This documents how I set up an Ubuntu linux cluster for our Computational Chemistry Lab at University of Illinois at Chicago.
The cluster includes one server and several clients. User login authentication is managed by OpenLDAP. Users' home and application directories are exported from the server using NFS. The clients use Autofs to mount users' home and applications directories on demand from the server.
After installing Ubuntu (16.04) on the server and clients, run update and upgrade.
sudo apt-get update
sudo apt-get upgrade
sudo apt-get dist-upgrade
Then we need to move the admin user out of /home direcrory
to avoid overriding when /home is mounted.
We need to also rename /home directory to /rhome and create a new empty
/home and mount /rhome to /home.
This will make things easiser when we want to move all the users' data to another disk partition.
This is done on the server only.
This is done on both server and clients.
Change user to root.
~$ sudo -i
Edit the passwd file.
~# vim /etc/passwd
Change the line near the end of the file.
adminuser:x:1001:1001:Admin,,,:/home/adminuser:/bin/bash
to
adminuser:x:999:999:Admin,,,:/home/adminuser:/bin/bash
Edit the group file.
~# vim /etc/group
Change the line near the end of the file.
adminuser:x:1001:
to
adminuser:x:999:
Change the ower
~# chown -R adminuser:adminuser /home/adminuser
~# chown -R adminuser:adminuser /home/adminuser/.*
Move the admin home
~# mv /home/adminuser /
Edit the passwd file again.
~# vim /etc/passwd
Change the line.
adminuser:x:999:999:Admin,,,:/home/adminuser:/bin/bash
to
adminuser:x:999:999:Admin,,,:/adminuser:/bin/bash
Edit the file login.defs.
~# vim /etc/login.defs
Change the line
UID_MIN 1000
to
UID_MIN 999
Change the line
GID_MIN 1000
to
GID_MIN 999
Reboot the computer.
We need to do this on the server.
sudo mv /home /rhome
Edit the file fstab
sudo vim /etc/fsatb
Add the line.
/rhome /home none bind
sudo mount -a
Create a file in /etc/lightdm/lightdm.conf.d
sudo vim /etc/lightdm/lightdm.conf.d/00-hide-user-list.conf
Add the following contents
[SeatDefaults]
greeter-hide-users=true
greeter-show-manual-login=true
allow-guest=false
Reboot.
On the server, install:
sudo apt-get update
sudo apt-get install slapd ldap-utils
Give the password for the admin of the LDAP directory. LDAP should run after installed. Check the status by
sudo /etc/init.d/slapd status
sudo dpkg-reconfigure slapd
Omit LDAP server configuration? No
DNS domain: mylab.xx.xx.edu
Organization name: MyLab
Administrator password: Same as above
Database backend to use: MDB
Do you want the database to be removed when slapd is purged? No
Move old databases? Yes
Allow LDAPv2 protocol? No
Create a file called base.ldif, with the following lines:
dn: ou=People,dc=mylab,dc=xx,dc=xx,dc=edu
objectClass: organizationalUnit
ou: People
dn: ou=Group,dc=mylab,dc=xx,dc=xx,dc=edu
objectClass: organizationalUnit
ou: Group
Add this file to the database.
sudo ldapadd -x -D cn=admin,dc=mylab,dc=xx,dc=xx,dc=edu -W -f base.ldif
To add the first LDAP user to the database, create a file called ldapuser1.ldif with the following lines
dn: cn=ldapuser1,ou=Group,dc=mylab,dc=xx,dc=xx,dc=edu
objectClass: posixGroup
cn: ldapuser1
gidNumber: 10000
dn: uid=ldapuser1,ou=People,dc=mylab,dc=xx,dc=xx,dc=edu
objectClass: inetOrgPerson
objectClass: posixAccount
objectClass: shadowAccount
uid: ldapuser1
sn: ldapuser1
givenName: ldapuser1
cn: ldapuser1
displayName: ldapuser1
uidNumber: 10000
gidNumber: 10000
userPassword: somepasswd
gecos: ldapuser1
loginShell: /bin/bash
homeDirectory: /home/ldapuser1
Add it to the database.
