MacroModel Reference Manual - ISP

Chapter 2: Running MacroModeltest calculation is performed on each of the hosts (this is recommended). Simple examples foreach of the supported types of distributed calculation are located in the directory:$SCHRODINGER/macromodel-vversion/test/dbmin after installation.After the NPRC line has been added to the .com file, MacroModel is run in the normal manner,e.g.:$SCHRODINGER/bmin test1Note:The -NO_REDIRECT command-line option to the $SCHRODINGER/bmin script is incompatiblewith distributed jobs.If a distributed MacroModel job is to be submitted to a queue, the following syntax should beused:$SCHRODINGER/bmin -LOCAL -HOST queue_name jobnameThe -LOCAL option keeps intermediate files in the local directory and facilitates inter-nodecommunication.Note:For the -LOCAL option to function properly, it is often necessary for the current directoryto be mounted on all computers involved in the process of running the job,including the machine on which the job is run and the machine that queues the job.The queue_name argument to the -HOST option specifies the name of the queue on which thejob should be run. Using the example schrodinger.hosts file in Section 2.3 on page 19,queue_name could be replaced with queue2.The jobname is the name of the command file for the job, without the .com extension.Note:It is currently necessary to submit such jobs from an NSF-mounted directory.A complete description of the syntax for running MacroModel from the command line can befound in Section 2.1.2 on page 12.Up to a total of 100 processors on up to 100 remote hosts can be requested for a single calculation.MacroModel looks through the hosts file for up to the number of processors requested bythe NPRC opcode, starting from the first entry. If insufficient hosts are listed, a message appearsin the .log file and the run continues, using the hosts listed. If the test calculation is requestedvia arg4, it is performed first. If there are significant differences amongst the energies returnedby the initial test calculations, the job stops and provides information as to which hosts gavedifferent answers. Since internally-distributed MacroModel calculations select hosts startingfrom the top of the schrodinger.hosts file, it can be advantageous to use customized filesfor different calculation. See Section 6.1 of the Installation Guide for information on setting upa schrodinger.hosts file.22MacroModel 9.7 Reference Manual