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==Genome-miner== ===Current Data Storage=== * Note 1:RO - Read only; RW - Read and write * Note 2: Our plan right now is to have people migrate to using new volumes once every 3-4 years and making older volumes become long-term storage. As our drives are getting older, we need a better way to monitor them so that failed disks can be replaced as soon as possible in order to avoid volume crashes. Raid 5 have 4+1 redundancy, so each 12-bay box can handle up to 2 disk failures. * Note 3: Home_Raid1 and Scratch_SSD are software raids. {| class="wikitable" | align="center" style="background:#f0f0f0;"|'''Directory Name''' | align="center" style="background:#f0f0f0;"|'''Total HDD size''' | align="center" style="background:#f0f0f0;"|'''Raid''' | align="center" style="background:#f0f0f0;"|'''Read speed''' | align="center" style="background:#f0f0f0;"|'''Write speed''' | align="center" style="background:#f0f0f0;"|'''Permissions''' | align="center" style="background:#f0f0f0;"|'''Descriptions''' |- | Home_Raid1||6TB||Raid 1||TBD||TBD||RW||Home directories with mirroring |- | Scratch_SSD||4TB||Raid 0||TBD||TBD||RW||Working directories, not good for long term storage |- | 12TB_ext ||12TB||Raid 0||TBD||TBD||RW||Working directories, not good for long term storage |- | NAS2_volume1||30TB||Raid 5||TBD||TBD||RO||Confocal Store & long term storage |- | NAS3_volume1||60TB||Raid 5||TBD||TBD||RO||SeqStore2016 & FreshReads |- | NAS3_volume2||60TB||Raid 5||TBD||TBD||RW||Long term storage & working |- | NAS1_volume1||30TB ||Raid 5||TBD||TBD||Not mounted||Long term storage & working |- | NAS1_volume2||30TB||Raid 5||TBD||TBD||Not mounted||Long term storage & working |- | NAS2_volume2||60TB||Raid 5||TBD||TBD||Not mounted|| '''Unused Volume''' |} ===Summer 2016=== * Summer 2016 - new Dell PowerEdge T630 server tower **Chassis with up to 8, 3.5" Hard Drives, Software RAID, Tower Configuration **Dual Intel® Xeon® E5-2697A v4 2.6GHz,40M Cache,9.60GT/s QPI,Turbo,HT,16C/32T (145W) Max Mem 2400MHz **2400MT/s RDIMMs **2x 32GB RDIMM, 2400MT/s, Dual Rank, x4 Data Width **No RAID with Embedded SATA (1 SATA HDD or SATA SSD) **Embedded SATA **1x 240GB Solid State Drive SATA Mix Use MLC 6Gbps 2.5in Hot-plug Drive,3.5in HYB CARR, SM863 **Single, Hot-plug Power Supply (1+0), 750W **3 Year Basic Hardware Warranty Repair, 5X10 HW-Only, 5x10 NBD On-site * Installation notes here: [[File:final_configurations.sh]] ===Dinh=== *Re-installed Ubuntu in December 2014. See notes [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh:Genome_Miner_Upgrades here]. ===Robert/Athurva Era=== *Recently reinstalled using MacOS instead of Ubuntu; see notes [[Genome_Miner_Reinstall |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 *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/ ===Apache Web Server=== * Brandon said we'd better have a web server on Genome-miner since majority of the data were analyzed there. * Make your own folder in /opt/lampp/htdocs/ * Put the files you want to share in your own folder * Example: http://132.239.25.238/shg047/ * Usage: http://132.239.25.238/hello.pl
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