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2009-05-19

[專案] 陽明生物資訊計算叢集設定

上次遇到 firmware-bnx2 的問題，在 Debian Lenny 上無法正常重建網路開機環境，因此改用 Ubuntu 9.04 進行網路安裝，過程很順利。
硬碟 I/O 很慢的主因是有做硬體 RAID，而且持續在做 SYNC 的動作，因此只要把 RAID 卡關掉就可以比較快速地開進作業系統。
參考Lustre on Debian，在 Ubuntu 9.04 上編譯 Lustre 核心模組。

[失敗] 因為 Lustre 目前官方只支援到 2.6.22，因此無法 patch 產生 2.6.28 的核心模組。

~$ sudo apt-get update
~$ sudo apt-get install linux-patch-lustre lustre-source linux-source kernel-package
~$ cd /usr/src
/usr/src$ sudo tar jxvf linux-source-2.6.28.tar.bz2
/usr/src$ cd linux-source-2.6.28/
/usr/src/linux-source-2.6.28$ sudo cp /boot/config-2.6.28-11-generic .config
/usr/src/linux-source-2.6.28$ sudo make oldconfig
/usr/src/linux-source-2.6.28$ sudo su
/usr/src/linux-source-2.6.28# tar jxvf ../lustre.tar.bz2
/usr/src/linux-source-2.6.28# export CONCURRENCY_LEVEL=3
/usr/src/linux-source-2.6.28# make-kpkg clean
/usr/src/linux-source-2.6.28# make-kpkg --rootcmd fakeroot --added-patches=lustre --initrd --append-to-version "-lustre-1.6.5.1-4" --revision=20090519 kernel_image

安裝 JDK
```
~$ sudo apt-get install sun-java6-jdk
```

安裝 R 及 Bioconductor

~$ sudo apt-get install r-base
~$ sudo R
> source("http://www.bioconductor.org/biocLite.R")
> biocLite()
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
  dependency ‘Matrix’ is not available
2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
  installation of package 'IRanges' had non-zero exit status
3: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
  installation of package 'Biostrings' had non-zero exit status

第一個錯誤是找不到 r-cran-matrix 套件，這裡用暴力法安裝所有在 apt 套件庫裡的 R 相關套件(除了 rjava 外)
```
~$ sudo apt-get install `apt-cache search --names-only "^r-cran" | awk '{ print $1 }' | grep -v "r-cran-rjava" `
```

裝好之後，重裝一次 Bioconductor 就沒有錯誤了。

~$ sudo apt-get install r-base
~$ sudo R
> source("http://www.bioconductor.org/biocLite.R")
> biocLite()
> library()
Packages in library '/usr/local/lib/R/site-library':

affy                    Methods for Affymetrix Oligonucleotide Arrays
affydata                Affymetrix Data for Demonstration Purpose
affyio                  Tools for parsing Affymetrix data files
affyPLM                 Methods for fitting probe-level models
affyQCReport            QC Report Generation for affyBatch objects
annaffy                 Annotation tools for Affymetrix biological
                        metadata
annotate                Annotation for microarrays
AnnotationDbi           Annotation Database Interface
Biobase                 Biobase: Base functions for Bioconductor
Biostrings              String objects representing biological
                        sequences, and matching algorithms
DynDoc                  Dynamic document tools
gcrma                   Background Adjustment Using Sequence
                        Information
genefilter              genefilter: methods for filtering genes from
                        microarray experiments
geneplotter             Grapics related functions for Bioconductor
GO.db                   A set of annotation maps describing the entire
                        Gene Ontology
hgu95av2.db             Affymetrix Human Genome U95 Set annotation data
                        (chip hgu95av2)
IRanges                 Low-level containers for storing sets of
                        integer ranges
KEGG.db                 A set of annotation maps for KEGG
limma                   Linear Models for Microarray Data
marray                  Exploratory analysis for two-color spotted
                        microarray data
matchprobes             Basic infrastructure for using oligonucleotide
                        microarray reporter sequence information for
                        preprocessing and quality assessment
multtest                Resampling-based multiple hypothesis testing
preprocessCore          A collection of pre-processing functions
ROC                     utilities for ROC, with uarray focus
RSQLite                 SQLite interface for R
simpleaffy              Very simple high level analysis of Affymetrix
                        data
vsn                     Variance stabilization and calibration for
                        microarray data
xtable                  Export tables to LaTeX or HTML

