[ale] HADTOO: Automatic-node-generating Hadoop cluster on Gentoo Linux

[Jeff Hubbs]

For the past few months, I've been operating an Apache Hadoop cluster at 
Emory University's Goizueta Business School. That cluster is 
Gentoo-Linux-based and consists of a dual-homed "edge node" and three 
16-GiB-RAM 16-thread two-disk "worker" nodes. The edge node provides NAT 
for the active cluster nodes and holds a complete mirror of the Gentoo 
package repository that is updated nightly. There is also an auxiliary 
edge node (a one-piece Dell Vostro 320) with xorg and xfce that I mostly 
use to display exported instances of xosview from all of the other nodes 
so that I can keep an eye on the cluster's operation. Each of the worker 
nodes carries a standalone Gentoo Linux instance that was flown in via 
rsync from another node while booted to a liveCD-style distribution 
(SystemRescueCD, which happens to be Gentoo-based).

I have since set up the main edge node to form a "shadow cluster" in 
addition to the one I've been operating. Via iPXE and dnsmasq on the 
edge node, any x86_64 system that is connected to the internal cluster 
network and allowed to PXE-boot will download a stripped-down Gentoo 
instance via HTTP (served up by nginx), boot to this instance in RAM, 
and execute a bash script that finds, partitions, and formats all of 
that system's disks, downloads and writes to those disks a complete 
Gentoo Linux instance, installs and configures the GRUB bootloader, sets 
a hostname based on the system's first NIC's MAC address, and reboots 
the system into that freshly-written instance.

At present, there is only one read/write NFS export on the edge node and 
it holds a flat file that Hadoop uses as a list of available worker 
nodes. The list is populated by the aforementioned node setup script 
after the hostname is generated.

Both the PXE-booted Gentoo Linux instance and the on-disk instance are 
managed within a chroot on the edge node in a manner not unlike how 
Gentoo Linux is conventionally installed on a system. Once set up as 
desired, these instances are compressed into separate squashfs files and 
placed in the nginx doc root. In the case of the PXE-booted instance, 
there is an intermediate step where much of the instance is stripped 
away just to reduce the size of the squashfs file, which is currently 
431MiB. The full cluster node distribution file is 1.6GiB but I 
sometimes exclude the kernel source tree and local package 
meta-repository to bring it down to 1.1GiB. The on-disk footprint of the 
complete worker node instance is 5.9GiB.

The node setup script takes the first drive it finds and GPT-partitions 
it six ways: 1) a 2MiB "spacer" for the bootloader; 2) 256MiB for /boot; 
3) 32GiB for root; 4) 2xRAM for swap (this is WAY overkill; it's set by 
ratio in the script and a ratio of one or less would suffice); 5) 64GiB 
for /tmp/hadoop-yarn (more about this later); 6) whatever is left for 
/hdfs1. Any remaining disks identified are single-partitioned as /hdfs2, 
/hdfs3, etc. All partitions are formatted btrfs with the exception of 
/boot, which is vfat for UEFI compatibility (a route I went down because 
I have one old laptop I found that was UEFI-only and I expect that will 
become more the case than less over time). A quasi-boolean in the script 
optionally enables compression at mount time for /tmp/hadoop-yarn.

One of Gentoo Linux's strengths is the ability to compile software 
specifically for the CPU but the node instance is set up with the gcc 
option -mtune=generic. Another quasi-boolean setting in the node setup 
script will change that to -march=native but that change will only 
effectuate when packages are built or rebuilt locally (as opposed to in 
chroot on the edge node, where everything must be built generic). I can 
couple this feature with another feature to optionally rebuild all the 
system's binaries native but that's an operation that would take a fair 
bit of time (that's over 500 packages and only some of them would affect 
cluster operation). Similarly, in the interest of run-what-ya-brung 
flexibility, I'm using Gentoo's genkernel utility to generate a kernel 
and initrd befitting a liveCD-style instance that will boot on basically 
any x86-64 along with whatever NICs and disk controllers it finds.

