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14. MPIクラスターを作ろう！ - qn24bを動かしてみる - 電子計算記
スパコンと言えばTOP500！
Home | TOP500 Supercomputer Sites
TOP500と言えばLinpack！
ということで、LinpackのMPIによる並列実装のHPLを動かしてTOP500のようなベンチマークスコアをはじき出しましょう。
ただ、本気でやるとキリがないほど奥深いので、時短で簡単に実行するやりかたを紹介します。
Linpackの根幹である行列演算、このライブラリとしてHPLはBLASを使うのでまずはその準備から。
本気で性能を出したい場合は、利用している環境に合わせてビルドするわけですが、ここは時短でUbuntu標準パッケージを利用します。
BLASの最近のOSS実装だと、OpenBLASかATLASが定番。Ubuntu16.04だと両方パッケージあるのでどっち使ってもよいですが、ここではOpenBLASの例ですすめます。
まずは、ビルド環境としてcompute-1を使うとして、OpenBLASをインストールします。
root@compute-1:~# apt install libopenblas-dev -y
これだけで/usr/lib配下にすぐに使えるOpenBLASのライブラリがインストールされます。
では下準備が整ったので、HPLをビルドしていきます。まずはファイルのダウンロード。オフィシャルからとってきます。
mpiuser@compute-1:~$ wget http://www.netlib.org/benchmark/hpl/hpl-2.2.tar.gz mpiuser@compute-1:~$ tar zxf hpl-2.2.tar.gz -C /nfs/ mpiuser@compute-1:~$ cd /nfs/hpl-2.2/
環境ごとのビルド用のMakefileのサンプルがsetupディレクトリの中にありますので、ここでは一番変更の少ないMake.Linux_PII_CBLAS_gmをベースとして編集します。
mpiuser@compute-1:/nfs/hpl-2.2$ cp ./setup/Make.Linux_PII_CBLAS_gm ./ mpiuser@compute-1:/nfs/hpl-2.2$ vi Make.Linux_PII_CBLAS_gm
編集箇所としては、
70行目のTOPdirをHPLを展開したディレクトリパスを指定
TOPdir = /nfs/hpl-2.2
95行目のLAdirをBLASをインストールしたライブラリのディレクトリパスを指定
LAdir = /usr/lib
97行目のLAlibをBLASをインストールしたライブラリのファイル自身を指定
LAlib = $(LAdir)/libopenblas.a
これだけです。（前回までの流れで、OpenMPI、gfortranをaptインストールしている前提）
わかりにくいかもなので全部のっけておきます。
/nfs/hpl-2.2/Make.Linux_PII_CBLAS_gm
#
# -- High Performance Computing Linpack Benchmark (HPL)
# HPL - 2.2 - February 24, 2016
# Antoine P. Petitet
# University of Tennessee, Knoxville
# Innovative Computing Laboratory
# (C) Copyright 2000-2008 All Rights Reserved
#
# -- Copyright notice and Licensing terms:
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions, and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
#
# 3. All advertising materials mentioning features or use of this
# software must display the following acknowledgement:
# This product includes software developed at the University of
# Tennessee, Knoxville, Innovative Computing Laboratory.
#
# 4. The name of the University, the name of the Laboratory, or the
# names of its contributors may not be used to endorse or promote
# products derived from this software without specific written
# permission.
#
# -- Disclaimer:
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE UNIVERSITY
# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# ######################################################################
#
# ----------------------------------------------------------------------
# - shell --------------------------------------------------------------
# ----------------------------------------------------------------------
#
SHELL = /bin/sh
#
CD = cd
CP = cp
LN_S = ln -s
MKDIR = mkdir
RM = /bin/rm -f
TOUCH = touch
#
# ----------------------------------------------------------------------
# - Platform identifier ------------------------------------------------
# ----------------------------------------------------------------------
#
ARCH = Linux_PII_CBLAS_gm
#
# ----------------------------------------------------------------------
# - HPL Directory Structure / HPL library ------------------------------
# ----------------------------------------------------------------------
#
TOPdir = /nfs/hpl-2.2
INCdir = $(TOPdir)/include
BINdir = $(TOPdir)/bin/$(ARCH)
LIBdir = $(TOPdir)/lib/$(ARCH)
