Attaching cloud storage to a campus grid using parrot, chirp, and hadoop

2nd IEEE International Conference on Cloud Computing Technology and Science

Attaching Cloud Storage to a Campus Grid
Using Parrot, Chirp, and Hadoop

Patrick Donnelly, Peter Bui, Douglas Thain
Computer Science and Engineering
University of Notre Dame
pdonnel3, pbui, dthain@nd.edu

Abstract the needs of web search engines and other scalable applica-
tions that require highly scalable streaming access to large
The Hadoop filesystem is a large scale distributed filesys- datasets. Hadoop excels at dealing with large files on the
tem used to manage and quickly process extremely large order of terabytes and petabytes while ensuring data in-
data sets. We want to utilize Hadoop to assist with data- tegrity and resiliency through checksums and data replica-
intensive workloads in a distributed campus grid environ- tion. Hadoop is typically used to enable the massive pro-
ment. Unfortunately, the Hadoop filesystem is not designed cessing of large data files through the use of distributed
to work in such an environment easily or securely. We computing abstractions such as Map Reduce [5].
present a solution that bridges the Chirp distributed filesys- In principle, we would like to deploy Hadoop as a scal-
tem to Hadoop for simple access to large data sets. Chirp able storage service in a central location, and allow jobs
layers on top of Hadoop many grid computing desirables in- running on the campus grid to access the filesystem. Unfor-
cluding simple deployment without special privileges, easy tunately, there are a number of practical barriers to accom-
access via Parrot, and strong and flexible security Access plishing this. Most applications are not designed to operate
Control Lists (ACL). We discuss the challenges involved in with the native Hadoop Java interface. When executing on a
using Hadoop on a campus grid and evaluate the perfor- campus grid, it is not possible to install any dependent soft-
mance of the combined systems. ware on the local machine. The Hadoop protocol was not
designed to be secure over wide area networks, and varies
in significant ways across versions of the software, making
if difficult to upgrade the system incrementally.
1 Introduction To address each of these problems, we have coupled
Hadoop to the Chirp filesystem, and employed the latter to
A campus grid is a large distributed system encompass- make the storage interface accessible, usable, secure, and
ing all of the computing power found in a large institution, portable. Chirp [15] is a distributed filesystem for grid com-
from low-end desktop computers to high end server clus- puting created at Notre Dame and used around the world. It
ters. In the last decade, a wide variety of institutions around has been shown to give favorable performance [15] [14] for
the world have constructed campus grids by deploying soft- distributed workflows. It is primarily used to easily export
ware such as the Condor [16] distributed computing system. a portion of the local filesystem for use by remote work-
One of the largest known public campus grids is BoilerGrid, ers. Chirp is built to be easily deployed temporarily for
consisting of over 20,000 cores harnessed at Purdue Uni- a job and then torn down later. It supports unprivileged
versity [2]; and systems consisting of merely a few thou- deployment, strong authentication options, sensible secu-
sand cores are found all around the country [13]. Campus rity of data, and grid-friendly consistency semantics. Using
grids have traditionally been most effective at running high- Parrot [12], we can transparently connect the application to
throughput computationally-intensive applications. How- Chirp and thereby to Hadoop.
ever, as the data needs of applications in the campus grid The remainder of this paper presents our solution for at-
increases, it becomes necessary to provide a system that can taching Hadoop to a campus grid via the Chirp filesystem.
provide high capacity and scalable I/O performance. We begin with a detailed overview of Hadoop, Parrot, and
To address this, we consider the possibility of using Chirp, explaining the limitations of each. We explored two
Hadoop [8] as a scalable filesystem to serve the I/O needs distinct solutions to this problem. By connecting Parrot
of a campus grid. Hadoop was originally designed to serve directly to Hadoop, we achieve the most scalable perfor-

