mongod command "corrupting" MongoDb installation? - mongodb

Question

I am using Ubuntu 14.04 LTS and I have installed MongoDB 3.2.1. I had various problems with it that I fixed by either finding help from the internet (thanks Google) or by uninstalling and re-installing MongoDb.
One persistent problem that I cannot fix, unless I re-install, is by running mongod on the terminal. Currently my mongodb installation is working properly. With sudo service mongod start I start mongodb (I commented out start on xxxx line at /etc/init/mongod.conf so it doesn't auto start.) and with sudo service mongod stop I can stop it normally atm. And it correctly uses /var/lib/mongodb path for saving my collections.
If however after I stop mongodb with sudo service mongod stop I hit, on the terminal, mongod then mongodb breaks. I have gotten all kinds of errors like
Unusable mongod.lock. I have gotten around it, in a previous install, by doing sudo mongod but that was not a proper solution.
/data/db folder not found !!. Why look for it in the first place? The /etc/mongod.conf specifies the dbpath /var/lib/mongodb which is also the default when mongodb gets installed !!?? I have gotten around it as well with the mongod --dbpath /var/lib/mongodb option.
I think there was one more error that I don't remember but I also fixed/gotten_around it by finding solutions online.
I know that by re-installing and by never running mongod I can - for now? - not face those problems again (which looks a much better solution that the "workarounds" I did whenever those problems arose. I am wondering however what it is that is going wrong when I type mongod instead of sudo service mongod start ?!
In case somebody tries to replicate the problem know that I ve done only two modifications on my system after installing:
Commenting out the start on xxxx line at /etc/init/mongod.conf
Disabling transparent hugepages as described on the answer here.
I don't think anyone of those should interfere with my installation.
Can anyone help me understand what is going on? Aren't those commands supposed to do the same thing??
Thanks for your help.

Answer 1

Ok, I will try to answer.
First, unless you know what you are doing, you should not start mongod manually.
In general (a bit simplified), calling [sudo] service mongod start, you instruct the system to read the according file in /etc/init and start the executable according to the configuration described in said file.
When you started mongod by hand, however, you actually called the mongod binary, the server software itself – while the name is the same as the service, the two commands have few things in common. The binary does not use the /etc/mongod.conf by default, falling back to its default values for the various settings. Actually, you can see that the config file is explicitly defined in the init script. This is why mongod tried to find /data/db.
You can find said binary by issuing
which mongod
Regarding the lock file: When mongod is started by the system, user root actually assumes the effective user id of mongod (or mongodb I don't know for Ubuntu of the top of my head). When you tried to start it from your user id, you do not have the privileges to overwrite the lock file. When you used sudo mongod afterwards, you assumed the effective user id of root which on the other hand is allowed to overwrite said file. However, mongod will the run as root which is a security no-no.
An init script defines which environment to use, which user to run under and a lot of other stuff. Unless you really know what you are doing, you should not even fiddle with them, much less skip it.
And now, with the finger up
sudo is not the UNIX way of saying "I mean it!"
It has security implications, and you should be very aware of those implications before using it – aka read the man pages of every command you issue before you use it until you have at least a fact based idea of what the command is doing.
And again: unless you really know (as opposed to assume) what you are doing, do not fiddle with the system configuration.