(r61) BioInformatics < CF

CF Web>Research>ResearchGroups>BioInformatics (revision 61) (raw view)~~EditAttach~~
---+ Bioinformatics Group
DC2582
   * Web site: http://monod.uwaterloo.ca/

%TOC%

---++ Printing
   * Note: you can now print to lj_dc2582 via print.cs using CUPS 
      * *Please See:* https://cs.uwaterloo.ca/twiki/view/CF/Printing 
         * *Please use CUPS method*
   * *Troubleshooting:* Please see: https://cs.uwaterloo.ca/twiki/view/CF/PrinterProblems

---+++ Manual Printer Setup for Direct to printer Access
---++++ Linux Setup
---++ Adding Printers manually
---+++ Your local Web Browser
   * Using a Web Browser open this url: http://127.0.0.1:631/admin
   * *Add Printer* button 
      * *LPD/LPR* is the most commonly supported type 
         * Most of our printers also support *ipp* , *http* and for HP printers *AppSocket/HP JetDirect*
      * *Connection:* 
         * Example: lpd://socket://lj-dc2582.cs.uwaterloo.ca 
            * Where: *printername.cs.uwaterloo.ca* is the internet address
            * You may find this by looking on http://print.cs.uwaterloo.ca:631/printers
            * Open the printer name link and look at the *Connection* field
      * *Name:* a local name you will give this printer
      * *Location:* Where the printer is located
      * *Sharing:* leave this unchecked
   * *Continue*
   * *Model:* Printer Model Goes Here. Typically; Postscript (recommended) (en) driver is preferred 
      * *Example: *HP LaserJet P2055 Prostscript (recommended) (en)*
   * *Authentication* 
      * Provide your normal Login Userid and Password
   * *Set Default Options* 
      * *Finishing Panel* - to change duplexing, etc to your wishes
      * *Image Quality* - *dpi* and print density
      * *General* - default page size and tray

   * Using a Web Browser open this url: http://127.0.0.1:631/admin
   * *Add Printer* button 
      * *LPD/LPR* is the most commonly supported type 
         * Most of our printers also support *ipp* , *http* and for HP printers *AppSocket/HP JetDirect*

---+++ Status and Troubleshooting
   * Please see: https://cs.uwaterloo.ca/twiki/view/CF/PrinterProblems
---++++ Printers Built in Web Server
   * You can view the printers status directly using to see if it is 
      1 ) out of papper
      1 ) paper jam
      1 ) low or out of toner
      1 ) ready to print
   * Visit the printers web page: http://lj-dc2582.cs.uwaterloo.ca/

---++++ print.cs print job status
   * You can view the print.cs job queue to see what is happing with your print job 
      * *Note: the printer can be ready but your job might have an error - or someone else may have a print job error blocking your printout.*
   * Visit: http://print.cs.uwaterloo.ca:631/printers/lj_dc2582 
      * If you need to delete a print job please contact [[https://cs.uwaterloo.ca/~magore/][Mike Gore]]

---++++ Very important note about Documents and Paper size
   * *Please note* if you send a PDF file to be printed and the document is *A4* paper type it will *fail and cause the printer to wait for manual intervention!* * *There are a vast number of PDF douments that are published on A4 peper type and this is the most common problem*
---++++ Replacement Toner
   * There are spare toners in DC2582 *If you use the last one you MUST contact Wendy Rush or* [[https://cs.uwaterloo.ca/~magore/][Mike Gore]] *to have news ones ordered!*

---+++ Printing - via monod - old method do not use
   * *This is just here for historical reference* 
      * *Please See:* https://cs.uwaterloo.ca/twiki/view/CF/Printing
   * Log into *monod* 
      * Add host IP to */etc/cups/cupsd.conf* to section starting with =&lt; Location &gt;= (look about 80% the way down the file)
      * restart cups */etc/init.d/cupsys restart*
   * Client computer needs the following changes to */etc/cups/cupsd.conf* <verbatim>
      # Show shared printers on the local network.
      Browsing On
      BrowseOrder allow,deny
      BrowseAllow all
      BrowseLocalProtocols CUPS dnssd
      BrowseAddress @LOCAL
      BrowsePoll print.cs.uwaterloo.ca
      BrowsePoll monod.uwaterloo.ca
      BrowseInterval 3600
      BrowseTimeout 3700
   </verbatim>
   * On Client computer restart cups: */etc/init.d/cups restart*
   * Add default printer: *lpadmin -d bif_bw2*

