use remote debugging
mvn exec:exec -Dexec.executable="java" -Dexec.args="-classpath %classpath -Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=1044 com.mycompany.app.App"
Then in your eclipse, you can use remote debugging and attach the debugger to localhost:1044.
Sunday, March 23, 2014
Tuesday, February 4, 2014
chkconfig replavement in Ubuntu
http://www.debuntu.org/how-to-managing-services-with-update-rc-d/
How-To: Managing Services With Update-Rc.D
Posted by chantra on July 5th, 2007
Wednesday, January 29, 2014
Configuring Supermicro IPMI interface NIC using ipmitool
Newer Supermicro IPMI interfaces come configured by default in
“failover” mode which means that the IPMI will bind to either the
dedicated IPMI NIC port or share with one the the machine NIC ports.
This can cause IPMI to come up on wrong NIC and hence be inaccessible if the dedicated NIC doesn’t detect a link.
You can use ipmitool to change this behavour
First query the current setting:
The result will be one of the following
Next to configure it you can use one of the following.
For older models:
For X9 motherboards:
References for this can be found here:
http://www.supermicro.com/support/faqs/faq.cfm?faq=9829
http://www.supermicro.com/support/faqs/faq.cfm?faq=14417
This can cause IPMI to come up on wrong NIC and hence be inaccessible if the dedicated NIC doesn’t detect a link.
You can use ipmitool to change this behavour
First query the current setting:
ipmitool raw 0x30 0x70 0x0c 0The result will be one of the following
0x00 = Dedicated
0x01 = Onboard / Shared
0x02 = Failover
Next to configure it you can use one of the following.
For older models:
ipmitool raw 0x30 0x70 0x0c 1 1 0For X9 motherboards:
ipmitool raw 0x30 0x70 0x0c 1 0References for this can be found here:
http://www.supermicro.com/support/faqs/faq.cfm?faq=9829
http://www.supermicro.com/support/faqs/faq.cfm?faq=14417
Thursday, January 23, 2014
eth* and em*
https://access.redhat.com/site/documentation/en-US/Red_Hat_Enterprise_Linux/6/html/Deployment_Guide/appe-Consistent_Network_Device_Naming.html
Monday, January 13, 2014
Difference bewteen Pylab and pyplot
Matplotlib is the whole package; pylab is a module in matplotlib that gets installed alongsidematplotlib; and matplotlib.pyplot is a module in matplotlib.
Pyplot provides the state-machine interface to the underlying plotting library in matplotlib. This means that figures and axes are implicitly and automatically created to achieve the desired plot. For example, calling plot from pyplot will automatically create the necessary figure and axes to achieve the desired plot. Setting a title will then automatically set that title to the current axes object:
Pylab combines the pyplot functionality (for plotting) with the numpy functionality (for mathematics and for working with arrays) in a single namespace, making that namespace (or environment) even more MATLAB-like. For example, one can call the sin and cos functions just like you could in MATLAB, as well as having all the features of pyplot.
The pyplot interface is generally preferred for non-interactive plotting (i.e., scripting). Thepylab interface is convenient for interactive calculations and plotting, as it minimizes typing. Note that this is what you get if you use the ipython shell with the -pylab option, which imports everything from pylab and makes plotting fully interactive.
Monday, December 30, 2013
[CC]IPMI over LAN on Ubuntu 12.04
Doing this on two of these machines:
After a reboot, visit the IP of the IPMI LAN device in a browser from a separate computer. I found everything worked except console redirection (SOL – Serial Over Lan,) as indeed this has to be setup inside the Linux Kernel.
These are the steps I took to make console redirection work:
1. The first thing I did was install the tools and setup the modules.
EDIT 07/06/13:
System Information
Manufacturer: Supermicro
Product Name: X9DBL-3F/X9DBL-iF
In the IPMI section of the BIOS,
set the IP/gateway/netmask addresses. (This can also be done from
inside the Linux Kernel with `ipmitool` after loading the modules.) I
left all the other IPMI settings as default.Manufacturer: Supermicro
Product Name: X9DBL-3F/X9DBL-iF
After a reboot, visit the IP of the IPMI LAN device in a browser from a separate computer. I found everything worked except console redirection (SOL – Serial Over Lan,) as indeed this has to be setup inside the Linux Kernel.
