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Subject: Re: [OMPI users] Running application with MPI_Comm_spawn() in multithreaded environment
From: Ralph Castain (rhc_at_[hidden])
Date: 2008-10-01 09:08:03


Okay, I believe I understand the problem. What this error is telling
you is that the Torque MOM is refusing our connection request because
it is already busy. So we cannot spawn another process.

If I understand your application correctly, you are spinning off
multiple threads, each attempting to comm_spawn a single process -
true? The problem with that design is that - since OMPI is not thread
safe yet - these threads are all attempting to connect to the MOM at
the same time. The MOM will only allow one connection at a time, and
so at some point we are requesting a connection while already connected.

Since we are some ways off from attaining thread safety in these
scenarios, you really have three choices:

1. you could do this with a single comm_spawn call. Remember, you can
provide an MPI_Info key to comm_spawn essentially telling it where to
place the various process ranks. Unless you truly want each new
process to be in its own comm_world, there is no real need to do this
with 10000 individual calls to comm_spawn.

2. you could execute your own thread locking scheme in your
application so that only one thread calls comm_spawn at a time.

3. remove the threaded launch scenario and just call comm_spawn in a
loop.

In truth, the threaded approach to spawning all these procs isn't
gaining you anything. Torque will only do one launch at a time anyway,
so you will launch them serially no matter what. You may just be
adding complexity for no real net gain.

Ralph

On Oct 1, 2008, at 1:56 AM, Roberto Fichera wrote:

