[Difx-users] (SOLVED) mpicorrdifx cannot be loaded correctly on more than a single node
Arash Roshanineshat
arash.roshanineshat at cfa.harvard.edu
Thu Jun 29 14:29:47 EDT 2017
Hi All
Thank you all for your help. I want to update you about what I did and
what the result was.
I tried executing "mpirun" on a target node using "--host" argument:
user at fringes-difx0$ mpirun --host fringes-difx1 ...
but it couldn't use more than 1 cpu. to use more than a cpu I had to
pass "--oversubscribe" argument to "mpirun". Furthermore, although the
node had 40 cpus (checked with "htop"), it couldn't use more than 20
cpus. I passed 20 and I also tried passing 90 threads to "mpirun", but
it didn't make any difference. only maximum of 20 of cpus were used.
I installed SLURM on the cluster and nodes and done the same experiment
using the following command:
$ salloc -N 2 mpirun ~/difx/bin/mpispeed
All 80 cpus (2 nodes) got involved in some processing. but no output, no
update and no results. the output was just bunch of:
About to run MPIInit on node fringes-difx0
About to run MPIInit on node fringes-difx0
About to run MPIInit on node fringes-difx0
About to run MPIInit on node fringes-difx0
About to run MPIInit on node fringes-difx0
About to run MPIInit on node fringes-difx1
and it stuck there and I had to Ctrl+C to get out.
Based on Adam's suggestion and the experiences above, I decided to try
other versions of "openmpi". The experiments above were done using
Ubuntu 16.04, openmpi 1.10.2 and SLURM 15.08.7.
I tried installing "Openmpi 2.1.1", but no success. I was getting an
error about "pmi" component. Although pmi2.h was included in the package
and I tried several ways to introduce it, I failed.
So I purged and removed Openmpi and its libraries and decided to move to
"mpich" (version 3.2) instead.
"startdifx" didn't work again. Because it tries to execute a command
which includes "mpirun" and "mca" and it seems "mpich" does not
recognize "mca".
However, the first try using difx and "mpirun" was successful and it
used the whole system resources. It also worked on several nodes at the
same time as well successfully. I executed a difx experiment and checked
the result and it was correct.
I would be grateful if you give your feedback and opinion. I also would
be happy to track the problem I had with "openmpi".
Best Regards
Arash Roshanineshat
On 06/28/2017 09:08 PM, Adam Deller wrote:
> OK, then there is clearly a problem with the mpirun command generated by
> startdifx, if it is giving the same error when you are only using a
> single node. What is the mpirun command you have used previously which
> *did* work, and on which machine are you running it?
>
> The other thing that might be an issue is mpirun simply getting confused
> about how many processes it should be allowed to start on the node. See
> https://www.open-mpi.org/doc/v2.0/man1/mpirun.1.php for a huge list of
> options (specifically the "Mapping, ranking and binding" section). What
> happens if you run the mpirun command manually, but add --report-bindings?
>
> Cheers,
> Adam/
> /
>
> On 29 June 2017 at 09:58, Arash Roshanineshat
> <arash.roshanineshat at cfa.harvard.edu
> <mailto:arash.roshanineshat at cfa.harvard.edu>> wrote:
>
> Hi Adam
>
> Thank you for your information.
>
> I disabled each node by putting 0 in the third column of cluster
> configuration file (C.txt) one by one and I doubled checked to see
> if the disabled node is removed from "threads" and "machines" file.
>
> However, the problem is still there with the same error message in
> both cases.
>
> Yes, the nodes in the cluster are connected to each other using 40G
> cables and the master node that I want it to run difx is connected
> to my workstation using a regular LAN (RJ-45) cable. So the master
> node has two interfaces up.
>
>
> Best Regards
> Arash Roshanineshat
>
>
> On 06/28/2017 07:42 PM, Adam Deller wrote:
>
> 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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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 <tel:%2B61%203%209214%205307>
> fax: +61 3 9214 8797 <tel:%2B61%203%209214%208797>
>
> office days (usually): Mon-Thu
> !=============================================================!
>
>
>
>
> --
> !=============================================================!
> 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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