1. download instant client
http://www.oracle.com/technetwork/topics/linuxx86-64soft-092277.html
select ones matched verion of oracle server.  (rpm)

2.
> mkdir /usr/lib/oracle
> cd /usr/lib/oracle
> rpm -Uvh oracle-instantclient-basic-10.2.0.4-1.x86_64.rpm
> rpm -Uvh oracle-instantclient-sqlplus-10.2.0.4-1.x86_64.rpm
> vi /usr/lib/oracle/10.2.0.4/client64/tnsnames.ora
HDA =
    (DESCRIPTION =
         (ADDRESS = (PROTOCOL = TCP)(HOST =IP_ADRESS)(PORT = 1521))
         (CONNECT_DATA =
              (SERVER = DEDICATED)
              (SERVICE_NAME = hda)
         )
    )
> vi /etc/profile.d/oracle.sh
# for Oracle Instant Client
if [ -d /usr/lib/oracle ]
then
     LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/oracle/10.2.0.4/client64/lib/;export   LD_LIBRARY_PATH
     TNS_ADMIN=/usr/lib/oracle/10.2.0.4/client64; export TNS_ADMIN;
     NLS_LANG=AMERICAN_AMERICA.KO16KSC5601;export NLS_LANG;
#   PATH=$PATH:/usr/lib/oracle;export PATH;
#   SQLPATH=/usr/lib/oracle; export SQLPATH;
fi
> source /etc/profile/oracle.sh
> sqlplus64 DBNAME@HDA

== sqlldr ==
> scp orahda@111.111.111.11:/oracle/orahda/product/10.2.0/bin/sqlldr /usr/bin/
> mkdir /usr/lib/oracle/10.2.0.4/client64/rdbms/mesg/
> scp orahda@111.111.111.11:/oracle/orahda/product/10.2.0/rdbms/mesg/ulus.msb /usr/lib/oracle/10.2.0.4/client64/rdbms/mesg/
> vi /etc/profile.d/oracle.sh
ORACLE_HOME=/usr/lib/oracle/10.2.0.4/client64; export ORACLE_HOME
> source /etc/profile.d/oracle.sh

 

Posted by 옥탑방람보
,
Parallel enviroment named by "smp" in SGE


# add "smp" parallel enviroment and correct like below

> qconf -ap smp

pe_name smp
slots 9999
user_lists NONE
xuser_lists NONE
start_proc_args /bin/true
stop_proc_args /bin/true
allocation_rule $pe_slots
control_slaves TRUE
job_is_first_task FALSE
urgency_slots min

# add a queue group, "secondary" and add the "smp" in "pe_list" parameter

> qconf -aq secondary

 

Posted by 옥탑방람보
,
create queue
> qconf -aq [queue_name]

delete queue
> qconf -dq [queue_name]

manage queue
> qconf -mq [queue_name]

list queue
> qconf -sql

create parallel environment
> qconf -ap [pe-name]

delete parallel environment
> qconf -dp [pe-name]

manage parallel environment
> qconf -mp [pe-name]

list parallel environment
> qconf -spl

create host_list
> qconf -ah [host_list_name]

* create host_list
The default hostgroup is called @allhosts. To create a new hostgroup use the qconf -Ahgrp file_name command where the configuration file file_name has the structure described in man hostgroup.

Example:
> cat merlin0809.hgrp
group_name @merlin0809
hostlist merlin08 merlin09

>qconf -Ahgrp merlin0809.hgrp
added "@merlin0809" to host group list

> qconf -shgrpl
@allhosts
@merlin0809

> qconf -shgrp @merlin0809
group_name @merlin0809
hostlist merlin08 merlin09

The host groups are stored in the directory $SGE_ROOT/$SGE_CELL/spool/qmaster/hostgroups, e.g.:
> cat /opt/gridengine/default/spool/qmaster/hostgroups/@merlin0809
# Version: GE 6.0u7
#
# DO NOT MODIFY THIS FILE MANUALLY!
#
group_name @merlin0809
hostlist merlin08 merlin09


delete host_list
> qconf -dh [host_list_name]

manage host_list
> qconf -mhgrp [host_list_name]

list host_list
> qconf -shgrpl

list hosts in host_list
> qconf -shgrp [host_list_name]

 

Posted by 옥탑방람보
,
1. Disk Full
This mostly happens when the disk is full.
Check disk storage or available disk of the account.

> df -h

2. Permission
Check "Write" permission of the account.

 

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Posted by 옥탑방람보
,

SRC-POINT -> DEST-POINT

1.
Setting up SSH key authentication (mostly skip this step)
First, you need to make sure the DEST-POINT has the ability to user key autherntication enabled.

> vi /etc/ssh/sshd_config
RSAAuthentication yes
PubkeyAuthentication yes
AuthorizedKeysFile .ssh/authorized_keys
> /etc/init.d/sshd restart
 
2. Generation SSH public key in SRC-POINT
> ssh-keygen -t rsa
(*note: do not enter any passphrases on this, just hit enter when prompted)
 
3. Planting the public key to DEST-POINT
> vi ~/.ssh/authorized_keys
Add the public key of SRC-POINT
(*note:  user1> cat ~/.ssh/id_rsa.pub | ssh user1@DEST-POINT 'cat >> ~/.ssh/authorized_keys')
> chmod 755 ~/.ssh  (DEST-POINT)
> chmod 644 ~/.ssh/authorized_keys  (DEST-POINT)
(*note: check permissions all above directories of the "~/.ssh". If Group or Other permissions in them have "Write", sync between the two points are broken.)
 
