This chapter describes the installation of PALM on the Linux workstation cluster of IMUK and a suitable remote computer (host), on which the model runs are actually carried out. The local cluster is used to start the batch job with mrun and to analyze the results produced by the model. In batch mode, runs can be carried on the IBM-Regatta system of the HLRN, on an IBM-Regatta at KISTI, Korea (via a local DEC-Alpha-workstation at the Department of Atmospheric Sciences of the Yonsei University, Seoul), and on an NEC-SX6 at DKRZ. The examples given in this chapter refer to an installation of PALM on the IMUK cluster, considering the IBM-Regatta system of the HLRN as the remote computer.
The installation process requires a valid
account on the IMUK cluster and on the remote host as well. In the
following the IMUK workstation is called the “local host”.
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-adddress>
In both cases you should nnot be prompted for a password. Before continuing the further installation process, this must be absolutely guaranteed! This must also be guaranteed for all other remote hosts, on which PALM shall run.
In the first installation step a set of directories must be created both on the local and on the remote host. These directories are:
~/job_queue
~/palm
~/palm/current_version
~/palm/current_version/SOURCE
~/palm/current_version/JOBS
The names of these directories are freely selectable (except ~/job_queue), however new users should use them as suggested, since many examples in this documentation as well as all example files are assuming these settings.
In the second step the PALM source code must be copied into directory ~/palm/current_version/SOURCE on the local host by carrying out the following commands:
cd ~/palm/current_version/SOURCE
ln -s /home/raasch/public_html/PALM_group/INSTALL/RCS .
cp RCS/*,v .
co *,v
rm -rf *,v
Afterwards, the directory ~/palm/current_version/SOURCE should contain all PALM routines as well as a file with the name Makefile. All files are write-protected, the source code files end on “.f90”. The user should never modify these files without further knowledge of the PALM code.
To avoid the
re-compilation of the complete source code for each model run, PALM
willl be pre-compiled once on the remote host. Due to the use of
FORTRAN modules in the source code, the subroutines must be compiled
in a certain sequence. Therefore the so-called make mechanism
is used (see the respective man-page of the Unix operating system),
requiring the file Makefile,
in which the dependencies are described. The compiled sources (object
files) are
stored on the remote computer in the directory
~/palm/current_version/SOURCE/MAKE_DEPOSITORY.
For pre-compilation the user has to call the
command mbuild, which requires some pre-settings. The path
variable must be extended on both computers, so that the
commands mbuild and mrun as well as further routines
needed by mrun can be found.
This is achieved on the local computer via::
PATH=$PATH:/home/raasch/pub,
and on the IBM Regatta system of the HLRN via
PATH=$PATH:/home/h/niksiraa/pub.
These path extensions must be automatically set in the profiles of the local and remote host (file "~/.myprofile" at IMUK, file "~/.profile" at HLRN).
It is now assumed that the working directory is ~/palm/current_version/SOURCE on the local host. Compilation of the PALM code via mbuild needs a configuration file, which must be copied to the working directory under name .mrun.config (please click on the link with <SHIFT> + left mouse button). This file contains typical installation parameters like compiler name, compiler options, etc. for a set of different remote hosts. This file is also needed later on for starting the model runs.
In the configuration file .mrun.config the user name on the respective remote host must be entered. In lines like
% remote_username <username> <remote-computer-shortcut>
After this, the pre-compilation for the IBM-Regatta of HLRN can be started by entering
mbuild - h ibmh .
mbuild will prompt some queries, which must all be answered "y" by the user. The compiling process will take some time. mbuild transfers the respective compiler calls to the remote host where they are carried out interactively. You can follow the progress at the terminal window, where also error messages are displayed (hopefully not for this standard installation). By just entering
mbuild
PALM will be (consecutively) pre-compiled for all remote hosts listed in the configuration file.
As a last step,
after the compilation has been finished, the PALM installation has to
be verified. For this
purpose a simple test run is carried out. This once again requires the mrun
configuration file (described in chapter
3.2), as well as the parameter
file (described in chapter
4.4). The parameter file must be
copied to
~/palm/current_version/JOBS/example/INPUT/example_p3d .
The test run can now be started by entering the command:
mrun -d example -h ibmh -K parallel -X 8 -T 8 -t 500 -q cdev -r “d3# pr#”
This specific run will be carried out on 8 PEs and is allowed to use up to 500 seconds CPU time. After pressing <return>, the most important settings of the job are displayed at the terminal window and the user is prompted for o.k. (“y”). Afterwards a message of the queuing system like “Request … Submitted to queue… by…” should be displayed. Now the job is queued either started immediately or at a later time, depending on the current workload of the remote host. Provided that it is executed immediately and that all things work as designed, the job protocol of this run will appear under the file name ~/job_queue/ibmh_example no more than 3 minutes later. The content of this file should be carefully examined for any error messages.
Beside the job protocol and according to
the configuration file and arguments given for mrun
options -d and -r,further files should be found in
the
directories
~/palm/current_version/JOBS/example/MONITORING
and
~/palm/current_version/JOBS/example/OUTPUT .
Please compare the contents of file
~/palm/current_version/JOBS/example/MONITORING/ibmh_example_rc
with those of the result example file (e.g. with the help of the UNIX-command diff). There should be not a single difference between these two files. If the file contents are identical, the installation is successfully completed.
If you have any problems with the PALM installation, the members of the PALM working group are pleased to help you.
Last change: 20/04/05 (SR)