fredag den 25. december 2015
Systemd conflicts with docker
The Problem:
Transaction check error:
file /usr/lib64/libsystemd-daemon.so.0 from install of systemd-libs-219-19.el7.x86_64 conflicts with file from package systemd-container-libs-208.20-6.el7.centos.x86_64
file /usr/lib64/libsystemd-id128.so.0 from install of systemd-libs-219-19.el7.x86_64 conflicts with file from package systemd-container-libs-208.20-6.el7.centos.x86_64
file /usr/lib64/libsystemd-journal.so.0 from install of systemd-libs-219-19.el7.x86_64 conflicts with file from package systemd-container-libs-208.20-6.el7.centos.x86_64
file /usr/lib64/libsystemd-login.so.0 from install of systemd-libs-219-19.el7.x86_64 conflicts with file from package systemd-container-libs-208.20-6.el7.centos.x86_64
file /usr/lib64/libudev.so.1 from install of systemd-libs-219-19.el7.x86_64 conflicts with file from package systemd-container-libs-208.20-6.el7.centos.x86_64
file /usr/lib64/security/pam_systemd.so from install of systemd-libs-219-19.el7.x86_64 conflicts with file from package systemd-container-libs-208.20-6.el7.centos.x86_64
Fix:
docker pull centos:latest or do: docker pull centos:7
But I have to use 7.1.1503!
RUN yum clean all && yum swap fakesystemd systemd
Source : http://seven.centos.org/?p=558
onsdag den 23. december 2015
A Batch of servers...
Finaly more servers added....
We got alot of Dell R730xd ( http://www.dell.com/us/business/p/poweredge-r730xd/pd )
Our iRODS help : http://www.hpc.dtu.dk/?page_id=324
Presentation of the DTU Supercomputer Computerome
https://www.youtube.com/watch?v=54kPOpf5dIYComputerome - 2015:
https://www.youtube.com/watch?v=XF5njN82l0YComputerome - A look back at 2014
https://www.youtube.com/watch?v=-WJG_rdUcVQ
torsdag den 10. december 2015
Videos about iRODS and why...
Big Data changes everything
https://www.youtube.com/watch?v=s_0xJEJSgv8The future starts in the Datacenter
https://www.youtube.com/watch?v=heOUObQ6dnciRODS - Control Your Data, 2015
https://www.youtube.com/watch?v=e-B_AM8i8Og
iRODS - Reagan Moore talks about iRODS
https://www.youtube.com/watch?v=-yCK5yE0glciRODS - Jason Coposky - Open Source Benefits
https://www.youtube.com/watch?v=BobGYQ2u798iRODS the Integrated Rule Oriented Data-management System:
https://www.youtube.com/watch?v=QwZTGzNJCnciRODS setup on Ubuntu :
iRods Basic Setup - April 2015
https://www.youtube.com/watch?v=A_I19sp5NE0
Policy Based Preservation Environments (iRODS)
https://www.youtube.com/watch?v=SYqEVgdtnesiRODS Consortium @ DDN’s Best Practices for Big Data in Genomics Workshop 2015 ( HERE )
https://www.youtube.com/watch?v=P067Xm6oHfo
mandag den 7. december 2015
Errors when installing/using iRODS
First ask your self: (Did I do this ?) -NOT "testpassword" Right? Please Note! This is on a CentOS 7
su postgres
psql
CREATE USER irods WITH PASSWORD 'testpassword';
CREATE DATABASE "ICAT";
GRANT ALL PRIVILEGES ON DATABASE "ICAT" TO irods;
\q
# Do remember : var/lib/pgsql/data/postgresql.conf
# listen_addresses = 'localhost' to listen_addresses = '*'
# and /var/lib/pgsql/data/pg_hba.conf # IDENT = trust
/var/lib/irods/packaging/setup_irods.sh ; iinit
Error:
su postgres
psql
CREATE USER irods WITH PASSWORD 'testpassword';
CREATE DATABASE "ICAT";
GRANT ALL PRIVILEGES ON DATABASE "ICAT" TO irods;
\q
# Do remember : var/lib/pgsql/data/postgresql.conf
# listen_addresses = 'localhost' to listen_addresses = '*'
# and /var/lib/pgsql/data/pg_hba.conf # IDENT = trust
/var/lib/irods/packaging/setup_irods.sh ; iinit
Docs » Manual » Troubleshooting>
Did you read : https://docs.irods.org/master/manual/troubleshooting/
Install problem:
Connection to iRODS server failed.
