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opencobra / COBRA.jl

High-level, high-performance, constraint-based reconstruction and analysis in Julia
https://git.io/COBRA.jl
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Trying to run doubleGeneDeeletion script on PALM.jl #74

Open ali-kishk opened 4 years ago

ali-kishk commented 4 years ago

I have only both the model.mat and KO script 'Macrophage_KO.m' in the test directory.

PALM(modelDir, "$(joinpath(dirname(pathof(COBRA)), "../test/Macrophage_KO.m"))", nMatlab=nWorkers, outputFile="modelCharacteristics.mat", varsCharact=varsCharact, cobraToolboxDir=installDir)

but I am getting this error:

Every worker will run 17 model(s). Load sharing is ideal.

-- Load distribution --

┌ Info: Directory with 17 models read successfully. └ @ COBRA ~/COBRA.jl/src/PALM.jl:247

The poolsize is equal to 1. PALM.jl is meant to be used in parallel, not serial or sequential.

Stacktrace: [1] error(::String) at ./error.jl:33 [2] PALM(::String, ::String; nMatlab::Int64, outputFile::String, varsCharact::Array{String,1}, cobraToolboxDir::String, printLevel::Int64, useCOBRA::Bool) at ~/COBRA.jl/src/PALM.jl:257

rmtfleming commented 4 years ago

Hi it may be that COBRA.jl needs to be updated to point to the new location of the models repo: https://github.com/opencobra/COBRA.models Alternatively, add that missing model to the new repo. Regards, Ronan

On Mon, 23 Mar 2020 at 12:43, ali-kishk notifications@github.com wrote:

I have only both the model.mat and KO script 'Macrophage_KO.m' in the test directory.

PALM(modelDir, "$(joinpath(dirname(pathof(COBRA)), "../test/Macrophage_KO.m"))", nMatlab=nWorkers, outputFile="modelCharacteristics.mat", varsCharact=varsCharact, cobraToolboxDir=installDir)

but I am getting this error:

Every worker will run 17 model(s). Load sharing is ideal.

-- Load distribution --

-

Number of models: 17

Number of workers: 1

True load (models/worker): 17.0

Realistic load (quotient): 17

Remaining load (remainder): 0

┌ Info: Directory with 17 models read successfully. └ @ COBRA ~/COBRA.jl/src/PALM.jl:247

The poolsize is equal to 1. PALM.jl is meant to be used in parallel, not serial or sequential.

Stacktrace: [1] error(::String) at ./error.jl:33 [2] PALM(::String, ::String; nMatlab::Int64, outputFile::String, varsCharact::Array{String,1}, cobraToolboxDir::String, printLevel::Int64, useCOBRA::Bool) at ~/COBRA.jl/src/PALM.jl:257

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu & Adjunct Lecturer, School of Medicine, National University of Ireland, Galway.

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