[Difx-users] mpicorrdifx cannot be loaded correctly on more than a single node

[Adam Deller]

Hi Arash,

I'm fairly sure this is an openmpi issue and not a DiFX issue, hence the
number of threads should not be important - it is barfing well before the
stage of trying to start processing threads.  For some reason, openmpi
thinks there are not enough CPUs available to bind processes on your first
machine (although there should be, given that you're only allocating 5
processes to it and it has 20 cores).  I know Lupin Liu posted a similar
problem about 2 years ago, but when I Iook at that thread there was never a
resolution - perhaps Lupin can comment?  (You can search through the
difx-users archive for "While computing bindings", and you'll see it).

If you change C.txt to only have one machine enabled (first fringes-difx0,
then fringes-difx1), does it work in both cases?  Do you have any funny
networking infrastructure like infiniband in parallel with ethernet?
Sometimes mpi gets confused when multiple interfaces are present.

If you can easily do so, I also suggest trying a different version of
openmpi.

Cheers,
Adam

On 29 June 2017 at 09:21, Arash Roshanineshat <arashroshani92 at gmail.com>
wrote:

> Thank you Chris.
>
> I reduced the number of threads to 5 in the cluster configuration file
> (C.txt) and the same problem is still there.
>
> As per your request, I have attached the files to this email.
>
> "errormon2" does not report anything when I execute startdifx. I mean the
> output of errormon2 is blank.
>
> It might be useful to say that, executing "mpispeed", as it was suggested
> in an archived mail-list email, using the following command and the same
> configuration files, works correctly. It uses 6 cpus in total in both
> cluster nodes and returns "done" outputs.
>
> $ mpirun -np 6 --hostfile /home/arash/Shared_Examples/Ex
> ample2/e17d05-Sm-Sr_1000.machines /home/arash/difx/bin/mpispeed
>
> Regarding the large number of threads, If I have understood correctly from
> NRAO's difx tutorial, MPI should handle the threads(and hyperthreads)
> automatically. So I chose a large number to use whole system's resources
> and speed up the difx.
>
> Best Regards
>
> Arash Roshanineshat
>
>
>
> On 06/28/2017 07:03 PM, Chris.Phillips at csiro.au wrote:
>
>> Hi Arash,
>>
>> Without the full setup, it is basically impossible to debug such
>> problems. We would need to see the .input file and preferably the .v2d and
>> .vex file also.  Also the full output from DIFX for the entire run (use
>> errormon or errormon2)
>>
>> Specifically how many antennas are being correlated? Maybe you just have
>> too few DIFX processes.
>>
>> Given you are running all the DataStream processes in a single node, I
>> would suggest you probably have too many threads running per core. I doubt
>> that is the problem you are seeing though.
>>
>> Actually maybe it is - stardifx maybe is being clever (I don't use it)
>> and not being willing to allocate more than 20 processes (ignore
>> hyperthreads, they tend to be useless for DIFX).  Try changing # threads
>> to, say, 5.
>>
>> Cheers
>> Chris
>>
>> ________________________________________
>> From: Difx-users <difx-users-bounces at listmgr.nrao.edu> on behalf of
>> Arash Roshanineshat <arashroshani92 at gmail.com>
>> Sent: Thursday, 29 June 2017 7:34 AM
>> To: difx-users at listmgr.nrao.edu
>> Cc: arash.roshanineshat at cfa.harvard.edu
>> Subject: [Difx-users] mpicorrdifx cannot be loaded correctly on more than
>> a     single node
>>
>> Hi,
>>
>> I could install difx but it can only be run on a single node cluster.
>>
>> The *.machines and *.threads files are attached to this email.
>>
>> Openmpi is installed on all nodes and difx folder and data folder is
>> shared among the clusters using NFS filesystem. Difx works perfectly
>> with correct output on single machines.
>>
>> executing "startdifx -v -f e17d05-Sm-Sr_1000.input" returns the
>> following error:
>>
>> DIFX_MACHINES -> /home/arash/Shared_Examples/Example2/C.txt
>> Found modules:
>> Executing:  mpirun -np 6 --hostfile
>> /home/arash/Shared_Examples/Example2/e17d05-Sm-Sr_1000.machines --mca
>> mpi_yield_when_idle 1 --mca rmaps seq  runmpifxcorr.DiFX-2.5
>> /home/arash/Shared_Examples/Example2/e17d05-Sm-Sr_1000.input
>> ------------------------------------------------------------
>> --------------
>> While computing bindings, we found no available cpus on
>> the following node:
>>
>>     Node:  fringes-difx0
>>
>> Please check your allocation.
>> ------------------------------------------------------------
>> --------------
>> Elapsed time (s) = 0.50417590141
>>
>> and executing
>>
>> $ mpirun -np 6 --hostfile
>> /home/arash/Shared_Examples/Example2/e17d05-Sm-Sr_1000.machines
>> /home/arash/difx/bin/mpifxcorr
>> /home/arash/Shared_Examples/Example2/e17d05-Sm-Sr_1000.input
>>
>> seems to be working but by observing the cpu usage, I see only 6 cpus
>> involving "5 in fringes-difx0 and 1 in fringes-difx1". I was expecting
>> it to use the number of cpus equal to the number in "*.threads" file.
>> How can I solve this issue?
>>
>> the specification of the cluster is Socket=2, Core per Socket=10 and
>> Threads per core=2.
>>
>> Best Regards
>>
>> Arash Roshanineshat
>>
>>
>>
>>
>>
>
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-- 
!=============================================================!
Dr. Adam Deller
ARC Future Fellow, Senior Lecturer
Centre for Astrophysics & Supercomputing
Swinburne University of Technology
John St, Hawthorn VIC 3122 Australia
phone: +61 3 9214 5307
fax: +61 3 9214 8797

office days (usually): Mon-Thu
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