PMLS安装
1. 系统环境
1.1 系统版本
文档使用的是 64-bit Ubuntu Desktop 14.04
本次安装使用的是 64-bit Ubuntu Desktop 16.04，18.04和20.04在安装过程会出现Python版本和编译错误
1.2 Python版本
Python 2.7.12
1.3 GCC版本
gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.12)
2. Obtaining PMLS
The best way to download PMLS is via the git command. Install git by running
sudo apt-get -y update
sudo apt-get -y install git
Then, run the following commands to download PMLS Bösen and Strads:
git clone -b stable https://github.com/sailing-pmls/bosen.git
git clone https://github.com/sailing-pmls/strads.git
cd bosen
git clone https://github.com/sailing-pmls/third_party.git third_party
cd ..
Next, for each machine that PMLS will be running on, execute the following commands to install dependencies:
sudo apt-get -y update
sudo apt-get -y install g++ make autoconf git libtool uuid-dev openssh-server cmake libopenmpi-dev openmpi-bin libssl-dev libnuma-dev python-dev python-numpy python-scipy python-yaml protobuf-compiler subversion libxml2-dev libxslt-dev zlibc zlib1g zlib1g-dev libbz2-1.0 libbz2-dev
Warning: Some parts of PMLS require openmpi, but are incompatible with mpich2 (e.g. in the Anaconda scientific toolkit for Python). If you have both openmpi and mpich2 installed, make sure mpirun points to openmpi’s executable.
3. Compiling PMLS
You’re now ready to compile PMLS. From the directory in which you started, run
cd strads
make
cd ../bosen/third_party
make
cd ../../bosen
cp defns.mk.template defns.mk
make
cd ..
If you are installing PMLS to a shared filesystem, the above steps only need to be done from one machine.
The first make builds Strads, and the second and third makes build Bösen and its dependencies. All commands will take between 5-30 minutes each, depending on your machine. We’ll explain how to compile and run PMLS’s built-in apps later in this manual.
4. Very important: Setting up password-less SSH authentication
PMLS uses ssh (and mpirun, which invokes ssh) to coordinate tasks on different machines, even if you are only using a single machine. This requires password-less key-based authentication on all machines you are going to use (PMLS will fail if a password prompt appears).
If you don’t already have an SSH key, generate one via
ssh-keygen
You’ll then need to add your public key to each machine, by appending your public key file ~/.ssh/id_rsa.pub to ~/.ssh/authorized_keys on each machine. If your home directory is on a shared filesystem visible to all machines, then simply run
cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys
If the machines do not have a shared filesystem, you need to upload your public key to each machine, and the append it as described above.
Note: Password-less authentication can fail if ~/.ssh/authorized_keys does not have the correct permissions. To fix this, run chmod 600 ~/.ssh/authorized_keys.