Getsetsolver

changeCobraSolver(solverName, problemType, printLevel, validationLevel)

Changes the Cobra Toolbox optimization solver(s)

USAGE

[solverOK, solverInstalled] = changeCobraSolver (solverName, problemType, printLevel, validationLevel)

INPUTS

• solverName – Solver name

• problemType – Problem type (‘LP’ by default) (a) One of the following: LP MILP, QP, MIQP ‘EP’, ‘CLP’ (b) ‘all’ attempts to change all applicable solvers to solverName. This is purely a shorthand convenience. (c) Cell array of problemTypes, e.g. {‘LP’,’QP’}

• printLevel – verbose level

  • if 0, warnings and errors are silenced

  • if > 0, warnings and errors are thrown. (default: 1)

OPTIONAL INPUT

validationLevel – how much validation to use

• -1: assign only the global variable. Do not assign any path.

• 0: adjust solver paths but don’t validate the solver

• 1: validate but remove outputs, silent (default)

• 2: validate and keep any outputs

OUTPUT

• solverOK – true if solver can be accessed, false if not

• solverInstalled – true if the solver is installed (not necessarily working)

USAGE

• The following is an example of how to change gurobi to be the LP solver

• [solverOK, solverInstalled] = changeCobraSolver (‘gurobi’,’LP’)

• If there are problems changing to a solver, use the following call to debug

• [solverOK, solverInstalled] = changeCobraSolver (‘gurobi’,’LP’,1,1)

Currently allowed LP solvers:

• fully supported solvers

  cplex_direct	CPLEX accessed directly through Tomlab cplex.m. This gives the user more control of solver parameters. e.g. minimising the Euclidean norm of the internal flux to get rid of net flux around loops
  dqqMinos	Double Quad Quad precision solver for ill scaled prob
  pronnb
  glpk	GLPK solver with Matlab mex interface (glpkmex)
  gurobi	Gurobi solver
  ibm_cplex	The IBM API for CPLEX using the CPLEX class
  matlab	MATLAB’s linprog function
  mosek	Mosek LP solver with Matlab API (using linprog.m from Mosek)
  pdco	PDCO solver
  quadMinos	quad solver
  tomlab_cplex	CPLEX accessed through Tomlab environment (default)
  cplexlp	CPLEX accessed through IBM matlab functions

• legacy solvers:

  lindo_new	Lindo API > v2.0
  lindo_legacy	Lindo API < v2.0
  lp_solve	lp_solve with Matlab API
  gurobi_mex	Gurobi accessed through Matlab mex interface (Gurobi mex)
  opti	CLP(recommended), CSDP, DSDP, OOQP and SCIP(recommended) solver installed and called with OPTI TB wrapper Lower level calls with installed mex files are possible but best avoided for all solvers

Currently allowed MILP solvers:

• fully supported solvers:

  cplex_direct	CPLEX accessed directly through Tomlab cplex.m. This gives the user more control of solver parameters. e.g. minimising the Euclidean norm of the internal flux to get rid of net flux around loops
  glpk	glpk MILP solver with Matlab mex interface (glpkmex)
  gurobi	Gurobi solver
  ibm_cplex	The IBM API for CPLEX using the CPLEX class
  mosek	Mosek LP solver with Matlab API (using linprog.m from Mosek)
  tomlab_cplex	CPLEX MILP solver accessed through Tomlab environment

• legacy solvers:

  gurobi_mex	Gurobi accessed through Matlab mex interface (Gurobi mex)
  opti	CLP(recommended), CSDP, DSDP, OOQP and SCIP(recommended) solver installed and called with OPTI TB wrapper Lower level calls with installed mex files are possible but best avoided for all solvers

Currently allowed QP solvers:

• fully supported solvers:

  cplex_direct	CPLEX accessed directly through Tomlab cplex.m. This gives the user more control of solver parameters. e.g. minimising the Euclidean norm of the internal flux to get rid of net flux around loops
  gurobi	Gurobi solver
  ibm_cplex	The IBM API for CPLEX using the CPLEX class
  mosek	Mosek QP solver with Matlab API
  pdco	PDCO solver
  tomlab_cplex	CPLEX QP solver accessed through Tomlab environment
  dqqMinos	Double Quad Quad precision solver for ill scaled prob

• experimental support:

  qpng	qpng QP solver with Matlab mex interface (in glpkmex package, only limited support for small problems)

• legacy solvers:

  gurobi_mex	Gurobi accessed through Matlab mex interface (Gurobi mex)
  opti	CLP(recommended), CSDP, DSDP, OOQP and SCIP(recommended) solver installed and called with OPTI TB wrapper. Lower level calls with installed mex files are possible

Currently allowed MIQP solvers:

• fully supported solvers:

  cplex_direct	CPLEX accessed directly through Tomlab cplex.m. This gives the user more control of solver parameters. e.g. minimising the Euclidean norm of the internal flux to get rid of net flux around loops
  gurobi	Gurobi solver
  ibm_cplex	The IBM API for CPLEX using the CPLEX class
  tomlab_cplex	CPLEX MIQP solver accessed through Tomlab environment

• legacy solvers:

  gurobi_mex

  Gurobi accessed through Matlab mex interface (Gurobi mex)

Currently allowed NLP solvers:

• fully supported solvers:

  matlab	MATLAB’s fmincon.m
  quadMinos	quad solver

• experimental support:

  tomlab_snopt

  SNOPT solver accessed through Tomlab environment

Note

It is a good idea to put this function call into your startup.m file (usually matlabinstall/toolboxes/local/startup.m)

getAvailableSolversByType()

Get the available solvers for the different solver types on the system.

USAGE

solvers = getAvailableSolversByType()

OUTPUT

solvers – struct containing one field per Problem type listing all solvers installed on the system for that problem type. Also contains an ALL field indicating all available solvers

getCobraSolver(solverType, validate)

Gets the current solver name given a solver type

INPUTS

solverType – Solver type, LP, MILP, QP, MIQP (opt, default LP, all). ‘all’ attempts to change all applicable solvers to solverName. This is purely a shorthand convenience.

validate

OUTPUT

• solverName – Solver name

• solverOK – true if solver can be accessed, false if not

• solverInstalled – true if the solver is installed (not necessarily working)

getCobraSolverVersion(solverName, printLevel, rootPathSolver)

detects the version of given COBRA solver

USAGE

solverVersion = getCobraSolverVersion (solverName, printLevel, rootPathSolver)

INPUT

• solverName – Name of the solver

• printLevel – verbose level (default: 0)

• rootPathSolver – Path to the solver installation

OUTPUT

solverVersion – string that contains the version number