I am using the Hadoop binary distribution (currently 3.1.1) as 
distributed directly by Apache (no HortonWorks; no Cloudera). Each 
cluster node has its own Hadoop distribution and each node's Hadoop 
distribution has configuration features both in common and specific to 
that node, modified in place by the node setup script. In the latter 
case, the amount of available RAM, the number of available CPU threads, 
and the list of available HDFS partitions on a system are flown into the 
proper local config files. Hadoop services run in a Java VM; I am 
currently using the IcedTea 3.8.0 source distribution supplied within 
Gentoo's packaging system. I have also run it under the IcedTea binary 
distribution and the Oracle JVM with equal success.

Hadoop has three primary constructs that make it up. HDFS (Hadoop 
Distributed File System) consists of a NameNode daemon that runs on a 
single machine and controls the filesystem namespace and user access to 
it; DataNode daemons run on each worker node and coordinate between the 
NameNode daemon and the local machine's on-disk filesystem. You access 
the filesystem with command-line-like options to the hdfs binary like 
-put, -get, -ls, -mkdir, etc. but in the on-disk filesystem underneath 
/hdfs1.../hdfsN, the files you write are cut up into "blocks" (default 
size: 128MiB) and those blocks are replicated (default: three times) 
among all the worker nodes. My initial cluster with standalone workers 
reported 7.2TiB of HDFS available spread across six physical spindles. 
As you can imagine, it's possible to accumulate tens of TiB of HDFS 
across only a handful of nodes but doing so isn't necessarily helpful.

YARN (Yet Another Resource Negotiator) is the construct that manages the 
execution of work among the nodes. Part of the whole point behind Hadoop 
is to /move the processing to where the data is /and it's YARN that 
coordinates all that. It consists of a ResourceManager daemon that 
communicates with all the worker nodes and NodeManager daemons that run 
on each of the worker nodes. You can run the ResourceManager daemon and 
HDFS' NameNode daemon on the same machines that act as worker nodes but 
past a point you won't want to and past /that/ point you'd want to run 
each of NameNode and ResourceManager on two separate machines. In that 
regime, you'd have two machines dedicated to those roles (their names 
would be taken out of the centrally-located workers file) and the rest 
would run both the DataNode and NodeManager daemons, forming the HDFS 
storage subsystem and the YARN execution subsystem.

There is another construct, MapReduce, whose architecture I don't fully 
understand yet; it comes into play as a later phase in Hadoop 
computations and there is a JobHistoryServer daemon associated with it.

Another place where the bridge is out with respect to my understanding 
of Hadoop is coding for it - but I'll get there eventually. There are 
other apps like Apache's Spark and Hive that use HDFS and/or YARN that I 
have better mental insight into, and I have successfully gotten 
Python/Spark demo programs to run on YARN in my cluster.

One thing I have learned is that Hadoop clusters do not "genericize" 
well. When I first tried running the Hadoop-supplied teragen/terasort 
example (goal: make a file of 10^10 100-character lines and sort it), it 
failed for want of space available in /tmp/hadoop-yarn but it ran 
perfectly when the file was cut down to 1/100th that size. For my 
PXE-boot-based cluster, I gave my worker nodes a separate partition for 
/tmp/hadoop-yarn and gave it optional transparent compression. There are 
a lot of parameters for controlling things like minimum size and minimum 
size increment of memory containers and JVM parameters that I haven't 
messed with but to optimize the cluster for a given job, one would 
expect to.

What I have right now - basically, a single Gentoo Linux instance for 
installation on a dual-homed edge node - is able to generate a working 
Hadoop cluster with an arbitrary number of nodes, limited primarily by 
space, cooling, and electric power (the Dell Optiplex desktops I'm using 
right now max out at about an amp, so you have to be prepared to supply 
at least N amps for N nodes). They can be purpose-built rack-mount 
servers, a lab environment full of thin clients, or wire shelf units 
full of discarded desktops and laptops.

- Jeff


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