[-] libnative.cpp:336:native_auth_client_response : status [CAT_INVALID_USER] errno [] -- message [Call to rcAuthResponseFailed.]
failed with error -827000 CAT_INVALID_USER
Fix :
DB user / password is wrong...
If you have nothing you care about in your database yet, you can drop the tables, and start again.
Error:
# iadmin
ERROR: _rcConnect: setRhostInfo error, irodsHost is probably not set correctly status = -302000 USER_RODS_HOST_EMPTY
ERROR: rcConnect failure USER_RODS_HOST_EMPTY () (-302000) _rcConnect: setRhostInfo faile
Fix:
This means that your environment is not defined for your current unix user. This user has an ~/.irods/irods_environment.json file?
If not, you can run iinit to create one (it will prompt you for four pieces of information).
After a drop of the DB named: ICAT ... and follow the guides from : https://docs.irods.org/master/manual/installation/ and last run : iinit and give the same info as I did on setup.sh
Error : if the install say something about Permission denied /tmp/irods/setup_irods_configuration.flag
Fix:
Disable SELinux. Because /tmp/ is protected by SElinux - nano /etc/sysconfig/selinux
Disable SELinux. Because /tmp/ is protected by SElinux - nano /etc/sysconfig/selinux
Change “SELINUX=enforcing” to “SELINUX=disabled” and save the configuration file and reboot ;-)
Error:
Enter your current iRODS password:
[-] libnative.cpp:336:native_auth_client_response : status [CAT_INVALID_AUTHENTICATION] errno [] -- message [Call to rcAuthResponseFailed.]
failed with error -826000 CAT_INVALID_AUTHENTICATION
Fix : This error is from iCOMMAND. Your iRODS id/password is wrong.
re-run iinit and type the right id / password (what you typed when running: setup.sh )
Error:
ils /remoteZone
ERROR: rcObjStat of /remoteZone failed status = -913000 REMOTE_SERVER_SID_NOT_DEFINED
Fix :
Error:
ils /remoteZone
ERROR: rcObjStat of /remoteZone failed status = -913000 REMOTE_SERVER_SID_NOT_DEFINED
Fix :
The new name for the 'RemoteZoneSID' is 'zone_key'. We have not yet converted all the error codes from the old naming conventions - this is on the roadmap for 4.2.
You are missing the 'zone_key' entry on one side or the other of the federation, defining the authentication mechanism between your two zones.
Both sides of the federation need to have a stanza that includes the following four pieces of information:
"federation": [
{
"icat_host": "otherzone.example.org",
"zone_name": "anotherZone",
"zone_key": "ghjk6789",
"negotiation_key": "
}
]
They will mutually authenticate and the errors will go away.
