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Subject: Re: [OMPI users] [EXTERNAL] Re: (OpenMPI for Cray XE6 ) How to set mca parameters through aprun?
From: Teranishi, Keita (knteran_at_[hidden])
Date: 2013-11-26 16:33:20


Nathan,

Please see the attached obtained from two cases (-np 2 and -np 4).

Thanks,
---------------------------------------------------------------------------

--
Keita Teranishi
Principal Member of Technical Staff
Scalable Modeling and Analysis Systems
Sandia National Laboratories
Livermore, CA 94551
+1 (925) 294-3738
On 11/26/13 1:26 PM, "Nathan Hjelm" <hjelmn_at_[hidden]> wrote:
>Seems like something is going wrong with processor binding. Can you run
>with
>-mca plm_base_verbose 100 . Might shed some light on why it thinks there
>are
>not enough slots.
>
>-Nathan Hjelm
>Application Readiness, HPC-5, LANL
>
>On Tue, Nov 26, 2013 at 09:18:14PM +0000, Teranishi, Keita wrote:
>> Nathan,
>> 
>> Now I remove strip_prefix stuff, which was applied to the other versions
>> of OpenMPI.  
>> I still have the same problem with msubrun command.
>> 
>> knteran_at_mzlogin01:~> msub -lnodes=2:ppn=16 -I
>> qsub: waiting for job 7754058.sdb to start
>> qsub: job 7754058.sdb ready
>> 
>> knteran_at_mzlogin01:~> cd test-openmpi/
>> knteran_at_mzlogin01:~/test-openmpi> !mp
>> mpicc cpi.c -o cpi
>> knteran_at_mzlogin01:~/test-openmpi> mpirun -np 4 ./cpi
>> 
>>-------------------------------------------------------------------------
>>-
>> There are not enough slots available in the system to satisfy the 4
>>slots
>> that were requested by the application:
>>   ./cpi
>> 
>> Either request fewer slots for your application, or make more slots
>> available
>> for use.
>> 
>>-------------------------------------------------------------------------
>>-
>> 
>> I set PATH and LD_LIBRARY_PATH to match with my own OpenMPI
>>installation.
>> knteran_at_mzlogin01:~/test-openmpi> which mpirun
>> /home/knteran/openmpi/bin/mpirun
>> 
>> 
>> 
>> 
>> Thanks,
>> 
>> 
>>-------------------------------------------------------------------------
>>--
>> --
>> Keita Teranishi
>> Principal Member of Technical Staff
>> Scalable Modeling and Analysis Systems
>> Sandia National Laboratories
>> Livermore, CA 94551
>> +1 (925) 294-3738
>> 
>> 
>> 
>> 
>> 
>> On 11/26/13 12:52 PM, "Nathan Hjelm" <hjelmn_at_[hidden]> wrote:
>> 
>> >Weird. That is the same configuration we have deployed on Cielito and
>> >Cielo. Does
>> >it work under an msub allocation?
>> >
>> >BTW, with that configuration you should not set
>> >plm_base_strip_prefix_from_node_names
>> >to 0. That will confuse orte since the node hostname will not match
>>what
>> >was
>> >supplied by alps.
>> >
>> >-Nathan
>> >
>> >On Tue, Nov 26, 2013 at 08:38:51PM +0000, Teranishi, Keita wrote:
>> >> Nathan,
>> >> 
>> >> (Please forget about the segfault. It was my mistake).
>> >> I use OpenMPI-1.7.2 (build with gcc-4.7.2) to run the program.  I
>>used
>> >> contrib/platform/lanl/cray_xe6/optimized_lustre and
>> >> --enable-mpirun-prefix-by-default for configuration.  As I said, it
>> >>works
>> >> fine with aprun, but fails with mpirun/mpiexec.
>> >> 
>> >> 
>> >> knteran_at_mzlogin01:~/test-openmpi> ~/openmpi/bin/mpirun -np 4 ./a.out
>> >> 
>> 
>>>>-----------------------------------------------------------------------
>>>>--
>> >>-
>> >> There are not enough slots available in the system to satisfy the 4
>> >>slots
>> >> that were requested by the application:
>> >>   ./a.out
>> >> 
>> >> Either request fewer slots for your application, or make more slots
>> >> available
>> >> for use.
