Tag: linux

HTTPSConnectionPool(host=’files.pythonhosted.org’, port=443): Read timed out

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I recently had an issue where one of our EMR clusters failed to bootstrap the python modules via PIP. I checked the logs and saw that we ran into the following error:

I wanted to have PIP not die if it timed out, I also wanted it to retry on failure. By adding the following to my bootstrap.sh I was able to have the PIP socket timeout at a longer interval, also bump up the retries to 10. I have not seen the issue since I applied the new settings.

From the PIP help page:

Upgrade Rocky Linux 8 to 9 CLI

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I thought I would share my version of how I updated the server that runs this blog from Rocky 8 to Rocky 9 without a clean install. I want to mention this is a do at your own risk post, this is not officially supported.

!!!Do not attempt this if you do not have backups and a way to fully recover your system.!!!

The first step I took was go to the rocky download site and make sure I grabbed the latest GPG, RELEASE and REPOS:

https://download.rockylinux.org/pub/rocky/9/BaseOS/x86_64/os/Packages/r/

You will need to modify the below command to match the version you find in the above site, once that is complete you can run it.

One road block was dnf did not like that I had remi and epel release 8, so I removed them and it went fine.

Find the epel and remi release rpms:

Remove them:

Upgrade your system to 9 from 8:

I ignored this error, it seems like its just a GPG error:

Verify:

Rebuild the RPM database to now use SQLITE:

Thats it, reboot:

I did have some issues with dnf where I needed to reset some modules.

I needed to reset the modules one by one, there may be more on your system:

That seemed to fix it, good luck.

Python Linux Find Files With Pattern Accessed Older Than N Days And Remove

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This is a neat utility that you can use to keep in your sysadmin bag of tricks, it walks the directory you define recursively and grabs all the file access times and stores them into a list, it then compares them against a command line parameter for days ago. If its older than N days it will remove the file. What’s really nice about this utility is it has a debug mode, this way you can see what will be deleted before you remove debug and execute it.

Node Application Stopped Sending Updates To Slack – can’t identify protocol

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I wanted to share my experience with a node application that I support. This particular application is an API, it happens to log each and every request it receives to a internal slack channel. Our team uses this channel for many things, to verify when the API is in maintenance, to check that requests are processing, to see status on the overall health of the API etc..

Once in a while out of nowhere we would stop receiving these updates to slack. I set out to troubleshoot why this may be happening, at first we thought that we were hitting the slack rate limits, which is clearly defined here:

https://api.slack.com/docs/rate-limits

However after reading the linked doc, I was skeptical. The API does serve a lot of requests, but not enough to hit their limit. We have 2 servers that send slack messages and process the API requests and when they stopped sending it would be both servers, not just one. Also we have run into this before and restarting the service fixed the issue, so I was sure we did not hit the rate limit. Also trying to send a manual slack update using curl would not work! I knew this had to be something with the linux OS itself, and not the Slack service.

I tried to use netstat to see if we were hitting some type of OS limit, and all looked well. Next I tried one of my favorite tools, LSOF, at first I grepped for deleted to see if something was being held and not released. I did not see anything that stood out, next I grepped for node and low and behold I saw this:

My eyes went right to the “can’t identify protocol”, I opened up a browser and started to research, first hit when searching “can’t identify protocol” was a stack overflow article with the solution.

https://stackoverflow.com/questions/7911840/seeing-too-many-lsof-cant-identify-protocol

When lsof prints “Can’t identify protocol”, this usually relates to sockets (it should also say ‘sock’ in the relevant output lines).

So, somewhere in your code you are probably connecting sockets and not closing them properly (perhaps you need a finally block).

I suggest you step through your code with a debugger (easiest to use your IDE, potentially with a remote debugger, if necesssary), while running lsof side-by-side. You should eventually be able to see which thread / line of code is creating these File Descriptors.

Turns out that the node application was opening file descriptors / sockets and not closing them properly, this caused the system to hit the hard limit on open files / file descriptors. You can view the hard and soft limit like so, switch to the user that application is running as and run:

So you can see that the nodeuser has a hard limit of 4096 open files, which due to the application not properly closing them, we hit the ceiling. This explains why restarting the server or the process fixed it. It would release the open file descriptors and the system was able to open sockets again. I spoke with the developer and we researched, looks like one of the modules we were using was the cause of the issue, perhaps we were using it wrong? I found this out from this article:
https://stackoverflow.com/questions/24922745/node-js-winston-how-to-safely-drain-a-logger

Question:

I have experimented with instantiating and closing winston loggers as (half) described on https://github.com/flatiron/winston#instantiating-your-own-logger, to no avail. I run into trouble closing file transports of Winston’s – walking through it’s source code, I found that the proper way to close off a logger would seem to be the close method. I expected this to take care of closing the transport file used by the logger – however that turned out to be not so.

