Difference: DocuMentacoes (4 vs. 5)

Revision 504 Feb 2012 - Main.RodrigoZucoloto

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  Proxy:
add no /etc/profile das estações (internet)
export http_proxy=http://192.168.1.1:3128

NFS
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

Changed:
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3) Arquivo de configuração do DHCP

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

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

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4) Clustal-mpi

4a) README 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
http://www.bii.a-star.edu.sg/software/clustalw-mpi/

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

or

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:

CFLAGS = -c -g -DSERIAL_NJTREE

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
tree:

%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.

KNOWN PROBLEM
------------
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.

Solutions:

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

or

(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

or

(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));
...
...
free((void
)rdiq);

4b) Manual de usdo 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

#!/bin/sh
#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
%qstat

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.

Command

Function

qalter

Alter a job's attributes.

qdel

Delete a job.

qhold

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

qmove

Move a job to a different queue or server

qmsg

Append a message to the output of an executing job.

qrerun

Terminate an executing job and return it to a queue.

qrls

Remove a hold from a job.

qselect

Obtain a list of jobs that met certain criteria.

qsig

Send a signal to an executing job.

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