{"id":6565,"date":"2022-12-06T16:45:32","date_gmt":"2022-12-06T16:45:32","guid":{"rendered":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=6565"},"modified":"2022-12-06T16:53:33","modified_gmt":"2022-12-06T16:53:33","slug":"modeltest-ng","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/modeltest-ng\/","title":{"rendered":"Modeltest-NG"},"content":{"rendered":"

Overview<\/h2>\n

Modeltest-NG<\/a> is a program for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces.<\/p>\n

Version 0.1.7 is installed on the CSF. Please note that the GUI has not been installed – all use should be via batch jobs.<\/p>\n

Restrictions on use<\/h2>\n

There are no restrictions on accessing Modeltest-NG on the CSF. The software is released under the Gnu GPL v3 license<\/a> and all usage must fall within that license.<\/p>\n

Set up procedure<\/h2>\n

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings<\/abbr>.<\/p>\n

Load one of the following modulefiles:<\/p>\n

\r\nmodule load apps\/gcc\/modeltest-ng\/0.1.7          # MPI and multithreaded version\r\n<\/pre>\n
Running the application<\/h2>\n
Please do not run Modeltest-NG on the login node. Jobs should be submitted to the compute nodes via batch. You may, however, run modeltest-ng --help<\/code> to see a list of command-line flags on the login node.<\/p>\n
Example jobs for the multicore and MPI executables are available in the following directory (after loading the modulefile.) You can copy the files you find there to your own scratch area if you like:<\/p>\n
\r\ncp -r $MODELTESTNGDIR\/example-jobs\/ ~\/scratch\r\n<\/pre>\n
Serial batch job submission<\/h3>\n
Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n                    # NO -V line - we load modulefiles in the jobscript\r\n\r\nmodule load apps\/gcc\/modeltest-ng\/0.1.7\r\n\r\n# $NSLOTS is automatically set to 1 for a serial job\r\nmodeltest-ng -p $NSLOTS -i input.fas<\/em> -t topology<\/em> -o results<\/em>\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Single-node Multicore Parallel batch job submission<\/h3>\n
This uses the multi-threaded executable so will only run on a single compute node (max 32 cores.)<\/p>\n
Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -pe smp.pe 8     # Number of cores (can be 2--32)\r\n\r\nmodule load apps\/gcc\/modeltest-ng\/0.1.7\r\n\r\n# $NSLOTS is automatically set to the number of cores requested above\r\nmodeltest-ng -p $NSLOTS flags...<\/em>\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Single-node small MPI Parallel batch job submission<\/h3>\n
This uses the MPI executable so can run on one or more compute nodes. The following is for use on a single compute node (up to 32 cores.)<\/p>\n
Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -pe smp.pe 8     # Number of cores (can be 2--32)\r\n\r\nmodule load apps\/gcc\/modeltest-ng\/0.1.7\r\n\r\n# $NSLOTS is automatically set to the number of cores requested above\r\nmpirun -n $NSLOTS modeltest-ng-mpi flags...<\/em>\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Multi-node large MPI Parallel batch job submission<\/h3>\n
This uses the MPI executable so can run on one or more compute nodes. The following is for use on a multiple compute nodes.<\/p>\n
Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd                    # Job will run from the current directory\r\n#$ -pe mpi-24-ib.pe 48     # Number of cores (48 or more in multiples of 24)\r\n\r\nmodule load apps\/gcc\/modeltest-ng\/0.1.7\r\n\r\n# $NSLOTS is automatically set to the number of cores requested above\r\nmpirun -n $NSLOTS modeltest-ng-mpi flags...<\/em>\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Further info<\/h2>\n