> Ralph Castain ha scritto:
>> Hi Roberto
>>
>> There is something wrong with this cmd line - perhaps it wasn't
>> copied
>> correctly?
>>
>> mpirun --verbose --debug-daemons --mca obl -np 1 -wdir `pwd`
>> testmaster 10000 $PBS_NODEFILE
>>
>> Specifically, the following is incomplete: --mca obl
>>
>> I'm not sure if this is the problem or not, but I am unaware of such
>> an option and believe it could cause mpirun to become confused.
> Ops! Sorry, I copied the wrong log, below there the right one:
>
> [roberto_at_master TestOpenMPI]$ qsub -I testmaster.pbs
> qsub: waiting for job 920.master.tekno-soft.it to start
> qsub: job 920.master.tekno-soft.it ready
>
> [roberto_at_master TestMPICH2]$ cd /data/roberto/MPI/TestOpenMPI/
> [roberto_at_master TestOpenMPI]$ mpirun --debug-daemons --mca btl
> tcp,self
> -wdir "`pwd`" -np 1 testmaster 100000 $PBS_NODEFILE
> [master.tekno-soft.it:05407] [[11340,0],0] orted_cmd: received
> add_local_procs
> [master.tekno-soft.it:05407] [[11340,0],0] node[0].name master
> daemon 0
> arch ffc91200
> [master.tekno-soft.it:05407] [[11340,0],0] node[1].name cluster4
> daemon
> INVALID arch ffc91200
> [master.tekno-soft.it:05407] [[11340,0],0] node[2].name cluster3
> daemon
> INVALID arch ffc91200
> [master.tekno-soft.it:05407] [[11340,0],0] node[3].name cluster2
> daemon
> INVALID arch ffc91200
> [master.tekno-soft.it:05407] [[11340,0],0] node[4].name cluster1
> daemon
> INVALID arch ffc91200
> Initializing MPI ...
> [master.tekno-soft.it:05407] [[11340,0],0] orted_recv: received
> sync+nidmap from local proc [[11340,1],0]
> [master.tekno-soft.it:05407] [[11340,0],0] orted_cmd: received
> collective data cmd
> [master.tekno-soft.it:05407] [[11340,0],0] orted_cmd: received
> message_local_procs
> [master.tekno-soft.it:05407] [[11340,0],0] orted_cmd: received
> collective data cmd
> [master.tekno-soft.it:05407] [[11340,0],0] orted_cmd: received
> message_local_procs
> Loading the node's ring from file
> '/var/torque/aux//920.master.tekno-soft.it'
> ... adding node #1 host is 'cluster4.tekno-soft.it'
> ... adding node #2 host is 'cluster3.tekno-soft.it'
> ... adding node #3 host is 'cluster2.tekno-soft.it'
> ... adding node #4 host is 'cluster1.tekno-soft.it'
> A 4 node's ring has been made
> At least one node is available, let's start to distribute 100000 job
> across 4 nodes!!!
> ****************** Starting job #1
> ****************** Starting job #2
> ****************** Starting job #3
> Setting up the host as 'cluster4.tekno-soft.it'
> Setting the work directory as '/data/roberto/MPI/TestOpenMPI'
> Spawning a task 'testslave' on node 'cluster4.tekno-soft.it'
> Setting up the host as 'cluster3.tekno-soft.it'
> Setting the work directory as '/data/roberto/MPI/TestOpenMPI'
> Spawning a task 'testslave' on node 'cluster3.tekno-soft.it'
> Setting up the host as 'cluster2.tekno-soft.it'
> Setting the work directory as '/data/roberto/MPI/TestOpenMPI'
> Spawning a task 'testslave' on node 'cluster2.tekno-soft.it'
> Setting up the host as 'cluster1.tekno-soft.it'
> Setting the work directory as '/data/roberto/MPI/TestOpenMPI'
> Spawning a task 'testslave' on node 'cluster1.tekno-soft.it'
> ****************** Starting job #4
> Daemon was launched on cluster3.tekno-soft.it - beginning to
> initialize
> Daemon [[11340,0],1] checking in as pid 9487 on host cluster3.tekno-
> soft.it
> Daemon [[11340,0],1] not using static ports
> --------------------------------------------------------------------------
> A daemon (pid unknown) died unexpectedly on signal 1 while
> attempting to
> launch so we are aborting.
>
> There may be more information reported by the environment (see above).
>
> This may be because the daemon was unable to find all the needed
> shared
> libraries on the remote node. You may set your LD_LIBRARY_PATH to
> have the
> location of the shared libraries on the remote nodes and this will
> automatically be forwarded to the remote nodes.
> --------------------------------------------------------------------------
> [master.tekno-soft.it:05407] [[11340,0],0] ORTE_ERROR_LOG: Resource
> busy
> in file base/plm_base_receive.c at line 169
> [master.tekno-soft.it:05414] [[11340,1],0] ORTE_ERROR_LOG: The
> specified
> application failed to start in file dpm_orte.c at line 677
> [master.tekno-soft.it:05414] *** An error occurred in MPI_Comm_spawn
> [master.tekno-soft.it:05414] *** on communicator MPI_COMM_WORLD
> [master.tekno-soft.it:05414] *** MPI_ERR_SPAWN: could not spawn
> processes
> [master.tekno-soft.it:05414] *** MPI_ERRORS_ARE_FATAL (goodbye)
>
> [master.tekno-soft.it:05407] [[11340,0],0] ORTE_ERROR_LOG: Resource
> busy
> in file base/plm_base_receive.c at line 169
> [master.tekno-soft.it:05407] [[11340,0],0] orted_cmd: received
> add_local_procs
> [master.tekno-soft.it:05407] [[11340,0],0] node[0].name master
> daemon 0
> arch ffc91200
> [master.tekno-soft.it:05407] [[11340,0],0] node[1].name cluster4
> daemon
> INVALID arch ffc91200
> [master.tekno-soft.it:05407] [[11340,0],0] node[2].name cluster3
> daemon
> 1 arch ffc91200
> [master.tekno-soft.it:05407] [[11340,0],0] node[3].name cluster2
> daemon
> INVALID arch ffc91200
> [master.tekno-soft.it:05407] [[11340,0],0] node[4].name cluster1
