beast and beagle-lib on amazon ec2 HPC-GPU instance

setup.md

• TODO: need to check block device mapping flags

• crank up an instance

    ec2-run-instances --key ec2-keypair ami-aa30c7c3 --instance-type=cg1.4xlarge \
    --block-device-mapping '/dev/sdb=ephemeral0' \
    --block-device-mapping '/dev/sdc=ephemeral1'
  

• check for instance status and to get ip address for ssh

    ec2-describe-instances
  

• if you haven't, allow ssh to default group (need this once)

    ec2-authorize default -p 22
  

• connect over ssh

    ssh -i ec2-keypair [email protected]
  

• get subversion client and some other items (can run as single command)

    yum install subversion
    yum install screen
    yum install automake
    yum install libtool
    yum install java-1.6.0-openjdk-devel.x86_64
    yum install gcc-c++
    yum install ant # to build beast
  

• add a user if you want

    useradd whoever
    passwd whoever
  

• get the newest CUDA toolkit

    cd /usr/local/src
    wget http://developer.download.nvidia.com/compute/cuda/3_2_prod/toolkit/cudatoolkit_3.2.16_linux_64_rhel5.5. run
    chmod 0755 cudatoolkit_3.2.16_linux_64_rhel5.5.run
    ./cudatoolkit_3.2.16_linux_64_rhel5.5.run
  

• update .bash_profile PATH and LD_LIBRARY_PATH to add CUDA goodies (filled these in from memory, may be wrong)

    export PATH=/usr/local/cuda/bin:$PATH
    export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH
  

• get the beagle library

    cd /usr/local/src && svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib
    cd beagle-lib
    ./autogen.sh # if you get an error here you may need to install libtool
    ./configure
    make
    sudo make install
    make check # tests passed
  

• go ahead and get BEAST

    cd /usr/local/src
    svn co http://beast-mcmc.googlecode.com/svn/trunk/ beast-mcmc
    cd beast-mcmc
    ant
  

• mount up some space (if not mounted; whoever is your user)

    mount /dev/sdc /mnt/data
    chown root:whoever /mnt/data
    chmod 0775 /mnt/data
  

• get data from somewhere

    wget http://my.data.from.somewhere/my_data.xml
  

• run beast-beagle with your data (or using $BEAST_HOME/examples/benchmark*.xml)

    screen # to start a session from which you can detach
    java -Xmx18000m -Djava.library.path=/usr/local/lib \
        -cp /usr/local/src/beast-mcmc/build/dist/beast.jar:/usr/local/src/beast-mcmc/lib/beagle.jar \
        dr.app.beast.BeastMain -beagle -beagle_GPU data.from.somewhere.xml
  

• detach from the session w/

    <ctrl><a><d>
  

Bonus Round

Assuming you have setup Amazon SES for your account, you can download the Amazon SES scripts (http://docs.amazonwebservices.com/ses/latest/GettingStartedGuide/) and email yourself that way ("normal" emails usually fail to arrive). You'll need to install openssl and openssl-devel, and perhaps some other thigns (can't remember):

    yum install openssl openssl-devel
    perl -MCPAN -e 'install Digest::SHA'
    perl -MCPAN -e 'install URI::Escape'
    perl -MCPAN -e 'install Bundle::LWP'
    perl -MCPAN -e 'install MIME::Base64'
    perl -MCPAN -e 'install Crypt::SSLeay'
    perl -MCPAN -e 'install XML::LibXML'

• Per the GettingStartedGuide, put your credentials somewhere (I put them on the ephemeral share)

    nano /mnt/data/aws-access.txt
    # paste in your credentials
  

• Per the user guide, give some access to your email addresses, and verify via the amazon email

• Now, start your run. The ses-send-email.pl runs on completion of the run.

    screen # to start a session from which you can detach
    java -Xmx18000m -Djava.library.path=/usr/local/lib \
    -cp /usr/local/src/beast-mcmc/build/dist/beast.jar:/usr/local/src/beast-mcmc/lib/beagle.jar \
    dr.app.beast.BeastMain -beagle -beagle_GPU -beagle_order 1,2,0 data.from.somewhere.xml \
    && perl -I/mnt/data/bin /mnt/data/bin/ses-send-email.pl \
    -k /mnt/data/aws-access.txt -s "Run Completed" -f [email protected] [email protected]
  

• The above assumes you use ATT. Some other service providers:

  • Alltel [10-digit phone number]@message.alltel.com
  • Boost Mobile [10-digit phone number]@myboostmobile.com
  • Sprint [10-digit phone number]@messaging.sprintpcs.com
  • T-Mobile [10-digit phone number]@tmomail.net
  • Verizon [10-digit phone number]@vtext.com
  • Virgin Mobile USA [10-digit phone number]@vmobl.com

Hi @brantfaircloth,

Thanks for this useful gist. I have been following your commands but I am struggling with the beagle installation. I get the flooding error

./autogen.sh 
Putting files in AC_CONFIG_AUX_DIR, `.config'.
configure.ac: installing `.config/install-sh'
configure.ac: installing `.config/missing'
examples/complextest/Makefile.am: installing `.config/depcomp'
Makefile.am: installing `./INSTALL'
configure.ac:388: required file `hmsbeagle-${GENERIC_API_VERSION}.pc.in' not found
autoreconf: automake failed with exit status: 1

Is this anything you have come across?

Could it be a result of changes to the beagle-lib ? Have you tried installing this recently?

Any help would be useful.

Cheers,
Joseph