sudo ldapadd -x -D cn=admin,dc=mylab,dc=xx,dc=xx,dc=edu -W -f ldapuser1.ldif
Create a file called uid_index.ldif with the contents:
dn: olcDatabase={1}mdb,cn=config
add: olcDbIndex
olcDbIndex: mail eq,sub
Run the command:
sudo ldapmodify -Q -Y EXTERNAL -H ldapi:/// -f uid_index.ldif
Create a file called schema_convert.conf with the contents:
include /etc/ldap/schema/core.schema
include /etc/ldap/schema/collective.schema
include /etc/ldap/schema/corba.schema
include /etc/ldap/schema/cosine.schema
include /etc/ldap/schema/duaconf.schema
include /etc/ldap/schema/dyngroup.schema
include /etc/ldap/schema/inetorgperson.schema
include /etc/ldap/schema/java.schema
include /etc/ldap/schema/misc.schema
include /etc/ldap/schema/nis.schema
include /etc/ldap/schema/openldap.schema
include /etc/ldap/schema/ppolicy.schema
include /etc/ldap/schema/ldapns.schema
include /etc/ldap/schema/pmi.schema
Create a directory:
mkdir ldif_output
Run the following commands:
slapcat -f schema_convert.conf -F ldif_output -n 0 | grep corba,cn=schema
slapcat -f schema_convert.conf -F ldif_output -n0 -H ldap:///cn={2}corba,cn=schema,cn=config -l cn=corba.ldif
Edit cn=corba.ldif to arrive at the following attributes:
dn: cn=corba,cn=schema,cn=config
...
cn: corba
And remove the following lines from the bottom:
structuralObjectClass: olcSchemaConfig
entryUUID: 52109a02-66ab-1030-8be2-bbf166230478
creatorsName: cn=config
createTimestamp: 20110829165435Z
entryCSN: 20110829165435.935248Z#000000#000#000000
modifiersName: cn=config
modifyTimestamp: 20110829165435Z
Run the command
sudo ldapadd -Q -Y EXTERNAL -H ldapi:/// -f cn\=corba.ldif
sudo apt-get install gnutls-bin ssl-cert
sudo sh -c "certtool --generate-privkey > /etc/ssl/private/cakey.pem"
sudo vim /etc/ssl/ca.info
With the following template
cn = My Lab
ca
cert_signing_key
Run the commands
sudo certtool --generate-self-signed --load-privkey /etc/ssl/private/cakey.pem --template /etc/ssl/ca.info --outfile /etc/ssl/certs/cacert.pem
sudo certtool --generate-privkey --bits 1024 --outfile /etc/ssl/private/mylab_slapd_key.pem
sudo vim /etc/ssl/mylab.info
Add the following lines
organization = My Lab
cn = mylab.xx.xx.edu
tls_www_server
encryption_key
signing_key
expiration_days = 3650
This crtificate is good for ten years. Then run
sudo certtool --generate-certificate --load-privkey /etc/ssl/private/mylab_slapd_key.pem --load-ca-certificate /etc/ssl/certs/cacert.pem --load-ca-privkey /etc/ssl/private/cakey.pem --template /etc/ssl/mylab.info --outfile /etc/ssl/certs/mylab_slapd_cert.pem
sudo chgrp openldap /etc/ssl/private/mylab_slapd_key.pem
sudo chmod 0640 /etc/ssl/private/mylab_slapd_key.pem
sudo gpasswd -a openldap ssl-cert
sudo systemctl restart slapd.service
Create the file called certinfo.ldif with the contents
dn: cn=config
add: olcTLSCACertificateFile
olcTLSCACertificateFile: /etc/ssl/certs/cacert.pem
-
add: olcTLSCertificateFile
olcTLSCertificateFile: /etc/ssl/certs/mylab_slapd_cert.pem
-
add: olcTLSCertificateKeyFile
olcTLSCertificateKeyFile: /etc/ssl/private/mylab_slapd_key.pem
Then run
sudo ldapmodify -Y EXTERNAL -H ldapi:/// -f certinfo.ldif
Since we will allow users to login into the server directly, we need to configure LDAP client on the server also.
