I have implemented some algorithms in C++ which are greatly affected by
shuffling time among nodes which is done by some broadcast calls. Up to
now, I have been testing them by running something like
mpirun -mca btl ^openib -mca plm_rsh_no_tree_spawn 1 ./my_test
which I think make MPI_Bcast to work serially. Now, I want to improve the
communication time so I have configured the appropriate SSH access from
every node to every other node and I have enabled the binary tree
implementation of Open MPI collective calls by running
mpirun -mca btl ^openib ./my_test
My problem is that throughout various experiments with files of different
sizes, I realized that there is no improvement in terms of transmission
time even though theoretically I would expect a gain of approximately
(log(k))/(k-1) where k is the size of the group that the communication
takes place within.
I compile the code with
mpic++ my_test.cc -o my_test
and all of the experiments are done on Amazon EC2 r3.large or m3.large
machines. I have also set different values of rate limits to avoid bursty
behavior of Amazon's EC2 transmission rate. The Open MPI I have installed
is described on the txt I have attached after running ompi_info.
What can be wrong here?
Package: Open MPI buildd@lgw01-57 Distribution
Open MPI: 1.10.2
Open MPI repo revision: v1.10.1-145-g799148f
Open MPI release date: Jan 21, 2016
Open RTE: 1.10.2
Open RTE repo revision: v1.10.1-145-g799148f
Open RTE release date: Jan 21, 2016
OPAL: 1.10.2
OPAL repo revision: v1.10.1-145-g799148f
OPAL release date: Jan 21, 2016
MPI API: 3.0.0
Ident string: 1.10.2
Prefix: /usr
Configured architecture: x86_64-pc-linux-gnu
Configure host: lgw01-57
Configured by: buildd
Configured on: Thu Feb 25 16:33:01 UTC 2016
Configure host: lgw01-57
Built by: buildd
Built on: Thu Feb 25 16:40:59 UTC 2016
Built host: lgw01-57
C bindings: yes
C++ bindings: yes
Fort mpif.h: yes (all)
Fort use mpi: yes (full: ignore TKR)
Fort use mpi size: deprecated-ompi-info-value
Fort use mpi_f08: yes
Fort mpi_f08 compliance: The mpi_f08 module is available, but due to
limitations in the gfortran compiler, does not
support the following: array subsections, direct
passthru (where possible) to underlying Open MPI's
C functionality
Fort mpi_f08 subarrays: no
Java bindings: no
Wrapper compiler rpath: runpath
C compiler: gcc
C compiler absolute: /usr/bin/gcc
C compiler family name: GNU
C compiler version: 5.3.1
C++ compiler: g++
C++ compiler absolute: /usr/bin/g++
Fort compiler: gfortran
Fort compiler abs: /usr/bin/gfortran
Fort ignore TKR: yes (!GCC$ ATTRIBUTES NO_ARG_CHECK ::)
Fort 08 assumed shape: yes
Fort optional args: yes
Fort INTERFACE: yes
Fort ISO_FORTRAN_ENV: yes
Fort STORAGE_SIZE: yes
Fort BIND(C) (all): yes
Fort ISO_C_BINDING: yes
Fort SUBROUTINE BIND(C): yes
Fort TYPE,BIND(C): yes
Fort T,BIND(C,name="a"): yes
Fort PRIVATE: yes
Fort PROTECTED: yes
Fort ABSTRACT: yes
Fort ASYNCHRONOUS: yes
Fort PROCEDURE: yes
Fort USE...ONLY: yes
Fort C_FUNLOC: yes
Fort f08 using wrappers: yes
Fort MPI_SIZEOF: yes
C profiling: yes
C++ profiling: yes
Fort mpif.h profiling: yes
Fort use mpi profiling: yes
Fort use mpi_f08 prof: yes
C++ exceptions: no
Thread support: posix (MPI_THREAD_MULTIPLE: no, OPAL support: yes,
OMPI progress: no, ORTE progress: yes, Event lib:
yes)
Sparse Groups: no
Internal debug support: no
MPI interface warnings: yes
MPI parameter check: runtime
Memory profiling support: no
Memory debugging support: no
dl support: yes
Heterogeneous support: yes
mpirun default --prefix: no
MPI I/O support: yes
MPI_WTIME support: gettimeofday
Symbol vis. support: yes
Host topology support: yes
MPI extensions:
FT Checkpoint support: no (checkpoint thread: no)
C/R Enabled Debugging: no
VampirTrace support: no
MPI_MAX_PROCESSOR_NAME: 256
MPI_MAX_ERROR_STRING: 256
MPI_MAX_OBJECT_NAME: 64
MPI_MAX_INFO_KEY: 36
MPI_MAX_INFO_VAL: 256
MPI_MAX_PORT_NAME: 1024
MPI_MAX_DATAREP_STRING: 128
MCA backtrace: execinfo (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA compress: gzip (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA compress: bzip (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA crs: none (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA db: print (MCA v2.0.0, API v1.0.0, Component v1.10.2)
MCA db: hash (MCA v2.0.0, API v1.0.0, Component v1.10.2)
MCA dl: dlopen (MCA v2.0.0, API v1.0.0, Component v1.10.2)
MCA event: libevent2021 (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA hwloc: external (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA if: posix_ipv4 (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA if: linux_ipv6 (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA installdirs: env (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA installdirs: config (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA memory: linux (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA pstat: linux (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA sec: basic (MCA v2.0.0, API v1.0.0, Component v1.10.2)
MCA shmem: posix (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA shmem: sysv (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA shmem: mmap (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA timer: linux (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA dfs: test (MCA v2.0.0, API v1.0.0, Component v1.10.2)
MCA dfs: app (MCA v2.0.0, API v1.0.0, Component v1.10.2)
MCA dfs: orted (MCA v2.0.0, API v1.0.0, Component v1.10.2)
MCA errmgr: default_hnp (MCA v2.0.0, API v3.0.0, Component
v1.10.2)
MCA errmgr: default_orted (MCA v2.0.0, API v3.0.0, Component
v1.10.2)
MCA errmgr: default_tool (MCA v2.0.0, API v3.0.0, Component
v1.10.2)
MCA errmgr: default_app (MCA v2.0.0, API v3.0.0, Component
v1.10.2)
MCA ess: slurm (MCA v2.0.0, API v3.0.0, Component v1.10.2)
MCA ess: env (MCA v2.0.0, API v3.0.0, Component v1.10.2)