Packages in library '/usr/lib/R/site-library':

abind                   Combine multi-dimensional arrays
acepack                 ace() and avas() for selecting regression
                        transformations
adapt                   adapt -- multidimensional numerical integration
bayesm                  Bayesian Inference for
                        Marketing/Micro-econometrics
bitops                  Functions for Bitwise operations
cairoDevice             Cairo-based cross-platform antialiased graphics
                        device driver.
car                     Companion to Applied Regression
caTools                 Tools: moving window statistics, GIF, Base64,
                        ROC AUC, etc.
chron                   Chronological objects which can handle dates
                        and times
coda                    Output analysis and diagnostics for MCMC
combinat                combinatorics utilities
date                    Functions for handling dates
DBI                     R Database Interface
Design                  Design Package
eco                     R Package for Ecological Inference in 2x2
                        Tables
effects                 Effect Displays for Linear, Generalized Linear,
                        Multinomial-Logit, and Proportional-Odds Logit
                        Models
fArma                   ARMA Time Series Modelling
fAsianOptions           EBM and Asian Option Valuation
fAssets                 Rmetrics - Assets Selection and Modelling
fBasics                 Rmetrics - Markets and Basic Statistics
fBonds                  Bonds and Interest Rate Models
fCalendar               Chronological and Calendarical Objects
fCopulae                Rmetrics - Dependence Structures with Copulas
fEcofin                 Economic and Financial Data Sets
fExoticOptions          Exotic Option Valuation
fExtremes               Rmetrics - Extreme Financial Market Data
fGarch                  Rmetrics - Autoregressive Conditional
                        Heteroskedastic Modelling
fImport                 Rmetrics - Economic and Financial Data Import
fMultivar               Multivariate Market Analysis
fNonlinear              Nonlinear and Chaotic Time Series Modelling
fOptions                Basics of Option Valuation
fPortfolio              Rmetrics - Portfolio Selection and Optimization
fRegression             Regression Based Decision and Prediction
fSeries                 Financial Time Series Objects
fTrading                Technical Trading Analysis
fUnitRoots              Trends and Unit Roots
fUtilities              Function Utilities
gdata                   Various R programming tools for data
                        manipulation
genetics                Population Genetics
getopt                  C-like getopt behavior.
gmaps                   Wrapper and auxilliary functions for maps
                        package to work with grid graphics system.
gmodels                 Various R programming tools for model fitting
gplots                  Various R programming tools for plotting data
gregmisc                Greg's Miscellaneous Functions
gtools                  Various R programming tools
haplo.stats             Statistical Analysis of Haplotypes with Traits
                        and Covariates when Linkage Phase is Ambiguous
hdf5                    HDF5
Hmisc                   Harrell Miscellaneous
its                     Irregular Time Series
jit                     Just-in-time compiler for the R language
latticeExtra            Extra Graphical Utilities Based on Lattice
lme4                    Linear mixed-effects models using S4 classes
lmtest                  Testing Linear Regression Models
lpSolve                 Interface to Lp_solve v. 5.5 to solve
                        linear/integer programs
mapdata                 Extra Map Databases
mapproj                 Map Projections
maps                    Draw Geographical Maps
MatchIt                 MatchIt: Nonparametric Preprocessing for
                        Parametric Casual Inference
Matrix                  Sparse and Dense Matrix Classes and Methods
MCMCpack                Markov chain Monte Carlo (MCMC) Package
misc3d                  Miscellaneous 3D Plots
mnormt                  The multivariate normal and t distributions
MNP                     R Package for Fitting the Multinomial Probit
                        Model
multcomp                Simultaneous Inference in General Parametric
                        Models
mvtnorm                 Multivariate Normal and t Distributions
nws                     R functions for NetWorkSpaces and Sleigh
polspline               Polynomial spline routines
pscl                    Political Science Computational Laboratory,
                        Stanford University
psy                     Various procedures used in psychometry
qtl                     Tools for analyzing QTL experiments
quadprog                Functions to solve Quadratic Programming
                        Problems.
qvalue                  Q-value estimation for false discovery rate
                        control
Rcmdr                   R Commander
RColorBrewer            ColorBrewer palettes
Rcpp                    Rcpp R/C++ interface package
relimp                  Relative Contribution of Effects in a
                        Regression Model
rggobi                  Interface between R and GGobi
rgl                     3D visualization device system (OpenGL)
Rglpk                   R/GNU Linear Programming Kit Interface
RGtk2                   R bindings for Gtk 2.8.0 and above
Rmetrics                Rmetrics - Financial Engineering and
                        Computational Finance
Rmpi                    Interface (Wrapper) to MPI (Message-Passing
                        Interface)
RMySQL                  R interface to the MySQL database
robustbase              Basic Robust Statistics
ROCR                    Visualizing the performance of scoring
                        classifiers.
RODBC                   ODBC Database Access
rpvm                    R interface to PVM (Parallel Virtual Machine)
RQuantLib               R interface to the QuantLib library
Rserve                  Binary R server
rsprng                  R interface to SPRNG (Scalable Parallel Random
                        Number Generators)
RUnit                   R Unit test framework
sandwich                Robust Covariance Matrix Estimators
sm                      Smoothing methods for nonparametric regression
                        and density estimation
sn                      The skew-normal and skew-t distributions
snow                    Simple Network of Workstations
strucchange             Testing, Monitoring and Dating Structural
                        Changes
timeDate                Rmetrics - Chronological and Calendarical
                        Objects
timeSeries              Rmetrics - Financial Time Series Objects
tkrplot                 TK Rplot
tseries                 Time series analysis and computational finance
urca                    Unit root and cointegration tests for time
                        series data
VGAM                    Vector Generalized Linear and Additive Models
XML                     Tools for parsing and generating XML within R
                        and S-Plus.
Zelig                   Everyone's Statistical Software
zoo                     Z's ordered observations