978-0-7695-4302-4/10 $26.00 © 2010 IEEE 488
DOI 10.1109/CloudCom.2010.74

mance, but a less robust system. By connecting Parrot to opers. A FUSE [1] module allows unmodified applica-
Chirp and then to Hadoop, we achieve a much more stable tions to access Hadoop through a user-level filesystem
system, but with a modest performance penalty. The final driver, but this method still suffers from the remaining
section of the paper evaluates the scalability of our solution three problems:
on both local area and campus area networks.
• Deployment. To access Hadoop by any method, it
is necessary to install a large amount of software, in-
2 Background cluding the Java virtual machine and resolve a number
of dependencies between components. Using FUSE
The following is an overview of the systems we are try- module requires administrator access to install the
ing to connect to allow campus grid users access to scalable FUSE kernel modules, install a privileged executable,
distributed storage. First, we examine the Hadoop filesys- and update the local administrative group definitions
tem and provide a summary of its characteristics and limita- to permit access. On a campus grid consisting of thou-
tions. Throughout the paper we refer to the Hadoop filesys- sands of borrowed machines, this level of access is
tem as HDFS or simply Hadoop. Next, we introduce the simply not practical.
Chirp filesystem, which is used at the University of Notre
• Authentication. Hadoop was originally designed with
Dame and other research sites for grid storage. Finally, we
the assumption that all of its components were oper-
describe Parrot, a virtual filesystem adapter that provides
ating on the same local area, trusted network. As a
applications transparent access to remote storage systems.
result, there is no true authentication between compo-
nents – when a client connects to Hadoop, it simply
2.1 Hadoop claims to represent principal X, and the server compo-
nent accepts that assertion at face value. On a campus-
Hadoop [8] is an open source large scale distributed area network, this level of trust is inappropriate, and a
filesystem modeled after the Google File System [7]. It pro- stronger authentication method is required.
vides extreme scalability on commodity hardware, stream-
ing data access, built-in replication, and active storage. • Interoperability. The communication protocols used
Hadoop is well known for its extensive use in web search between the various components of Hadoop are also
by companies such as Yahoo! as well as by researchers for tightly coupled, and change with each release of the
data intensive tasks like genome assembly [10]. software as additional information is added to each in-
A key feature of Hadoop is its resiliency to hardware teraction. This presents a problem on a campus grid
failure. The designers of Hadoop expect hardware failure with many simultaneous users, because applications
to be normal during operation rather than exceptional [3]. may run for weeks or months at a time, requiring up-
Hadoop is a ”rack-aware” filesystem that by default repli- grades of both clients and servers to be done indepen-
cates all data blocks three times across storage components dently and incrementally. A good solution requires
to minimize the possiblty of data loss. both forwards and backwards compatibility.
Large data sets are a hallmark of the Hadoop filesystem.
File sizes are anticipated to exceed hundreds of gigabytes 2.2 Chirp
to terabytes in size. Users may create millions of files in a
single data set and still expect excellent performance. The Chirp [15] is a distributed filesystem used in grid com-
file coherency model is ”write once, read many”. A file that puting for easy userlevel export and access to file data. It is a
is written and then closed cannot be written to again. In regular user level process that requires no privileged access
the future, Hadoop is expected to provide support for file during deployment. The user simply specifies a directory on
appends. Generally, users do not ever need support for ran- the local filesystem to export for outside access. Chirp of-
dom writes to a file in everyday application. fers flexible and robust security through per-directory ACLs
Despite many attractive properties, Hadoop has several and various strong authentication modes. Figure 1a pro-
essential problems that make it difficult to use from a cam- vides a general overview of the Chirp distributed filesystem
pus grid environment: and how it is used.
A Chirp server is set up using a simple command as a
• Interface. Hadoop provides a native Java API for ac- regular user. The server is given the root directory as an op-
cessing the filesystem, as well as a POSIX-like C API, tion to export to outside access. Users can authenticate to
which is a thin wrapper around the Java API. In princi- the server using various schemes including the Grid Secu-
ple, applications could be re-written to access these in- rity Infrastructure (GSI) [6], Kerberos [11], or hostnames.
terfaces directly, but this is a time consuming and intru- Access to data is controlled by a per-directory ACL system
sive change that is unattractive to most users and devel- using these authentication credentials.

489

tcsh emacs perl appl tcsh emacs perl appl

ordinary unix system calls ordinary unix system calls
custom custom
parrot fuse tools parrot fuse tools
file file
cache libchirp libchirp libchirp cache libchirp libchirp libchirp

chirp network protocol chirp network protocol

chirp Hadoop chirp
server Headnode server

unix
filesys
Hadoop
datanode
Hadoop
datanode
... Hadoop
datanode

(a) The Chirp Filesystem (b) The Chirp Filesystem Bridging Hadoop

Figure 1: Applications can use Parrot, FUSE, or libchirp directly to communicate with a Chirp server on the client side. The
modifications presented in this paper, Chirp can now multiplex between a local unix filesystem and a remote storage service
such as Hadoop.