---++ Ming Li - m160 research cluster
   * [[m160]] - Ming Li's research cluster
---++ Bioinformatics Wiki
   * https://www.bioinformatics.uwaterloo.ca/wiki/index.php
---++ NOVO Bin Ma - Research cluster
   * [[NOVO]] - Bin Ma research cluster

---++ Contacting the group
   * biolab@lists
   * (or bif@lists ??) - Mike - do you know the difference between these two lists?

---++ BIF CGL machine room cluster - next to CS racks
   * Physical Machines: 
      * Solaris Hosts: hmsbarracouta,hmsbeagle
      * Ubuntu Hosts: codon chromosome histone chromatin
   * VMs (hosted by codon) 
      * dna monod evlove
   * Spare Unused machines: 
      * Proteome,Genome,Element

---+++ Access from the CS Core
   * user *root* on *cscf* can log into the BIF servers listed below as *cscf-adm* using public key
   * See notes below for becoming *root*

---+++ Remote IPMI management
   * *Note: port A19 on dc2305d controlls access to the IPMI interfaces* 
      * *it is left DISABLED when not in use for added security!!!*
      * https://istns.uwaterloo.ca/ona/editport.php?ipname=dc2305d-cs1&port=A19
   * See IPMI documentation and [[https://cs.uwaterloo.ca/twiki/view/CF/IPMI#IPMIView][IPMIView]] for access
   * The following hosts have *unconfigured IPMI management interfaces* 
      * IPMI: chromatin-mgmt.cs HOST: chromatin.cs
      * IPMI: histone-mgmt.cs HOST: histone-mgmt.cs
      * IPMI: ilom-chromosome.cs HOST: ilom-chromosome.cs
      * IPMI: ilom-codon.cs HOST: ilom-codon.cs

---+++ KVM
   * There is an 8 port KVM attached to all of the Servers listed below, it is located in the bottom of the main BIF rack in DC2302A, with the keyboard and screen in the rack to the left. 
      * KVM Port Assignments:
      * Port 1 - [[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/chromosome.cs/][chromosome]]- note: no KM - use USB keyboard
      * Port 2 - [[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/hmsbeagle.cs/][hmsbeagle]]
      * Port 3 - [[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/hmsbarracouta.cs/][hmsbarracouta]]
      * Port 4 - [[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/codon.cs/][codon]] - note: no KM - use USB keyboard
      * Port 5 - [[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/chromatin.cs/][chromatin]] - note: no KM - use USB keyboard
      * Port 6 - proteome
      * Port 7 - histone - note: no KM - use USB keyboard
      * Port 8 - genome
--+++ Networking * 17 Oct 2011 Must be revised - everything is connected to dc2303a-cs1b all of the wall jack connections except one have been disconnected

   * SunFire x2200 Network Jacks - rear view:
<verbatim>
   |1|3|4|
   |2|
</verbatim>
   * Switches 
      * Netgear24 (internal private network 192.168.0.0/24)
      * Netgear5-5 -&gt; I11 vlan:7