>> >> 
>> >> 
>> 
>>>>-----------------------------------------------------------------------
>>>>--
>> >>--
>> >> -
>> >> 
>> >> Thanks,
>> >> 
>> >> 
>> 
>>>>-----------------------------------------------------------------------
>>>>--
>> >>--
>> >> --
>> >> Keita Teranishi
>> >> Principal Member of Technical Staff
>> >> Scalable Modeling and Analysis Systems
>> >> Sandia National Laboratories
>> >> Livermore, CA 94551
>> >> +1 (925) 294-3738
>> >> 
>> >> 
>> >> 
>> >> 
>> >> 
>> >> On 11/25/13 12:55 PM, "Nathan Hjelm" <hjelmn_at_[hidden]> wrote:
>> >> 
>> >> >Ok, that should have worked. I just double-checked it to me sure.
>> >> >
>> >> >ct-login1:/lscratch1/hjelmn/ibm/collective hjelmn$ mpirun -np 32
>> >>./bcast
>> >> >App launch reported: 17 (out of 3) daemons - 0 (out of 32) procs
>> >> >ct-login1:/lscratch1/hjelmn/ibm/collective hjelmn$
>> >> >
>> >> >
>> >> >How did you configure Open MPI and what version are you using?
>> >> >
>> >> >-Nathan
>> >> >
>> >> >On Mon, Nov 25, 2013 at 08:48:09PM +0000, Teranishi, Keita wrote:
>> >> >> Hi Natan,
>> >> >> 
>> >> >> I tried qsub option you
>> >> >> 
>> >> >> mpirun -np 4  --mca plm_base_strip_prefix_from_node_names= 0 ./cpi
>> >> >> 
>> >> 
>> 
>>>>>>---------------------------------------------------------------------
>>>>>>--
>> >>>>--
>> >> >>-
>> >> >> There are not enough slots available in the system to satisfy the
>>4
>> >> >>slots
>> >> >> that were requested by the application:
>> >> >>   ./cpi
>> >> >> 
>> >> >> Either request fewer slots for your application, or make more
>>slots
>> >> >> available
>> >> >> for use.
>> >> >> 
>> >> 
>> 
>>>>>>---------------------------------------------------------------------
>>>>>>--
>> >>>>--
>> >> >>-
>> >> >> 
>> >> >> 
>> >> >> Here is I got from aprun
>> >> >> aprun  -n 32 ./cpi
>> >> >> Process 8 of 32 is on nid00011
>> >> >> Process 5 of 32 is on nid00011
>> >> >> Process 12 of 32 is on nid00011
>> >> >> Process 9 of 32 is on nid00011
>> >> >> Process 11 of 32 is on nid00011
>> >> >> Process 13 of 32 is on nid00011
>> >> >> Process 0 of 32 is on nid00011
>> >> >> Process 6 of 32 is on nid00011
>> >> >> Process 3 of 32 is on nid00011
>> >> >> :
>> >> >> 
>> >> >> :
>> >> >> 
>> >> >> Also, I found a strange error in the end of the program
>> >>(MPI_Finalize?)
>> >> >> Can you tell me what is wrong with that?
