Installation and Running NPB-3.3 on Ubuntu 9.04

2011.03.03 11:24

Download from #1

Installation
># tar -xzvf NPB3.3.1.tar.gz
># cd NPB3.3.1
># cp config/make.def.template config/make.def
># cp config/suite.def.template config/suite.def

* Make some changes in the make.def file. 
># vim config/make.def
MPIF77 = mpif77
FMPI_LIB  = -L/usr/lib -lmpi
FMPI_INC = -I/usr/lib/mpich-mpd/include/mpif.h
#FFLAGS = -O
FFLAGS  = -O -fPIC

FLINKFLAGS = -O
#FLINKFLAGS = -O -fPIC
#CMPI_LIB  = -L/usr/local/lib -lmpi
CMPI_LIB  = -L/usr/lib/mpich-mpd/lib -lmpi

#CMPI_INC = -I/usr/local/include
CMPI_INC = -I/usr/lib/mpich-mpd/include

RAND   = randi8


Compile
># apt-get install fort77 libmpich-mpd1.0-dev
># make suite
or
make individual benchmark like this
># make bt NPROCS=1 CLASS=A

Running benchmark on single host (just for a test)
># ls bin
># lamboot
># time ./bt.A.1

Let's try running the MPI program on multiple machines using LAM [4, 5]
Copy binary to all machines.

># scp -r bin green1
.. 
># scp -r bin green4

># su ykoh
># ssh-keygen -t rsa -P '' -f ~/.ssh/id_rsa
># ssh-copy-id -i ~/.ssh/id_rsa.pub ykoh@green1
..
># ssh-copy-id -i ~/.ssh/id_rsa.pub ykoh@green4

green10 ># vim lamhosts
green10
green11
green12
green13

green10 ># recon -v lamhosts
Since ssh or rsh is not configured so it fails to connect to other machines.


green10>#  export LAMRSH="ssh -x"
We need to configure ssh (without password prompt). If it is properly configured right, then the message 
should show up like the following:


># lamboot -v lamhosts


># mpirun -v -np 4 ./bt.B.4


Side notes...
epio uses lots of IO as far as I know. I am not sure. 

References
3. 네트워크 벤치마크 툴, http://blog.seabow.pe.kr/65
4. One-step Tutorial: Getting started with LAM, http://www.lam-mpi.org/tutorials/one-step/lam.php
5. How-to setup LAM and run mpi executables, http://www.cis.gvsu.edu/den/doc/mpi/lam-HOWTO.shtml
6. 
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Installing and Running SPECmpi 2007 on Ubuntu 9.04

2011.03.02 21:07
It seems that installing and running SPECmpi2007 is very similiar to SPECcpu benchmark. 
OS: Ubuntu 9.04

Installation
># ./install.sh




Usages
># cd /usr/mpi2007
># . ./shrc

Make a config file
># cd config
># cp example-amd-linux-amd-intel-hpmpi.cfg linux-amd-intel-hpmpi.cfg

Modify
># apt-get install mpich-bin  libmpich1.0gf  lam4-dev
># vim linux-amd-intel-hpmpi.cfg
...
 #BOPTS= -O3 -ipo  -no-prec_div
BOPTS= -O3

#FC = mpif90 -mpif90 ifort
#CC = mpicc -mpicc icc
#CXX= mpiCC -mpicxx icpc
FC = mpif77
CC = mpicc
CXX= mpiCC


default=default=default=default:
COPTIMIZE = ${BOPTS}
FOPTIMIZE = ${BOPTS}
CXXOPTIMIZE= ${BOPTS}

use_submit_for_speed=1

121.pop2:
CPORTABILITY= -DSPEC_MPI_CASE_FLAG

127.wrf2:
CPORTABILITY =  -DSPEC_MPI_LINUX  -DSPEC_MPI_CASE_FLAG  


#include: example_appfile.cfg


Building
># runspec --config=linux-amd-intel-hpmpi.cfg --action=build --tune=base -size=mref 104.milc
># runspec --config=1--action=build --tune=base -size=mref 137.lu

Testing
># runspec --config=linux-amd-intel-hpmpi.cfg  --ranks=16 --noreportable --tune=base --size=mtest --iterations=1 137.lu

Running with reference workload
* This will take about 50 mins
># runspec --config=linux-amd-intel-hpmpi.cfg --ranks=16 --noreportable --tune=base --size=mref --iterations=1 137.lu

Benchmarks List



References
3. 
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iozone, bonnie++, postmark, filebench - IO benchmark

2011.01.09 20:33

iozone - Filesystem benchmark
The benchmark generates and measures a variety of file operations. The benchmark tests file I/O performance for the following operations:

Read, write, re-read, re-write, read backwards, read strided, fread, fwrite, random read/write, pread/pwrite variants

We are going to use iozone to simulate IO operations against a VM. Then what should we do??