These are the steps I took to make console redirection work:
1. The first thing I did was install the tools and setup the modules.
- Install the needed software:
sudo apt-get install ipmitool freeipmi-tools
- Find the information about the BMC (press ‘q’ to ‘quit’ less when done):
sudo ipmi-locate | less
- I found the information needed in the first few lines of the output as seen here:
Probing KCS device using DMIDECODE... done IPMI Version: 2.0 IPMI locate driver: DMIDECODE IPMI interface: KCS BMC driver device: BMC I/O base address: 0xCA2 Register spacing: 1
- Add the appropriate modules into the Kernel, for the ‘ipmi_si’ one use the information found with ipmi-locate like this:
sudo modprobe ipmi_si type=kcs ports=0xCA2 regspacings=1 sudo modprobe ipmi_devintf sudo modprobe ipmi_msghandler sudo modprobe ipmi_poweroff sudo modprobe ipmi_watchdog
- Now if you “ls -ahl /dev/ipmi*” you should see an ipmi0
- Make a copy of an existing tty and edit it. I’m using vim, but use whatever editor you like:
sudo cp /etc/init/tty1.conf /etc/init/ttyS1.conf sudo vi /etc/init/ttyS1.conf
- Edit the file to reflect ‘ttyS1′ instead of just ‘tty1′. Also edit the last line to use a baud rate of 115200, and tell it the type ’vt100′. Mine looks like this when done:
# ttyS1 - getty # # This service maintains a getty on ttyS1 from the point the system is # started until it is shut down again. start on stopped rc RUNLEVEL=[2345] stop on runlevel [!2345] respawn exec /sbin/getty -8 115200 ttyS1 vt100
- We must pass “console=tty1 console=ttyS1,115200n8″ as options to the command in our boot loader that starts the kernel. Note: the order of options passed to the kernel is important, the last “console” entry defines the ‘default’ console for the kernel. For grub-pc open up /etc/default/grub with your favorite editor and with sudo permissions and change GRUB_CMDLINE_LINUX=”" line to look like this:
GRUB_CMDLINE_LINUX="console=tty1 console=ttyS1,115200n8"
- Don’t forget to update grub after this: (I also changed ‘GRUB_HIDDEN_TIMEOUT_QUIET’ to false, and I uncommented the ‘GRUB_TERMINAL=console’ line.)
sudo update-grub3. Now we’re pretty much ready to connect. The only problem I found was with the launch.jnlp file that the Supermicro webUI spits at you. I’ll show you the edits I made to make it work:
- Again visit the IP pointed at your IPMI and login in to the webUI. Click the ‘Launch SOL’ button under the ‘Remote Control’ tab, choose to save the file instead of opening it in your browser’s web java application (‘IcedTea java web start’ in my case.)
- Towards the beginning of the file, look for these lines:
<property name="jnlp.packEnabled" value="true"/> <property name="jnlp.versionEnabled" value="true"/>
- Copy those two lines and scroll down a little until you see the distribution you are running and paste them into the there. I did it for each distribution so I didn’t have to think about it. I ended up with entries looking like this:
<resources os="Linux" arch="x86_64"> <property name="jnlp.packEnabled" value="true"/> <property name="jnlp.versionEnabled" value="true"/> <nativelib href="liblinux_x86_64.jar" download="eager" version="1.0.3"/> </resources>
- Lastly, scroll to the end of the file where you will see a list of “argument” xml tags. The one below the one that contains your IP probably contains a seemingly random string of letters, but it needs to be changed to the username you setup to login to the IPMI webUI, and the one below needs to be your password. Like this:
<argument>123.123.123.123</argument> <argument>[username]</argument> <argument>[password]</argument>
- Save the file and run it and you should now be ready to sit in front
of the machine remotely. Reboot the server to watch it boot up, offer
you the opportunity to enter the BIOS, and then offer you a login
prompt.