#
HPLlib = $(LIBdir)/libhpl.a
#
# ----------------------------------------------------------------------
# - Message Passing library (MPI) --------------------------------------
# ----------------------------------------------------------------------
# MPinc tells the C compiler where to find the Message Passing library
# header files, MPlib is defined to be the name of the library to be
# used. The variable MPdir is only used for defining MPinc and MPlib.
#
MPdir =
MPinc =
MPlib =
#
# ----------------------------------------------------------------------
# - Linear Algebra library (BLAS or VSIPL) -----------------------------
# ----------------------------------------------------------------------
# LAinc tells the C compiler where to find the Linear Algebra library
# header files, LAlib is defined to be the name of the library to be
# used. The variable LAdir is only used for defining LAinc and LAlib.
#
LAdir = /usr/lib
LAinc =
LAlib = $(LAdir)/libopenblas.a
#
# ----------------------------------------------------------------------
# - F77 / C interface --------------------------------------------------
# ----------------------------------------------------------------------
# You can skip this section if and only if you are not planning to use
# a BLAS library featuring a Fortran 77 interface. Otherwise, it is
# necessary to fill out the F2CDEFS variable with the appropriate
# options. **One and only one** option should be chosen in **each** of
# the 3 following categories:
#
# 1) name space (How C calls a Fortran 77 routine)
#
# -DAdd_ : all lower case and a suffixed underscore (Suns,
# Intel, ...), [default]
# -DNoChange : all lower case (IBM RS6000),
# -DUpCase : all upper case (Cray),
# -DAdd__ : the FORTRAN compiler in use is f2c.
#
# 2) C and Fortran 77 integer mapping
#
# -DF77_INTEGER=int : Fortran 77 INTEGER is a C int, [default]
# -DF77_INTEGER=long : Fortran 77 INTEGER is a C long,
# -DF77_INTEGER=short : Fortran 77 INTEGER is a C short.
#
# 3) Fortran 77 string handling
#
# -DStringSunStyle : The string address is passed at the string loca-
# tion on the stack, and the string length is then
# passed as an F77_INTEGER after all explicit
# stack arguments, [default]
# -DStringStructPtr : The address of a structure is passed by a
# Fortran 77 string, and the structure is of the
# form: struct {char *cp; F77_INTEGER len;},
# -DStringStructVal : A structure is passed by value for each Fortran
# 77 string, and the structure is of the form:
# struct {char *cp; F77_INTEGER len;},
# -DStringCrayStyle : Special option for Cray machines, which uses
# Cray fcd (fortran character descriptor) for
# interoperation.
#
F2CDEFS =
#
# ----------------------------------------------------------------------
# - HPL includes / libraries / specifics -------------------------------
# ----------------------------------------------------------------------
#
HPL_INCLUDES = -I$(INCdir) -I$(INCdir)/$(ARCH) $(LAinc) $(MPinc)
HPL_LIBS = $(HPLlib) $(LAlib) $(MPlib)
#
# - Compile time options -----------------------------------------------
#
# -DHPL_COPY_L force the copy of the panel L before bcast;
# -DHPL_CALL_CBLAS call the cblas interface;
# -DHPL_CALL_VSIPL call the vsip library;
# -DHPL_DETAILED_TIMING enable detailed timers;
#
# By default HPL will:
# *) not copy L before broadcast,
# *) call the BLAS Fortran 77 interface,
# *) not display detailed timing information.
#
HPL_OPTS = -DHPL_CALL_CBLAS
#
# ----------------------------------------------------------------------
#
HPL_DEFS = $(F2CDEFS) $(HPL_OPTS) $(HPL_INCLUDES)
#
# ----------------------------------------------------------------------
# - Compilers / linkers - Optimization flags ---------------------------
# ----------------------------------------------------------------------
#
CC = mpicc
CCNOOPT = $(HPL_DEFS)
CCFLAGS = $(HPL_DEFS) -fomit-frame-pointer -O3 -funroll-loops -W -Wall
#
# On some platforms, it is necessary to use the Fortran linker to find
# the Fortran internals used in the BLAS library.
#
LINKER = mpif77
LINKFLAGS = $(CCFLAGS)
#
ARCHIVER = ar
ARFLAGS = r
RANLIB = echo
#
# ----------------------------------------------------------------------Makefileができあがればあとはmakeするだけです。
mpiuser@compute-1:/nfs/hpl-2.2$ make arch=Linux_PII_CBLAS_gm mpiuser@compute-1:/nfs/hpl-2.2$ cd bin/Linux_PII_CBLAS_gm/ mpiuser@compute-1:/nfs/hpl-2.2/bin/Linux_PII_CBLAS_gm$ ls -alh total 22M drwxrwxr-x 2 mpiuser mpiuser 4.0K Jan 10 00:35 . drwxrwxr-x 3 mpiuser mpiuser 4.0K Jan 10 00:35 .. -rw-r--r-- 1 mpiuser mpiuser 1.2K Jan 10 00:35 HPL.dat -rwxrwxr-x 1 mpiuser mpiuser 22M Jan 10 00:35 xhpl
無事ビルドに成功するとbin/(arch)/の中にxhplというバイナリが出来上がっています。
では最後にREADMEにあるとおりテストしてみましょう。
mpiuser@compute-1:/nfs/hpl-2.2/bin/Linux_PII_CBLAS_gm$ mpirun -np 4 ./xhpl
〜省略〜
================================================================================
T/V N NB P Q Time Gflops
--------------------------------------------------------------------------------
WR00R2R2 35 4 4 1 0.00 4.775e-02
HPL_pdgesv() start time Wed Jan 10 00:38:25 2018
HPL_pdgesv() end time Wed Jan 10 00:38:25 2018
--------------------------------------------------------------------------------
||Ax-b||_oo/(eps*(||A||_oo*||x||_oo+||b||_oo)*N)= 0.0247304 ...... PASSED
================================================================================
T/V N NB P Q Time Gflops
--------------------------------------------------------------------------------
WR00R2R4 35 4 4 1 0.00 4.915e-02
HPL_pdgesv() start time Wed Jan 10 00:38:25 2018
HPL_pdgesv() end time Wed Jan 10 00:38:25 2018
--------------------------------------------------------------------------------
||Ax-b||_oo/(eps*(||A||_oo*||x||_oo+||b||_oo)*N)= 0.0199397 ...... PASSED
================================================================================
Finished 864 tests with the following results:
864 tests completed and passed residual checks,
0 tests completed and failed residual checks,
0 tests skipped because of illegal input values.
--------------------------------------------------------------------------------
End of Tests.
================================================================================テストでは4プロセス以上が必要でノード内でまずは動かしてみましょう。
failedやskippedがなければ成功です。
Light.S1でも1秒程度で実行完了できると思います。
しかし、複数ノードでLight.S1を4台で動かすと同じテストを終えるまでに30分以上かかります。
ということで、次回はHPLの実行パラメータのチューニングにせまっていきたいと思います。