> daemon
> INVALID arch ffc91200
> [cluster3.tekno-soft.it:09487] [[11340,0],1] orted: up and running -
> waiting for commands!
>
>
>
>>
>> Ralph
>>
>>
>> On Sep 30, 2008, at 8:24 AM, Roberto Fichera wrote:
>>
>>> Roberto Fichera ha scritto:
>>>> Hi All on the list,
>>>>
>>>> I'm trying to execute dynamic MPI applications using
>>>> MPI_Comm_spawn().
>>>> The application I'm using for tests, basically is
>>>> composed by a master, which spawn a slave in each assigned node
>>>> in a
>>>> multithreading fashion. The master is started with a
>>>> number of jobs to perform and a filename, containing the list of
>>>> assigned nodes. The idea is to handle all the dispatching
>>>> logic within the application, so that the master will try to take
>>>> as
>>>> busy as possible each assigned node. Said that, for each spawned
>>>> job, the master allocate a thread for spawning and handling the
>>>> communication, than generate a random number, send it to the
>>>> slave which simply send it back to the master. Finally the slave
>>>> terminate its job and the relative node become free for a new one.
>>>> The things will continue until all the requested jobs are done.
>>>>
>>>> The test program I'm using *doesn't* work flawless in mpich2
>>>> because it
>>>> has a ~24k spawned job limitation, due to a monotonically
>>>> increasing of its internal context id which basically stops the
>>>> application due to a library internal overflow. The internal
>>>> context
>>>> id,
>>>> allocated
>>>> for each terminated spawned job, are never recycled at moment. The
>>>> unique MPI-2 implementation, so supporting MPI_Comm_spawn(),
>>>> which was able to complete the test is currently the HP MPI. So
>>>> now I
>>>> would start to check OpenMPI if it's suitable for our dynamic
>>>> parallel
>>>> applications.
>>>>
>>>> The test application is linked against OpenMPI v1.3a1r19645,
>>>> running of
>>>> Fedora8 x86_64 + all updates.
>>>>
>>>> My first attempt end up on the error below which I basically
>>>> don't know
>>>> where to look further. Note that I've already checked PATHs and
>>>> LD_LIBRARY_PATH, the application is basically configured correctly
>>>> since
>>>> it uses two scripts for starting and all the paths are set there.
>>>> Basically I need to start *one* master application which will
>>>> handle
>>>> all
>>>> the things for managing slave applications. The communication is
>>>> *only*
>>>> master <-> slave and never collective, at moment.
>>>>
>>>> The test program is available on request.
>>>>
>>>> Does any one have an idea what's going on?
>>>>
>>>> Thanks in advance,
>>>> Roberto Fichera.
>>>>
>>>> [roberto_at_cluster4 TestOpenMPI]$ orterun -wdir
>>>> /data/roberto/MPI/TestOpenMPI -np
>>>> 1 testmaster 10000 $PBS_NODEFILE
>>>> Initializing MPI ...
>>>> Loading the node's ring from file
>>>> '/var/torque/aux//909.master.tekno-soft.it'
>>>> ... adding node #1 host is 'cluster3.tekno-soft.it'
>>>> ... adding node #2 host is 'cluster2.tekno-soft.it'
>>>> ... adding node #3 host is 'cluster1.tekno-soft.it'
>>>> ... adding node #4 host is 'master.tekno-soft.it'
>>>> A 4 node's ring has been made
>>>> At least one node is available, let's start to distribute 10000 job
>>>> across 4
>>>> nodes!!!
>>>> ****************** Starting job #1
>>>> ****************** Starting job #2
>>>> ****************** Starting job #3
>>>> ****************** Starting job #4
>>>> Setting up the host as 'cluster3.tekno-soft.it'
>>>> Setting the work directory as '/data/roberto/MPI/TestOpenMPI'
>>>> Spawning a task './testslave.sh' on node 'cluster3.tekno-soft.it'
>>>> Setting up the host as 'cluster2.tekno-soft.it'
>>>> Setting the work directory as '/data/roberto/MPI/TestOpenMPI'
>>>> Spawning a task './testslave.sh' on node 'cluster2.tekno-soft.it'
>>>> Setting up the host as 'cluster1.tekno-soft.it'
>>>> Setting the work directory as '/data/roberto/MPI/TestOpenMPI'
>>>> Spawning a task './testslave.sh' on node 'cluster1.tekno-soft.it'
>>>> Setting up the host as 'master.tekno-soft.it'
>>>> Setting the work directory as '/data/roberto/MPI/TestOpenMPI'
>>>> Spawning a task './testslave.sh' on node 'master.tekno-soft.it'
>>>> --------------------------------------------------------------------------
>>>>
>>>> A daemon (pid unknown) died unexpectedly on signal 1 while
>>>> attempting to
>>>> launch so we are aborting.
>>>>
>>>> There may be more information reported by the environment (see
>>>> above).
>>>>
>>>> This may be because the daemon was unable to find all the needed
>>>> shared
>>>> libraries on the remote node. You may set your LD_LIBRARY_PATH to
>>>> have the
>>>> location of the shared libraries on the remote nodes and this will
>>>> automatically be forwarded to the remote nodes.
>>>> --------------------------------------------------------------------------
>>>>
>>>> [cluster4.tekno-soft.it:21287] [[30014,0],0] ORTE_ERROR_LOG:
>>>> Resource busy in
>>>> file base/plm_base_receive.c at line 169
>>>> [cluster4.tekno-soft.it:21287] [[30014,0],0] ORTE_ERROR_LOG:
>>>> Resource busy in
>>>> file base/plm_base_receive.c at line 169
>>>>
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