># sudo apt-get install iozone3

This takes about 15 mins 
># iozone -a


-a : full automatic mode. Test all file operations for record sizes of 4k to 16M for file sizes of 64k to 512M.

To run single read test
># iozone -i0 -c -e -S256 -n16 -s2g
-i: read test
-c: close
-e: flush
-S: CPU cache is set to 256kB
-s2g: file size 2GB

># iozone -a -c -f -s2G -S256

Throughput test

># iozone -t -T -u1024
-u: 1024 processes
file size per process is 512kB

bonnie++ - program to test hard drive performance. 
This program is used to test how fast the hard drive or file system is. 
Compare to iozone, it has less feature, but it is suitable to get a rough idea of the performance. 
Typically, just run the command like this
>#  bonnie++
* this takes about 33 mins or so. 
or more specifically

>#bonnie++ -s 2048 -m `hostname` -n 100
-s: size of files (megabytes), 2GB of data
-n: the number of files for the file creation
100 * 1024 files


postmark - this file benchmark simulates email server 
># vim postmark.run
set location /tmp
set transactions 10000000000
run

># time postmark < postmark.run
PostMark v1.51 : 8/14/01
pm>pm>pm>Creating files...Done
Performing transactions.out of files!
For this workload, either increase the number of files or
decrease the number of transactions.
Deleting files...Done

real 4m40.208s
user 0m25.146s
sys 3m35.597s

filebench - this file benchmark simulates different types of applications. 
* I could not be able to compile this source code on debian. Is there a deb for this, anyone?
> #

dbench - filesystem benchmark
># dbench -D /tmp 1

tbench - net? system benchmark. This tool is a part of dbench benchmark suite
># tbench_srv &
># tbench -t 60 1 infi11

lmbench - microbenchmark too that tests Linux kernel API
To test all
># lmbench-run
To measure TCP bandwidth between two hosts
># cd ./bin/x86_64-linux-gnu
># bw_tcp -s
># bw_tcp servername

kernbench - compilng kernel source code
* requires actual kernel source code
># wget http://www.kernel.org/pub/linux/kernel/people/ck/apps/kernbench/kernbench-0.50.tar.gz
># tar -xzvf kernbench-0.50
>#

nepim - network pipemeter
># apt-get install liboop-dev
># cd src
># make
># cp nepim /usr/bin

ccrypt - not a benchmark tool, but it's a popular tool for encrypting/decrypting text file
># ccrypt text.txt
># ccrypt -d text.txt

StratusLab benchmark - To measure performance of cloud implementation
># git clone https://user@code.stratuslab.eu/git/benchmarks.git

Fhourstones  - integer benchmark that solves positions in the game of connect-4
># wget http://homepages.cwi.nl/~tromp/c4/Fhourstones.tar.gz
># tar -xzvf Fhourstones.tar.gz
># make
># time ./SearchGame < inputs
real    3m25.745s
user    3m25.701s
sys    0m0.036s

BYTE Unix benchmark - determine if a system is BSD or SysV.
* Dhrystone benchmark
># wget http://www.anime.net/~goemon/bench.tar.gz
># tar -xzvf bench.tar.gz
># make
To run all tests
># ./Run

To run individual tests
># ./Run -h
># time ./Run dhry2
real    2m0.185s
user    0m59.984s
sys    0m0.024s

References
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Frank kenshin579 linux/benchmarks Bonnie, bonnie++, byte, ccrypt, dbench, disk benchmark, fhourstone, filebench, iozone, nepim, postmark, stratuslab, tbench

netperf - Network, Benchmark tool

2011.01.09 20:01
Netperf is the de-facto standard for network bandwidth testing between two hosts on a network. It blasts TCP data from a client host to a server host. This is different than transferring a file over the network, as you avoid any disk bottlenecks, and are using a standardized client and server for testing. 

Since we need to check the network performance of a virtual machine (VM)

Installation
># sudo apt-get install netperf

Running the server inside of a VM
>#  vm console green1
># netserver

Running the client (from remote client)
># netperf -H green1 -l 60 -f K
-l: run for 60 seconds. 




Reference
1. Netperf homepage, http://www.netperf.org/netperf/
4. HTTP 서버 성능 체크, http://chokori.tistory.com/tag/HTTP
5. 
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SPECcpu2006 Installation & Basic Usages on Ubuntu 10.04 VM

2011.01.09 16:38
I need to install SPECcpu2006 on VM machine. 

