My life with BigData: august 2016

tirsdag den 30. august 2016

Update iRODS from 4.1.x to a 4.2 with YUM (Repo)

There was a note on the google chat for iRODS fans about updating to 4.2 via YUM,Zypper or APT.

-----

renci-irods-unstable/7/x86_64/signature | 819 B 00:00

Retrieving key from https://unstable.irods.org/irods-unstable-signing-key.asc

Importing GPG key 0x9086C490:

Userid : "iRODS Consortium - Unstable <info@irods.org>"

Fingerprint: 5909 3cb7 0f18 8588 25ac 778f 5054 912c 9086 c490

From : https://unstable.irods.org/irods-unstable-signing-key.asc

Is this ok [y/N]: y

----Just say Y

Dependencies Resolved

================================================================================

Package Arch Version Repository Size

================================================================================

Installing:

irods-icommands x86_64 4.2.0-1 renci-irods-unstable 313 k

replacing irods-icat.x86_64 4.1.9-0

irods-server x86_64 4.2.0-1 renci-irods-unstable 1.7 M

replacing irods-icat.x86_64 4.1.9-0

Updating:

irods-database-plugin-postgres x86_64 4.2.0-1 renci-irods-unstable 895 k

irods-runtime x86_64 4.2.0-1 renci-irods-unstable 3.3 M

Installing for dependencies:

irods-externals-avro1.7.7-0 x86_64 1.0-1 renci-irods-unstable 1.5 M

irods-externals-boost1.60.0-0 x86_64 1.0-1 renci-irods-unstable 13 M

irods-externals-clang-runtime3.8-0 x86_64 1.0-1 renci-irods-unstable 347 k

irods-externals-jansson2.7-0 x86_64 1.0-1 renci-irods-unstable 159 k

irods-externals-libarchive3.1.2-0 x86_64 1.0-1 renci-irods-unstable 1.4 M

irods-externals-zeromq4-14.1.3-0 x86_64 1.0-1 renci-irods-unstable 549 k

Transaction Summary

================================================================================

Install 2 Packages (+6 Dependent packages)

Upgrade 2 Packages

Total download size: 23 M

Is this ok [y/d/N]: Y

-----------------------

The Note says:

This server hosts both APT and YUM repositories for the iRODS Consortium.

Installation

Add this server to your package manager's list of repositories to check for new software.

APT

Install the public key and add the repository:

wget -qO - https://unstable.irods.org/irods-unstable-signing-key.asc

| sudo apt-key add -
echo "deb [arch=amd64] https://unstable.irods.org/apt/ $(lsb_release -sc)

main" | sudo tee /etc/apt/sources.list.d/renci-irods-unstable.list
sudo apt-get update

YUM

Install the public key and add the repository:

sudo rpm --import https://unstable.irods.org/irods-unstable-signing-key.asc
wget -qO - https://unstable.irods.org/renci-irods-unstable.yum.repo

| sudo tee /etc/yum.repos.d/renci-irods-unstable.yum.repo

ZYPPER

Install the public key and add the repository:

sudo rpm --import https://unstable.irods.org/irods-unstable-signing-key.asc
wget -qO - https://unstable.irods.org/renci-irods-unstable.zypp.repo

| sudo tee /etc/zypp/repos.d/renci-irods-unstable.zypp.repo

Source : https://groups.google.com/forum/#!topic/irod-chat/5cg24SHQ79w

tirsdag den 23. august 2016

Doing a FreeIPA for the server

What is FreeIPA : https://www.freeipa.org/page/Main_Page

Turn off SeLinux : setenforce 0

in the file : nano /etc/sysconfig/selinux
SELINUX=permissive
#SELINUX=enforcing

Install with :
yum -y install ipa-server bind-dyndb-ldap ipa-server-dns
ipa-server-install --setup-dns

The log file for this installation can be found in /var/log/ipaserver-install.log
==============================================================================
This program will set up the IPA Server.

This includes:
* Configure a stand-alone CA (dogtag) for certificate management
* Configure the Network Time Daemon (ntpd)
* Create and configure an instance of Directory Server
* Create and configure a Kerberos Key Distribution Center (KDC)
* Configure Apache (httpd)
* Configure DNS (bind)

To accept the default shown in brackets, press the Enter key.

Enter the fully qualified domain name of the computer
on which you're setting up server software. Using the form
<hostname>.<domainname>
Example: master.example.com.