On the client, install
sudo apt-get install ldap-utils
On the client, edit
sudo vim /etc/ldap/ldap.conf
Change the parameters BASE and URI to
BASE dc=mylab,dc=xx,dc=xx,dc=edu
URI ldap://IP of the server
On the server, edit
sudo vim /etc/ldap/ldap.conf
Change the parameters BASE and URI to
BASE dc=mylab,dc=xx,dc=xx,dc=edu
URI ldap://localhost
On both the server and client, install.
sudo apt-get install libnss-ldapd libpam-ldapd nslcd
It will ask which services to use, choose at least the three: passwd, group and shadow.
Check authentication:
getent passwd
getent group
getent shadow
We should see ldapuser1 in the output.
Now we should able to login to ldapuser1. Maybe reboot is needed.
On the server, run
sudo pam-auth-update
In addition to the defaults, select Automatically create user's home on first login
On the server
su ldapser1
This first login will create the directory /home/ldapuser1.
sudo apt-get install nfs-kernel-server
Edit the file /etc/exports
sudo vim /etc/exports
Add the following lines
/rhome nn.nn.nn.0/24(rw,sync)
/share nn.nn.nn.0/24(rw,sync)
Need to do this on the server:
sudo mkdir -p /share/apps
sudo /etc/init.d/nfs-kernel-server restart
sudo apt-get install autofs
Check directories shared by the server
showmount -e server's IP
Edit /etc/auto.master
sudo vim /etc/auto.master
and add
/home /etc/auto.home --timeout=600
/share /etc/auto.share --timeout=600
Create two map files.
sudo vim /etc/auto.home
and add
* -fstype=nfs,rw,hard,intr,nodev,exec,nosuid,rsize=8192,wsize=8192 server's IP:/rhome/&
sudo vim /etc/auto.share
and add
apps -fstype=nfs,rw,hard,intr,nodev,exec,nosuid,rsize=8192,wsize=8192 server's IP:/share/apps
Restart Autofs service.
sudo /etc/init.d/autofs restart
Check if the user's home directory is mounted:
cd /home/ldapuser1
Do this on both server and clients.
Install dependencies as listed here:
https://modules.readthedocs.io/en/stable/INSTALL.html
sudo apt-get install autopoint
sudo apt-get install tcl-dev
Download Modules here: http://modules.sourceforge.net/
tar -xzf modules-4.1.3.tar.gz
cd modules-4.1.3/
sudo mkdir /share/apps/modules # need to do this on the server
./configure --prefix=/usr/share/Modules --with-modulepath=/share/apps/modules
make
sudo make install
sudo ln -s /usr/share/Modules/init/profile.sh /etc/profile.d/modules.sh
sudo ln -s /usr/share/Modules/init/profile.csh /etc/profile.d/modules.csh
Do this on the server only.
Download VMD here: http://www.ks.uiuc.edu/Research/vmd/
sudo mkdir /share/apps/vmd/1.9.4
Follow the installation instruction to install vmd in /share/apps/vmd/1.9.4
Add a module file for vmd.
sudo mkdir /share/apps/modules/vmd
sudo vim /share/apps/modules/vmd/1.9.4
Put in the following contents
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "VMD v. 1.9.4 \n\thttp://www.ks.uiuc.edu/Research/vmd"
}
module-whatis "VMD Molecular Visualization Package"
prepend-path PATH /share/apps/vmd/1.9.4/bin
setenv VMD_PLUGIN_PATH /share/apps/vmd/1.9.4/lib/plugins/LINUXAMD64/molfile
Test loading the module.
module avail
module load vmd/1.9.4
[1] https://help.ubuntu.com/lts/serverguide/openldap-server.html
[2] https://help.ubuntu.com/community/LDAPClientAuthentication
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