Difference: DocuMentacoes (13 vs. 14)

Revision 1401 Oct 2013 - Main.RodrigoZucoloto

Line: 1 to 1

1. WebHome. 2. DocuMentacoes. 3. HistoricoLabiocomp


1) Configurações do Ldap nos nós do Cluster

# apt-get install libnss-ldap libpam-ldap nscd

LDAP server URI: ldap://
Distinguished name of the search base: dc=republica,dc=star,dc=wars
LDAP version to use: 3
LDAP account for root: cn=admin,dc=republica,dc=star,dc=wars

LDAP root account password: <vocês sabem qual né? Não vou colocar aqui>
Allow LDAP admin account to behave like local root? No
Does the LDAP database require login?: No

No arquivo /etc/ldap/ldap.conf adicione as seguintes linhas:

BASE dc=republica,dc=star,dc=wars
URI ldap://

No arquivo /etc/nsswitch.conf modifique conforme as linhas abaixo:

passwd: compat ldap
group: compat ldap
shadow: compat ldap

# /etc/init.d/nscd restart

Teste a conf:

# id testeldap

Deve retornar o seguinte:

uid=2000(testeldap) gid=100(users) grupos=100(users)

Rafael Gomes
Consultor em TI

(71) 8318-0284
2) Configurações do SSH sem senha, proxy, NFS e torque:
Vitor Vilas Boas vitorvilas@gmail.com
to r2d2_ufba
Galera, já está ok para meu usuário o SSH sem senha no cluster02 a partir do darthvader.

O que ainda falta fazer:

- Colocar o darthvader em todos os arquivos hosts.
- Cada usuário criar sua chave no ssh do darthvader e criar o arquivo authorized_keys.
- Modificar o fstab de todos os nós para que utilize o /home do darthvader e não do clustermaster como está setado.

Vou fazer isso hoje, até o final da tarde concluo.

Para os usuários fazerem a chave SSH, vou colocar aqui como fazer, e se alguém puder colocar na wiki (Gomex se puder...)

1 - Logar no darthvader com o próprio usuário;

2 - Gerar a chave com o comando --> ssh-keygen -t rsa

3 - Dar enter até terminar o processo, não colocando frase alguma, deixando a frase em branco.

4 - Entrar no diretório que estão localizadas as chaves ---> cd ~/.ssh

5 - Gerar o authorized_keys --> cat id_rsa.pub >> authorized_keys

6 - Fazer o teste logando no cluster02 --> ssh cluster02 (Caso precise, aceitar o certificado com yes) e refazer o teste.


add no /etc/profile das estações (internet)
export http_proxy=

add no /etc/fstab (monta home NFS)
darthvader.bio.intranet.ufba.br:/home /home nfs rw,hard,intr 0 0

Torque nas estações:
/var/spool/torque/server_name > uma única linha com o nome do servidor "darthvader"
/var/spool/torque/mom_priv/config > adicionar nome do servidor "darthvader"

Solução para qualquer máquina que possa ter sido desligada incorretamente:

rm -rf /var/run/network$ rm -rf /var/run/network/mountnfs


3) Arquivo de configuração do DHCP

/etc/dhcp/dhcpd.conf (Aqui estão as configurações que ligam os IPs com seus respectivos MACs)

/etc/init.d/isc-dhcp-server restart (Comando para reiniciar o serviço sem a necessidade de reiniciar o sistema todo)


4) Clustal-mpi




CLUSTALW-MPI: ClustalW? Analysis Using Grid and Parallel Computing

based on ClustalW? , the multiple sequence alignment program
(version 1.82, Feb 2001)


This README contains the help with INSTALLATION

ClustalW? is a popular tool for multiple sequence alignment. The
alignment is achieved via three steps: pairwise alignment,
guide-tree generation and progressive alignment. ClustalW? -MPI is an
MPI implementation of ClustalW? . Based on
version 1.82 of the original ClustalW? , both the pairwise
and progressive alignments are parallelized with MPI, a
popular message passing programming standard.

ClustalW? -MPI is freely available to the user community.

The software is available at

The original ClustalW? /ClustalX can be found at ftp://ftp-igbmc.u-strasbg.fr.

Please send bug reports, comments etc. to "kuobin@bii.a-star.edu.sg".

INSTALLATION (for Unix/Linux)

This is an extremely quick installation guide.

