[gmx-developers] thread problem on AMD 12 core chips?

[David van der Spoel]

On 2012-01-12 13:31, Ake Sandgren wrote:
> On Thu, 2012-01-12 at 13:18 +0100, David van der Spoel wrote:
>> On 2012-01-12 11:36, Berk Hess wrote:
>>> On 01/12/2012 11:24 AM, David van der Spoel wrote:
>>>> On 2012-01-12 11:17, Berk Hess wrote:
>>>>> Which compiler is this?
>>>>> We get lots of warnings with gcc4.6, but we run regularly on 32 and 64
>>>>> core nodes.
>>>>
>>>> Thread model: posix
>>>> gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5)
>>>>
>>>> Is intel more reliable?
>>> This is not a matter of platform I would think.
>>> We have only used AMD platform with 32 or more MPI threads.
>>> I would guess this is a thread-mpi bug or a compiler issue.
>> Compiling with Intel C 12.0.3.174 gives the same error, but the same
>> pthread library is linked in.
>>
>> Other tips for debugging this?
>>
>>>
>>> Berk
>>>>>
>>>>> Berk
>>>>>
>>>>> On 01/12/2012 11:04 AM, David van der Spoel wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I'm trying to compile and install gromacs release-4-5-patches on a new
>>>>>> cluster with four 12-core AMD chips (abisko in Umea, Sweden). However
>>>>>> the threaded code bails out with the following message:
>>>>>>
>>>>>> Reading file topol.tpr, VERSION 4.5.5-dev-20120111-9181e (double
>>>>>> precision)
>>>>>> Starting 32 threads
>>>>>> tMPI error: tMPI Initialization error (in valid comm)
>>>>>>
>>>>>> First, I'm a bit confused why the code detects only 32 cores, second
>>>>>> it shows above error and quits.
>>>>>>
>>>>>> Any clues?
>
>
> Abisko's current nodes are 4-socket 8-core (the 12-cores are still under
> test)
>
> If you are using openmpi it does not have support for MPI threads
> compiled in (the openib part of openmpi doesn't support this yet) that
> probably explains your problem.
>
I see, that explains the 32. But gromacs uses it's own mpi-over-threads 
implementation that does not use any MPI whatsoever.


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se