Preparing installation
Need to extend VM (currently 2GB) image size. 
># cd /home/xen/domains/green1

Add extra space (4GB) to existing disk image using dd. 
># dd if=/dev/zero bs=1M count=4096 >> root.img
># xm create /etc/xen/green1.cfg
># xm console green1
># df -h
># resize2fs /dev/xvda2
># df -h

Installation
># mount -o loop SPEC_CPU2006v1.1.iso /mnt/iso; cd /mnt/iso
># ./install.sh



># cd /usr/cpu2006

Setting the path
># . ./shrc

Create the default config file
># cd config
># cp Example-linux64-amd64-gcc43.cfg vm.cfg
># vim vm.cfg
This is necessary, but we just changed it.  When you run any spec benchmark,
the extension would look something like this, gobmk_base.proc 
...
ext=proc
...

># apt-get install build-essential

Build one benchmark and test with dataset 
"--tune=base" indicates that we want to use only  the simple tuning. 
># runspec --config=vm.cfg --action=build --tune=base bzip2

Run the benchmark with the test dataset
># runspec --config=vm.cfg --size=test --tune=base --noreportable --iterations=1 bzip2
At the output, "Success: 1x164.gzip" is the msg that we want to see. 

Running with real data set (takes about 8 mins or so)
># runspec --config=vm.cfg --size=ref --noreportable --iterations=1 bzip2

Check the result under result/

For the detail benchmark description, please refer to #5. 

Run a full run (reportable)
* You must specify int, fp, or all. 
># runspec --config=vm.cfg int
...
Running Benchmarks
Running (#1) 400.perlbench ref base vm default
/usr/cpu2006/bin/specinvoke -d /usr/cpu2006/benchspec/CPU2006/400.perlbench/run/run_base_ref_vm.0000 -e speccmds.err -o speccmds.stdout -f speccmds.cmd -C
...
Instead of executing runspec command, we can always use specinvoke command to actually invoke specific benchmark without going through each build, setup, and invoking setups. 

Since we need to monitor (cpu, memory, I/O, etc) each benchmark's resource usage, we just need to run individual command like this
Build all benchmarks and do runsetup as well. 
># runspec --config=vm.cfg --size=ref --action build all
># runspec --config=vm.cfg --size=ref --action runsetup all

># runspec --config=vm.cfg --size=ref --noreportable --delay=5 --nobuild bzip2
or 
># /usr/cpu2006/bin/specinvoke -d /usr/cpu2006/benchspec/CPU2006/401.bzip2/run/run_base_ref_vm.0001 -e speccmds.err -o speccmds.stdout -f speccmds.cmd -C

Reference
4. SPEC cpu 2006 alpha binary 생성, http://holypsycho.egloos.com/3084145
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Frank kenshin579 linux/benchmarks benchmark, cpu, extend vm disk, speccpu, SPECcpu2006

Well-known Benchmarks

2011.01.05 21:58

I just want to share some of benchmarks that I know and have used often. 


>> Macrobenchmarks

CPU
- SPECcpu2006


GPU

Memory

Network
- Web Servers
   > SPECweb2009
   * this measures power as well. 

- Network File System (NFS)
- Mail Servers


Virtualization
- SPECvirt_sc2010
  * 

Power
- SPECpower_ssj2008

Applications
- Hadoop 
  > ??



>> Microbenchmarks
- stress

References
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Frank kenshin579 linux/benchmarks benchmarks, macrobenchmarks, microbenchmark, spec, workload

Virtualization Benchmarks Notes

2009.09.15 22:38

지금까지 Virtualization에 대한 Benchmarking이 있었는지 그리고 부족한 부분들은 어떤 것들이 있는지 정리해보자.

1. Virtualization of Linux servers
(KQEMU, KVM, Linux-VServer, OpenVZ, VirtualBox, Xen)
Goal:

  • 여러 가상화 기술의 overhead를 평가함 (CPU, disk, network, sysbench, …)
    Scalability도 평가 (Sysbench-OLTP사용)
  • 여러 가상화 기술 에 대한

Possible TODO LIST

  • Scalability를 체크할 때 다른 workload를 mix해서 해보기

2. Survey of Virtualization Workloads

3. Benchmarking Amazon EC2 for high-performance scientific computing
Amazon EC2의 성능이 안좋다 due to network issues.
NPB, mpptest
여기서는 컴퓨터간의 어떤 네트워크 device를 사용하느냐에 따라서 성능 차이가 많이 날 것 같다. 그면 램 실에서 테스트할 때도 문제가 있을 것 같다. Network Bonding을 사용해야 하는지. 어떻게 네트워크를 구성해야 하는지가 큰 issue가 될 것 같다.