1. Make sure you have MPICH or LAM installed on your system.

2. Unpack the package in any working directory:

tar xvfp clustalw-mpi-0.1.tar.gz

3. Take a look at the Makefile and make the modifications that you might desire,
in particular:

CC = mpicc
CFLAGS = -c -g


CFLAGS = -c -O3

4. Build the whole thing simply by typing "make".

5. If you wanted to use serial codes to compute the neighbor-joining tree,
you would have to define the macro "SERIAL_NJTREE" when compiling trees.c:


This macro is defined in the default Makefile. That is, to use
MPI codes in neighbor-joining tree, you have to "undefine" the
macro "SERIAL_NJTREE" in your Makefile.

SAMPLE USAGE (for Unix/Linux)

1. To make a full multiple sequence alignment:
(using one master node and 4 computing nodes)

%mpirun -np 5 ./clustalw-mpi -infile=dele.input
%mpirun -np 5 ./clustalw-mpi -infile=CFTR.input

2. To make a guide tree only:

%mpirun -np 5 ./clustalw-mpi -infile=dele.input -newtree=dele.mytree
%mpirun -np 5 ./clustalw-mpi -infile=CFTR.input -newtree=CFTR.mytree

3. To make a multiple sequence alignment out of an existing

%mpirun -np 5 ./clustalw-mpi -infile=dele.input -usetree=dele.mytree
%mpirun -np 5 ./clustalw-mpi -infile=CFTR.input -usetree=CFTR.mytree

4. The environment variable, CLUSTALG_PARALLEL_PDIFF, could be used to
run the progressive alignment based on the parallelized pdiff().

By default the variable CLUSTALG_PARALLEL_PDIFF is not set, and
the progressive alignment will be parallelized accroding the structure
of the neighbor-joining tree. However, parallelized pdiff() will still
be used in the later stage when prfalign() tries to align more distant
sequences to the profiles. If you don't understand this,
simply leave the variable unset.

1. On Intel IA32 platforms, slightly different neighbor-joining trees
might be obtained with and without enabling the compiler's optimization flags.

This is due to the fact that Intel processors use 80-bit FPU registers
to cache "double" variables, which are supposed to be 64-bit long. With '-O1'
or above optimizer flag, the compiler would not always immediately save the
variables involved in a double operation back to memory. Instead, intermediate
results will be saved in registers, having 80-bit of precision. This would
cause problem for nj_tree() because it is sensitive to the precision of floating
point numbers.


(1) Other platforms, including Intel's IA64, don't seem to have this problem.


(2) Building "trees.c" with optios like the below: (potentially
with high performance overhead)

%gcc -c -O3 -ffloat-store trees.c // GNU gcc

%icc -c -O3 -mp trees.c // Intel C compiler


(3) Decalring relevant variables as "volatile" in nj_tree():

volatile double diq, djq, dij, d2r, dr, dio, djo, da;
volatile double *rdiq;

rdiq = (volatile double *)malloc(((last_seq-first_seq+1)+1)*
sizeof(volatile double));

4b) Manual de uso extraído de: http://www.cuhk.edu.hk/itsc/compenv/research-computing/organon/cwmpi.html#ii

OBS: o clustalw-mpi já está instalado em todo o cluster.

1. Introduction of ClustalW? -MPI

ClustalW? is a general-purpose multiple sequence alignment program for DNA or proteins.

The alignment is achieved via three steps:

  • pairwise alignment;
  • guide-tree generation; and
  • progressive alignment.
ClustalW? -MPI is an MPI and GRID-aware implementation of ClustalW? . Based on version 1.82 of the original ClustalW? , both the pairwise and progressive alignments are parallelized with MPI, a popular message passing programming standard.

2. Input Sequences

p All sequences input must be in 1 file, one after another. 7 formats are automatically recognised: NBRF/PIR, EMBL/SWISSPROT, Pearson (Fasta), Clustal ( .aln), GCG/MSF (Pileup), GCG9/RSF and GDE flat file. All non-alphabetic characters (spaces, digits, punctuation marks) are ignored except "-" which is used to indicate a GAP ("." in GCG/MSF).

p If the input file is in GenBank? (
.gb) or other formats which is not supported by the Clustal W and can't be converted by Clustal X, you can used EMBOSS-3.0($ seqret -osformat fasta) and convert the file to Fasta ( .fasta) format beforehand.

