WFN for NONMEM 7.3.0 - version 731

Hi, I have uploaded a new version of Wings for NONMEM (version 731) to http://wfn.sourceforge.net/ . New features are noted below. Of particular note are support for NONMEM 7.3.0 and simplifed parallel execution methods. Monolix users may use WFN to perform non-parametric and parametric bootstraps with Monolix 4.2.2. NeSI grid users may submit WFN runs to the PAN cluster in Auckland. Please let me know when you find bugs. Nick *A change is required to wfn.bat to complete the installation of this version. Version compatible with NONMEM 7.3.0 and NONMEM Version 7.2.* The NMVERMIN environment variable should be set in wfn.bat after the NMVER variable to reflect the minor version number e.g. For NONMEM 7.3: set NMVER=7 set NMVERMIN=3 For NONMEM 7.2: set NMVER=7 set NMVERMIN=2 If the –prdefault option is not used then a common directory is created for recompiled modules which is shared by all models (this mimics the default behavior of standard NONMEM). A user specified directory for recompiled modules may be defined by setting the nmpdir environment variable e.g. set nmpdir=temp.dir. The –mapall option has been added to the MPI pnm files. This allows Windows network drives to be used as the data source drive when using the MPI parallel method. The runname.ext file created by NM7.2 and later is no longer deleted at the end of a run. Visual predictive checks may be created using nmvpc.bat and any version of NONMEM or WFN. The R statistical programming system must be installed in order to create VPCs. See the VPC instructions. Because of internal errors within NONMEM it may not be possible to simulate with more than 1 subproblem. When using nmgosim to perform a parametric bootstrap the default is to request NONMEM to simulate the required number of replications using a data file representing one replication. Setting the NSUBPROBLEM environment variable to 1 will set the $SIMULATION option NSUB to the value of NSUBPROBLEM instead of the number or replications. The user should supply a data file containing the required number of replications. If the environment variable nmraw is set (e.g. set nmraw=n) then if a nmbs.cov file is created during a nmbs or nmbsgosim run it will be saved in nmbsall.cov in the results directory. The nmbs.cov file is only created if the covariance step is successful. The nmbsall.cov file records if the covariance step failed and collects nmbs.cov if it was successful. Parallelised thread execution has been simplified. The separate mpi parafiles provided with WFN720 are no longer needed. The environment variable cpus should be set to the desired number of parallel execution nodes e.g. to use 4 nodes when running nmgo: set cpus=4 nmgo theopd Note that the number of cpus assumes they are available on the same host. Parallelised command execution has been added. This is more efficient than parallelized thread execution with WFN commands that have multiple calls to NONMEM e.g. nmbs, nmgosim, nmrt. The environment variable cmds should be set to the desired number of parallel commands e.g. to use 4 commands when running nmbs: set cmds=4 nmbs theopd 1 100 The number of bootstrap runs will be divided among each of the parallel commands. Parallelised thread and parallelised command execution maybe combined. There should be at least as many nodes as cmds*cpus for this to be time efficient e.g. on a cluster with at least 400 nodes this following commands will execute 100 bootstrap runs in parallel with each run performing one bootstrap with 4 parallelised thread nodes. Depending on the cluster overhead this can complete the bootstrap runs in not much more time than it takes to perform one run. set cmds=100 set cpus=4 nmbs theopd 1 100 Support for Monolix command line execution with non-parametric and parametric bootstrap. Support for $THETAI and $THETAR records allowing reference to THETA parameters by name. Support for NESI grid submission. -- Nick Holford, Professor Clinical Pharmacology Dept Pharmacology & Clinical Pharmacology University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New Zealand tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23 53 email:[email protected] http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford