Sad state of medical profession

Today when a friend told me about an ad at olx.in about medical seats being sold (for those unaware of the concept, it means paying and getting into medical colleges irrespective of one's qualifications and intellectual merit), I was appalled. I knew that such things do happen. However, these deals were always secretly done. Openly selling seats in colleges is equivalent to committing theft in broad daylight and proudly announcing that it is the thief's right to do so. I believe it is blasphemy against humanity. It is a pity that people consider religious blasphemy very seriously but blasphemy against humanity is so simply ignored.

There is a propagation of crime going on here. These colleges bribe their way out of accreditation process or make a temporary show of fulfilling the requirements of the accreditation. Very rarely some are caught. Obviously the quality of education in such institutes is not up to the mark. The grave question then is whether we can trust diagnoses done by doctors passing our from such institutes that offer seats for sale. This actually is a more serious concern than global warming because incorrect diagnoses will cause undeserved deaths; but sadly no politician talks of it in his/her agenda.

Uninstalling python packages

Continuing my system cleanup, I decided to get rid of all unnecessary python packages.

pip2 list | awk -F ' ' '{print $1}' | grep -vE "django-paypal|boto|mercurial|MySQL-python|nltk" | xargs pip2 uninstall -y

The -y flag indicates confirmation of uninstallation.

Uninstalling all gems

Some time back I was trying out jruby. I had installed multiple gems for it. Today, while cleaning up my system I was trying to get rid of it because it does not have much use to me. However, uninstalling the gems one by one is a pain. So, I wrote the following line to uninstall all gems.

jruby -S gem list | awk -F ' ' '{print $1}' | xargs jruby -S gem uninstall

P.S. : To understand how to construct such one liners please look at my previous post.

Call by reference in Ruby

In Ruby, some objects are passed by value and some by reference. In case, we want to pass by reference some object which by default gets passed by value, we can just use the id value of the object in Ruby's memory, i.e. the object space. The id can be obtained as follows.

some_object = "some intialization"
some_object.object_id

Here is how pass by reference would work using object id values.

def caller
    blah = "blahblueblah"
    callee(blah.object_id)
end

def callee(object_id)
    puts ObjectSpace._id2ref(doc.object_id)
end

Such use should be highly improbable and might even turn out to be bad practice; but sometimes we just want to do things for the heck of it.

Bypassing ActiveRecord cache

ActiveRecord is the default object relational model of the Rails web framework. It obviously follows the active record architectural pattern. Now, ActiveRecord maintains it own query cache which is different from the query cache of the underlying database server. This query cache is a rather simplistic one.

The issue that brought the requirement of query cache bypassing into picture was as follows.

1. a call to first object of the model to check if any records existed (Model.first)
2. raw SQL query to truncate the table
3. a call again to first object of the model to check if any records existed (Model.first)

Now, #1 and #3 obviously generated same SQL query. So, ActiveRecord served #3 from its cache.

We found multiple approaches of bypassing the ActiveRecord cache.

Approach 1
Clear the entire ActiveRecord cache. In Rails 2 this can be done using

ActiveRecord::Base.query_cache.clear_query_cache

In Rails 3, the same can be achieved using the following line.

 ActiveRecord::Base.connection.clear_query_cache

This approach however would clear the entire ActiveRecord cache which in production environment means increasing load on database server which is already the bottleneck. Plus, this approach is like using a jack hammer where a finger-tap would work.

Approach 2
This approach exploits the simplicity of the ActiveRecord cache. It forms the query in such a manner that the query string is very likely to be different from previous queries.

r = call random number generator
where_clause = "r = r"

Appending the above where clause to #1 and #3, we obtained queries that are very likely to be different from previous ones at least within the life time of the cache. This approach is obviously not elegant.

Approach 3
In this approach, we went with raw SQL queries not only for #2 but also for #1 and #3. ActiveRecord does not seem to cache raw SQL queries. So we could replace the call to the 'first' method of the model with something similar to the following.


sql = "select * from table_name limit 1"
ActiveRecord::Base.connection.execute sql

Although we can get the job done by this approach, it is bad practice to execute raw SQL.

Approach 4
Finally, we found a way of doing it through Rails. We need to explicitly tell Rails not to serve our queries from its cache for #1 and #3. This can be done as follows.

Model.uncached do
    Model.first
end

As this method does the job using the Rails framework, the abstraction all provided by ActiveRecord remains unbroken.

Memory snapshot in Jetbrains RubyMine on linux

I use RubyMine on linux for Ruby on Rails development. Of late, it had been hanging up frequently. I reported this to Jetbrains. They got back to me asking me to provide more details so that the concerned developer can try and find more details about the issue. On a side note, their customer support was so fast in responding, I was amazed. Also, the guy responding back was pretty technical himself.

Getting back to the topic, they had asked me to provide a memory snapshot. The process of generating a memory snapshot is described here. However, that process requires users to download YourKit Java Profiler, which apart from being a large download, comes with a 15-day license. To me it did not make sense. So, I got back to them about it and it turns out on linux, you don't really need it. The linux version of RubyMine, comes with the profiler libraries bundled.

$RUBYMINE_HOME/bin/libyjpagent-linux.so
$RUBYMINE_HOME/bin/libyjpagent-linux64.so

To enable its usage all you need to do is, edit the following script and set IS_EAP to "true".