A Chirp server requires neither special privileges nor code to a Chirp filesystem without having to interface di-
kernel modification to operate. Chirp can both be deployed rectly with libchirp. While applications may also use FUSE
to a grid by a regular user to operate on personal data se- to remotely mount a Chirp fileserver, Parrot is more practi-
curely. We use Chirp at the University of Notre Dame to cal in a campus grid system where users may not have the
support workflows that require a personal file bridge to ex- necessary administrative access to install and run the FUSE
pose filesystems such as AFS [9] to grid jobs. Chirp is also kernel module. Because Parrot runs in userland and has
used for scratch space that harnesses the extra disk space of minimal dependencies, it is easy to distribute and deploy in
various clusters of machines. One can also use Chirp as a restricted campus grid environments.
cluster filesystem for greater I/O bandwidth and capacity.
3 Design and Implementation
2.3 Parrot

To enable existing applications to access distributed This section describes the changes we have made to im-
filesystems such as Chirp, the Parrot [12] virtual filesys- plement a usable and robust system that allows for appli-
tem adapter is used to redirect I/O operations for unmod- cations to transparently access the Hadoop filesystem. The
ified applications. Normally, applications would need to be first approach is to connect Parrot directly to HDFS, which
changed to allow them to access remote storage services provides for scalable performance, but has some limita-
such Chirp or Hadoop. With Parrot attached, unmodified tions. The second approach is to connect Parrot to Chirp
applications can access remote distributed storage systems and thereby Hadoop, which allows us to overcome these
transparently. Because Parrot works by trapping program limitations with a modest performance penalty.
system calls through the ptrace debugging interface, it can
be deployed and installed without any special system privi- 3.1 Parrot + HDFS
leges or kernel changes.
One service Parrot supports is the Chirp filesystem pre- Our initial attempt at integrating Hadoop into our cam-
viously described. Users may connect to Chirp using a va- pus grid environment was to utilize the Parrot middleware
riety of methods. For instance, the libchirp library provides filesystem adapter to communicate with our test Hadoop
an API that manages connections to a Chirp server and al- cluster. To do this we used libhdfs, a C/C++ binding for
lows user to construct custom applications. However, a user HDFS provided by the Hadoop project, to implement a
will generally use Parrot to transparently connect existing HDFS service for Parrot. As with other Parrot services, the