Packages in library '/usr/lib/R/library':

base                    The R Base Package
boot                    Bootstrap R (S-Plus) Functions (Canty)
class                   Functions for Classification
cluster                 Cluster Analysis Extended Rousseeuw et al.
codetools               Code Analysis Tools for R
datasets                The R Datasets Package
foreign                 Read Data Stored by Minitab, S, SAS, SPSS,
                        Stata, Systat, dBase, ...
graphics                The R Graphics Package
grDevices               The R Graphics Devices and Support for Colours
                        and Fonts
grid                    The Grid Graphics Package
KernSmooth              Functions for kernel smoothing for Wand & Jones
                        (1995)
lattice                 Lattice Graphics
MASS                    Main Package of Venables and Ripley's MASS
methods                 Formal Methods and Classes
mgcv                    GAMs with GCV smoothness estimation and GAMMs
                        by REML/PQL
nlme                    Linear and Nonlinear Mixed Effects Models
nnet                    Feed-forward Neural Networks and Multinomial
                        Log-Linear Models
rpart                   Recursive Partitioning
spatial                 Functions for Kriging and Point Pattern
                        Analysis
splines                 Regression Spline Functions and Classes
stats                   The R Stats Package
stats4                  Statistical Functions using S4 Classes
survival                Survival analysis, including penalised
                        likelihood.
tcltk                   Tcl/Tk Interface
tools                   Tools for Package Development
utils                   The R Utils Package

額外加裝 R ape 套件 - 參考步驟 (nlme, lattice 均有新版)

# apt-get install libc6-dev gfortran liblapack-dev
# wget http://cran.r-project.org/src/contrib/gee_4.13-13.tar.gz
# R CMD INSTALL gee_4.13-13.tar.gz
# wget http://cran.r-project.org/src/contrib/nlme_3.1-91.tar.gz
# R CMD INSTALL nlme_3.1-91.tar.gz
# wget http://cran.r-project.org/src/contrib/lattice_0.17-25.tar.gz
# R CMD INSTALL lattice_0.17-25.tar.gz
# wget http://cran.r-project.org/src/contrib/ape_2.3.tar.gz
# R CMD INSTALL ape_2.3.tar.gz

加裝 Intel C++ Compiler for Linux - 先註冊要序號，然後下載 IA-32 與 IA-64 的版本。這次裝的 Ubuntu 9.04 是用 i686 32 位元版本，因此這次先裝 IA-32 版本。
- [備忘] 安裝前建議先裝 libstdc++5 的套件，否則會有找不到 libstdc++.so.5 的訊息。
```
# apt-get install libstdc++5
```

測試讓 Lenny 產生內含 bnx2-06-4.0.5.fw 的 DRBL initrd.pxe 核心。

手動修改 initrd-pxe.2.6.26-2-amd64.img

# cd /tftpboot/nbi_img
/tftpboot/nbi_img# mv initrd-pxe.2.6.26-2-amd64.img initrd-pxe.2.6.26-2-amd64.img.gz
/tftpboot/nbi_img# gunzip initrd-pxe.2.6.26-2-amd64.img.gz
/tftpboot/nbi_img# mkdir temp
/tftpboot/nbi_img# cd temp
/tftpboot/nbi_img/temp# cpio -i < ../initrd-pxe.2.6.26-2-amd64.img
/tftpboot/nbi_img/temp# mkdir lib/firmware
/tftpboot/nbi_img/temp# cp /lib/firmware/* lib/firmware/
/tftpboot/nbi_img/temp# find . | cpio -H newc -o | gzip -9 > ../initrd-pxe.2.6.26-2-amd64.img

[參考] 修改 initrd 之後，發生錯誤

cpio 有很多種格式，用來開機的要用 cpio -H newc -o，必須用 newc 格式才可以正常開機

Virtualization

[備忘] 裝 Xen 要記得裝 bridge-utils

Mobile Computing

同步機制一直是行動裝置一個極為關鍵的需求，無論是否採用雲端運算，大家還是希望可以自己保有自己的私人資料在行動裝置上。最近 Synthesis AG 釋出開放原始碼的 libsynthesis 可以讓開發者在 Linux 平台上撰寫自己的 SyncML-DS (SyncML Data Sync) 應用程式。還在 Moblin 的 Git 上維護了一份原始碼。-- 相關新聞

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Last modified 15 years ago Last modified on May 20, 2009, 6:39:21 PM

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