Server host name [labipa.example.com]:

Please see ; https://www.youtube.com/watch?v=8wc4MO3LXQI

Please note : If you get the error : "Your system is running out of entropy"
Please install haveged [ http://www.issihosts.com/haveged/ ] or just wait some time.... ;-)

Look at : http://serverfault.com/questions/406038/server-suddenly-running-out-of-entropy

mandag den 22. august 2016

I need to change my passwd on a .pl site?

We got Spammed agian.... with a "we need your password on a .pl site"

Come on guys!! It's Amateur Night Agian.....

-------------------------------------------The Mail---------------

Kære bruger ,

Vi har bemærket nogle usædvanlige aktiviteter i din postkasse , og det er midlertidigt låst. Vær venlig at validere din e-mail- adresse ved hjælp af linket nedenfor for at gøre os i stand genaktivere din e-mail- konto . Hvis dette ikke gøres , vil føre til permanent blokering , og du vil være i stand du sende og modtage post .

Tak for dit samarbejde

Hilsen,

Help Desk

ENGLISH

Dear user,

We have noticed some unusual activities in your mail box and it has been temporarily locked. Please kindly validate your email address using the link below to enable us reactivate your email account. Failure to do this will lead to permanent blocking and you will be unable you send and receive mail.

Thank you for your cooperation

Regards,

Help Desk

The site the (removed) link pointed at :

torsdag den 4. august 2016

Getting NodeJS 6.x.x to run on CentOS7

On one of the servers we got an error running the new NodeJS script.

How was it installed ?? yum install nodejs -y

[root@server1 ~]# node -v
v0.10.42
-- How to fix???
[root@server1 ~]# rpm -qa |grep node
---cut----------
nodejs-inherits-2.0.0-4.el7.noarch
nodejs-fstream-0.1.24-1.el7.noarch
nodejs-slide-1.1.5-1.el7.noarch
nodejs-tar-0.1.18-1.el7.noarch
nodejs-abbrev-1.0.4-6.el7.noarch
nodejs-mime-1.2.11-1.el7.noarch
nodejs-cryptiles-0.2.2-1.el7.noarch
nodejs-cmd-shim-1.1.0-3.el7.noarch
nodejs-delayed-stream-0.0.5-5.el7.noarch
nodejs-read-1.0.5-1.el7.noarch
nodejs-npmconf-0.1.3-1.el7.noarch
nodejs-ctype-0.5.3-3.el7.noarch
nodejs-json-stringify-safe-5.0.0-1.el7.noarch
nodejs-normalize-package-data-0.2.1-1.el7.noarch
nodejs-minimatch-0.2.12-2.el7.noarch
nodejs-read-installed-0.2.4-1.el7.noarch
nodejs-asn1-0.1.11-3.el7.noarch

---cut----------

rpm -e nodejs-inherits-2.0.0-4.el7.noarch

error: Failed dependencies:

npm(inherits) >= 2.0.0 is needed by (installed) nodejs-fstream-0.1.24-1.el7.noarch

npm(inherits) < 2.1 is needed by (installed) nodejs-fstream-0.1.24-1.el7.noarch

npm(inherits) >= 2.0.0 is needed by (installed) nodejs-block-stream-0.0.7-1.el7.noarch

npm(inherits) < 2.1 is needed by (installed) nodejs-block-stream-0.0.7-1.el7.noarch

npm(inherits) >= 2 is needed by (installed) nodejs-tar-0.1.18-1.el7.noarch

---cut----------

Uninstall all NodeJS and fix the error....

[root@server1 ~]# rpm -qa |grep node > awk 'BEGIN{ORS=","}1' > node.txt

Please node : Node.txt is a full list of NodeJS files...

Just add "rpm -e " at the beginning of the file and it will uninstall all NodeJS files.

