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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):
- A Korn-shell (AT&T ksh or public domain ksh); must be available under /bin/ksh.
- A netCDF-library with version number not earlier than 3.6.2 (for netCDF, see under http://www.unidata.ucar.edu).
- A FORTRAN90/95 compiler.
- The Message Passing Interface (MPI), at least on the remote host, if the parallel version of PALM shall be used.
- 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:
- A job queueing system on the remote host. Currently, mrun can handle LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).
- 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://130.75.105.7/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://130.75.105.7/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://130.75.105.7/palm/trunk trunk
This version may contain new features (they might not be documented well), but it may also contain bugs.
Package Configuration
To use the PALM scripts, the PATH-variable has to be extended and the environment variable PALM_BIN has to be set (on local and remote host) in the respective profile of the users default shell (e.g. in .profile, if ksh is used):
export PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH export PALM_BIN=$HOME/palm/current_version/trunk/SCRIPTS
You may have to login again in order to activate these settings.
On the local and on the remote host, some small helper/utility programs have to be installed, which are later used by mrun e.g. for PALM data postprocessing. The installation is done by mbuild. This script requires a configuration file .mrun.config, which will be also used by mrun in the following. A copy has to be put into the working directory under the name .mrun.config by
cp trunk/SCRIPTS/.mrun.config.default .mrun.config
Beside many other things, this file contains typical installation parameters like compiler name, compiler options, etc. for a set of different (remote) hosts. Please edit this file, uncomment lines like
#%remote_username <replace by your ... username> <host identifier>
by removing the first hash (#) character and replace the string "<replace by ...>" by your username on the respective host given in the <host identifier>. You only have to uncomment lines for those hosts on which you intend to use PALM.
Warning: When editing the configuration file, please NEVER use the TAB key. Otherwise, very confusing errors may occur when mrun is executing.
Beside the default configuration file .mrun.config.default, the directory trunk/SCRIPTS contains additional configuration files which are already adjusted for special hosts, e.g. .mrun.config.imuk can be used at Hannover University, etc.. These files have to be edited in the same way as described above.
After modifying the configuration file, the respective executables are generated by executing
mbuild -u -h lcmuk mbuild -u -h lcsgih
The second call also copies the PALM scripts (like mrun and mbuild) to the remote host.
Pre-Compilation of 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 by again using the script mbuild. Due to the use of FORTRAN modules in the source code, the subroutines must be compiled in a certain order. Therefore the so-called make mechanism is used (see the respective man-page of the Unix operating system), requiring a Makefile, in which the dependencies are described. This file is found in subdirectory trunk/SOURCE, where also the PALM code is stored. The compiled sources (object files) are stored on the remote computer in the default directory ~/palm/current_version/MAKE_DEPOSITORY_<block_descriptor>, where <block_descriptor> is composed of the third (and fourth, if existing) column of the respective block in the configuration file (e.g. lcsgih_parallel for HLRN).
The pre-compilation for the remote host (here the SGI-ICE system of HLRN) is done by
mbuild -h lcsgih
'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. If you want to compile for the local host only, please enter
mbuild -h lcmuk
Installation Verification
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 4.4.1?). The parameter file must be copied from the PALM working copy by
mkdir -p JOBS/example_cbl/INPUT cp trunk/INSTALL/example_cbl_p3d JOBS/example_cbl/INPUT/example_cbl_p3d
The test run can now be started by executing the command
mrun -d example_cbl -h lcsgih -K parallel -X 8 -T 8 -t 500 -q testq -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"). Next, a message of the queuing system like "Request … Submitted to queue… by…" should be displayed. Now the job is queued and 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/lcsgih_example no more than a few 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_cbl/MONITORING
and
~/palm/current_version/JOBS/example_cbl/OUTPUT
Please compare the contents of file
~/palm/current_version/JOBS/example_cbl/MONITORING/lcsgih_example_rc
with those of the example result file which can be found under trunk/INSTALL/example_cbl_rc, e.g. by using the standard diff command
diff JOBS/example_cbl/MONITORING/lcsgih_example_cbl_rc trunk/INSTALL/example_cbl_rc
where it is assumed that your working directory is ~/palm/current_version.
You should not find any difference between these two files, except of the run date and time displayed at the top of the file header. If the file contents are identical, the installation is successfully completed.
Configuration for other machines
Starting from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also be installed and run on other Linux-Cluster-, IBM-AIX, or NEC-SX-systems. To configure PALM for a non-default host only requires to add some lines to the configuration file .mrun.config.
First, you have to define the host identifier (a string of arbitrary length) under which your local host shall be identified by adding a line
%host_identifier <hostname> <host identifier>
to the configuration file (best to do this in the section where the other default host identifiers are defined). Here <hostname> must be the name of your local host as provided by the unix-command "hostname". The first characters of <host identifier> have to be "lc", if your system is (part of) a linux-cluster, "ibm", or "nec" in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if you want to install on a linux-cluster, the line may read as
%host_identifier foo lc_bar
In the second step, you have to give all informations neccessary to compile and run PALM on your local host by adding an additional section to the configuration file:
%remote_username <1> <host identifier> parallel %tmp_user_catalog <2> <host identifier> parallel %compiler_name <3> <host identifier> parallel %compiler_name_ser <4> <host identifier> parallel %cpp_options <5> <host identifier> parallel %netcdf_inc <6> <host identifier> parallel %netcdf_lib <7> <host identifier> parallel %fopts <8> <host identifier> parallel %lopts <9> <host identifier> parallel
The section consists of four columns each separated by one or more blanks. The first column gives the name of the respective environment variable used by mrun and mbuild, while the second column defines its value. The third column has to be the host identifier as defined above, and the last column in each line must contain the string "parallel". Otherwise, the respective line(s) will be interpreted as belonging to the setup for compiling and running a serial (non-parallel) version of PALM.
All brackets have to be replaced by the appropriate settings for your local host:
- <1> is the username on your LOCAL host
- <2> is the temporary directory in which PALM runs will be carried out
- <3> is the compiler name which generates parallel code
- <4> is the compiler name for generating serial code
- <5> are the preprocessor options to be invoked. In most of the cases, it will be neccessary to adjust the MPI data types to double precision by giving -DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION. To switch on the netCDF support, you also have to give -D__netcdf and -D__netcdf4 (if you like to have netCDF4/HDF5 data format; this requires a netCDF4 library!).
- <6> is the compiler option for specifying the include path to search for the netCDF module/include files
- <7> are the linker options to search for the netCDF library
- <8> are the general compiler options to be used. You should allways switch on double precision (e.g. -r8) and code optimization (e.g. -O2).
- <9> are the linker options
- <host identifier> is the host identifier as defined before
A typical example may be:
%remote_username raasch lc_bar parallel %tmp_user_catalog /tmp lc_bar parallel %compiler_name mpif90 lc_bar parallel %compiler_name_ser ifort lc_bar parallel %cpp_options -DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf lc_bar parallel %netcdf_inc -I:/usr/local/netcdf/include lc_bar parallel %netcdf_lib -L/usr/local/netcdf/lib:-lnetcdf lc_bar parallel %fopts -axW:-cpp:-openmp:-r8:-nbs lc_bar parallel %lopts -axW:-cpp:-openmp:-r8:-nbs:-Vaxlib lc_bar parallel
Currently (version 3.7a), depending on the MPI version which is running on your local host, the options for the execution command (which may be mpirun or mpiexec) may have to be adjusted manually in the mrun-script. A future version will allow to give the respective settings in the configuration file.
If you have any problems with the PALM installation, the members of the PALM working group are pleased to help you.
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