This section describes the process of installing the Linda software you have purchased through Gaussian, Inc. and building a distributed-memory parallel version of Gaussian. It assumes that you have already built and tested the regular version of the program. It also assumes that you have read the normal installation instructions and also that you have access to the Gaussian 09 User’s Reference.
HF, CIS=Direct, and DFT calculations on molecules are Linda parallel, including energies, optimizations and frequencies. TDDFT energies and gradients and MP2 energies and gradients are also Linda parallel. Portions of MP2 frequency and CCSD calculations are Linda parallel, but others are only SMP-parallel, so they see some speedup from using a few nodes but no further improvement from larger numbers of nodes.
It is always best to use SMP-parallelism within nodes and Linda only between nodes. For example on a cluster of 4 nodes, each with a dual quad-core EM64T, one should use
%NProcShared=8 %LindaWorkers=node1,node2,node3,node4
rather than using more than one Linda worker per node.
If you have purchased Gaussian binaries, Linda is distributed on the same CD as the Gaussian binaries and no additional installation is necessary.
The Linda parallel programming model involves a master process, which runs on the current processor, and a number of worker processes which can run on other nodes of the network. So a Gaussian 09/Linda run must specify the number of processors to use, the list of processors where the jobs should be run, and occasionally other job parameters. An environment variable is generally the easiest way to specify this information (as we will see).
Each of these nodes needs to have some access to the Gaussian 09 directory tree. The recommended configuration is to have G09 on each system that will be used for the parallel job. Note that the Linda binaries need to have the same path on each machine. If this is not feasible, the G09 tree can be made accessible via a network-mounted disk which is accessed in an identical way on all nodes.
For MP2 calculations, each node must also have some local disk where Gaussian 09 can put temporary files.
Gaussian 09 gets configuration information from three primary sources
Details about %Link0 commands and the Default.Route file can also be found in the Gaussian 09 User’s Reference manual. Entries specific to Gaussian 09/Linda are described below.
The %LindaWorkers directive is used to specify computers where Linda worker processes should run. It has the following syntax:
%LindaWorkers=node1[:n1][,node2[:n2]] […]
This lists the TCP node name for each node to use. By default, one Linda worker is started on each node, but the optional value allows this to be varied. A worker is always started on the node where the job is started (the master node) whether or not it appears in the node list. %LindaWorkers may be combined with %NProcShared. In this case, one or more parallel worker processes will be run on each node (the number still determined by the values in %LindaWorkers). The value to %NProcShared specifies the number of SMP processors/cores to use on each system in the worker node list.
Do not use the obsolete %NProcLinda directive. G09 will compute the total number of Linda workers based on the %LindaWorkers input.
The following directive causes a network parallel job to be run across the specified 5 nodes. Nodes hamlet and ophelia will each run two worker processes.
%LindaWorkers=hamlet:2,ophelia:2,laertes,horatio,lear
The following directives specify that a parallel job will be executed on hosts norway, italy and spain. Nodes norway and italy will each run one 4-way SMP parallel worker, and spain will run two such workers:
%NProcShared=4 Specifies four-way SMP parallelism. %LindaWorkers=norway,italy,spain:2
These directives make sense when norway and italy are 4 processor/core computers, and spain is an 8 processor/core computer.
Note that the %NProc directive used in earlier Gaussian versions is obsolete.
Memory is specified using the %Mem Link0 command, just as for serial calculations.
By default, Linda uses rsh to communicate between nodes. You can use ssh instead by including the following option in the GAUSS_LFLAGS environment variable:
% setenv GAUSS_LFLAGS '… -opt "Tsnet.Node.lindarsharg: ssh"'
Another way to override this default, you need to create a configuration file in your home directory on the master node named .tsnet.config which contains the following line:
Tsnet.Node.lindarsharg: ssh
This will cause ssh to be used instead. Note that passwordless ssh logins must already be configured from the master to all worker nodes.
A few Linda options that are sometime useful are:
-v Display verbose messages -vv Display very verbose messages
Use the GAUSS_LFLAGS environment variable to set them.
For example, one could turn on very verbose Linda output using:
% setenv GAUSS_LFLAGS -vv
There are many other Linda options but most of them are not used by Gaussian. Check the Linda manual on the Internet at www.lindaspaces.com/downloads/lindamanual.pdf. The -opt form can be used in GAUSS_LFLAGS to invoke any valid .tsnet.config file directive. Note that Gaussian 09/Linda does not use the native Linda resources minworker and maxworker.
Last updated on: 10 May 2009