Varying in frequency according to node.js server load, winston would still hold on to many transport files, infinitely long after the close method had been called for them, indefinitely long after no new writes were being initiated to them. I observed that through the node.js process file descriptors table (lsof -p). Even though close has been called for a Winston logger, it would indefinitely keep the file descriptor of the log file “in use”, i.e. the log file never gets really closed. Thus leaking file descriptors and eventually making the node.js process bump into the ulimit (-n) limit after my application has been up for long.

Should there be a specific programming pattern for draining a Winston logger such that it can be eventually closed?

Answer:

Create only one logger instance and then derive children from it. In this case, winston will hold only one open file handler. Might also be better for performance.

So that was it, the developers agreed and set out to create a patch, problem solved.

AWS CLI Max Concurrent Requests Tuning

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In this post I would like to go over how I tuned a test server for copying / syncing files from the local filesystem to S3 over the internet. If you ever had the task of doing this, you will notice that as the file count grows, so does the time it takes to upload the files to S3. After some web searching I found out that AWS allows you to tune the config to allow more concurrency than default.
AWS CLI S3 Config

The parameter that we will be playing with is max_concurrent_requests
This has a default value of 10, which allows only 10 requests to the AWS API for S3. Lets see if we can make some changes to that value and get some performance gains. My test setup is as follows:

I have 56 102MB files in the test directory:

For the first test I am going to run aws s3 sync with no changes, so out of the box it should have 10 max_concurrent_requests. Lets use the Linux time command to gather the time result to copy all 56 files to S3. I will delete the folder on S3 with each iteration to keep the test the same. You can also view the 443 requests via netstat and count them as well to show whats going on. In all the tests my best result was 250. So as you can see you will need to play with the settings to get the best result, these settings will change along with the server specs.

1. 1m25.919s with the default configuration:

2. Now lets set the max conqurent requests to 20 and try again, you can do this with the command below, after running we can see a little gain.

3. Bumped up to 50 shows a bit more gain:

4. Bumped up to 100, I start to notice that we lost some speed:

5. Bumped up to 250 we see the best result so far:

6. Bumped up to 500, we lose performance, most likely due to the machine resources.

So to wrap up, you can tune the amount of concurrent requests allowed from the aws cli to s3, you will need to play with this setting to get the best results for your machine.

Python Backup WORDPRESS Site / DATABASE and HTML

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I have this blog hosted on a LINODE dedicated LINUX server. It’s about 10 dollars a month for a 1 core system with about 250GB of disk space and 1GB of RAM, this server runs the common LAMP stack, I needed a quick and dirty script to backup MYSQL database and the PHP code contained in the /var/www/html folder. I wanted the script to compress the contents of both and move them into a directory with the correct date. See the comments below outlining the code and the action of running it.

So you can see we generated 2 files in a dated directory, I chose to use both zip and gunzip for compression algoritims. To view the contents you can run the normal linux commands to extract the files.

So there you have it, I can tar up the entire dated directory for easy offsite backup now of my entire site jasonralph.org. Hope this helps someone, feel free to copy the source code and change at will.

Best,
Jason

PYTHON – Script to download youtube videos for offline viewing

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I was interested in viewing this video of a news conference (USENIX 2016) on my trip home on Metro North Train, NYC => CT. The trip is about an hour an 10 minutes from Manhattan’s Grand Central Terminal to Milford CT, express train that is. My concern was that I would have choppy internet service on the way since I recently updated my laptop and the built in Verizon Mobile card was not activated yet. I would need to use my ATT iPhone as a hotspot, which proved to be very shakey at times. A colleague of mine recommended a website for making youtube videos available for offline viewing. The name of this site was:

http://www.keepvid.com

Right off the rip I was concerned that this site was infested with malware and any other bullshit associated with a free video ripping service. I used the site and was able to create a download of the video I was interested in, however who knows how sick my Windows based machine just got. I could of contracted anything from this site.

I thought about this and said, there has to be a better way, or a python lib for this, and low and behold a search came up with PYTUBE:
https://github.com/nficano/pytube

This library had some interesting features and literally blew away the keepvid site in regards to flexibility. Here is some explaining of what this library can do. Please have a look at the examples below, I will do my best to narrate them.

Here I use PIP to install the PYTUBE lib, you can ignore the DEPRECATION: warning for my outdated python that blares at you for being such an idiot.

Next up you can see that I am setting a variable yt(this is the video you want to download). Using python’s Pretty Print Lib you can run the pprint(yt.get_videos() method to see what formats are available for download.

Please have a look at the comments in the code for a bit more details in regards to what is going on, in this example I am using the filename Pulp_Fiction.mp4 for my filename I want to be when downloaded.

Ok so here is what it looks like when you execute the program:

As you can see we have a new filename with the video we asked for to watch without a streaming internet connection, here is a ls to show:

As always, I am sure there are better ways to do this and I am sure there is cleaner code. Most of this code was taken right from the authors site who is a badass, here is his link:

https://github.com/nficano/pytube

Hope you liked,
J$0N