MCA ess: singleton (MCA v2.0.0, API v3.0.0, Component
v1.10.2)
MCA ess: tool (MCA v2.0.0, API v3.0.0, Component v1.10.2)
MCA ess: hnp (MCA v2.0.0, API v3.0.0, Component v1.10.2)
MCA filem: raw (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA grpcomm: bad (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA iof: tool (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA iof: mr_orted (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA iof: orted (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA iof: mr_hnp (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA iof: hnp (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA odls: default (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA oob: tcp (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA plm: slurm (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA plm: rsh (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA plm: isolated (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA ras: slurm (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA ras: simulator (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA ras: loadleveler (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA ras: gridengine (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA rmaps: rank_file (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA rmaps: seq (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA rmaps: mindist (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA rmaps: staged (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA rmaps: ppr (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA rmaps: resilient (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA rmaps: round_robin (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA rml: oob (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA routed: binomial (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA routed: radix (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA routed: debruijn (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA routed: direct (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA state: staged_orted (MCA v2.0.0, API v1.0.0, Component
v1.10.2)
MCA state: hnp (MCA v2.0.0, API v1.0.0, Component v1.10.2)
MCA state: staged_hnp (MCA v2.0.0, API v1.0.0, Component
v1.10.2)
MCA state: orted (MCA v2.0.0, API v1.0.0, Component v1.10.2)
MCA state: app (MCA v2.0.0, API v1.0.0, Component v1.10.2)
MCA state: dvm (MCA v2.0.0, API v1.0.0, Component v1.10.2)
MCA state: tool (MCA v2.0.0, API v1.0.0, Component v1.10.2)
MCA state: novm (MCA v2.0.0, API v1.0.0, Component v1.10.2)
MCA allocator: basic (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA allocator: bucket (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA bcol: basesmuma (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA bcol: ptpcoll (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA bml: r2 (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA btl: self (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA btl: tcp (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA btl: openib (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA btl: sm (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA btl: vader (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA coll: self (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA coll: sm (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA coll: libnbc (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA coll: tuned (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA coll: hierarch (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA coll: basic (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA coll: inter (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA coll: ml (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA dpm: orte (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA fbtl: posix (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA fcoll: dynamic (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA fcoll: two_phase (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA fcoll: ylib (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA fcoll: static (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA fcoll: individual (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA fs: ufs (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA io: romio (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA io: ompio (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA mpool: grdma (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA mpool: sm (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA osc: sm (MCA v2.0.0, API v3.0.0, Component v1.10.2)
MCA osc: pt2pt (MCA v2.0.0, API v3.0.0, Component v1.10.2)
MCA pml: v (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA pml: cm (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA pml: bfo (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA pml: ob1 (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA pubsub: orte (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA rcache: vma (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA rte: orte (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA sbgp: basesmsocket (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA sbgp: basesmuma (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA sbgp: p2p (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA sharedfp: lockedfile (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA sharedfp: individual (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
MCA sharedfp: sm (MCA v2.0.0, API v2.0.0, Component v1.10.2)
MCA topo: basic (MCA v2.0.0, API v2.1.0, Component v1.10.2)
MCA vprotocol: pessimist (MCA v2.0.0, API v2.0.0, Component
v1.10.2)
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