[root@server1 ~]# echo 'rpm -e' | cat - node.txt | tee node.txt

-and run your uninstall bash script with sh ./node.txt

Then do:

curl --silent --location https://rpm.nodesource.com/setup_6.x | bash - ; yum -y install nodejs ; yum install gcc-c++ make

[root@server1 ~]# node -v

v6.3.1

tirsdag den 2. august 2016

Get Julia to run on CentOS 7

What is Julia???
"Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments. "

Info about the language : https://julialang.org/

Install Info from : https://copr.fedorainfracloud.org/coprs/nalimilan/julia/
wget https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
rpm -ivh epel-release-latest-7.noarch.rpm

cd /etc/yum.repos.d

wget https://copr.fedorainfracloud.org/coprs/nalimilan/julia/repo/epel-7/nalimilan-julia-epel-7.repo

The Repo file :

[nalimilan-julia]
name=Copr repo for julia owned by nalimilan
baseurl=https://copr-be.cloud.fedoraproject.org/results/nalimilan/julia/epel-7-$basearch/
skip_if_unavailable=True
gpgcheck=1
gpgkey=https://copr-be.cloud.fedoraproject.org/results/nalimilan/julia/pubkey.gpg
enabled=1
enabled_metadata=1

Or you can : (Source : http://julialang.org/downloads/platform.html )

sudo dnf copr enable nalimilan/julia
or
sudo dnf copr enable nalimilan/julia-nightlies

yum -y install julia

yum -y install mc nano vim libXp openmotif openmotif22 python.x86_64 numpy* ncurses-devel gcc gcc-c++ autoconf automake; yum -y groupinstall "Development Tools"

julia

That was easy ;-) Next comes the cluster setup ....

Building iRODS 4.1.9 from source on CentOS7

##  Install from a .gz file ( ftp://ftp.renci.org/pub/irods/releases/4.1.9/  )
yum -y install gcc-c++ make python-devel rpm-build help2man unixODBC fuse-devel curl-devel
yum -y install --enablerepo=centosplus openssl-devel pam-devel bzip2-devel zlib-devel pam-devel openssl-devel libxml2-devel perl-JSON
yum -y install rsync unixODBC-devel epel-release net-tools wget nano mc mlocate ImageMagick python-devel rpm-build help2man
yum -y install bzip2-devel libxml2-devel unixODBC pam-devel openssl-devel wget nano mc tomcat tomcat-webappsl tomcat-admin-webapps
yum -y install tomcat-docs-webapp tomcat-javadoc net-tools postgresql postgresql-serverl postgresql-contrib postgresql-libs
yum -y install postgresql-odbc fuse-libs.x86_64 perl-JSON* python-requests.noarch python-jsonschema python-psutil lsof
yum -y install authd postgresql postgresql-libs postgresql-plperl postgresql-plpython postgresql-server python-jsonschema python-psutil python-requests postgresql-odbc
###NodeJS 6.x install

curl --silent --location https://rpm.nodesource.com/setup_6.x | bash - ; yum -y install nodejs ; yum install gcc-c++ make

yum -y groupinstall "Development Tools"
yum -y install python-pip git gettext-devel openssl-devel perl-CPAN perl-devel zlib-devel
##############
git clone https://github.com/DICE-UNC/irods-cloud-browser.git
git clone https://github.com/sunadtudk/irods_2_figshare.git
##############
pip install git+git://github.com/iPlantCollaborativeOpenSource/pycommands.git
pip install --upgrade pip
pip install --upgrade git+git://github.com/irods/python-irodsclient.git
pip install pigshare
#pip install --upgrade pigshare
###############################

#############Build iRODS server###############
wget ftp://ftp.renci.org/pub/irods/releases/4.1.9/irods-4.1.9.tar.gz
tar -zxvf irods-4.1.9.tar.gz
cd irods-4.1.9/packaging/
./build.sh  icat postgres
./build.sh -s resource
./build.sh -s icommands
###############Install###############
cd ~/irods-4.1.9/build/
rpm -ivh irods-icat-4.1.9-64bit-centos7.rpm
rpm -ivh irods-database-plugin-postgres-1.9-centos7.rpm
rpm -ivh irods-dev-4.1.9-64bit-centos7.rpm
rpm -ivh irods-runtime-4.1.9-64bit-centos7.rpm
#rpm -ivh irods-database-plugin-postgres93-1.9-centos7.rpm
#rpm -ivh irods-resource-4.1.9-64bit-centos7.rpm
postgresql-setup initdb
systemctl start postgresql
systemctl enable postgresql
######config iRODS server#######
sudo /var/lib/irods/packaging/setup_irods.sh

# rpm -ivh irods-icommands-4.1.9-64bit-centos7.rpm

Cracking my Technicolor TG788vn open

A look inside my Technicolor TG788vn.

With a RaspBerry PI you can do funny things ;-)