| Name | Model | Net 1 | Net 2 | Net 3 | Net 4 | KVM |
| Chromosome | Sunfire x2200 | NC | DC2303a-i17 vlan:1896 | DC2303a-i19 vlan:7 | Netgear24-22 vlan:private | KVM1 |
| Codon | Sunfire x2200 | NC | DC2303a-i18 vlan:1896 | DC2303a-i20 vlan:7 | Netgear24-23 vlan:private | KVM4 |
| Chromatin | Sunfire x2200 | NC | NC | Netgear5-1 vlan:7 | Netgear24-11 vlan:private | KVM5 |
| Histon | Sunfire x2200 | NC | DC2303a-i10 vlan:1896 | Netgear5-3 vlan:7 | Netgear24-12 vlan:private | KVM7 |
| Hmsbarracouta | Super Micro | Netgear5-2 vlan:7 | Netgear24-21 vlan:private | - | - | KVM3 |
| Hmsbeagle | Super Micro | DC2303A-i9 vlan:7 | Netgear24-24 vlan:private | - | - | KVM2 |
| Element | Dell GX260 | DC2303A-i12 vlan:7 | - | - | - | - |
| Proteome | Dell Poweredge 6650 | DC2303A-i15 vlan:7 | Netgear24-15 vlan:private | - | - | KVM6 |
| Genome | Dell Poweredge 6650 | DC2303A-i14 vlan:78 | Netgear24-13 vlan:private | - | - | KVM8 |

---+++ Servers
---++++ Access
   * See Bioinformatics and cscf-adm in safe for all of the following
#FileServers
---++++ Primary File Servers

Use *su* to become root - password is in safe
   * *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/hmsbarracouta.cs/][hmsbarracouta]]* - primary
   * *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/hmsbeagle.cs/][hmsbeagle]]* - backup
#FixingBootErrors
---+++++ Fixing boot errors
   * If you have a *boot_archive* or *repository.db*
   * Fix *boot_archive* 
      * boot failsafe image
      * *yes* to mount file system on /a
      * *rm -f /a/platfore/i86pc/boot_archive*
      * *bootadm update-archive -R /a*
      * *reboot*
   * Fix *repository.db* 
      * */lib/svc/method/fs-root*
      * */lib/svc/method/fs-usr*
      * */lib/svc/bin/restore_repository*
      * pick *boot*

---+++++ Fixing NFS mount LDAP related errors
   * Many of the NFS mounts exported by *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/hmsbarracouta.cs/][hmsbarracouta]]* and *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/hmsbeagle.cs/][hmsbeagle]]* need LDAP to be working 
      * LDAP runs on *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/evolve.cs/][evolve]]* - a VM hosted by *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/codon.cs/][codon]]* 
         * So make sure that *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/codon.cs/][codon]]* is running and that *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/evolve.cs/][evolve]]* is up
#LdapService
---++++++ Restarting LDAP service on evolve

*Make sure codon and the VM's are running* <br /> Note: *LDAP SERVICE ON EVOLVE MUST BE STARTED BEFORE ANY LDAP CLIENTS ARE STARTED*
   * Dependencies: *codon* must be up and running *and* the VM *evolve* must be up and running
   * Manual method: 
      1 ) log into *evolve* as *cscf-adm* and *sudo bash* to become root
      1 ) */etc/init.d/slapd restart* restarts the ldap service
   * Automatic method: 
      1 ) log onto codon as cscf-adm
      1 ) *./fixit* - this will fix all services on all hosts provided they are powered up and online
#FixingFileServers
---++++++ Restarting LDAP clients - exporting NFS shares from hmsbarracouta and hmsbeagle

*Make sure codon and the VM's are running*
   * *Initialize LDAP*: run *ldap_init* on *BOTH* of *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/hmsbarracouta.cs/][hmsbarracouta]]* AND *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/hmsbeagle.cs/][hmsbeagle]]*
   * Manual method: 
      1 ) login as *cscf-adm*
      1 ) *su* - password in safe
      1 ) *./ldap_init _password* (BIF_LDAP_password is in the safe) 
         * Note: the *ldap_init* script does this: <verbatim>
               ldapclient -v init \
                  -a proxyDN=cn=proxyagent,ou=profile,dc=bioinformatics,dc=uwaterloo,dc=ca \
                  -a proxyPassword=<proxypassword> evolve-local
                Note:  <proxypassword> is the LDAP password - in safe
         </verbatim>
      1 ) *exportfs -a* (fixes LDAP related NFS errors)
      1 ) Debugging 
         * *showmount -a* will show the exported mounts
         * *showmount -d* will show the mounts in use
   * Automatic method: 
      1 ) log onto codon as cscf-adm
      1 ) *./fixit* - this will fix all services on all hosts provided they are powered up and online
#LdapClients
---++++++ Restart all other LDAP clients and services everywhere and remount
   * We need to bring up services on *dna,codon,chromosome,histone,chromatin* 
      1 ) login to *codon* as *cscf-adm* 
         * *./fixit* - ignore any errors

