hpc
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| - | ====== Changelog ====== | ||
| - | * **November 30, 2009**: Added '' | ||
| - | * **December 2, 2009**: Installed several bioinformatics tools into ''/ | ||
| - | * dca (with costs in ''/ | ||
| - | * msa | ||
| - | * toppred: ftp:// | ||
| - | * gnuplot | ||
| - | * **December 4, 2009**: Installed new versions of 454 software (version 2.3, taken from the flx cluster) | ||
| - | * **January 12, 2010**: Installed '' | ||
| - | * **January 13, 2010**: Changed the number of nfs daemon instances in ''/ | ||
| - | * **January 14, 2010**: Installed '' | ||
| - | * **January 18, 2010**: Installed ''/ | ||
| - | * **January 19, 2010**: | ||
| - | * Deleted three lines from SGE's conf ('' | ||
| - | < | ||
| - | rsh_command | ||
| - | rlogin_command | ||
| - | * Created link from ''/ | ||
| - | < | ||
| - | $ sudo ln -s /scratch/ / | ||
| - | $ sudo chmod 777 /scratch/ | ||
| - | $ sudo chmod o+t / | ||
| - | * **January 20, 2010**: Installed 32-bit compatibility libraries '' | ||
| - | * **January 22, 2010**: | ||
| - | * Removed 32-bit packages from HPC: [[hpc: | ||
| - | * Ran some trivial application updates: ''# | ||
| - | * **January 26, 2010**: Ran trivial application updates: ''# | ||
| - | * **February 23, 2010**: Disabled '' | ||
| - | * **March 4, 2010**: Added '' | ||
| - | * **March 5, 2010**: Added options to ''/ | ||
| - | < | ||
| - | ForwardX11Trusted | ||
| - | * **March 9, 2010**: Changed the SGE configuration ('' | ||
| - | < | ||
| - | rlogin_command | ||
| - | rsh_daemon | ||
| - | rlogin_daemon | ||
| - | qlogin_command | ||
| - | qlogin_daemon | ||
| - | See http:// | ||
| - | |||
| - | * **March 19, 2010**: Installed B2G4PIPE (blast2go- A version for B2G annotation without FrontEnd (GUI) for Pipeline Integration) http:// | ||
| - | * **March 30, 2010**: Installed Staden packages 1.7 and 2.0.0b6 to ''/ | ||
| - | < | ||
| - | $ sudo ln -s / | ||
| - | $ sudo ln -s / | ||
| - | * **April 8, 2010**: Archived '' | ||
| - | < | ||
| - | Note, it is gzipped so you must use '' | ||
| - | < | ||
| - | * **April 12, 2010**: Installed '' | ||
| - | * **April 20, 2010**: Installed PhyML 3.0 to ''/ | ||
| - | * **April 21, 2010**: Installed latest PHYLIP to ''/ | ||
| - | * **April 23, 2010**: | ||
| - | * **May 12, 2010**: Ran trivial software updates: | ||
| - | < | ||
| - | libxml2-python.x86_64 ntp.x86_64 openssh.x86_64 sudo.x86_64 strace perl tcp_wrappers.x86_64 tzdata.noarch \ | ||
| - | openssl.x86_64 openssh-clients.x86_64 python26.x86_64 openssl-devel.x86_64 openssh-server.x86_64 | ||
| - | sqlite-dev.x86_64 psmisc.x86_64 pciutils.x86_64 pciutils-dev.x86_64 iptables.x86_64 dhclient.x86_64 \ | ||
| - | chkrootkit.x86_64</ | ||
| - | It's easy to run trivial software updates after looking at the output to the '' | ||
| - | * **May 13, 2010**: Copied some missing files to the compute nodes... parse the output of '' | ||
| - | < | ||
| - | * **May 18, 2010**: Install Biopython and NumPy for '' | ||
| - | * **May 18, 2010**: Head node crashed after a heavy python script was run (using python 2.6 and Biopython) so we used it as an opportunity to upgrade several packages which require a reboot since there was downtime anyways (kernel, udev, hal, etc). | ||
| - | * **May 18, 2010**: Installed a new Python 2.6.5 to ''/ | ||
| - | * **May 20, 2010**: Downloaded [[http:// | ||
| - | * **May 22, 2010**: Install the [[http:// | ||
| - | * **May 25, 2010**: Several ports have been allowed to the HPC: SSH, NTP, ICMP. | ||
| - | * Limit SSH access to users in the '' | ||
| - | * Limit compiler access to users in the '' | ||
| - | * **June 4, 2010**: | ||
| - | * **June 22, 2010**: Installed some software for the Phylogenetics course: | ||
| - | * BEAST | ||
| - | * RAxML | ||
| - | * **June 29, 2010**: Installed more software for the Phylogenetics course: | ||
| - | * Dendroscope 2.7.3 | ||
