Auxiliary I/O Systems¶

I/O Systems Supported¶

Currently, the I/O systems supported are:

• Lustre
• HDFS
• Curl

Setting up HDFS¶

HDFS is the Hadoop Distributed Filesystem. This section demonstrates how to set up a Hadoop installation. If you already have access to an HDFS filesystem, you can skip ahead to Enabling HDFS Support.

The HDFS functionality in Chapel is dependent Hadoop being installed. The HADOOP_INSTALL, JAVA_INSTALL and CLASSPATH environment variables must be set as described below. Without this it will not compile with HDFS, even if the flags are set. As well, the HDFS functionality is also dependent upon the CHPL_AUXIO_INCLUDE and CHPL_AUXIO_LIBS environment variables being set properly.

If you have a working installation of Hadoop already, you can skip this section, other than to set up your CLASSPATH environment variable. This section is written so that people without sudo permission can install and use HDFS. If you do have sudo permissions, you can usually install all of these via a package manager.

The general outline for these instructions are:

• Step 1: Install and point to the jdk to provide code Chapel needs to compile against libhdfs
• Step 2: Install Hadoop
• Step 3: Set up Hadoop on (a) the local host or (b) a cluster of hosts
• Step 4: Start up HDFS
• Step 5: Stop HDFS when you're done
• Step 6: Set up Chapel to run in distributed mode

First reflect your directory structure and version numbers (etc) in the sample .bashrc and put it in your .bashrc (or other shell rc file of your choice) and source whichever one you put it into.

1. Make sure you have a SERVER edition of the jdk installed and point JAVA_INSTALL to it (see the sample .bashrc below)

2. Install Hadoop

   • Download the latest version of Hadoop and unpack it

   • Now in the unpacked directory, open conf/hadoop-env.sh and edit:

     • set JAVA_INSTALL to be the part before bin/ when you do:

       which java
       

     • set HADOOP_CLASSPATH=$HADOOP_HOME/""*:$HADOOP_HOME/lib/""*:

   • Now in conf/hdfs-site.xml put the replication number that you want for the field dfs.replication (this will set the replication of blocks of the files in HDFS)

   • Now set up passwordless ssh, if you haven't yet:

     ssh-keygen -t dsa -P '' -f ~/.ssh/id_dsa
     cat ~/.ssh/id_dsa.pub >> ~/.ssh/authorized_keys
     

3. Set up Hadoop

   1. For the local host - See the Hadoop website for good documentation on how to do this.

   2. For a cluster of hosts. If you want to run Hadoop over a cluster, there are good tutorials online. Although it is usually as easy as making edits to the following files in $HADOOP_HOME/conf:

      • adding the name of the nodes to slaves

      • putting what you want to be the namenode in masters

      • putting the master node in core-site.xml and mapred-site.xml

      • running:

        hadoop-daemon.sh start datanode
        hadoop-daemon.sh start tasktracker
        

      After this go to your datanode site and you should see a new datanode.

      A good online tutorial for this as well can be found here on the Hadoop Cluster Setup Documentation

4. Start HDFS

   • Now all we need to do is format the namenode and start things up:

     hadoop namenode -format
     start-all.sh  # (This will start hdfs and the tasktracker/jobtracker)
     

   • In general, hadoop has the same type of commands as bash, usually in the form:

     hadoop dfs -<command> <regular args to that command>
     

   • At this point, you can compile and run Chapel programs using HDFS

   • You can check the status of Hadoop via http, for example on a local host (e.g., for 3a above), using:

     • http://localhost:50070/
     • http://localhost:50030/

     For cluster mode (3b), you'll use the name of the master host in the URL and its port (see the web for details).

5. Shut things down:

   stop-all.sh   # (This will stop hdfs and mapreduce)
   

6. Set up Chapel to run in distributed mode:
   • You'll need to set up your Chapel environment to target multiple locales in the standard way (see Multilocale Chapel Execution and the "Settings to run Chapel on multiple nodes" section of the Sample .bashrc below).
   • After this you should be able to run Chapel code with HDFS over a cluster of computers the same way as you normally would.

