Create mechanism instance struct in LLVM IR

[iomaganaris]

Create a stuct declaration in LLVM IR module similar to <mech>_Instance struct declared in cpp files.

An example of such struct declaration is:
test.mod (based on hh.mod)

NEURON {
    USEION na READ ena WRITE ina
    USEION k READ ek WRITE ik
    NONSPECIFIC_CURRENT il
    RANGE gnabar
    RANGE minf, hinf, ninf, mtau, htau, ntau
}

STATE {
    m h n
}

PARAMETER {
    gnabar = .12 (S/cm2)    <0,1e9>
}

ASSIGNED {
    v (mV)
    celsius (degC)

    minf hinf ninf
    mtau (ms) htau (ms) ntau (ms)
}

test.cpp

/** all mechanism instance variables */
    struct _Instance  {
        const double* __restrict__ gnabar;
        double* __restrict__ minf;
        double* __restrict__ hinf;
        double* __restrict__ ninf;
        double* __restrict__ mtau;
        double* __restrict__ htau;
        double* __restrict__ ntau;
        double* __restrict__ m;
        double* __restrict__ h;
        double* __restrict__ n;
        double* __restrict__ ena;
        double* __restrict__ ina;
        double* __restrict__ ek;
        double* __restrict__ ik;
        double* __restrict__ Dm;
        double* __restrict__ Dh;
        double* __restrict__ Dn;
        double* __restrict__ v_unused;
        const double* __restrict__ ion_ena;
        double* __restrict__ ion_ina;
        double* __restrict__ ion_dinadv;
        const double* __restrict__ ion_ek;
        double* __restrict__ ion_ik;
        double* __restrict__ ion_dikdv;
    };

In LLVM IR we generate the following:

%unknown_Instance = type { double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double* }

The variables that are taken into account are:

88:  * Variable added to instance struct: gnabar
88:  * Variable added to instance struct: minf
88:  * Variable added to instance struct: hinf
88:  * Variable added to instance struct: ninf
88:  * Variable added to instance struct: mtau
88:  * Variable added to instance struct: htau
88:  * Variable added to instance struct: ntau
88:  * Variable added to instance struct: m
88:  * Variable added to instance struct: h
88:  * Variable added to instance struct: n
88:  * Variable added to instance struct: ena
88:  * Variable added to instance struct: ina
88:  * Variable added to instance struct: ek
88:  * Variable added to instance struct: ik
88:  * Variable added to instance struct: Dm
88:  * Variable added to instance struct: Dh
88:  * Variable added to instance struct: Dn
88:  * Variable added to instance struct: v_unused
88:  * Variable added to instance struct: ion_ena
88:  * Variable added to instance struct: ion_ina
88:  * Variable added to instance struct: ion_dinadv
88:  * Variable added to instance struct: ion_ek
88:  * Variable added to instance struct: ion_ik
88:  * Variable added to instance struct: ion_dikd

These variables include any float pointers or int pointers that are indexes to other vectors.

This PR also includes:

• Refactoring CodegeCVisitor and moving some functions to CodegenInfo
• Updating hpc-coding-conventions
• Small fixes in breaking unit tests (Maybe this only happened to my machine? I am using LLVM 11 on Ubuntu 20.04)

[georgemitenkov]

@iomaganaris A quick question about the Mech struct. The pointers point to the arrays of these variables that define current, conductivity, etc, across different points on the membrane. (By that I mean that NEURON user can define segments within the model that have their own properties). Do we know the sizes of the arrays they point to at compile time?

[iomaganaris]

@iomaganaris A quick question about the Mech struct. The pointers point to the arrays of these variables that define current, conductivity, etc, across different points on the membrane. (By that I mean that NEURON user can define segments within the model that have their own properties). Do we know the sizes of the arrays they point to at compile time?

@georgemitenkov As far as I know the sizes of the arrays are defined during run time according to the number of cells and segments per cell. @pramodk can correct me if I am wrong.

[pramodk]

What Ioannis mentioned is correct! we will know the trip count at runtime unless we do JIT (but that's different topic for now).