Code Installation

This chapter describes the installation of PALM on a Linux workstation (local host). There are two methods to install and run PALM. With the simple method, you can run PALM interactively on the local computer. This method is using the scripts palm_simple_install and palm_simple_run. The simple method cannot create batch jobs itself, and cannot be used to create restart runs. Also file handling and most other features of the advanced method are not available. This method is only recommended for those who like to test PALM quickly.

The advanced method is for running PALM in batch mode on a suitable remote computer. The installation procedure is using the script mbuild. All jobs are started on the local host using the script mrun. The PALM output is automatically sent back from the remote host to the local host. Alternatively, mrun can also be used to start PALM in interactive mode on the local host, or as a batch job on the local host (if a queueing system like NQS, PBS, or LoadLeveler is available).

Only the advanced method gives full access to all PALM features.

Requirements

The installation and operation of PALM requires at mimimum (for the advanced method on both, the local and the remote host, unless stated otherwise):

1. A Korn-shell (AT&T ksh or public domain ksh); must be available under /bin/ksh.
2. A NetCDF-library with version number not earlier than 3.6.2 (for NetCDF, see under ​http://www.unidata.ucar.edu).
3. A FORTRAN90/95 compiler.
4. The Message Passing Interface (MPI), at least on the remote host, if the parallel version of PALM shall be used.
5. On the local host, the revision control system subversion (see ​http://subversion.tigris.org). This is already included in many Linux distributions (e.g. SuSe). subversion requires port 3690 to be open for tcp/udp. If there are firewall restrictions concerning this port, the PALM code cannot be accessed. The user needs a permit to access the PALM repository. For getting a permit please contact the PALM group (​raasch@muk.uni-hannover.de) and define a username under which you like to access the repository. You will then receive a password which allows access under this name.
   

The advanced method additionally requires:

6. A job queueing system on the remote host. Currently, mrun can handle LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).
7. ssh/scp-connections to and from the remote host must not be blocked by a firewall.

Currently, mrun is configured to be used on a limited number of selected machines. These are SGI-ICE systems at computing center HLRN in Hannover (lcsgih), Berlin (lcsgib), IBM-Regatta systems at Yonsei University (ibmy), and at DKRZ, Hamburg (ibmh), an NEC-SX8 system at RIAM, Kyushu University, Fukuoka (necriam), as well as on the Linux cluster of IMUK (lcmuk), Tokyo Institute of Technology (lctit), Kyoto computing center (lckyoto), and Cray-XT4/5 systems at the Bergen Center for Computational Science (lcxt4) and at the Finish Meteorological Institute (lcxt5m). The strings given in brackets are the systems names (host identifiers) under which mrun identifies the different hosts.

You can also use mrun/PALM on other Linux-Cluster, IBM-AIX, or NEC-SX machines. See below? on how to configure mrun for other machines. However, these configurations currently (version 3.7a) allow to run PALM in interactive mode only. Batch mode requires manual adjustments for the respective queing system and MPI installation in scripts mrun, mbuild, and subjob.

The examples given in this chapter refer to an installation of PALM on an IMUK Linux workstation and (for the advanced method) the SGI-ICE system of HLRN, used as remote host. They are just referred to as local and remote host from now on.

The installation process for the advanced method requires a valid account on the local and on the remote host as well.

The advanced installation method is described below. For the simple method see the end of this chapter.

Advanced installation method

All hosts (local as well as remote) are accessed via the secure shell (ssh). The user must establish passwordless login using the private/public-key mechanism (see e.g. the ​HLRN documentation). To ensure proper function of mrun, passwordless login must be established in both directions, from the local to the remote host as well as from the remote to the local host! Test this by carrying out e.g. on the local host:

  ssh  <username on remote host>@<remote IP-address>

and on the remote host:

  ssh  <username on local host>@<local IP-address>

In both cases you should not be prompted for a password. Before continuing the further installation process, this must be absolutely guaranteed! It must also be guaranteed for all other remote hosts, on which PALM shall run.

Please note that on many remote hosts, passwordless login must also work within the remote host, i.e. for ssh connections from the remote host to itself. Test this by executing on the remote host:

  ssh <username on remote host>@<remote IP-address>

You should not be prompted for a password.

Package Installation

The first installation step requires creating a set of directories on the local and, for the advanced method, on the remote host. These are:

  ~/job_queue
  ~/palm
  ~/palm/current_version
  ~/palm/current_version/JOBS

The names of these directories can be freely selected (except ~/job_queue), however new users should choose them as suggested, since many examples in this documentation as well as all example files are based on these settings. The directory ~/palm/current_version on the local host will be called the working directory from now on.

In the second step a working copy of the recent PALM version, including the source code, scripts, documentation, etc. must be copied to the working directory (local host!) by executing the following commands. Replace <your username> by the name that you have chosen to access the repository, and <#> by any of the available PALM releases, e.g. "3.7a" (new releases will be announced to members of the PALM mailing list).

  cd ~/palm/current_version
  svn checkout --username <your username> svn://130.75.105.2/palm/tags/release-<#> trunk

You will then be prompted for your password. After completion, there should be a subdirectory trunk in your working directory. It contains a number of further subdirectories, which contain e.g. the PALM source code (SOURCE) and the scripts for running PALM (SCRIPTS).

Alternatively, executing

  svn checkout --username <your username> svn://130.75.105.2/palm/tags/release-<#> abcde

will place your working copy in a directory named abcde (instead of a directory named trunk). But keep in mind that you will have to adjust several paths given below, if you do not use the default directory trunk.

Please never touch any file in your working copy of PALM, unless you know what you are doing.

You can also get a copy of the most recent developer code by executing

  svn checkout --username <your username> svn://130.75.105.2/palm/trunk trunk

This version may contain new features (they might not be documented well), but it may also contain bugs.