490

ever, were fully supported. The parrot hdfs module did not
tcsh emacs perl appl provide a means of overcoming this limitation.
Finally, the biggest impediment to using both Hadoop
and the parrot hdfs module was the lack of proper access
ordinary unix system calls
controls. Hadoop’s permissions can be entirely ignored as
parrot there is no authentication mechanism. The filesystem ac-
libhdfs cepts whatever identity the user presents to Hadoop. So
while a user may partition the Hadoop filesystem for dif-
Hadoop RPC ferent groups and users, any user may report themselves as
any identity thus nullifying the permission model. Since
parrot hdfs simply provides the underlying access control
system, this problem is not mitigated in anyway by the ser-
Hadoop
Headnode
Hadoop
Datanode
Hadoop
Datanode
... Hadoop
Datanode
vice. For a small isolated cluster filesystem this is not a
problem, but for a large campus grid, such a lack of permis-
sions is worrisome and a deterent for wide adoption, espe-
cially if sensitive research data is being stored.
Figure 2: In the parrot hdfs tool, we connect Parrot directly So although parrot hdfs is a useful tool for integrating
to Hadoop using libhdfs, which allows client applications to Hadoop into a campus grid environment, it has some limita-
communicate with a HDFS service. tions that prevent it from being a complete solution. More-
over, Hadoop itself has limitations that need to be addressed
before it can be widely deployed and used in a campus grid.
HDFS Parrot module (parrot hdfs) allows unmodified end
user applications to access remote filesystems, in this case 3.2 Parrot + Chirp + HDFS
HDFS, transparently and without any special priviledges.
This is different from tools such as FUSE which require To overcome these limitations in both parrot hdfs and
kernel modules and thus adminstrative access. Since Par- Hadoop, we decided to connect Parrot to Chirp and then
rot is a static binary and requires no special priviledges, it Hadoop. In order to accomplish this, we had to implement
can easily be deployed around our campus grid and used to a new virtual multiplexing interface in Chirp to allow it to
access remote filesystems. to use any backend filesystem. With this new capability, a
Figure 2 shows the architecture of the parrot hdfs mod- Chirp server could act as a frontend to potentially any other
ule. Applications run normally until an I/O operation is filesystem, such as Hadoop, which is not usually accessible
requested. When this occurs, Parrot traps the system call with normal Unix I/O system calls.
using the ptrace system interface and reroutes to the appro- In our modified version of Chirp, the new virtual mul-
priate filesystem handler. In the case of Hadoop, any I/O tiplexing interface routes each I/O Remote Procedure Call
operation to the Hadoop filesytem is implemented using the (RPC) to the appropriate backend filesystem. For Hadoop,
libhdfs library. Of course, the trapping and redirection of all data access and storage on the Chirp server is done
system calls incurs some overhead, but as shown in a pre- through Hadoop’s libhdfs C library. Figure 1b illustrates
vious paper [4], the parrot hdfs module is quite serviceable how Chirp operates with Hadoop as a backend filesystem.
and provides adequate performance. With our new system, a simple command line switch
Unfortunately, the parrot hdfs module was not quite a changes the backend filesystem during initialization of the
perfect solution for integrating Hadoop into our campus in- server. The command to start the Chirp server remains sim-
frastructure. First, while Parrot is lightweight and has mini- ple to start and deploy:
mal dependencies, libhdfs, the library required for commu-
nicating to Hadoop, does not. In fact, to use libhdfs we $ chirp_server -f hdfs
must have access to a whole Java virtual machine installa- -x headnode.hadoop:9100
tion, which is not always possible in a heterogeneous cam-
pus grid with multiple administrative domains. Clients that connect to the Chirp server such as the one
Second, only sequential writing was supported by the above will work over HDFS instead of on the the server’s
module. This is because Hadoop, by design, is a write-once- local filesystem. The head node of Hadoop and port it
read-many filesystem and thus is optimized for streaming listens on are specified using the -x <host>:<port>
reads rather than frequent writes. Moreover, due to the in- switch. The root of the Hadoop filesystem is the exported
stability of the append feature in the version of Hadoop de- directory by Chirp changed via the -r switch. Because
ployed in our cluster, it was also not possible to support ap- Hadoop and Java require multiple inconvenient environ-
pends to existing files. Random and sequential reads, how- ment variables to be setup prior to execution, we have also

491

provided the chirp_server_hdfs wrapper which sets replication and correctly dealing with the (now) muta-
these variables to configuration defined values before run- ble last block of a file. As of now, turning appends on
ning chirp_server. requires setting experimental parameters in Hadoop.
Recall that Hadoop has no internal authentication sys- Chirp provides some support for appends by imple-
tem; it relies on external mechanisms. A user may de- menting the operation through other primitives within
clare any identity and group membership when establishing Hadoop. That is, Chirp copies the file into memory,
a connection with the Hadoop cluster. The model naturally deletes the file, writes the contents of memory back to
relies on a trustworthy environment; it is not expected to be the file, and returns the file for further writes – effec-
resilient to malicious use. In a campus environment, this tively allowing appends. Support for appends to small
may not be the case. So, besides being an excellent tool for files fit most use cases, logs in particular. Appending
grid storage in its own right, Chirp brings the ability to wall to a large file is not advised. The solution is naturally
off Hadoop from the campus grid while still exposing it in less than optimal but is necessary until Hadoop pro-
a secure way. To achieve this, we would expect the admin- vides non-experimental support.
istrator to firewall off regular Hadoop access while still ex-
posing Chirp servers running on top of Hadoop. This setup
is a key difference to parrot hdfs, discussed in the previous • Random Writes Random writes to a file are not al-
section. Chirp brings its strong authentication mechanisms lowed by Hadoop. This type of restriction generally
and flexible access control lists to protect Hadoop from un- affects programs, like linkers, that do not write to a file
intended or accidental access whereas parrot hdfs connects sequentially. In Chirp, writes to areas other than the
to an exposed, unprotected Hadoop cluster. end of the file are silently changed to appends instead.