---++++++ Autofs
   * The *fixit* script will redo the client machines *ldap* authenticated mounts that are done with *autofs*
   * */etc/init.d/autofs restart*
   * Autofs Status Example <verbatim>
      root@codon:~# /etc/init.d/autofs status
   Configured Mount Points:
   ------------------------
   /usr/sbin/automount --timeout=60 /net/home file /etc/auto.home 

   Active Mount Points:
   --------------------
   /usr/sbin/automount --pid-file=/var/run/autofs/_net_home.pid --timeout=60 /net/home file /etc/auto.home
   </verbatim>
   * */etc/auto.home* example: <verbatim>
   root@codon:~# more /etc/auto.home
   #
   # Mount home directories from zfs server.
   #

   *   -fstype=nfs,rw,rsize=32768,wsize=32768,hard,intr,bg,noacl   hmsbarracouta-local:/export/zfs/&

   </verbatim>
#NameServers
---++++++ Restarting caching name service on machines

*Note: if you have problems resolving names from a host restart the caching name service*
   * the *fixit* script we runs the *nscd* command on *dna,codon,chromosome,histone,chromatin* 
      1 ) */etc/init.d/nscd restart* restart caching name service
---+++++ LDAP on Evolve - docs
   * Documents: *https://help.ubuntu.com/community/LDAPClientAuthentication*
---+++++ Files
   * */etc/ldap.conf* - config file
---+++++ Testing

*PAM*: evolve pam is configured like this:
<verbatim>
root@evolve:/etc/puppet/modules# grep ldap /etc/pam.d/common*
   /etc/pam.d/common-auth:auth    sufficient      pam_ldap.so ignore_unknown_user
   /etc/pam.d/common-password:password   sufficient  pam_ldap.so ignore_unknown_user
</verbatim>

*PUPPET*:
<verbatim>
   root@evolve:/etc/puppet/modules/ldap# ls *
   files:
   ldapcert.key  ldap.conf    nsswitch.conf    pamldap.conf
   ldapcert.pem  ldap.secret  oldpamldap.conf

   manifests:
   authclient.pp  client.pp
</verbatim>

   * *ldap.secret* contains the master password
---++++ Understanding ZFS exports and LDAP access from hmsbarracouta
   * ZFS TWIKI page: CF.ZFS
   * Useful documents outlining Solaris and Linux shares: http://docstore.mik.ua/orelly/networking_2ndEd/nfs/ch06_02.htm
   * List exports: *showmount -e hmsbarracouta.cs*
   * Local export file: */etc/dfs/sharetab* 
      * Example entry: */export/vm - nfs sec=sys,rw=codon-local,root=codon-local* 
         * The share */export/vm* is shared to *codon-local* as root with *rw* perms granted to host *codon-local* using *sys* security (*sys is a host based trust)
         * In this case codon-local is defined in */etc/hosts* as 192.168.0.12
      * Example entry: */opt - nfs sec=sys,rw=nfsclients,root=nfsclients* 
         * The share */opt* is shared to *nfsclients* as root with *rw* perms granted to hosts *nfsclients* using *sys* security (*sys is a host based trust)
      * Example entry: */export/databases - nfs sec=sys,rw=nfsclients,root=nfsclients* 
         * The share */export/databases* is shared to *nfsclients* as root with *rw* perms granted to hosts *nfsclients* using *sys* security (*sys is a host based trust)

---++++ services solaris 10
   * *svcs* - list service status
   * *svcadm* - control services * svcadm restart puppetd

