Lab IT: Difference between revisions
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** Can access via smb://132.239.135.123/Brother%20HL-5250DN on Macs. | ** Can access via smb://132.239.135.123/Brother%20HL-5250DN on Macs. | ||
*Brother HL-4040CN, PFBH402, network printer, IP=172.16.25. | *Brother HL-4040CN, PFBH402, network printer, IP=172.16.25.21. | ||
*Brother MFC-7220, PFBH402, attached to Time Capsule through USB. | *Brother MFC-7220, PFBH402, attached to Time Capsule through USB. | ||
Revision as of 21:14, 5 November 2012
NAS
- Apple Time Capsule 877b54
- MAC address: 00:1F:00:1F:5B:87:7B:54
- Wireless password: Zhang lab's common password.
- Backup of lab wiki, also serves as a wireless router.
Wiki server
- MacMini, Mac OS X,
- Hostname: genome-tech.ucsd.edu
- IP address: 132.239.25.34
- Public site: http://genome-tech.ucsd.edu/public
- Private wiki: http://genome-tech.ucsd.edu/LabNotes , password protected.
- How to add a new user:
cd /etc/httpd/ sudo htpasswd passwords new_user_name Edit the httpd.conf file. Add the new_user_name to the following line: Require user kunzhang ...some_existing_user_name
- Wiki backup
Launchd deamon: /Library/LaunchDeamons/labwiki.backup Script for backup: /Library/Scripts/wiki_backup.sh
- Server migration from Mac Mini to Mac Pro: Migration Log
- Reads from genome-miner are shared in /Volumes/genome-miner-SeqStore2/ (See [1])
- MediaWiki was upgrade from v 1.13.2 to v 1.15.1
apachectl stop #backup the mysql databases mv LabNotes LabNotes.v1.13.2 tar -xzvf mediawiki-1.15.1.tar.gz mv mediawiki-1.15.1 LabNotes cp LabNotes.v1.13.2/LocalSettings.php LabNotes cp -r LabNotes.v1.13.2/extensions LabNotes cp /LabNotes/AdminSettings.sample /LabNotes/AdminSettings.php #edit the /LabNotes/AdminSettings.php file for the admin previlege cd LabNotes/maintenance php update.php --aconf ../AdminSettings.php cd ../.. mv LabNotes.v1.13.2/upload LabNotes mv LabNotes.v1.13.2/zhangloupload LabNotes apachectl start
- 0.9.9 full text search engine installed (Jan-23-2010)
- MediaWiki was upgrade from v 1.15.1 to v 1.18.2 (April-08-2012)
mv LabNotes LabNotes.v1.13.2 tar -xzvf mediawiki-1.18.2.tar.gz mv mediawiki-1.18.1 LabNotes.v1.18.2 cp LabNotes/LocalSettings.php LabNotes.v1.18.2 cp -r LabNotes.v1.13.2/extensions LabNotes cd LabNotes.v1.18.2/maintenance php update.php sudo mv LabNotes/upload LabNotes.v1.18.2 sudo mv LabNotes/zhangloupload LabNotes.v1.18.2 sudo mv probedesign ../LabNotes.v1.18.2/ sudo mv PeakPicker.jar ../LabNotes.v1.18.2/ sudo mv SeqScannerInstall.exe ../LabNotes.v1.18.2/ sudo mv RobertsLabNotesSupplement ../LabNotes.v1.18.2/ mv LabNotes LabNotes.v1.15.1 mv LabNotes.v1.18.2 LabNotes download the latest version of Sphinx extension: SphinxSearch-MW1.18-r92378.tar.gz Extract the tarball and copy all the files to LabNote/extension/SphinxSearch folder.
To rebuild the mysql database from mysql dump: /usr/local/mysql/bin/mysql -u wikiuser -pPASSWORD wikidb < wiki_db_current.sql
Meangenemachine
- Duel Intel Xeon X5645 (12 cores), 32 GB RAM
- Booting from 500GB drive
- Drive space: 600GB_store, 1TB_store1, 1TB_store2, 2TB_store1, 2TB_store2
- Ubuntu 11.04
- For general use
- address: meangenemachine.dynamic.ucsd.edu
- Setting up DHCP network:
- Request DHCP-only networking with ACS
- In: /etc/network/interfaces
auto lo eth0 iface eth0 inet dhcp iface lo inet loopback
- Restart networking
sudo /etc/init.d/networking restart
- Get IP
sudo dhclient
Genemapster
- Dual Intel Xeon X5520 (8 cores), 32 GB RAM, Tesla C1060 GPU
- Ubuntu 10.04.3 LTS
- For general use and for running GPU softwares
- address: genemapster.dynamic.ucsd.edu
Genome-miner
- Recently reinstalled using MacOS instead of Ubuntu; see notes here
- A MacPro (8 core, 16GB RAM, 4TB), dedicated for GA Pipeline (PFBH406)
- MAC addresses:
- Port 1: 00:25:00:ee:6f:c8; connected to the campus network;
- IP=132.239.135.41;
- Subnet: 255.255.0.0
- Gateway: 132.239.135.1
- DNS: 132.239.0.252, 128.54.16.2
- Port 2: 00:25:00:ee:3f:85; connected to GA PC;
- IP=192.168.137.11
- Port 1: 00:25:00:ee:6f:c8; connected to the campus network;
- MAC addresses:
- Installation of Ubuntu 9.04 (AMD64 Desktop).