| - | * Dendroscope 2.7.4 | ||
| - | * Splitstree 4.11.3 | ||
| - | * **June 30, 2010**: Installed the Celera Whole Genome Shotgun Assembler and appropriate module files: | ||
| - | * /// | ||
| - | * **August 2, 2010**: Change the SGE queue to '' | ||
| - | * Add '' | ||
| - | * '' | ||
| - | * **August 10, 2010**: Updates from yum: | ||
| - | * < | ||
| - | * **August 12, 2010**: Edit R script to use SGE for picking a random node, /// | ||
| - | * < | ||
| - | qrsh $PROGRAM_CMD --save</ | ||
| - | * The commented out way requires that R runs via an xterm (and fails if X11 isn't active). | ||
| - | * **September 8, 2010**: | ||
| - | * Fine tune SSH access to HPC. The ssh daemon only accepts connections from people in the '' | ||
| - | * < | ||
| - | + : | ||
| - | + : | ||
| - | |||
| - | # some special accounts who can access from anywhere | ||
| - | + : | ||
| - | + : | ||
| - | + : | ||
| - | + : | ||
| - | |||
| - | # everyone else from the corporate network: 192.168.1.2 | ||
| - | + : | ||
| - | |||
| - | # deny everything else | ||
| - | - : | ||
| - | * This allows root locally, a few people from '' | ||
| - | * **September 19, 2010**: | ||
| - | * It appears HPC crashed this weekend... the hardware RAID hiccuped or something, so I had to reboot the server. | ||
| - | * I took that opportunity to run some system updates as well: kernel, openssh-server, | ||
| - | * **September 30, 2010**: | ||
| - | * Updated the zabbix agent: | ||
| - | * < | ||
| - | * Still not working for monitoring, need to add a zabbix user and configure the agent... | ||
| - | * **October 1, 2010**: | ||
| - | * Couldn' | ||
| - | * Deleted all zabbix-related stuff and reinstalled to start from scratch: | ||
| - | * < | ||
| - | # rm -rf / | ||
| - | # rm -rf / | ||
| - | # rm -rf / | ||
| - | # yum remove zabbix zabbix-agent | ||
| - | # yum install zabbix-agent</ | ||
| - | * Update /// | ||
| - | * < | ||
| - | PidFile=/ | ||
| - | DisableActive=1</ | ||
| - | * Create the zabbix run directory to store the pid: | ||
| - | * < | ||
| - | # chown -R zabbix / | ||
| - | * Start the zabbix agent: | ||
| - | * < | ||
| - | * **October 12, 2010**: | ||
| - | * Move SSH-specific PAM access rules to the appropriate file, /// | ||
| - | * I had mistakenly added some to /// | ||
| - | * See the configuration of pam_access related to SSH in /// | ||
| - | * Also, comment out the root rules in /// | ||
| - | * **October 19, 2010**: | ||
| - | * Power problems at ILRI, had to rebuild the nodes. | ||
| - | *< | ||
| - | rocks set host installaction compute action=" | ||
| - | * Then physically reboot them. They will PXE boot to their installers... | ||
| - | * **November 8, 2010**: | ||
| - | * Install bowtie, samtools, python 2.6.6, and corresponding module files. | ||
| - | * Add /// | ||
| - | * Find directories in the PATH which don't exist anymore, crude one-liner: | ||
| - | * < | ||
| - | PATH=$PATH | ||
| - | / | ||
| - | / | ||
| - | / | ||
| - | * ... and remove them from the PATH. | ||
| - | * Move the existing /// | ||
| - | * Link a few binaries into the new bin folder for easy access: | ||
| - | * < | ||
| - | # ln -s / | ||
| - | # ln -s / | ||
| - | # ln -s / | ||
| - | # ln -s / | ||
| - | * Now these binaries can be easily accessed without having to use environment modules. | ||
| - | * One bonus of this method seems to be that the nodes can access them... seems to work well? | ||
| - | * **November 18, 2010**: | ||
| - | * Add excludes to headnode' | ||
| - | * < | ||
| - | * from the Rocks wiki here: https:// | ||
| - | * **November 19, 2010**: | ||
| - | * Install mira 3.2.0rc2, and remove older versions. | ||
| - | * **November 21, 2010**: | ||
| - | * Power failure on HPC this weekend, maybe someone shut it down because of the problems in the server room? Still not sure... | ||
| - | * Ran the following updates: | ||
| - | * < | ||
| - | * Noticed a problem with the /// | ||
