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From Mangirish Wagle <vaglomangir...@gmail.com>
Subject Re: Running MPI jobs on Mesos based clusters
Date Tue, 18 Oct 2016 05:54:03 GMT
Hello Devs,

Here is an update on some new learnings and thoughts based on my
interactions with Mesos and Aurora devs.

MPI implementations in Mesos repositories (like MPI Hydra) rely on obsolete
MPI platforms and no longer supported my the developer community. Hence it
is not recommended that we use this for our purpose.

One of the known ways of running MPI jobs over mesos is using "gang
scheduling" which is basically distributing the MPI run over multiple jobs
on mesos in place of multiple nodes. The challenge here is the jobs need to
be scheduled as one task and any job errored should collectively error out
the main program including all the distributed jobs.

One of the Mesos developer (Niklas Nielsen) pointed me out to his work on
gang scheduling: https://github.com/nqn. This code may not be fully tested
but certainly a good starting point to explore gang scheduling.

One of the Aurora developer (Stephen Erb) suggests using gang scheduling on
top of Aurora. Aurora scheduler assumes that every job is independent.
Hence, there would be a need to develop some external scaffolding to
coordinate and schedule these jobs, which might not be trivial. One
advantage of using Aurora as a backend for gang scheduling is that we would
inherit the robustness of Aurora, which otherwise would be a key challenge
if targeting bare mesos.

Alternative to all the options above, I think we should probably be able to
run a 1 node MPI job through Aurora. A resource offer with CPUs and Memory
from Mesos is abstracted as a single runtime, but is mapped to multiple
nodes underneath, which eventually would exploit distributed resource
capabilities.

I intend to try out the 1 node MPI job submission approach first and
simultaneously explore the gang scheduling approach.

Please let me know your thoughts/ suggestions.

Best Regards,
Mangirish



On Thu, Oct 13, 2016 at 12:39 PM, Mangirish Wagle <vaglomangirish@gmail.com>
wrote:

