[gmx-users] multinode issue

[Éric Germaneau]

Thank you Mark,

Yes this was the end of the log.
I tried an other input and got the same issue:

    Number of CPUs detected (16) does not match the number reported by
    OpenMP (1).
    Consider setting the launch configuration manually!
    Reading file yukuntest-70K.tpr, VERSION 4.6.3 (single precision)
    [16:node328] unexpected disconnect completion event from [0:node299]
    Assertion failed in file ../../dapl_conn_rc.c at line 1179: 0
    internal ABORT - process 16

Actually, I'm running some test for our users, I'll talk with the admin 
about how to  return information
to the standard sysconf() routine in the usual way.
Thank you,

            Éric.

On 12/05/2014 07:38 PM, Mark Abraham wrote:
> On Fri, Dec 5, 2014 at 9:15 AM, Éric Germaneau <germaneau at sjtu.edu.cn>
> wrote:
>
>> Dear all,
>>
>> I use impi and when I submit o job (via LSF) to more than one node I get
>> the following message:
>>
>>     Number of CPUs detected (16) does not match the number reported by
>>     OpenMP (1).
>>
> That suggests this machine has not be set up to return information to the
> standard sysconf() routine in the usual way. What kind of machine is this?
>
>     Consider setting the launch configuration manually!
>>     Reading file test184000atoms_verlet.tpr, VERSION 4.6.2 (single
>>     precision)
>>
> I hope that's just a 4.6.2-era .tpr, but nobody should be using 4.6.2 mdrun
> because there was a bug in only that version affecting precisely these
> kinds of issues...
>
>     [16:node319] unexpected disconnect completion event from [11:node328]
>>     Assertion failed in file ../../dapl_conn_rc.c at line 1179: 0
>>     internal ABORT - process 16
>>
>> I submit doing
>>
>>     mpirun -np 32 -machinefile nodelist $EXE -v -deffnm $INPUT
>>
>> The machinefile looks like this
>>
>>     node328:16
>>     node319:16
>>
>> I'm running the release 4.6.7.
>> I do not set anything about OpenMP for this job, I'd like to have 32 MPI
>> process.
>>
>> Using one node it works fine.
>> Any hints here?
>>
> Everything seems fine. What was the end of the .log file? Can you run
> another MPI test program thus?
>
> Mark
>
>
>>                                                               Éric.
>>
>> --
>> Éric Germaneau (???), Specialist
>> Center for High Performance Computing
>> Shanghai Jiao Tong University
>> Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China
>> M:germaneau at sjtu.edu.cn P:+86-136-4161-6480 W:http://hpc.sjtu.edu.cn
>> --
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-- 
Éric Germaneau (???), Specialist
Center for High Performance Computing
Shanghai Jiao Tong University
Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China
Email:germaneau at sjtu.edu.cn Mobi:+86-136-4161-6480 http://hpc.sjtu.edu.cn