3.3 Limitations when Bridging Hadoop • Other POSIX Incompatibilities Hadoop has other
with Chirp peculiar incompatibilities with POSIX. The execute bit
for regular files is nonexistent in Hadoop. Chirp gets
The new modified Chirp provides users with an approxi- around this by reporting the execute bit set for all users.
mate POSIX interface to the Hadoop filesystem. Certain re- Additionally, it does not allow renaming a file to one
strictions are unavoidable due to limitations stemming from that already exists. This would be equivalent to the
design decisions in HDFS. The API provides most POSIX Unix mv operation from one existing file to another ex-
operations and semantics that are needed for our bridge with isting file. Further, opening, unlinking, and closing a
Chirp, but not all. We list certain notable problems we have file will result in Hadoop failing with an EINTERNAL
encountered here. error. For these types of semantic errors, the Chirp
server and client have no way of reasonably respond-
• Errno Translation The Hadoop libhdfs C API binding
ing or anticipating such an error. We expect that as the
interprets exceptions or errors within the Java runtime
HDFS binding matures many of these errors will be
and sets errno to an appropriate value. These trans-
responded to in a more reasonable way.
lations are not always accurate and some are missing.
A defined errno value within libhdfs is EINTERNAL
which is the generic error used when another is not
found to be more appropriate. Chirp tries to sensi- 4 Evaluation
bly handle these errors by returning a useful status to
the user. Some errors must be caught early because
Hadoop does not properly handle all error conditions. To evaluate the performance characteristics of our Par-
For example, attempting to open a file that is a direc- rot + Chirp + HDFS system, we ran a series of benchmark
tory results errno being set to EINTERNAL (an HDFS tests. The first is a set of micro-benchmarks designed to
generic EIO error) rather than the correct EISDIR. test the overhead for individual I/O system calls when us-
ing Parrot with various filesystems. The second is a data
• Appends to a File Appends are largely unsupported transfer performance test of our new system versus the na-
in Hadoop within production environments. Hadoop tive Hadoop tools. Our tests ran on a 32 node cluster of
went without appends for a long time in its history be- machines (located off Notre Dame’s main campus) with the
cause the Map Reduce abstraction did not benefit from Hadoop setup using 15 TB of aggregate capacity. The clus-
it. Still, use cases for appends surfaced and work to ter is using approximately 50% of available space. The
add support – and determine the appropriate semantics Hadoop cluster shares a 1 gigabit link to communicate with
– has been in progress since 2007. The main barri- the main campus network. We have setup a Chirp server as
ers to its developement are coherency semantics with a frontend to the Hadoop cluster on one of the data nodes.

492

50 50
2 Clients 2 Clients
4 Clients 4 Clients
8 Clients 8 Clients
40 16 Clients 40 16 Clients
Bandwidth (MB/s)

Bandwidth (MB/s)
30 30

20 20

10 10

0 0
0 1000 2000 3000 4000 5000 6000 7000 8000 0 1000 2000 3000 4000 5000 6000 7000 8000
File Size (MB) File Size (MB)

(a) Campus Network Reads to Chirp+HDFS. (b) Campus Network Reads to HDFS.

50 50
2 Clients 2 Clients
4 Clients 4 Clients
8 Clients 8 Clients
Bandwidth (MB/s)

Bandwidth (MB/s)
30 30

20 20

10 10

0 0
0 1000 2000 3000 4000 5000 6000 7000 8000 0 1000 2000 3000 4000 5000 6000 7000 8000

(c) Campus Network Writes to Chirp+HDFS. (d) Campus Network Writes to HDFS.

Figure 3

35
Parrot+Chirp+Unix
The results of these micro-benchmarks are shown in Fig-
ure 5. As can be seen, our new Parrot + Chirp + HDFS
Latency (Milliseconds)

30 Parrot+HDFS
Parrot+Chirp+HDFS
25 systems has some overhead when compared to accessing a
20 Chirp server or HDFS service using Parrot. In particular, the
15 metadata operations of stat and open are particularly heavy
10 in our new system while read and close are relatively close.
5 The reason for this high overhead on metadata-intensive op-
0 erations is because of the access control lists Chirp uses to
stat open read close
Micro-Operations implement security and permissions. For each stat or open,
multiple files must be opened and checked in order to verify
Figure 5: Latency of I/O Operations using Microbench valid access, which increases the latencies for these system
calls.