---++++ Managing accounts

*Note:* You *must* do the next two steps before managing account
   1 ) Log onto *evolve* as *cscf-adm*
   1 ) make sure */net/opt/bin* is in your path
---+++++ Adding users
   * *bif-adduser userid* 
      * Enter ldap password: (see BIF LDAP password in safe) <verbatim>
   Full name : Test User
   Office : DC1234
   Phone : 1-519-123-4567
   Current email testuser@cs.uwaterloo.ca (leave blank for default)
   Email :
   Purpose : Test User
   Date created 2010-02-09.
   ex. browndg, mli
   Supervisor: nobody
   Generated password: ucsyiderg
   </verbatim>
---+++++ Deleting users

*Deleting user accounts* <br /> We have no policy on deleting user accounts at this time. If you make an error in creating an account and really need to delete it, you must do so manually. <br /> First, use *ldapvi* as *bifadmin* on *evolve* and delete all entries related to the user. There should be a group, a user, and an entry in the research group. You may use another LDAP editor if you prefer. <br /> Second, you must log into hmsbarracouta and hmsbeagle and delete the users ZFS home directory using zfs destroy. If you have just created the user, only hmsbarracouta will have an account as the backup task will not yet have backed up the new directory.

---++++ Changing password
   * To change a userÃ&fnof;Â&fnof;Ã&sbquo;Â&fnof;Ã&fnof;Â&sbquo;Ã&sbquo;Â&fnof;Ã&fnof;Â&fnof;Ã&sbquo;Â&sbquo;Ã&fnof;Â&sbquo;Ã&sbquo;Â&sbquo;Ã&fnof;Â&fnof;Ã&sbquo;Â&fnof;Ã&fnof;Â&sbquo;Ã&sbquo;Â&sbquo;Ã&fnof;Â&fnof;Ã&sbquo;Â&sbquo;Ã&fnof;Â&sbquo;Ã&sbquo;Â&rsquo;s password in LDAP, they must use the *bif-passwd* program. This program will change both the unix and samba password hashes.
   * The default shell configuration for both bash and csh/tcsh is currently set to alias *passwd* to *bif-passwd*. If this alias is corrupted for any reason, it will result in difficulty changing passwords.
   * The bifpassword program is subject to the same special character bug as *bif-adduser*.
   * *bif-passwd userid* - you can change someones password without knowing it fist - even if you are *root* - need to fix this
---+++++ password or user update problems

Notes: If the LDAP server is not running you will not get an obvious error - *solution restart the LDAP server and clients first. Example error: as root you try to change a password - you get prompted for the old password - regardless nothing you try will work

---+++++ Exports
   * */etc/dfs/shareall* - automatically created

---++++ Other Servers

Use *sudo bash* to become root - will not be prompted for a password

---+++++ Sunfire X2200
   * *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/chromosome.cs/][chromosome]]*
   * *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/codon.cs/][codon]]* 
      * VMware console for VM's https://codon.cs:8333 - must use IE Web browser
   * *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/chromatin.cs/][chromatin]]*
   * *histone*

---+++++ Dell Power Edge 6650

*Currently offline - spare machines*
   * *proteome*
   * *genome*
#VirtualMachines
---+++ Virtual Machines
---++++ Vmware Infrastructure Web Access

Note: make sure the NFS shares are working - problems with LDAP (see below) can cause access errors and weird errors!
   * Web admin interface: https://codon.cs:8333 - must use IE Web browser 
      * *cscf-adm* or *bifadmin* - password in safe
---+++++ Virtual Machines
   * cscf-adm - sudo bash to become root
   * VM Locations: 
      * *dna* //codon.cs.uwaterloo.ca/vm/dna.cs.uwaterloo.ca (was //hmsbarracouta/export/vm/dna.cs.uwaterloo.ca)
      * *monod* //codon.cs.uwaterloo.ca/vm/monod
      * *evolve* //codon.cs.uwaterloo.ca/vm/evlove.vmwarevm

---+++++ Trouble shooting VM server on Codon
   * some times a VM will not start no matter what you try 
      1 ) */etc/init.d/vmware stop*
      1 ) /home/cscf-adm/bin/kill-vmware
      1 ) */home/bifadmin/vmware-server-distrib/bin/vmware-config.p* 
         * If you see any errors like the network module not loading see Reinstalling VMware server * Answer 8333 for the secure port for web management - for some reason this keeps changing to 443
      1 ) now wait for a long time for the vms to start 
         * You can open https://codon.cs:8333/ui/# using cscf-adm (password in safe) - must use IE Web browser
         * verify the VM's start!