 
* in Cluster (rocks)
In the default Rocks cluster configuration, /home is an automount directory. All nodes in the cluster system can mount the Home directory when an user accesses to each node.
Therefore, in cluster system, directories generated public key of SRC-POINT and DEST-POINT are same. "id_rsa.rsa" and "authorized_keys" files are located in same directory of an user home.
> ssh-keygen -t rsa
> cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys

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,

[ssh] slow SSH login

TA/Common 2012. 12. 24. 17:11

1. Make sure DNS is properly configured on your system. Slow SSH logins are often caused by a name resolution timeout. Does your primary name server have entries for the systems from which you are connecting? Are the reverse lookup entries in place?  (from rocks-discuss)

2. If the server can not use DNS, enroll your local IP into /etc/hosts.
> vi /etc/hosts
IP_ADRESS   YOURHOSTNAME

 

Posted by 옥탑방람보
,
SGE would not read your .bashrc or .bash_profile when starting jobs.
You need to include -V or -v option.
ex) qsub -V -cwd -j y script.sh

-V
Specifies that all environment variables active within the qsub utility be exported to the context of the job.
 
-v variable[=value],...
Defines or redefines the environment variables to be exported to the execution context of the job. If the -v option is present Grid Engine will add the environment variables defined as arguments to the switch and, optionally, values of specified variables, to the execution context of the job.

You can also set as default option.
> vi /opt/gridengine/default/common/sge_request
(ADD) -V

 

Posted by 옥탑방람보
,
Use liftOver provided from UCSC web site.
The liftOver is designed to work between differenct assemblies of the same organism. This program does not have multiple alignment function but allows to lift genomic coordinates in the same organism. So, this requires a map.chain file which has the old genome as the target and the new genome as the query. For human genome you can get it at UCSC download page.

Usage: liftOver oldFile map.chain newFile unMapped
oldFile : BED format (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) (optional)
  ==> It works with a input file having first 3 columns only. All positions MUST be zero base.
map.chain: (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/)
newFile : output file name
unMapped: output file name for un-lifted positions
ex) ./liftOver hg18.positions hg18ToHg19.over.chain ./output/hg19.positions ./output/unmapped.positions

Download liftOver: (http://hgdownload.cse.ucsc.edu/admin/exe/)

 

Posted by 옥탑방람보
,

[linux] my bashrc

TA/Common 2012. 12. 24. 16:24

#User specific

#alias
alias vi='vim'
alias rm='rm -i'
alias ll='ls -lF --color'
alias ls='ls --color'
alias python='time python'
alias pyt='time python'
alias qstat='qstat -u "*"'
alias du='du -c'

#kimps path
export KIMPS=/home/user/kimps/
#kimps bin
export KIMPSUTILS=$KIMPS/bin/
if [ -d ${KIMPSUTILS} ]
then
   for i in ${KIMPSUTILS}/*; do
      if [ -d "$i" ]; then
         PATH=$PATH:$i/
      fi
   done
   unset i
fi
export PATH=$KIMPSUTILS:$PATH

#user bin
export USERBIN=/home/user/bin/
if [ -d ${USERBIN} ]
then
   for i in ${USERBIN}/*; do
      if [ -d "$i" ]; then
         PATH=$PATH:$i/
      fi
   done
   unset i
fi
export PATH=$USERBIN:$PATH

#exports
export PYTHONPATH=/home/user/install/Python-2.6.7/Lib/site-packages:$PYTHONPATH
export CATALINA_HOME=/home/user/install/apache-tomcat-6.0.20/
export DRMAA_LIBRARY_PATH=/opt/gridengine/lib/lx26-amd64/libdrmaa.so
export JAVA_HOME=/home/user/install/java/
export HADOOP_HOME=/home/user/install/hadoop/
export HADOOP_CLASSPATH=/home/user/install/hadoop/lib/

Posted by 옥탑방람보
,

$> nmap -v 서버아이피

 

예)

$> nmap -v ftp.kaist.ac.kr

    Starting Nmap 4.11 ( http://www.insecure.org/nmap/ ) at 2012-09-24 15:57 KST

    DNS resolution of 1 IPs took 6.50s.

    Initiating SYN Stealth Scan against ftp.kaist.ac.kr (143.248.234.110) [1680 ports] at 15:57

    Discovered open port 21/tcp on 143.248.234.110

    The SYN Stealth Scan took 23.95s to scan 1680 total ports.

    Host ftp.kaist.ac.kr (143.248.234.110) appears to be up ... good.

    Interesting ports on ftp.kaist.ac.kr (143.248.234.110):

    Not shown: 1679 filtered ports

    PORT   STATE SERVICE

    21/tcp open  ftp

     

    Nmap finished: 1 IP address (1 host up) scanned in 30.569 seconds

                   Raw packets sent: 3365 (148.040KB) | Rcvd: 6 (276B)

 

 

<아이피 확인>

$> nslookup ftp.kaist.ac.kr

 

예)

$> nslookup ftp.kaist.ac.kr

    Server:     203.241.132.34

    Address:    203.241.132.34#53

     

    Non-authoritative answer:

    Name:   ftp.kaist.ac.kr

    Address: 143.248.234.110

 

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Posted by 옥탑방람보
,