#
# For Hadoop
#
export HADOOP_INSTALL=<Place where you have Hadoop installed>
export HADOOP_HOME=$HADOOP_INSTALL
export HADOOP_VERSION=<Your Hadoop version number>
#
# Note that the following environment variables might contain more paths than
# those listed below if you have more than one IO system enabled. These are all
# that you will need in order to use HDFS (only)
#
export CHPL_AUXIO_INCLUDE="-I$JAVA_INSTALL/include -I$JAVA_INSTALL/include/linux  -I$HADOOP_INSTALL/src/c++/libhdfs"
export CHPL_AUXIO_LIBS="-L$JAVA_INSTALL/jre/lib/amd64/server -L$HADOOP_INSTALL/c++/Linux-amd64-64/lib"

#
# So we can run things such as start-all.sh etc. from anywhere and
# don't need to be in $HADOOP_INSTALL
#
export PATH=$PATH:$HADOOP_INSTALL/bin

#
# Point to the JDK installation
#
export JAVA_INSTALL=<Place where you have the jdk installed>

#
# Add Hadoop directories to the Java class path
#
export CLASSPATH=$CLASSPATH:$HADOOP_HOME/""*:$HADOOP_HOME/lib/""*:$HADOOP_HOME/conf/""*:$(hadoop classpath):

#
# So we don't have to "install" these things
#
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HADOOP_HOME/c++/Linux-amd64-64/lib:$HADOOP_HOME/src/c++/libhdfs:$JAVA_INSTALL/jre/lib/amd64/server:$JAVA_INSTALL:$HADOOP_HOME/lib:$JAVA_INSTALL/jre/lib/amd64:$CLASSPATH

#
# Settings to run Chapel on multiple nodes
#
export GASNET_SPAWNFN=S
export SSH_SERVERS=<the names of the computers in your cluster>
export SSH_CMD=ssh
export SSH_OPTIONS=-x
export GASNET_ROUTE_OUTPUT=0

# C/C++ implementation
export CHPL_AUX_FILESYS=hdfs3

# Java implementation. Also set environment variables noted above.
export CHPL_AUX_FILESYS=hdfs

make

Installing Curl Dependencies¶

The Curl functionality in Chapel is dependent on libcurl. For information on how to install libcurl, see the curl installation instructions

The environment variables CHPL_AUXIO_INCLUDE and CHPL_AUXIO_LIBS must be set to point to the include and lib directories for libcurl respectively.

export CHPL_AUX_FILESYS=curl

make

CHPL_AUXIO_INCLUDE & CHPL_AUXIO_LIBS¶

These paths are for the extra libraries that will be linked in with the runtime when it is compiled. For instance, if I installed libcurl, and had it install in ~/include and ~/lib you would set them to be:

export CHPL_AUXIO_LIBS="-L~/include"
export CHPL_AUXIO_INCLUDE="-I~/lib"

In general, you want it so that if you had a .c file that used the libraries that you wish to compile Chapel with, all you would need to do to compile this file would be:

cc $CHPL_AUXIO_LIBS $CHPL_AUXIO_INCLUDE <any libraries> <the .c file>

where <any libraries> might be -lcurl, -lhdfs, -lhdfs3, -ljvm etc.

CHPL_AUX_FILESYS¶

This is a space delimited string detailing what AIO systems we wish to compile Chapel with (and use). For example if we wanted to enable Curl and HDFS support simultaneously we would set:

CHPL_AUX_FILESYS="hdfs curl"

Assuming that you have correctly defined CHPL_AUXIO_INCLUDE and CHPL_AUXIO_LIBS as detailed above, and have the correct libraries installed.

If you only have one AIO system that you wish to use, you may simply set CHPL_AUX_FILESYS=<system>. For example, if we only wanted Apache Hadoop HDFS support, we would set:

CHPL_AUX_FILESYS=hdfs

Parallel and Distributed I/O Features¶

We support two functions for Parallel and Distributed file systems (these also work on "standard" file systems as well).

file.getchunk(start:int(64), end:int(64)):(int(64), int(64))

• This returns the first logical chunk of the file that is inside this section. If no chunk can be found inside this region, (0,0) is returned. If no arguments are provided, we return the start and end of the first logical chunk for this file.

  • On Lustre, this returns the first stripe for the file that is inside this region.
  • On HDFS, this returns the first block for the file that is inside this region.
  • On local file systems, it returns the first optimal transfer block (from fstatfs) inside this section of the file.

file.localesForRegion(start:int(64), end:int(64)):domain(locale)

• This returns the best locales for a given chunk of the file. If no individual or set of locales are best (i.e., there is some sort of data affinity that we can exploit), we return all locales.

  • On Lustre, no locale are best, so we return all locales
  • On HDFS, we return the block owners for that specific block
  • On local file systems, we return all locales, since no individual locale is best.