4.1 Micro-benchmarks 4.2 Performance benchmarks

The first set of tests we ran were a set of micro- For our second set of benchmarks, we stress test the
benchmarks that measure the average latency of various I/O Chirp server by determining the throughput achieved when
system calls such as stat, open, read, close. For this test we putting and getting very large files. These types of com-
wanted to know the cost of putting Chirp in front of HDFS mands are built into Chirp as the RPC’s getfile and
and using Parrot to access HDFS through our Chirp server. putfile. Our tests compared the equivalent Hadoop
We compared these latencies to those for accessing a Chirp native client hadoop fs get and hadoop fs put
server hosting a normal Unix filesystem through Parrot, and commands to the Chirp ones. The computer on the cam-
accessing HDFS directly using Parrot. pus network initiating the tests used the Chirp command

493

100 100
2 Clients 2 Clients
4 Clients 4 Clients
8 Clients 8 Clients
Bandwidth (MB/s)

Bandwidth (MB/s)
60 60

40 40

20 20

0 0
0 1000 2000 3000 4000 5000 6000 7000 8000 0 1000 2000 3000 4000 5000 6000 7000 8000

(a) LAN Network Reads to Chirp+HDFS. (b) LAN Network Reads to HDFS.

50 50
2 Clients 2 Clients
4 Clients 4 Clients
8 Clients 8 Clients
Bandwidth (MB/s)

Bandwidth (MB/s)
30 30

20 20

10 10

0 0
0 1000 2000 3000 4000 5000 6000 7000 8000 0 1000 2000 3000 4000 5000 6000 7000 8000

(c) LAN Network Writes to Chirp+HDFS. (d) LAN Network Writes to HDFS.

Figure 4

line tool, which uses the libchirp library without any ex- chines will follow access the Hadoop storage in this way.
ternal dependencies, and the Hadoop native client, which For contrast, in the next tests, we remove this barrier.
requires all the Hadoop and Java dependencies. We want to
Next, we place the clients on the same LAN as the
test how the Chirp server performs under load compared to
Hadoop cluster and the Chirp server frontend. We expect
the Hadoop cluster by itself. For these tests, we communi-
that throughput will not be hindered by the link rate of the
cated with the Hadoop cluster and the Chirp server frontend
network and parallelism will allow Hadoop to scale. Similar
from the main campus. All communication went through
to the tests from the main campus grid, the clients will put
the 1 gigabit link to the cluster.
and get files to the Chirp server and via the Hadoop native
The graphs in Figures 3a and 3b show the results of read- client.
ing (getting) a file from the Chirp server frontend and via The graphs in Figures 4a and 4b show the results of read-
the the native Hadoop client, respectively. We see that the ing a file over the LAN setup. We see that we get simi-
Chirp server is able to maintain throughput comparable to lar throughput over the Chirp server as in the main campus
the Hadoop native client; the Chirp server does not present tests. While the link to the main campus grid is no longer
a real bottleneck to reading a file from Hadoop. In Fig- a limiting factor, the Chirp server’s machine still only has
ures 3c and 3d, we have the results of writing (putting) a a gigabit link to the LAN. Meanwhile, Hadoop achieves
file to the Chirp server frontend and native Hadoop client, respectably good performance, as expected, when reading
again respectively. These graphs similarly show that the files with a large number of clients. The parallelism gives
Chirp server obtains similar throughput to the Hadoop na- Hadoop almost twice the throughput. For a larger number
tive client for writes. For these tests, the 1 gigabit link plays of clients, Hadoop’s performance outstrips chirp by a large
a major role in limiting the exploitable parallelism obtain- factor of 10. The write performance in Figures 4c and 4d,
able via writing to Hadoop over a faster (local) network. show similar results. The writes over the LAN bottleneck
Despite hamstringing Hadoop’s potential parallelism, we on the gigabit link to the Chirp server while Hadoop main-
find these tests valuable because the campus network ma- tains minor performance hits as the number of clients in-

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