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

Wed Jun 28 23:06:57 EDT 2017

Dear Adam,

I forgot whether I really reported the problem in using startdifx two years ago, but I indeed post the problem about startdifx on Nov. 4 of 2016 and Apr. 10 of 2017.
I noted these problems because we were installing the DiFX (both trunk and ver 2.4) in the new computers; and one is for Ubuntu 16.04 while the second time is for Scientific Linux 6.8.
(Please note the error messages obtained from two posts are not the same.)
But I think my problem is not similar to what Arash met.

In reality, I did not fully solve my problems in startdifx, but just find other way to replace the usage on “startdifx”.
Now we use "mpirun --machinefile xxxx.machines -np xx mpifxcorr xxxx.input” in correlation to replace the original "startdifx -v -v -n -f xxxx.input”.
In the previous post, I followed Walter’s suggestion to examine the mpispeed problem, but I can successfully pass the test.
I also checked the installation of different openmpi versions, but I still cannot solve the problem in using “startdifx”.
Since my purpose is to correlate the data, I have not been seriously tied by the problem of "startdifx” …….. 
I also wish to solve this problem, but I have no idea on other tests even I checked some documents related to openmpi. 
(But in reality, I only have basic experiences in using openmpi as well …)

Sincerely,
--
Lupin Chun-Che Lin
Supporting Scientist of GLT (GreenLand Telescope) project 
in Institute of Astronomy and Astrophysics, Academia Sinica,
14F of Astronomy-Mathematics Building (Rm: 1405), 
National Taiwan University. 
No.1, Sec. 4, Roosevelt Rd, Taipei 10617, Taiwan.
Tel: +886-2-2366-5464
Fax: +886-2-2367-7849

> Adam Deller <adeller at astro.swin.edu.au> 於 2017年6月29日 上午7:42 寫道：
> 
> 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 <mailto: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/Example2/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 <mailto:difx-users-bounces at listmgr.nrao.edu>> on behalf of Arash Roshanineshat <arashroshani92 at gmail.com <mailto:arashroshani92 at gmail.com>>
> Sent: Thursday, 29 June 2017 7:34 AM
> To: difx-users at listmgr.nrao.edu <mailto:difx-users at listmgr.nrao.edu>
> Cc: arash.roshanineshat at cfa.harvard.edu <mailto: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
> 
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