More fixes on : https://groups.google.com/forum/#!forum/irod-chat
tirsdag den 1. december 2015
Install script for iRODS 4.1.7 on a CentOS7
### Other resource :
## OS : https://www.centos.org/
## https://groups.google.com/forum/#!forum/irod-chat
## https://docs.irods.org/master/
## http://trafficserver.apache.org/
## https://pods.iplantcollaborative.org/wiki/display/DS/Using+the+Data+Store
yum -y update;
yum -y upgrade;
yum -y update;
yum -y install net-tools wget nano mc
##FirewallD -please Note! This will open full on public! (we got a filter on front)
## please note big files need tcp ports : Range (Begin): 20000 (End):20199
firewall-cmd --zone=public --add-port=1248/tcp --permanent
firewall-cmd --zone=public --add-service=http --permanent
firewall-cmd --zone=public --add-service=https --permanent
firewall-cmd --reload
wget ftp://ftp.renci.org/pub/irods/releases/4.1.7/centos7/irods-database-plugin-postgres-1.7-centos7-x86_64.rpm
wget ftp://ftp.renci.org/pub/irods/releases/4.1.7/centos7/irods-database-plugin-postgres93-1.7-centos7-x86_64.rpm
wget ftp://ftp.renci.org/pub/irods/releases/4.1.7/centos7/irods-dev-4.1.7-centos7-x86_64.rpm
wget ftp://ftp.renci.org/pub/irods/releases/4.1.7/centos7/irods-icat-4.1.7-centos7-x86_64.rpm
wget ftp://ftp.renci.org/pub/irods/releases/4.1.7/centos7/irods-icommands-4.1.7-centos7-x86_64.rpm
wget ftp://ftp.renci.org/pub/irods/releases/4.1.7/centos7/irods-resource-4.1.7-centos7-x86_64.rpm
wget ftp://ftp.renci.org/pub/irods/releases/4.1.7/centos7/irods-runtime-4.1.7-centos7-x86_64.rpm
rpm --import https://www.elrepo.org/RPM-GPG-KEY-elrepo.org
yum -y install http://www.elrepo.org/elrepo-release-7.0-2.el7.elrepo.noarch.rpm
yum -y install epel-release
yum -y install http://rpms.famillecollet.com/enterprise/remi-release-7.rpm
sed -i 's/enabled=0/enabled=1/g' /etc/yum.repos.d/remi.repo
yum -y install http://pkgs.repoforge.org/rpmforge-release/rpmforge-release-0.5.3-1.el7.rf.x86_64.rpm
yum -y install unixODBC pam-devel openssl-devel wget nano mc tomcat tomcat-webapps
yum -y install tomcat-admin-webapps tomcat-docs-webapp tomcat-javadoc net-tools postgresql postgresql-server
yum -y install postgresql-contrib postgresql-libs postgresql-odbc fuse-libs.x86_64 perl-JSON* python-requests.noarch
yum -y install python-jsonschema python-psutil lsof authd
rpm -ivh irods-dev-4.1.7-centos7-x86_64.rpm
rpm -ivh irods-icat-4.1.7-centos7-x86_64.rpm
rpm -ivh irods-runtime-4.1.7-centos7-x86_64.rpm
rpm -ivh irods-database-plugin-postgres-1.7-centos7-x86_64.rpm
postgresql-setup initdb
systemctl start postgresql
systemctl enable postgresql
## If your webserver are heavy loaded... use : Varnish
#[varnish-4.0]
#name=Varnish 4.0 for Enterprise Linux
#baseurl=https://repo.varnish-cache.org/redhat/varnish-4.0/el7/$basearch
#enabled=1
#gpgcheck=0
#gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-VARNISH
############
#su postgres
#psql
#CREATE USER irods WITH PASSWORD 'testpassword';
#CREATE DATABASE "ICAT";
#GRANT ALL PRIVILEGES ON DATABASE "ICAT" TO irods;
#\q
# Do remember : var/lib/pgsql/data/postgresql.conf
# listen_addresses = 'localhost' to listen_addresses = '*'
# and /var/lib/pgsql/data/pg_hba.conf # IDENT = trust
###########################################################################################