4. Modeling Virtual Machine Performance: Challenges and Approaches

  • VM perf. Depends heavily on visible & invisible resources
  • Offline/online monitoring techniques 을 통해서 multiple VMs sharing resources에 대한 characterize한다.
  • Offline/online monitoring techniques을 통해서 성능을 예측한다
  • Issues: core/cache interference,

Possible TODO LIST

  • Consider other resources (core pipeline resources, memory bandwidth, etc)
  • Other virtualization benchmarks & VMMs를 사용해서 modeling이 맞는 지 확인하다.

5. Characterization & Analysis of a Server Consolidation Benchmark
vConsolidate Benchmark으로 문제점을 확인하고 구체적으로 어떤 부분에서 성능 문제가 있는지 확인한다. (문제점: core/cache interference, etc)

Possible TODO LIST

  • Additional virtualization overhead due to consolidation (context switching, interrupt, page fault, service VM instantiations, etc.)
  • Scaling 부족: testing Multiple CSUs.

6. Quantifying the Performance Isolation Properties of Virtualization Systems.
가상화 기술(VMware, OpenVZ, Xen)에 각각 Stress test를 적용하여 가상 머신간에 어떤 영향을 주는지에 대한 조사이다.

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Frank kenshin579 linux/benchmarks

Free Benchmark Tools

2009.09.09 10:48

CPU

  • SPEC CPU2006 (not free)
  • Kernel build (CPU intensive+filesystem)
  • Bzip2 (CPU intensive : -9 options)

Virtualization

Mail Server

  • SPECmail2009 (not free)
  • LoadSim (Requires Microsoft Exchange Server), well-known load generation utility that simulates users of the Exchange mail server

Java Client/Server

  • SPECjAPPServer2004 (not free)
  • SPECjbb2005 (not free): entirely standalone benchmark - no external DB server requires

HPC (High Parallel Computing)

Database Server

File Server

Web server

  • ApacheBench, measuring the performance of HTTP web servers, how many requests per second the server is capable of serving
    ># sudo apt-get install apache2-utils
  • *JMeter, analyzing and measuring the performance of a variety of services with a focus on web applications (DB, FTP, LDAP, Mail, etc)
    http://jakarta.apache.org/jmeter
    ,
  • Webbench, simple HTTP benchmarking tool.
    http://home.tiscali.cz/~cz210552/webbench.html
  • SPECweb2009 (not free)

Network

System Performance


Java benchmarking

  • Dacapo, benchmark tool for Java benchmarking by the programming language, memory management, 
    and computer architecture
    http://www.dacapobench.org/


References

  1. www.clarkson.edu/class/cs644/xen
  2. Linux Benchmark Suite, http://lbs.sourceforge.net/
  3. Benchmark tools, http://lxc.sourceforge.net/bench/benchs.php

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Frank kenshin579 linux/benchmarks benchmark

NAS Parallel Benchmarks (NPB)

2009.09.04 17:08

Class

Description

S

Testing

W, A

Desktop Workstations

B, C

Multiprocessor Systems

 

How to Compile NPB
NPB-OMP

># cd NPB3.3/NPB3.3-OMP
># cd config
># cp make.def.template make.def
># cp suite.def.template

Edit make.def & suite.def
># cd ..
># make suite

NPB-MPI

># cd NPB3.3/NPB3.3-MPI
># cd config
># cp make.def.template make.def
># cp suite.def.template

Edit make.def(make sure to change /usr/include/mpi) & suite.def
># cd ..
># make suite


Running Benchmark
NPB-OMP

># vi run-omp.sh
#!/bin/bash
# NCSA Abe

#PBS -l walltime=6:00:00,nodes=1:ppn=8
#PBS –V

cd $HOME/NPB3.3/NPB3.3-OMP

echo "Class B:"
cnt=2
while [ $cnt -ge 1 ] ; do
echo "$cnt processors"
export OMP_NUM_THREADS=$cnt
mkdir -p output/${cnt}_proc
./bin/bt.B > output/${cnt}_proc/bt.B
./bin/cg.B > output/${cnt}_proc/cg.B
./bin/ep.B > output/${cnt}_proc/ep.B
./bin/ft.B > output/${cnt}_proc/ft.B
./bin/is.B > output/${cnt}_proc/is.B
./bin/lu.B > output/${cnt}_proc/lu.B
./bin/mg.B > output/${cnt}_proc/mg.B
./bin/sp.B > output/${cnt}_proc/sp.B
./bin/ua.B > output/${cnt}_proc/ua.B
cnt=$[ $cnt - 1 ]
done

NPB-MPI

># vi run-mpi.sh
>#

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Frank kenshin579 linux/benchmarks MPI, nas parallel benchmark, NPB, openmpi