---+++++ Reinstalling VMware server
   1 ) Make sure you stop all vmware tasks - see Trouble shooting VM server section first
   1 ) *cd /home/bifadmin/vmware-server-distrib* 
      * Answer 8333 for the secure port for web management - for some reason this keeps changing to 443
   1 ) *./vmware-install.pl* - pick all defaults

---+++++ Reconfiguring VMware Tools on client machines

* Notes: you might have to reconfigure vmware tools after a Kernel upgrade*
   * Reinstall/Install: */usr/bin/vmware-config-tools.pl* 
      * Note if this does not work open 
         1 ) Vmware Infrastructure Web Access
         1 ) Inventory
         1 ) (highlight your VM)
         1 ) Commands
         1 ) Configure VM
         1 ) Power
         1 ) Check and install VMware tools before Power on
   * Network is broken 
      * check */etc/udev/ruls.d/70-persistent-net.rules* and make sure the assumptions match */etc/network/interfaces*

---++++ evolve
   * To restart all services everywhere: 
      1 ) log onto codon as cscf-adm
      1 ) *./fixit* - this will fix all services on all hosts provided they are powered up and online
   * Manual steps follow in the next sections for reference:
#StartCplex
---+++++ Restart CPLEX license Server:
   * 
      * */etc/init.d/ilog-ilm restart*
#StartGridEngine
---+++++ Restart Sun Grid Engine:
   * 
      * */etc/init.d/sgemaster.uwbif stop*
      * */etc/init.d/sgemaster.uwbif start*
#CheckGridEngine
---+++++ Check Grid Engine
   1 
      1 ) *ssh cscf-adm@dna*
      1 ) *qstat -f*
      * Fail Example: <verbatim>
   cscf-adm@dna:~$ qstat -f
   error: commlib error: can't connect to service (Connection refused)
   error: unable to contact qmaster using port 6444 on host "evolve-local"
   </verbatim> * Working Example: <verbatim>
   cscf-adm@dna:~$ qstat -f
   queuename                      qtype resv/used/tot. load_avg arch          states
   ---------------------------------------------------------------------------------
   all.q@chromosome.cs.uwaterloo. BP    0/0/4          0.02     lx24-amd64    E
   ---------------------------------------------------------------------------------
   all.q@codon.cs.uwaterloo.ca    BP    0/0/0          -NA-     lx24-amd64    au
   ---------------------------------------------------------------------------------
   all.q@histone.cs.uwaterloo.ca  BP    0/0/4          -NA-     lx24-amd64    auE
   ---------------------------------------------------------------------------------
   brown@chromatin.cs.uwaterloo.c BP    0/0/3          -NA-     lx24-amd64    au
   ---------------------------------------------------------------------------------
   verylong@codon.cs.uwaterloo.ca BP    0/0/1          -NA-     lx24-amd64    au
   ---------------------------------------------------------------------------------
   web@chromatin.cs.uwaterloo.ca  BIP   0/0/1          -NA-     lx24-amd64    au
       </verbatim>
---++++ monod

---++++ dna
---++++ Procedures documentation
   * Mike's notes: http://www.cs.uwaterloo.ca/~magore/bioinformatics.htm
   * Accounts Setup: https://www.bioinformatics.uwaterloo.ca/wiki/index.php?Account%20Setup

---++++ CUPS admin
   * Cups printing admin commands like *cupsenable* can be run from the command line without the cups server web interface - this is great for restarting queues on *monod*. *Print queues dies rather often*