| - | * < | ||
| - | * **November 23, 2010**: | ||
| - | * Replace CMOS in 8 nodes, should help with nodes not remembering boot order(PXE first!) after power failure. | ||
| - | * **November 26, 2010**: | ||
| - | * Install consed 20.0 | ||
| - | * < | ||
| - | $ sudo mkdir -p / | ||
| - | $ sudo cp consed_linux64bit / | ||
| - | $ sudo ln -s / | ||
| - | $ cd misc/ | ||
| - | $ make | ||
| - | $ sudo cp phd2fasta / | ||
| - | $ cd ../mktrace | ||
| - | $ make | ||
| - | $ sudo cp mktrace / | ||
| - | $ cd ../454/ | ||
| - | $ gcc sff2scf.c -o sff2scf | ||
| - | $ gcc sff2scfAndPhd.c -o sff2scfAndPhd | ||
| - | $ gcc sffinfo.c -o sffinfo | ||
| - | $ sudo cp sff2scf sff2scfAndPhd sffinfo / | ||
| - | $ cd ../ | ||
| - | $ sudo cp * / | ||
| - | $ sudo mkdir / | ||
| - | $ sudo cp / | ||
| - | $ sudo mkdir / | ||
| - | $ cd ../misc/ | ||
| - | $ sudo cp *.fa *.fasta *.seq / | ||
| - | </ | ||
| - | * I disabled 454's '' | ||
| - | * Created a module file for consed | ||
| - | * **January 17, 2010**: | ||
| - | * < | ||
| - | * HPC was shutdown in the weekend due to a power outage, so it was a good chance to reboot it anyways before too many people started running jobs. | ||
| - | * Still haven' | ||
| - | * **January 20, 2011**: | ||
| - | * Updated 454 applications to 2.5.3 (gsAssembler, | ||
| - | * the official installers put the files in /// | ||
| - | * **January 28, 2011**: | ||
| - | * Install ARB in /// | ||
| - | * HPC crash because of Anne's ARB... had to sysrq... | ||
| - | * **February 6, 2011**: | ||
| - | * Had to restart lsf on the head and compute nodes to fix the " | ||
| - | * **February 11, 2011**: | ||
| - | * Resurrect some compute nodes by fixing their grub parameters at boot: '' | ||
| - | * Shut some compute nodes down to save heat during the weekend' | ||
| - | * **February 14, 2011**: | ||
| - | * Turn compute nodes back on | ||
| - | * Install mira 3.2.1, /// | ||
| - | * **February 18, 2011**: | ||
| - | * Install marthlab' | ||
| - | * Install Strand' | ||
| - | * **March 31, 2011**: | ||
| - | * Reboot HPC because some problems with the KVM's mouse, and the tape drive is behaving funny | ||
| - | * Update Storix SBadmin from 6.3.4.4 to 6.3.4.5 | ||
| - | * Trying to clean up the log files, drop packets from CIP's HPC trying to grid with us: | ||
| - | * < | ||
| - | * **May 3, 2011**: | ||
| - | * Run updates: | ||
| - | * < | ||
| - | * **May 5, 2011**: | ||
| - | * Reconfigure the NFS server' | ||
| - | * < | ||
| - | LOCKD_UDPPORT=32769 | ||
| - | MOUNTD_PORT=892 | ||
| - | RQUOTAD_PORT=875 | ||
| - | STATD_PORT=662 | ||
| - | STATD_OUTGOING_PORT=2020</ | ||
| - | * Reconfigure iptables to allow connections from the corporate ILRI network, /// | ||
| - | * < | ||
| - | -A INPUT -s 192.168.1.2/ | ||
| - | -A INPUT -s 192.168.1.2/ | ||
| - | -A INPUT -s 192.168.1.2/ | ||
| - | -A INPUT -s 192.168.1.2/ | ||
| - | -A INPUT -s 192.168.1.2/ | ||
| - | -A INPUT -s 192.168.1.2/ | ||
| - | -A INPUT -s 192.168.1.2/ | ||
| - | -A INPUT -s 192.168.1.2/ | ||
| - | -A INPUT -s 192.168.1.2/ | ||
| - | -A INPUT -s 192.168.1.2/ | ||
| - | -A INPUT -s 192.168.1.2/ | ||
| - | * **May 11, 2011**: | ||
| - | * Reboot HPC again and REALLY apply the updates from May 3. Appears they didn't get run last time. | ||
| - | * **May 16, 2011**: | ||
| - | * Update SSH access configuration in /// | ||
| - | * < | ||
| - | + : | ||
| - | * **May 17, 2011**: | ||
| - | * Re-enable the system MySQL. | ||
| - | * **May 27, 2011**: | ||
| - | * Hmmm, for some reason the Rocks MySQL wasn't running on HPC. Start it: | ||
| - | * < | ||
| - | * **May 31, 2011**: | ||
| - | * Install new version of clustalw into /// | ||
| - | * Update module files for R, python, clustalw, and dendroscope to use a cleaner, more-robust syntax for conflicts and man pages | ||
| - | ====== New HPC! ====== | ||
| - | * **June 18, 2011**: | ||
| - | * Install new HPC! | ||