*3. Job Submission and Monitoring

Sample PBS Script for a 4-node job - "clustalw.pbs"
You can use the following script to build a full multiple sequence alignment job using 4 computing nodes (8 CPUs): To edit the script, you may run pico, e.g. % pico clustalw.pbs

#PBS -q q4n16g
#PBS -N cpu8
#PBS -lnodes=4:ppn=2
#PBS -m bea
#PBS -M s800000@organon.itsc.cuhk.edu.hk
export PATH=/usr/pbs/bin:$PATH;
cd clustalw-mpi-0.13
source /usr/local/etc/mpich.sh
time pbs_mpirun clustalw-mpi -infile=test.fasta >& test8.out

Job Submission
Then, you can run the job by submitting the script to PBS as follows:
% qsub clustalw.pbs

For other PBS commands, please refer to the section "Starter Guide for PBS"

Job Monitoring

List the current jobs on the cluster

List the currently running jobs on the cluster
%qstat –a

Lists nodes allocated to running jobs
%qstat –r

Show detailed information on a specific job
% qstat –n

Show detailed information for all queues
%qstat -f <jobid>

Advance PBS command:

Advanced users can type % man q_command to see the details of the following command.




Alter a job's attributes.


Delete a job.


Place a hold on a job to keep it from being scheduled for running.


Move a job to a different queue or server


Append a message to the output of an executing job.


Terminate an executing job and return it to a queue.


Remove a hold from a job.


Obtain a list of jobs that met certain criteria.


Send a signal to an executing job.


5) Instalar Mega no Debian squeeze

5.1) Adicionar #deb http://ubuntu.mirror.cambrium.nl/ubuntu/ natty main universe no sources.list

5.2) Instalar o wine1.2: aptitude install wine 1.2

5.3) Baixar wine1.2-gecko do mirror: mirror.pnl.gov/ubuntu/

5.4) Instalar o wine1.2-gecko usando Gdebi

5.5) Adicionar o repositório do mega "deb http://update.megasoftware.net/deb/ mega main" no sources.list

5.6) Instalar o mega: aptitude install mega



6) MPICH2 - Debian e RedHat?

Copiado de http://www.flaviotorres.com.br/fnt/artigos/mpich2.php

Por: Flavio Torres - ftorres[@]ymail.com
Publicado em: 03/08/2007

Instalando MPICH2 em Sistemas Linux.

MPICH é uma das implementações existentes para o padrão MPI (Message-Passing Interface) de bibliotecas de passagem de mensagem.

Além da biblioteca MPI, MPICH contém um ambiente de programaçao que inclui um conjunto de bibliotecas para análise de performance (profiling) de programas MPI e uma interface gráfica para todas as ferramentas.

Em outras palavras, com o MPI é possível você ter um único processo sendo executado em múltiplos servidores, um Cluster.

Este é um segundo artigo, para aqueles que não possuem um ubuntu dapper, ou brigaram muito com o python 2.3 smile

Arquivos necessários:

* gcc
* cpp
* libc6
* lib6c-dev
* g77
* g++
* Python 2.2 ou superior

Instalando os arquivos necessários:

apt-get install gcc cpp libc6 libc6-dev g77 g++

Python, em 99% das instalações já vem na versão 2.4 ou 2.5.

Obtendo o tarball do mpich2, site do projeto: http://www-unix.mcs.anl.gov/mpi/mpich/

wget http://www-unix.mcs.anl.gov/mpi/mpich/downloads/mpich2-1.0.5p4.tar.gz

Descompacte o arquivo dentro de seu home:

tar -xvzf mpich2-1.0.5p4.tar.gz ; cd mpich2-1.0.5p4

Compile e instale:

./configure -prefix=/home/you/mpich2-install |& tee configure.log
make |& tee make.log
make install |& tee install.log

Se não utilizar um prefix, o default será /usr/local/bin.

Adicione o local de instalação em seu $PATH;

Para csh e tcsh:

setenv PATH /home/you/mpich2-install/bin:$PATH

Para Bash e sh:

export PATH=/home/you/mpich2-install/bin:$PATH

Checando se está tudo em ordem:

which mpd
which mpiexec
which mpirun

O which deve te retornar o local de instalação dos executáveis.

Após instalar em todos os hosts, devemos configurar os nomes para a resolução, edite o seu /etc/hosts e configure todas as máquinas:

vi /etc/hosts host1 host2 host3

Agora, devemos configurar o ssh para conexão sem senha, entre todos os hosts.