$RUBYMINE_HOME/bin/rubymine.sh

Restarting RubyMine after that change, will show the memory and CPU snapshot icons. It is also advised to provide thread dumps, as described here, along with the memory snapshot.

Extracting logs out of journalctl

Journalctl gives us nice consolidated logs. However, on a number of occasions, we need to extract parts of the logs. There are multiple ways of doing it. To filter by process, you can use PID numbers as shown below.

journalctl _PID=<pid number>

To obtain PID number when you have the process name [or part of the process name], use the following:

ps aux | grep -i <process name>

The manual page only refers to it in examples. A commonly used slicing option is to see logs of current boot only. This can be done as follows.

journalctl -b

Another option is to look at logs of a particular unit only. This can be done in the following way.

journalctl -u <unit name>

The unit name could be some daemon name like 'mysqld'. Unfortunately, this does not work with 'kernel' as a unit. It can be combined with the -b option though. However, I find myself dealing with messages from various units. So, I scan through all messages and find the messages I need. To filter them out, I can use time stamps in the messages using the following format.

journalctl --since='2013-03-06 22:58:34' --until='2013-03-06 23:00:34'

The beginning time stamp works fine; but the ending time stamp does not work. I talked about it at #systemd IRC channel. It is fixed and will be released soon.

Setting up an FTP server on AWS

Recently for testing some code, I had to host an FTP server. I tried doing it on my local first. It was easy. I just had to follow the Arch wiki for vsftpd. File transfers in both directions were working so I thought I can try it on an Amazon instance too.

My local machine ran Arch linux on while the Amazon instance ran Fedora 8. After looking up the details of the package manager for Fedora and some help from a friend, I installed vsftpd on it, applied the same config and started the FTP service. When we started testing it, we could operate successfully from command line but not from the code. From the command line, we were using active mode of operation while the code was using the passive mode, so we looked into the config to check settings related to passive mode of operation. It turned out that the passive mode is enabled by default. However, going through the various options we found an option called pasv_address. From prior experience I know that AWS machines have a private LAN IP and a separate public IP. Now, the OS on the cloud instance is not aware of what public IP it is serving. So, we suspected that in its response it must be asking the client to connect on the private LAN IP which would obviously fail. So we just set the pasv_address option to the public IP of the instance and passive mode started working fine. We could successfully connect to it and get file transfers done. So, we decided to use it for testing our code. However, when we tested it, we saw that our application was trying to post files but it was failing every time. The error we were getting each time said '500: Invalid Port command'.

The FTP protocol really goes funky with ports. It uses separate ports for control and data. The behaviour of data ports is dependent upon the mode of operation. In active mode, the client initiates the data connection and therefore the port selection is done by the client, while in passive mode, the server initiates the data connection and therefore the port selection is done by the server. We were using the passive mode of operation and the server was hitting the client at a port that later turned out to be blocked. To debug the situation, we tried connecting to the FTP server from the command line utility 'ftp' using the following command.

ftp ip address of FTP server

To turn on the passive mode and debug mode, we can use the commands 'passive' and 'debug' respectively. However, they only set the options on the client without actually sending any control data to the server. To test the FTP service, try some command that sends some control data. We went with an 'ls'. The following FTP commands were executed in sequence.

PASV
LIST

The PASV commands [1] outputs a line, like the following, indicating the port the data transfer will happen.

Entering Passive Mode (1,2,3,4,224,186)

The port has to be calculated from the last two numbers using the following formula.

n1 x 256 + n2

In the above instance, it is 224 x 256 + 186 = 57530. Once we knew that the issue was the port that the FTP server was trying to communicate to the application machine on was blocked, we decided to configure the FTP server to connect on some port within the open port range. This can be done setting the pasv_min_port and pasv_max_port options correctly in vsftpd.conf. Once we got the server connect to the client on proper ports, the transfers worked fine.

[1] A reference of FTP commands.

Getting to know the Syslog protocol

Recently I was looking into FTP issues, when I learnt some details about Syslog. I was using vsftpd for hosting an FTP service. I had enabled logging but I was not seeing anything in journalctl output. The reason for that turned out to be a configuration flaw. I had not turned on the option for vsftpd to use syslog. Once I turned the option on, proper log files were created.

I do not have Syslog-ng or any other syslog package installed. I had uninstalled it when I switched to systemd. So, I had not enabled that option in vsftpd. However, as it turns out when I turn that option on vsftpd uses the syslog protocol for logging. Systemd listens for messages sent using that protocol and creates appropriate logs.

This is a great way of unifying all logging. Individual packages do not have to bother about logging. They just act as clients of the protocol and the listener will take care of maintaining the logs. There are instances of similar architecture being followed for logging in other domains too.

As it turns out, there are standardized versions of the syslog protocol:

• Syslog protocol
• BSD Syslog protocol

The version used commonly is the BSD one even the former is more advanced. Now syslog is being replaced by systemd's journal because it capitalizes over syslog. It provides efficient transfer of binary data and supports JSON. Maintaining logs is much easier.

It was interesting to know that even though syslog packages are becoming obsolete, the syslog protocol is still the logging standard. It is actually a nice example of robust architecture surviving over the years.