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########################
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