> > >> compatible
>> > >>   #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
>> > >> compatible
>> > >>
>> > >> 2 GPUs auto-selected to be used for this run: #0, #1
>> > >>
>> > >> Using CUDA 8x8x8 non-bonded kernels
>> > >> Making 1D domain decomposition 1 x 2 x 1
>> > >>
>> > >> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
>> > >> We have just committed the new CPU detection code in this branch,
>> > >> and will commit new SSE/AVX kernels in a few days. However, this
>> > >> means that currently only the NxN kernels are accelerated!
>> > >> In the mean time, you might want to avoid production runs in 4.6.
>> > >>
>> > >> --
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>> > >
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>>
>>
>> --
>>
>> ======================================================================
>>
>> 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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>
>