# Do remember!!!!
#/var/lib/irods/packaging/setup_irods.sh
#iinit
###################Done########################
## OS : https://www.centos.org/
## https://groups.google.com/forum/#!forum/irod-chat
## https://docs.irods.org/master/
## http://trafficserver.apache.org/
## https://pods.iplantcollaborative.org/wiki/display/DS/Using+the+Data+Store
yum -y update;
yum -y upgrade;
yum -y update;
yum -y install net-tools wget nano mc
##FirewallD -please Note! This will open full on public! (we got a filter on front)
## please note big files need tcp ports : Range (Begin): 20000 (End):20199
firewall-cmd --zone=public --add-port=1248/tcp --permanent
firewall-cmd --zone=public --add-port=1247/tcp --permanent
firewall-cmd --zone=public --add-port=5432/tcp --permanentfirewall-cmd --zone=public --add-service=http --permanent
firewall-cmd --zone=public --add-service=https --permanent
firewall-cmd --reload
##FirewallD
wget ftp://ftp.renci.org/pub/irods/releases/4.1.7/centos7/irods-database-plugin-postgres93-1.7-centos7-x86_64.rpm
wget ftp://ftp.renci.org/pub/irods/releases/4.1.7/centos7/irods-dev-4.1.7-centos7-x86_64.rpm
wget ftp://ftp.renci.org/pub/irods/releases/4.1.7/centos7/irods-icat-4.1.7-centos7-x86_64.rpm
wget ftp://ftp.renci.org/pub/irods/releases/4.1.7/centos7/irods-icommands-4.1.7-centos7-x86_64.rpm
wget ftp://ftp.renci.org/pub/irods/releases/4.1.7/centos7/irods-resource-4.1.7-centos7-x86_64.rpm
wget ftp://ftp.renci.org/pub/irods/releases/4.1.7/centos7/irods-runtime-4.1.7-centos7-x86_64.rpm
rpm --import https://www.elrepo.org/RPM-GPG-KEY-elrepo.org
yum -y install http://www.elrepo.org/elrepo-release-7.0-2.el7.elrepo.noarch.rpm
yum -y install epel-release
yum -y install http://rpms.famillecollet.com/enterprise/remi-release-7.rpm
sed -i 's/enabled=0/enabled=1/g' /etc/yum.repos.d/remi.repo
yum -y install http://pkgs.repoforge.org/rpmforge-release/rpmforge-release-0.5.3-1.el7.rf.x86_64.rpm
yum -y install unixODBC pam-devel openssl-devel wget nano mc tomcat tomcat-webapps
yum -y install tomcat-admin-webapps tomcat-docs-webapp tomcat-javadoc net-tools postgresql postgresql-server
yum -y install postgresql-contrib postgresql-libs postgresql-odbc fuse-libs.x86_64 perl-JSON* python-requests.noarch
yum -y install python-jsonschema python-psutil lsof authd
rpm -ivh irods-dev-4.1.7-centos7-x86_64.rpm
rpm -ivh irods-icat-4.1.7-centos7-x86_64.rpm
rpm -ivh irods-runtime-4.1.7-centos7-x86_64.rpm
rpm -ivh irods-database-plugin-postgres-1.7-centos7-x86_64.rpm
postgresql-setup initdb
systemctl start postgresql
systemctl enable postgresql
## If your webserver are heavy loaded... use : Varnish
#[varnish-4.0]
#name=Varnish 4.0 for Enterprise Linux
#baseurl=https://repo.varnish-cache.org/redhat/varnish-4.0/el7/$basearch
#enabled=1
#gpgcheck=0
#gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-VARNISH
############
#su postgres
#psql
#CREATE USER irods WITH PASSWORD 'testpassword';
#CREATE DATABASE "ICAT";
#GRANT ALL PRIVILEGES ON DATABASE "ICAT" TO irods;
#\q
# Do remember : var/lib/pgsql/data/postgresql.conf
# listen_addresses = 'localhost' to listen_addresses = '*'
# and /var/lib/pgsql/data/pg_hba.conf # IDENT = trust
###########################################################################################
# Do remember!!!!
#/var/lib/irods/packaging/setup_irods.sh
#iinit
###################Done########################
onsdag den 28. oktober 2015
iRODs 4.1.6 on my CentOS
My First test with iRODS 4.1.6 on a CentOS 7
From : https://groups.google.com/forum/#!forum/irod-chat
I did : chmod -R 755 /var/lib/irods
-- My Server files---
By default Postgresql uses IDENT-based authentication.
All you have to do is allow username and password based authentication for your network or webserver.
IDENT will never allow you to login via -U and -W options. Append following to allow login via localhost only:
-----
---the file-------
nano /etc/varnish/varnish.params
Setup : DAEMON_OPTS="-a :80 -T localhost:6082 -f /etc/varnish/default.vcl -S /etc/varnish/secret -s malloc,256m"
From : https://groups.google.com/forum/#!forum/irod-chat
I did : chmod -R 755 /var/lib/irods
-- My Server files---
#rpm -qa postgre*
postgresql-server-9.2.13-1.
postgresql-9.2.13-1.el7_1.x86_
postgresql-odbc-09.03.0100-2.
postgresql-devel-9.2.13-1.el7_
postgresql-contrib-9.2.13-1.
postgresql-server-9.2.13-1.
postgresql-9.2.13-1.el7_1.x86_
postgresql-odbc-09.03.0100-2.
postgresql-devel-9.2.13-1.el7_
postgresql-contrib-9.2.13-1.