Gerando a chave, lembre-se de fazer em todos os servidores:

ssh-keygen -t dsa -b 1024
* Não digite a senha quando for questionado, tecle <enter>

Agora devemos configurar o ssh para autenticar sem senha:

Passo1) Copiando a chave do host1 para o host2 e host3:

host1$ scp .ssh/id_dsa.pub usuario@host2:
host1$ scp .ssh/id_dsa.pub usuario@host3:

Passo2) Configurando a chave para autenticação no host2:

host2$ cat id_dsa.pub >> .ssh/authorized_keys
host2$ chown 600 .ssh/authorized_keys

Passo3) Configurando a chave para autenticação no host3:

host3$ cat id_dsa.pub >> .ssh/authorized_keys
host3$ chown 600 .ssh/authorized_keys

Agora, repita os 3 Passos para as 3 máquinas, no final de tudo, você deve realizar ssh sem senha da máquina:

host1 > host2 e host3
host2 > host1 e host3
host3 > host2 e host1

Configurando os arquivos do mpi que são:

* mpd.conf
* mpd.hosts

O arquivo mpd.conf contém a informação de autenticação do mpi entre as máquinas, por isto,a senha deve ser a MESMA em todos os hosts.

Se você está utilizando o root para realizar os testes, este arquivo deve estar dentro de /etc, caso esteja utilizando algum usuário comum, este arquivo deve estar dentro de $HOME.

Adicionando a senha do mpd.conf e copiando para as outras máquinas:

host1$ echo "MPD_SECRETWORD=mr45-j9z" > .mpd.conf
host1$ chmod 600 .mpd.conf
host1$ scp .mpd.conf host2:
host1$ scp .mpd.conf host3:

O arquivo mpd.hosts contém as máquinas que fazem parte do cluster para ESTE usuário;

Adicionando as máquinas do cluster no arquivo .mpd.hosts, e replicando para as outras máquinas:

host1$ echo "host1" > .mpd.hosts
host1$ echo "host2" >> .mpd.hosts
host1$ echo "host3" >> .mpd.hosts
host1$ scp .mpd.hosts host2:
host1$ scp .mpd.hosts host3:

Pronto, a parte chata já passou smile

Agora vamos iniciar o daemon do mpi, com o mpdboot:

host1$ mpdboot -n 3 -f .mpd.hosts
host1$ mpdtrace

Perfeito, estão todos respondendo!!

Agora é só brincar com um teste simples:

host1$ mpiexec -n 5 mpich2-1.0.5p4/examples/cpi
Process 0 of 5 is on host1
Process 2 of 5 is on host2
Process 1 of 5 is on host3
Process 4 of 5 is on host3
Process 3 of 5 is on host1
pi is approximately 3.1415926544231230, Error is 0.0000000008333298

wall clock time = 0.925560


7) mrbayes-multi
7) mrbayes-multi

Fonte: http://nebc.nerc.ac.uk/bioinformatics/docs/mrbayes-multi.html

Name mrbayes-multi

MrBayes is a program for the Bayesian estimation of phylogeny. mrbayes-multi provides a multi-processor version of MrBayes.

In order to run the parallel version of Mr Bayes (across multiple processors) you must have mpi and installed, and MrBayes? must be launched using the mpirun command (i.e. it cannot be executed in the standard interactive mode). Finally you will need to have mpd configured on your system.

To achieve the above, you can run commands similar to the following:

echo "MPD_SECRETWORD=secret"
chmod 600 ~/.mpd.conf
mpd &
mpirun -np 4 mrbayes-multi

In the first command above, you will want to change the text "secret" to a password only you know. In the final command, change the number 4 to the number of cores you wish to run mrbayes over.

Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes? uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.

Remote Documentation http://mrbayes.csit.fsu.edu/wiki/index.php/Main_Page
Local Documentation


MPI Alternatives
This package uses the Debian Alternatives system to allow you to choose
between the different MPI implementations.

You can check which version of MPI you use with
update-alternatives --list mpirun
update-alternatives --list mpi (for the development files)

Use 'update-alternatives --display' to list all installed implementations,
and 'update-alternatives --config' to configure which implementation to use.

update-alternatives --config mpirun para fazer o setup do mpirun (usar este).


-- RodrigoZucoloto - 02 Nov 2011 \ No newline at end of file

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