mpi and mrbayes on ec2

start an image:

  ec2-run-instances --key keypair ami-74f0061d \
      --instance-type=c1.xlarge \
      --block-device-mapping '/dev/sda2=ephemeral0' \
      --block-device-mapping '/dev/sda3=ephemeral1'

  ssh -i ec2-keypair [email protected]

install compilers and stuff (including mpich2 and screen):

  yum groupinstall "Development Tools"
  yum install mpich2-devel.x86_64 mpich2.x86_64 screen readline-devel

mount ephemeral store

  sudo su
  mkdir /mnt/data
  mount /dev/sda2 /mnt/data
  chown ec2-user:ec2-user /mnt/data
  exit

get mrbayes and compile mpi version (as ec2-user is fine)

  mkdir ~/src/ ~/bin/
  cd src && wget http://downloads.sourceforge.net/project/mrbayes/mrbayes/3.1.2/mrbayes-3.1.2.tar.gz
  tar -xzvf mrbayes-3.1.2.tar.gz
  cd mrbayes-3.1.2

edit makefile and at very least
```
  MPI ?= yes
```
run make - ensure compiling w/ mpicc
```
  make
  mv mb ../../bin/
```

set mpi password, restrict access to pwd file, and start daemon

  cd ~
  echo "MPD_SECRETWORD=kittens" > .mpd.conf
  chmod 0600 /home/ec2-user/.mpd.conf
  mpd &

rsync data up to ec2 instance

  rsync -avz -e "ssh -i /path/to/my/ec2-keypair" \
      ./ [email protected]:/mnt/data/

run mrbayes with

  cd /mnt/data
  # start screen
  screen
  mpirun -np 8 /home/ec2-user/bin/mb
  # do mrbayes stuff...
  # detach from screen
  <ctrl-a>,<ctrl-d>
  # wait

log back in to instance, and re-attach (-r) to screen session
```
  screen -r
```

when done, pull data down with:

  rsync -avz -e "ssh -i /path/to/my/ec2-keypair" \
      [email protected]:/mnt/data/ ./

you can pull data down while a run is in progress, but you may need to edit the *.p and *.t files to make the number of iterations equal in the *.p files and the *.t files and add "End;" to the *.t files.

brantfaircloth/gist:950010