| - | * **June 20, 2011**: | ||
| - | * Install muscle 3.8.31 into /// | ||
| - | * IPtables rules for samba seem to need some work, windows clients are having problems connecting so I've disabled iptables for now. | ||
| - | * **June 28, 2011**: | ||
| - | * Install phred, phrap, and cap3 + module files. | ||
| - | * **June 30, 2011**: | ||
| - | * Install seqclean, estscan, and tgcil + module files. | ||
| - | * **July 1, 2011**: | ||
| - | * Remove the DefaultTime from the slurm '' | ||
| - | * Allow '' | ||
| - | * < | ||
| - | # allow Alan to query the RAID status remotely. | ||
| - | aorth ALL = NOPASSWD: RAIDSTATUS</ | ||
| - | * Remove Rocks' Wordpress because Ian Moore said it showed up in an external security scan and we're not using it. | ||
| - | * < | ||
| - | * **July 5, 2011**: | ||
| - | * Make changes to allow the RAID monitoring script to run via a cron job (disallow the " | ||
| - | * < | ||
| - | # see `man sudoers` cuz this syntax is confusing. | ||
| - | Defaults!RAIDSTATUS !requiretty</ | ||
| - | * **July 12, 2011**: | ||
| - | * Change php's mysqli and mysql sockets to the system mysql (they were set to Rocks' | ||
| - | * Installed formtools | ||
| - | * Remove the pre-installed mediawiki as it's just going to get out of date! | ||
| - | * Install VirtualBox 4.0.10: | ||
| - | * < | ||
| - | sudo rpm --import oracle_vbox.asc | ||
| - | wget http:// | ||
| - | sudo cp virtualbox.repo / | ||
| - | sudo yum list available virtual\* | ||
| - | sudo yum install VirtualBox-4.0.x86_64</ | ||
| - | * **July 21, 2011**: | ||
| - | * Interproscan done installing. | ||
| - | * Installed glimmer3 + module file but it seems Rocks already has a glimmer3... hmmm. | ||
| - | * **August 4, 2011**: | ||
| - | * Installed Affymetrix Powertools (APT) in /// | ||
| - | * Installed updates: '' | ||
| - | * Update VirtualBox to 4.1.0 | ||
| - | * **August 5, 2011**: | ||
| - | * Fix the lims server' | ||
| - | * Add root user to the ssh group | ||
| - | * Edit /// | ||
| - | * < | ||
| - | + : | ||
| - | * **August 10, 2011**: | ||
| - | * Installed git from the webtatic repo, see here: http:// | ||
| - | * **August 11, 2011**: | ||
| - | * Enable java plugin on Firefox: | ||
| - | * < | ||
| - | * **August 22, 2011**: | ||
| - | * Install boost 1.47.0, samtools 0.1.17, and cufflinks 1.0.3 | ||
| - | * Write documentation and module files for each | ||
| - | * Update galaxy to use newer samtools (0.1.17 instead of 0.1.16) | ||
| - | * **September 1, 2011**: | ||
| - | * Install MEGAN: | ||
| - | * /// | ||
| - | * set the default memory allocation to 16G in /// | ||
| - | * **September 2, 2011**: | ||
| - | * Install kernel updates | ||
| - | * Install new SAS card to prepare for tape library | ||
| - | * Enable virtualization support in the BIOS | ||
| - | * Apparently MySQL and munge weren' | ||
| - | * < | ||
| - | sudo chkconfig --level 2345 munge on</ | ||
| - | * Install '' | ||
| - | * **September 6, 2011**: | ||
| - | * Fix the module files for '' | ||
| - | * Update CrossmatchSearchEngine.pm to fix a minor bug in RepeatMasker (more info here: http:// | ||
| - | * Install rmblast 2.2.23+ in /// | ||
| - | * **September 22, 2011**: | ||
| - | * Install the new tape library (but haven' | ||
| - | * **September 23, 2011**: | ||
| - | * Install mira 3.4.0 (and module file) in /// | ||
| - | * Install staden 2.0.0b8 (and module file) in /// | ||
| - | * **September 27, 2011**: | ||
| - | * Install clview: | ||
| - | * < | ||
| - | tar zxf clview_linux_i386.tar.gz -C clview | ||
| - | cd clview | ||
| - | sudo cp libFOX-1.0.so.0* /usr/lib/ | ||
| - | sudo cp clview / | ||
| - | sudo chmod 755 / | ||
| - | clview</ | ||
| - | * **September 29, 2011**: | ||
| - | * Add Harry Noyes to the '' | ||
| - | * Access to GFHPC and HPC from outside is still down though, James Indimuli in ICT says he'll get back to me. | ||
hpc.1317305841.txt.gz · Last modified: by aorth