- Installed rEFIt for dual booting (http://refit.sourceforge.net/).
- Installed Ubuntu 9.04 Desktop from ISO image.
- Turned out that all the hard drives were not recognized with the RAID card. Removed the RAID card.
- Press "c" to boot from the CD.
- The OS was install in the hard drive in Bay 4.
- The other two hard drives in Bay 2&3 were also reformatted to ext3
- Ubuntu booted up correctly, but without network connection. Turned out that the Ethernet card was too new.
- Downloaded the driver from sf.net/projects/e1000, manually changed the following two files, compiled and installed the driver.
Added the following to the netdev.c: {PCI_VDEVICE(INTEL, 0x10F6), board_82574} and to hw.h #define E1000_DEV_ID_82574L_NEW 0x10F6
- Installed GA_pipeline 1.4
- Install the Ubuntu Development Package:
apt-get install build-essential
- Installed fftw-3.2.1, need to compile with --enable-single;
- Installed gnuplot;
- Installed ImageMagik (for the convert function);
- Installed zlib, bzlib2;
- Install XML::Simple perl module.
- Run make, all prerequisites passed.
- Installed UNAFold (http://dinamelt.bioinfo.rpi.edu/) in /usr/local/
Printers
- Brother HL-5250DN, PFBH406, attached to ZhangLab-VGN through USB. IP=132.239.135.123. (Used to be attached to ZhangLab-GelDoc through USB. IP=132.239.25.45)
- Can access via smb://132.239.135.123/Brother%20HL-5250DN on Macs.
- Brother HL-4040CN, PFBH402, network printer, IP=172.16.25.21.
- Brother MFC-7220, PFBH402, attached to Time Capsule through USB.
- ZhangLab-GelDoc, PC desktop, attached to the BioRad GelDocXL system.
- IP: 132.239.25.45.
- To map the shared data folder, use the network path: \\132.239.25.45\GelImages
- To map the shared data folder on mac, use the network smb: \\132.239.25.45\GelImages
- ZhangLab-Chromo4, PC desktop, attached to Biorad Chromo4 Thermalcycler.
- IP: 132.239.135.43.
- To map the shared data folder, use the network path: \\132.239.135.43\Users
- ZhangLab-VGN, PC laptop.
- ZhangLab-IX81, the WinXP workstation attached to the Olympus IX81 microscope. \\172.16.25.86 MAC address: 00-25-64-A8-9D-1C, the password is "GenomeClub".
Biogem Data
- To obtain data from Biogem, you must have sudo privileges.
- On genome-miner, issue the command:
sudo mount /media/Biogem
- To unmount the drive once you are done, type:
sudo umount /media/Biogem
Synology NAS - Diskstation
- Synology DS2411+
Install Notes
- Installed Synology Diskstation with 6 Hitachi 3 TB Drives
- Part numbers: 0S03230 (Bays 1-3) and 0F12460 (Bays 4-6)
- Seems to be the same drive, but from different production cycles?
- Diskstation recognizes these as the same drive model
- Installed Synology DSM Software using included disk
- Currently formatting all six drives as a RAID5 - ~15 Tb storage space
- Decided to perform full disk check to make sure we do not have any failures
Administering the NAS
- Visit its IP Address (currently 192.168.1.22:5000, you must be on the ZhangLab wireless router) with any web browser
- Username is admin, password is Zhang lab's common password
- Can control disks, file sharing, and more from web interface
Installation Plans
Step 1
- Copy SeqStore2 and other contents of Ext9T and Ext6T to 15 Tb partition
- Erase Ext9T and Ext6T
- Move the 3 functional 3TB drives from Ext9T to Diskstation
- Set them up as either individual drives or RAID0 most likely (Scratch Space)
- Load a backup 2TB drive into Ext9T
- Re-setup each as either RAID5 or RAID0
Step 2
- Dr. Zhang has ordered 5 more 3TB hard drives - load 3 of them into Diskstation
- Set them up as either individual drives or RAID1? (Use for more long-term storage
Step 3
- Next, temporarily back up Ext4T to Diskstation
- Erase Ext4T, remove the two drives
- Load two 3TB drives into Ext4T, set up as a 6 TB RAID0
- Move data back from Diskstation to Ext4T
Results
- This will leave us with:
- Synology Diskstation: 15 TB RAID5, 18 TB individual disks, joined, or RAID0
- Ext9T: 6-8 TB RAID5 or RAID0
- Ext6T: 6-8 TB RAID5 or RAID0
- Ext4T: 6 TB RAID0
- Internal Storage on Genome-Miner: 8 TB in 4 disks
- This will leave us with 3 2TB hard drives left over for backups.
- Should order more Hitachi drives of this model; can use them as hotswaps when RAID fails