>> >> >> [nid00010:23511] [ 0] /lib64/libpthread.so.0(+0xf7c0)
>> >>[0x2aaaacbbb7c0]
>> >> >> [nid00010:23511] [ 1]
>> >> >> 
>> >> 
>> 
>>>>>>/home/knteran/openmpi/lib/libmpi.so.0(opal_memory_ptmalloc2_int_free+
>>>>>>0x
>> >>>>57
>> >> >>)
>> >> >> [0x2aaaaaf38ec7]
>> >> >> [nid00010:23511] [ 2]
>> >> >> 
>> >>/home/knteran/openmpi/lib/libmpi.so.0(opal_memory_ptmalloc2_free+0xc3)
>> >> >> [0x2aaaaaf3b6c3]
>> >> >> [nid00010:23511] [ 3]
>> >> >> /home/knteran/openmpi/lib/libmpi.so.0(mca_pml_base_close+0xb2)
>> >> >> [0x2aaaaae717b2]
>> >> >> [nid00010:23511] [ 4]
>> >> >> /home/knteran/openmpi/lib/libmpi.so.0(ompi_mpi_finalize+0x333)
>> >> >> [0x2aaaaad7be23]
>> >> >> [nid00010:23511] [ 5] ./cpi() [0x400e23]
>> >> >> [nid00010:23511] [ 6] /lib64/libc.so.6(__libc_start_main+0xe6)
>> >> >> [0x2aaaacde7c36]
>> >> >> [nid00010:23511] [ 7] ./cpi() [0x400b09]
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> Thanks,
>> >> >> 
>> >> >> 
>> >> 
>> 
>>>>>>---------------------------------------------------------------------
>>>>>>--
>> >>>>--
>> >> >>--
>> >> >> --
>> >> >> Keita Teranishi
>> >> >> 
>> >> >> Principal Member of Technical Staff
>> >> >> Scalable Modeling and Analysis Systems
>> >> >> Sandia National Laboratories
>> >> >> Livermore, CA 94551
>> >> >> +1 (925) 294-3738
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> On 11/25/13 12:28 PM, "Nathan Hjelm" <hjelmn_at_[hidden]> wrote:
>> >> >> 
>> >> >> >Just talked with our local Cray rep. Sounds like that torque
>>syntax
>> >>is
>> >> >> >broken. You can continue
>> >> >> >to use qsub (though qsub use is strongly discouraged) if you use
>>the
>> >> >>msub
>> >> >> >options.
>> >> >> >
>> >> >> >Ex:
>> >> >> >
>> >> >> >qsub -lnodes=2:ppn=16
>> >> >> >
>> >> >> >Works.
>> >> >> >
>> >> >> >-Nathan
>> >> >> >
>> >> >> >On Mon, Nov 25, 2013 at 01:11:29PM -0700, Nathan Hjelm wrote:
>> >> >> >> Hmm, this seems like either a bug in qsub (torque is full of
>> >>serious
>> >> >> >>bugs) or a bug
>> >> >> >> in alps. I got an allocation using that command and alps only
>> >>sees 1
>> >> >> >>node:
>> >> >> >> 
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: Trying ALPS
>> >> >> >>configuration file: "/etc/sysconfig/alps"
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: parser_ini
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: Trying ALPS
>> >> >> >>configuration file: "/etc/alps.conf"
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate:
>> >> >> >>parser_separated_columns
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: Located ALPS
>> >> >>scheduler
>> >> >> >>file: "/ufs/alps_shared/appinfo"
>> >> >> >> [ct-login1.localdomain:06010]
>> >> >> >>ras:alps:orte_ras_alps_get_appinfo_attempts: 10
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: begin
>>processing
>> >> >> >>appinfo file
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: file
>> >> >> >>/ufs/alps_shared/appinfo read
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: 47 entries in
>> >>file
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3492 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3492 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3541 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3541 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3560 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3560 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3561 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3561 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3566 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3566 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3573 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3573 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3588 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3588 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3598 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3598 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3599 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3599 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3622 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3622 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3635 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3635 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3640 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3640 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3641 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3641 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3642 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3642 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3647 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3647 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3651 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3651 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3653 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3653 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3659 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3659 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3662 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3662 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3665 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3665 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for
>> >>resId
>> >> >> >>3668 - myId 3668
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:read_appinfo(modern):
>> >> >>processing
>> >> >> >>NID 29 with 16 slots
>> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: success
>> >> >> >> [ct-login1.localdomain:06010] [[15798,0],0]
>>ras:base:node_insert
>> >> >> >>inserting 1 nodes
>> >> >> >> [ct-login1.localdomain:06010] [[15798,0],0]
>>ras:base:node_insert
>> >> >>node 29
>> >> >> >> 
>> >> >> >> ======================   ALLOCATED NODES
>>======================
>> >> >> >> 
>> >> >> >>  Data for node: 29	Num slots: 16	Max slots: 0
>> >> >> >> 
>> >> >> >> 
>>=================================================================
>> >> >> >> 
>> >> >> >> 
>> >> >> >> Torque also shows only one node with 16 PPN:
>> >> >> >> 
>> >> >> >> $ env | grep PBS
>> >> >> >> ...
