Systems Lab-Book
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Most Recent
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- 2009-11-19
A must try article http://hep.kbfi.ee/index.php/IT/KernelTuning
- 2009-11-13
- Updated to libstdc++6 (4.3.2-1.1) from Lenny on headnodes and computenodes
- 2009-07-13
I stopped courier-mta on Owl to see if Thomas stops getting spam. We need to setup an independent mail server.
- 2009-07-13
- Owl got frozen due to an unknown NFS defect. This happened at 4AM, I restarted Owl at 9:30AM. Some things are becoming clear about the NFS defect, it was probably triggered by this:
owl ib1 errors WARNINGs: packets is 10452405.01 (outside range [:1]).
- Owl got frozen due to an unknown NFS defect. This happened at 4AM, I restarted Owl at 9:30AM. Some things are becoming clear about the NFS defect, it was probably triggered by this:
- 2009-07-07
- Today I created about 5 different containers for various purposes. One command that I always forget is:
sudo dpkg-reconfigure locales # and select en_US.UTF-8 UTF-8
- Today I created about 5 different containers for various purposes. One command that I always forget is:
- 2009-07-02
- On node 27 there are R processes in a Noninterruptible sleep state:
grep " D " all-processes node08 : 275 ? D 0:09 \_ [pdflush] node27 : 5200 ? D 6:55 /opt/R-2.9.0/lib64/R/bin/exec/R node27 : 30255 ? D 0:00 [R] node27 : 30320 ? D 0:00 [R] node27 : 19151 ? D 0:00 [R] node27 : 19227 ? D 0:00 [R] node27 : 32241 ? D 0:00 [R]
- On node 27 there are R processes in a Noninterruptible sleep state:
- 2009-06-11
- Some links from the USENIX09 ZFS tutorial:
- 2009-06-11
- Restarting the NFS server on Bicluster takes a very long time. Something is unhealthy about that.
Running /usr/sbin/rpc.mountd and /usr/sbin/rpc.nfsd could un-freeze the nfs-kernel restart init script.
- 2009-05-31
On Biocluster, when eth2 (192.168.2....) is down, many many problems occur Details.
- 2009-05-30
- Fstabs on Biocluster changed to
Projects in Bioinformatics
High Performance Computing
General Linux Solutions
TODO List
BUG Check echo "echo \$PATH" | qsub. /usr/local/bin did not show up on several occasions. (Added 2009-05-30) (fixed 2009-11-19)
Must read http://marc.info/?l=linux-kernel&m=123732127919368&w=2 (added 2008-04-09) (Compleated 2009-11-19)
Discuss Updating R (and possibly a lot of other software) on Bioweb. (added 2008-12-09)
Make the User Guide wiki for Biocluster (qsub, taskset, .forward)
Give professor Girke the capability to install R packages on a system-wide level
A complete /etc/init.d/biocluster-check-config - script that checks the syntax and some semantics of /etc/biocluster
A complete /etc/init.d/biocluster-network-config - script that generates the proper fstab on the head nodes.
A complete /etc/init.d/biocluster-fs-config - script that generates the proper fstab on the head nodes.
A complete /etc/init.d/biocluster-kerberos-config - script that configures the master and the slave KDCs.
A complete /etc/init.d/biocluster-torque - script that start pbs_server and pbs_sched on Biocluster
A map of the topology of the networks
A documented procedure for reverting the golden and owl images to an earlier state
A script that adds new users
Install Munin system monitoring on Biocluster (added 2008-08-25)
Install EMBOSS (added 2008-08-25) (completed 2009-04-14)
Upgrade Phred/Phrap/Consed (added 2009-02-23) (completed 2009-03-05)
Discuss and install ELAND (added 2008-08-25) (completed 2009-03-13)
Test out the reliable NFS problem test (added 2008-09-02) Test script is not good (added 2008-09-29)
Set up an HTTP/FTP cache for for the compute nodes to set of common data sources: NCBI, UniProt, etc... (added 2008-04-14)