#rpm -qa irod*
irods-dev-4.1.6-0.x86_64
irods-icat-4.1.6-0.x86_64
irods-runtime-4.1.6-0.x86_64
irods-database-plugin-
irods-dev-4.1.6-0.x86_64
irods-icat-4.1.6-0.x86_64
irods-runtime-4.1.6-0.x86_64
irods-database-plugin-
in the file : /var/lib/pgsql/data/
you need to change : listen_addresses = 'localhost' to listen_addresses = '*'
you need to change : listen_addresses = 'localhost' to listen_addresses = '*'
Also remember to add it to firewall-cmd with the option : --permanent
To fix this error open PostgreSQL client authentication configuration file /var/lib/pgsql/data/pg_hba.
# vi /var/lib/pgsql/data/pg_hba.
To fix this error open PostgreSQL client authentication configuration file /var/lib/pgsql/data/pg_hba.
# vi /var/lib/pgsql/data/pg_hba.
This file controls: Which hosts are allowed to connect
How clients are authenticated which PostgreSQL user names they can use Which databases they can access
How clients are authenticated which PostgreSQL user names they can use Which databases they can access
By default Postgresql uses IDENT-based authentication.
All you have to do is allow username and password based authentication for your network or webserver.
Other usefull stuff: (systemD)
systemctl status postgresql.service
systemctl stop postgresql.service
systemctl start postgresql.service
--
Test your iRODS password with : iinit
Wrong password will give :
Enter your current iRODS password:
[-] libnative.cpp:336:native_auth_
failed with error -826000 CAT_INVALID_AUTHENTICATION
systemctl status postgresql.service
systemctl stop postgresql.service
systemctl start postgresql.service
--
Test your iRODS password with : iinit
Wrong password will give :
Enter your current iRODS password:
[-] libnative.cpp:336:native_auth_
failed with error -826000 CAT_INVALID_AUTHENTICATION
Right password will give :
Enter your current iRODS password:
#
Enter your current iRODS password:
#
-----
install postgresql93: (NOT the latest one!!! )
rpm -iUvh http://yum.postgresql.org/9.3/
yum -y install postgresql93 postgresql93-server postgresql93-contrib postgresql93-libs postgresql93-odbc fuse-libs.x86_64 perl-JSON* python-jsonschema.noarch
rpm -iUvh http://yum.postgresql.org/9.3/
yum -y install postgresql93 postgresql93-server postgresql93-contrib postgresql93-libs postgresql93-odbc fuse-libs.x86_64 perl-JSON* python-jsonschema.noarch
Get the rpm from.... ftp://ftp.renci.org/pub/irods/
Please Note : IDROP-web need : TomCat 7 or 8 (and Varnish???)
--
I'm still testing with Varnish vs. Apache Traffic Server as a Reverse Proxy
---
--My Setup:
Varnish : nano /etc/yum.repos.d/varnish.repo
Varnish : nano /etc/yum.repos.d/varnish.repo
---the file-------
[varnish-4.0]
name=Varnish 4.0 for Enterprise Linux
baseurl=https://repo.varnish-
enabled=1
gpgcheck=0
gpgkey=file:///etc/pki/rpm-
---------
yum install varnish varnish-libs varnish-libs-devel
name=Varnish 4.0 for Enterprise Linux
baseurl=https://repo.varnish-
enabled=1
gpgcheck=0
gpgkey=file:///etc/pki/rpm-
---------
yum install varnish varnish-libs varnish-libs-devel
firewall-cmd --zone=public --add-port=80/tcp --permanent
firewall-cmd --reload
firewall-cmd --reload
nano /etc/varnish/varnish.params
Setup : DAEMON_OPTS="-a :80 -T localhost:6082 -f /etc/varnish/default.vcl -S /etc/varnish/secret -s malloc,256m"
Please let me know how you did your CentOS 7 or RedHat ES 7
Abonner på:
Opslag (Atom)