>> >> >> >> PBS_NUM_PPN=16
>> >> >> >> 
>> >> >> >> 
>> >> >> >> $ cat /var/spool/torque/aux//915289.sdb
>> >> >> >> login1
>> >> >> >> 
>> >> >> >> Which is wrong! I will have to ask Cray what is going on here.
>>I
>> >> >> >>recommend you switch to
>> >> >> >> msub to get an allocation. Moab has fewer bugs. I can't even
>>get
>> >> >>aprun
>> >> >> >>to work:
>> >> >> >> 
>> >> >> >> $ aprun -n 2 -N 1 hostname
>> >> >> >> apsched: claim exceeds reservation's node-count
>> >> >> >> 
>> >> >> >> $ aprun -n 32 hostname
>> >> >> >> apsched: claim exceeds reservation's node-count
>> >> >> >> 
>> >> >> >> 
>> >> >> >> To get an interactive session 2 nodes with 16 ppn on each run:
>> >> >> >> 
>> >> >> >> msub -I -lnodes=2:ppn=16
>> >> >> >> 
>> >> >> >> Open MPI should then work correctly.
>> >> >> >> 
>> >> >> >> -Nathan Hjelm
>> >> >> >> HPC-5, LANL
>> >> >> >> 
>> >> >> >> On Sat, Nov 23, 2013 at 10:13:26PM +0000, Teranishi, Keita
>>wrote:
>> >> >> >> >    Hi,
>> >> >> >> >    I installed OpenMPI on our small XE6 using the configure
>> >>options
>> >> >> >>under
>> >> >> >> >    /contrib directory.  It appears it is working fine, but it
>> >> >>ignores
>> >> >> >>MCA
>> >> >> >> >    parameters (set in env var).  So I switched to mpirun (in
>> >> >>OpenMPI)
>> >> >> >>and it
>> >> >> >> >    can handle MCA parameters somehow.  However,  mpirun
>>fails to
>> >> >> >>allocate
>> >> >> >> >    process by cores.  For example, I allocated 32 cores (on 2
>> >> >>nodes)
>> >> >> >>by "qsub
>> >> >> >> >    -lmppwidth=32 -lmppnppn=16", mpirun recognizes it as 2
>>slots.
>> >> >> >>Is it
>> >> >> >> >    possible to mpirun to handle mluticore nodes of XE6
>>properly
>> >>or
>> >> >>is
>> >> >> >>there
>> >> >> >> >    any options to handle MCA parameters for aprun?
>> >> >> >> >    Regards,
>> >> >> >> >    
>> >> >> 
>> >> 
>> 
>>>>>>>>-------------------------------------------------------------------
>>>>>>>>--
>> >>>>>>--
>> >> >>>>--
>> >> >> >>----
>> >> >> >> >    Keita Teranishi
>> >> >> >> >    Principal Member of Technical Staff
>> >> >> >> >    Scalable Modeling and Analysis Systems
>> >> >> >> >    Sandia National Laboratories
>> >> >> >> >    Livermore, CA 94551
>> >> >> >> >    +1 (925) 294-3738
>> >> >> >> 
>> >> >> >> > _______________________________________________
>> >> >> >> > users mailing list
>> >> >> >> > users_at_[hidden]
>> >> >> >> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>> >> >> >> 
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >> _______________________________________________
>> >> >> >> users mailing list
>> >> >> >> users_at_[hidden]
>> >> >> >> http://www.open-mpi.org/mailman/listinfo.cgi/users
>> >> >> >
>> >> >> 
>> >> >> _______________________________________________
>> >> >> users mailing list
>> >> >> users_at_[hidden]
>> >> >> http://www.open-mpi.org/mailman/listinfo.cgi/users
>> >> 
>> >> _______________________________________________
>> >> users mailing list
>> >> users_at_[hidden]
>> >> http://www.open-mpi.org/mailman/listinfo.cgi/users
>> 
>> _______________________________________________
>> users mailing list
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>> http://www.open-mpi.org/mailman/listinfo.cgi/users