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:n.holf...@auckland.ac.nz
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