---+++ Puppet
   * *evolve* is the *puppet master*
   * resolv.conf = evolve:/etc/puppet/modules/network/files/solaris-resolv.conf 
      * dns-nameservers mentioned in /etc/puppet/modules/network/templates/interfaces.erb
   * autofs 
      * /etc/puppet/modules/net/files/*

---++++ Configuration files

Our puppet configuration files are on evolve in the */etc/puppet* directory. The majority of the configuration logic is in the */etc/puppet/modules* directory. We follow standard puppet module procedures.
| *Module* | *Purpose* |
| *acct* | Process accounting. |
| *apt* | apt config files |
| *bash* | bash config files and associated default profiles |
| *bifaccounttools* | Dependencies for BIF password change and user addition tools |
| *cluster* | Various cluster configurations including package installation list for compute nodes and interactive nodes |
| *cron* | cron entries that do not fit anywhere else University of Waterloo |
| *csh* | csh package and related configuration files. |
| *cups* | Printer client files. |
| *ldap* | LDAP client and server configuration. |
| *motd* | Message of the day. |
| *net* | NFS mounts. |
| *network* | Configuration for interfaces and DNS. |
| *nfs* | NFS services and configs. |
| *ntp* | Time management configuration through ntp. |
| *pam* | Authentication services. This includes modifications for LDAP as well as limiting user logins to interactive nodes. |
| *postfix* | Default mail services for all machines. |
| *puppet* | Mostly client configuration. Puppet can manage itself if you are careful. |
| *security* | Limits and access configuration to go with the PAM configuration files. |
| *ssh* | SSH services. |
| *tcsh* | tcsh and related configuration files. |
| *user* | Local users such as bifadmin, cscf-admin, and database admin. |

*Notes:*
   * The remaining configuration is in */etc/puppet/manifests*. Here, *templates.pp* provides basic templates for various types of machines including cluster nodes, interactive nodes, servers, and Solaris machines. We configures machines themselves in the *nodes.pp* file. The *site.pp* file only loads our templates and nodes at this point. Known problems and fixes
   * Puppet clients seem to freeze or break occasionally. We use a cron entry to restart the puppet client every two hours, if it is stopped. To find frozen clients, we run *puppet_check* on *evolve*. This script looks at the puppet master database and emails a warning for any clients that have node checked in within a day.
   * PuppetÃ&fnof;Â&fnof;Ã&sbquo;Â&fnof;Ã&fnof;Â&sbquo;Ã&sbquo;Â&fnof;Ã&fnof;Â&fnof;Ã&sbquo;Â&sbquo;Ã&fnof;Â&sbquo;Ã&sbquo;Â&sbquo;Ã&fnof;Â&fnof;Ã&sbquo;Â&fnof;Ã&fnof;Â&sbquo;Ã&sbquo;Â&sbquo;Ã&fnof;Â&fnof;Ã&sbquo;Â&sbquo;Ã&fnof;Â&sbquo;Ã&sbquo;Â&rsquo;s management of Solaris is currently somewhat limited and thus we manually manage our Solaris machines for the most part. Initially we managed cron through puppet, but it turns out that you can only install root cron entries on Solaris machines.
---++++ CPLEX
---+++++ CPLEX users on remote computers and the CS firewall
   * Have CS open port *3000* between your desktop and evolve
   * port *3000* is the ILOG LIcense Server Port
---+++++ License Server

Note: runs on *evolve* so make sure the machine is running
   * Restart CPLEX license Server:
   * */etc/init.d/ilog-ilm restart*
---+++++ License File
   * *hmsbarracouta:/export/zfs/akhudek/cplex/access.ilm*
   * on evolve see */home/cscf-adm/plex/access.ilm*

---+++ Power Up
---++++ Circuit Breakers
   * All of the *UPS* are fed from CS panel breaker *12B6A #20* and *PDS* breaker *1C

---++++ UPS notes
---+++++ APC SUA3000XL
   * CS panel breaker *12B6A #20* - attached to 
      * Physical Machines 
         * Solaris Hosts: hmsbarracouta,hmsbeagle
         * Ubuntu Hosts: codon chromosome histone chromatin
      * VMs (hosted by codon) 
         * dna monod evlove
   * *PDS breaker 1C* 
      * secondary power supply for *hmsbarracouta,hmsbeagle*

---+++++ No power
   * Spare Unused machines: 
      * Proteome,Genome,Element

---++++ Startup order

Note: chicken and egg issue - *evolve* ruins the *LDAP* service - *evolve* is a VM on *codon* <br /> which needs *NFS* shares from *hmsbrracouta* which needs *LDAP* service from *evolve*! *sigh*

   * Start *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/codon.cs/][codon]]* 
      * *Wait for VM's to come up*
      * *More Info:* CF.BioInformatics#VirtualMachines
   * Verify [[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/evolve.cs/][evolve]] is up before continuing 
      * *restart LDAP service on evolve 
         * */etc/init.d/slapd restart*
         * *More Info:* CF.BioInformatics#LdapService
   * Start *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/hmsbarracouta.cs/][hmsbarracouta]]*
   * Start *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/hmsbeagle.cs/][hmsbeagle]]* 
      * Wait for them to finish booting 
         * Boot Errors: CF.BioInformatics#FixingBootErrors
      * Start File Server *LDAP* clients: CF.BioInformatics#FixingFileServers
      * *More Info:* CF.BioInformatics#FileServers
   * Start chromosome histone chromatin
   * Start All other LDAP Clients and services 
      * See CF.BioInformatics#LdapClients 
         * *NOTE this link has you run a script called "fixit" which does ALL of the remaining steps automatically!*
This section is for reference
   * Restart All other caching name servers 
      * See CF.BioInformatics#NameServers
   * Start CPLEX 
      * See CF.BioInformatics#StartCplex
   * Start Grid Engine 
      * See CF.BioInformatics#StartGridEngine
      * Test it! run *qstat -f* on *dna** 
         * See CF.BioInformatics#CheckGridEngine

---+++ Power Down
---++++ Shutdown order
   * *dna*,*monod*, *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/evolve.cs/][evolve]]*
   * *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/codon.cs/][codon]]*,*[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/chromosome.cs/][chromosome]]*,*[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/chromatin.cs/][chromatin]]*,*histone*
   * *proteome*, *genome*
   * *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/hmsbarracouta.cs/][hmsbarracouta]]* and *[[https://www.cs.uwaterloo.ca/cscf/internal/edocs/machines/hmsbeagle.cs/][hmsbeagle]]*
---+++++ Documents
   * https://www.bioinformatics.uwaterloo.ca/wiki/index.php?CPLEX
If you are using *cplex*, change '*monod*' to '*monod.uwaterloo.ca*' in your *~/cplex/access.ilm* file. You may have to log out and back in to *dna* to pick up a new path for the cplex interactive utility as well.

---++++ Mailing Lists
   * http://monod.uwaterloo.ca/mailman/listinfo/

---++++ External Documentation
   * Documentation: http://reductivelabs.com/products/puppet/

---++++ Special Machine notes
   * [[%ATTACHURL%/BIFserverdesignandpolicy.pdf][BIFserverdesignandpolicy.pdf]]: BIF server design and policy - 15Apr 2010 Alex Hudek
   * BioinformaticsMachines - notes on the Bioinformatics machines and how they're organized
   * http://raindrop.cs.uwaterloo.ca - Special web server for a research project

---++++ CSCF Subscription Info
   * http://www.cs.uwaterloo.ca/~magore/cgi-bin/sub?__form_list=all#dd-bioinformatics-1
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I	Attachment	History	Action	Size	Date	Who	Comment
pdf	BIFserverdesignandpolicy.pdf	r2 r1	manage	191.2 K	2010-04-15 - 12:50	MikeGore	BIF server design and policy - 15Apr 2010 Alex Hudek
Topic revision: r61 - 2014-01-15 - MikeGore
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