> Hi Marlon,
> Thanks for confirming and sharing the legal link.
>
> -Mangirish
>
> On Thu, Oct 13, 2016 at 12:13 PM, Pierce, Marlon <marpierc@iu.edu> wrote:
>
>> BSD is ok: https://www.apache.org/legal/resolved.
>>
>>
>>
>> *From: *Mangirish Wagle <vaglomangirish@gmail.com>
>> *Reply-To: *"dev@airavata.apache.org" <dev@airavata.apache.org>
>> *Date: *Thursday, October 13, 2016 at 12:03 PM
>> *To: *"dev@airavata.apache.org" <dev@airavata.apache.org>
>> *Subject: *Re: Running MPI jobs on Mesos based clusters
>>
>>
>>
>> Hello Devs,
>>
>> I needed some advice on the license of the MPI libraries. The MPICH
>> library that I have been trying claims to have a "BSD Like" license (
>> http://git.mpich.org/mpich.git/blob/HEAD:/COPYRIGHT).
>>
>> I am aware that OpenMPI which uses BSD license is currently used in our
>> application. I had chosen to start investigating MPICH because it claims to
>> be a highly portable and high quality implementation of latest MPI
>> standard, suitable to cloud based clusters.
>>
>> If anyone could please advise on the acceptance of the MPICH libraries
>> MSD Like license for ASF, that would help.
>>
>> Thank you.
>>
>> Best Regards,
>>
>> Mangirish Wagle
>>
>>
>>
>> On Thu, Oct 6, 2016 at 1:48 AM, Mangirish Wagle <vaglomangirish@gmail.com>
>> wrote:
>>
>> Hello Devs,
>>
>>
>>
>> The network issue mentioned above now stands resolved. The problem was
>> with the iptables had some conflicting rules which blocked the traffic. It
>> was resolved by simple iptables flush.
>>
>>
>>
>> Here is the test MPI program running on multiple machines:-
>>
>>
>>
>> [centos@mesos-slave-1 ~]$ mpiexec -f machinefile -n 2 ./mpitest
>>
>> Hello world!  I am process number: 0 on host mesos-slave-1
>>
>> Hello world!  I am process number: 1 on host mesos-slave-2
>>
>>
>>
>> The next step is to try invoking this through framework like Marathon.
>> However, the job submission still does not run through Marathon. It seems
>> to gets stuck in the 'waiting' state forever (For example
>> http://149.165.170.245:8080/ui/#/apps/%2Fmaw-try). Further, I notice
>> that Marathon is listed under 'inactive frameworks' in mesos dashboard (
>> http://149.165.171.33:5050/#/frameworks).
>>
>>
>>
>> I am trying to get this working, though any help/ clues with this would
>> be really helpful.
>>
>>
>>
>> Thanks and Regards,
>>
>> Mangirish Wagle
>>
>>
>>
>>
>> On Fri, Sep 30, 2016 at 9:21 PM, Mangirish Wagle <
>> vaglomangirish@gmail.com> wrote:
>>
>> Hello Devs,
>>
>>
>>
>> I am currently running a sample MPI C program using 'mpiexec' provided by
>> MPICH. I followed their installation guide
>> <http://www.mpich.org/static/downloads/3.2/mpich-3.2-installguide.pdf> to
>> install the libraries on the master and slave nodes of the mesos cluster.
>>
>>
>>
>> The approach that I am trying out here is that I am equipping the
>> underlying nodes with MPI handling tools and then use the Mesos framework
>> like Marathon/ Aurora to submit jobs to run MPI programs by invoking these
>> tools.
>>
>>
>>
>> You can potentially run an MPI program using mpiexec in the following
>> manner:-
>>
>>
>>
>> # *mpiexec -f machinefile -n 2 ./mpitest*
>>
>>    - *machinefile *-> File which contains an inventory of machines to
>>    run the program on and number of processes on each machine.
>>    - *mpitest *-> MPI program compiled in C using mpicc compiler. The
>>    program returns the process number and he hostname of the machine running
>>    the process.
>>    - *-n *option indicates number of processes that it needs to spawn
>>
>> Example of machinefile contents:-
>>
>>
>>
>> # Entries in the format <hostname/IP>:<number of processes>
>>
>> mesos-slave-1:1
>>
>> mesos-slave-2:1
>>
>>
>>
>> The reason for choosing slaves is that Mesos runs the jobs on slaves,
>> managed by 'agents' pertaining to the slaves.
>>
>>
>>
>> Output of the program with '-n 1':-
>>
>>
>>
>> # mpiexec -f machinefile -n 1 ./mpitest
>>
>> Hello world!  I am process number: 0 on host mesos-slave-1
>>
>>
>>
>> But when I try for '-n 2', I am hitting the following error:-
>>
>>
>>
>> # mpiexec -f machinefile -n 2 ./mpitest
>>
>> [proxy:0:1@mesos-slave-2] HYDU_sock_connect
>> (/home/centos/mpich-3.2/src/pm/hydra/utils/sock/sock.c:172): unable to
>> connect from "mesos-slave-2" to "mesos-slave-1" (No route to host)
>>
>> [proxy:0:1@mesos-slave-2] main (/home/centos/mpich-3.2/src/pm/hydra/pm/pmiserv/pmip.c:189):
>> *unable to connect to server mesos-slave-1 at port 44788* (check for
>> firewalls!)
>>
>>
>>
>> It seems to not allow the program execution due to network traffic being
>> blocked. I checked security groups in scigap openstack for mesos-slave-1,
>> mesos-slave-2 nodes and it is set to 'wideopen' policy. Furthermore, I
>> tried adding explicit rules to the policies to allow all TCP and UDP
>> (Currently I am not sure what protocol is used underneath), even then it
>> continues throwing this error.
>>
>>
>>
>> Any clues, suggestions, comments about the error or approach as a whole
>> would be helpful.
>>
>>
>>
>> Thanks and Regards,
>>
>> Mangirish Wagle
>>
>>
>>
>> *Error! Filename not specified.*
>>
>>
>>
>> On Tue, Sep 27, 2016 at 11:23 AM, Mangirish Wagle <
>> vaglomangirish@gmail.com> wrote:
>>
>> Hello Devs,
>>
>>
>>
>> Thanks Gourav and Shameera for all the work w.r.t. setting up the
>> Mesos-Marathon cluster on Jetstream.
>>
>>
>>
>> I am currently evaluating MPICH (http://www.mpich.org/about/overview/)
>> to be used for launching MPI jobs on top of mesos. MPICH version 1.2
>> supports Mesos based MPI scheduling. I have been also trying to submit jobs
>> to the cluster through Marathon. However, in either cases I am currently
>> facing issues which I am working to get resolved.
>>
>>
>>
>> I am compiling my notes into the following google doc. You may please
>> review and let me know your comments, suggestions.
>>
>>
>>
>> https://docs.google.com/document/d/1p_Y4Zd4I4lgt264IHspXJli3
>> la25y6bcPcmrTD6nR8g/edit?usp=sharing
>>
>>
>>
>> Thanks and Regards,
>>
>> Mangirish Wagle
>>
>>
>>
>> *Error! Filename not specified.*
>>
>>
>>
>> On Wed, Sep 21, 2016 at 3:20 PM, Shenoy, Gourav Ganesh <
>> goshenoy@indiana.edu> wrote:
>>
>> Hi Mangirish,
>>
>>
>>
>> I have set up a Mesos-Marathon cluster for you on Jetstream. I will share
>> with you with the cluster details in a separate email. Kindly note that
>> there are 3 masters & 2 slaves in this cluster.
>>
>>
>>
>> I am also working on automating this process for Jetstream (similar to
>> Shameera’s ansible script for EC2) and when that is ready, we can create
>> clusters or add/remove slave machines from the cluster.
>>
>>
>>
>> Thanks and Regards,
>>
>> Gourav Shenoy
>>
>>
>>
>> *From: *Mangirish Wagle <vaglomangirish@gmail.com>
>> *Reply-To: *"dev@airavata.apache.org" <dev@airavata.apache.org>
>> *Date: *Wednesday, September 21, 2016 at 2:36 PM
>> *To: *"dev@airavata.apache.org" <dev@airavata.apache.org>
>> *Subject: *Running MPI jobs on Mesos based clusters
>>
>>
>>
>> Hello All,
>>
>>
>>
>> I would like to post for everybody's awareness about the study that I am
>> undertaking this fall, i.e. to evaluate various different frameworks that
>> would facilitate MPI jobs on Mesos based clusters for Apache Airavata.
>>
>>
>>
>> Some of the options that I am looking at are:-
>>
>>    1. MPI support framework bundled with Mesos
>>    2. Apache Aurora
>>    3. Marathon
>>    4. Chronos
>>
>> Some of the evaluation criteria that I am planning to base my
>> investigation are:-
>>
>>    - Ease of setup
>>    - Documentation
>>    - Reliability features like HA
>>    - Scaling and Fault recovery
>>    - Performance
>>    - Community Support
>>
>> Gourav and Shameera are working on ansible based automation to spin up a
>> mesos based cluster and I am planning to use it to setup a cluster for
>> experimentation.
>>
>>
>>
>> Any suggestions or information about prior work on this would be highly
>> appreciated.
>>
>>
>>
>> Thank you.
>>
>>
>>
>> Best Regards,
>>
>> Mangirish Wagle
>>
>> *Error! Filename not specified.*
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>

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