EDIT 07/06/13:
Corrected the line:
GRUB_CMDLINE_LINUX="console=tty0 console=ttyS1,115200n8"
to:
GRUB_CMDLINE_LINUX="console=tty1 console=ttyS1,115200n8"Also,
Corrected the line:
exec /sbin/getty -8 115200 tty1 vt100
to:
exec /sbin/getty -8 115200 ttyS1 vt100Also,
Removed the lines from ttyS1.conf pertaining to ‘containers’:
and (
not-container or
container CONTAINER=lxc or
container CONTAINER=lxc-libvirt)
Everything is running smoothly after this, even when networking is turned off in the kernel.
Tuesday, September 24, 2013
mapping Probe ID to Gene ID by using R
1) in or after 2006, there should be good Probe Id to GENE id map.
2) necessary package:
Biobase,
GEOquery
3) load the GPL platform file:
gpl5425 = getGEO('GPL5425',destdir=".")
## get annotation table
gpl5425_ann = Table(gpl5425)
#make the rownames to be ID
rownames(gpl5425_ann) = gpl5425_ann$ID
--------------------------------------------------------------------------------
ID GB_ACC GENE_SYMBOL
AA799301_PROBE1 AA799301_PROBE1 AA799301 LOC498225
AA799313_PROBE1 AA799313_PROBE1 AA799313 Siat10 ST3
AA799329_PROBE1 AA799329_PROBE1 AA799329 Col10a1
AA799331_PROBE1 AA799331_PROBE1 NM_001007634 Pelo
--------------------------------------------------------------------------------
#assume the expression data is:
gse24417
--------------------------------------------------------------------------------
ID_REF GSM204540 GSM204503 GSM204587 GSM204994
1 NM_016986_Probe1 14.5383 15.6827 14.0196 15.0969
2 NM_016987_Probe1 12.7629 15.6014 13.1481 14.4640
3 NM_016988_Probe1 14.0954 14.0583 13.6035 14.3924
4 M27893_Probe1 12.4787 12.6605 11.6335 14.0050
5 NM_012490_Probe1 8.9914 8.2654 9.2640 6.5239
2) necessary package:
Biobase,
GEOquery
3) load the GPL platform file:
gpl5425 = getGEO('GPL5425',destdir=".")
## get annotation table
gpl5425_ann = Table(gpl5425)
#make the rownames to be ID
rownames(gpl5425_ann) = gpl5425_ann$ID
--------------------------------------------------------------------------------
ID GB_ACC GENE_SYMBOL
AA799301_PROBE1 AA799301_PROBE1 AA799301 LOC498225
AA799313_PROBE1 AA799313_PROBE1 AA799313 Siat10 ST3
AA799329_PROBE1 AA799329_PROBE1 AA799329 Col10a1
AA799331_PROBE1 AA799331_PROBE1 NM_001007634 Pelo
--------------------------------------------------------------------------------
#assume the expression data is:
gse24417
--------------------------------------------------------------------------------
ID_REF GSM204540 GSM204503 GSM204587 GSM204994
1 NM_016986_Probe1 14.5383 15.6827 14.0196 15.0969
2 NM_016987_Probe1 12.7629 15.6014 13.1481 14.4640
3 NM_016988_Probe1 14.0954 14.0583 13.6035 14.3924
4 M27893_Probe1 12.4787 12.6605 11.6335 14.0050
5 NM_012490_Probe1 8.9914 8.2654 9.2640 6.5239
--------------------------------------------------------------------------------
rownames(gse24417) = gse24417$ID_REF
#get the probe id, with upper character
pid = toupper(gse24417$ID_REF)
#get the gene symbol id
gid = gpl5425_ann[pid,]$GENE_SYMBOL
## gid contains empty value: "" , and NA value "NA", find the index of them and delete the lines.
blank_id = which( gid == "")
na_id = which(is.na(gid))
#now combine the final data
unwanted_index = c(blank_id,na_id)
gid = gid[-unwanted_index]
gse24417 = gse24417[-unwanted_index]
gse24417$ID_REF = gid
## now remove the repeated genes
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