# CNS Installation

The computational engine for most of HADDOCK3's modules is the [Crystallography and NMR System (CNS)](http://cns-online.org/v1.3/).
Once you have [cloned the HADDOCK3 repository](INSTALL.md), please follow these instructions to compile a CNS executable that can be used to run HADDOCK.

## 1 Download CNS

Downloading CNS requires a license, which academic users can [request for free](http://cns-online.org) (click on the `Download` menu and fill the form). You will be sent a password for the download via e-mail.
Using the link provided in the same e-mail, download CNS ("Source installer (compilation required on your system)") to the directory in which you want to install it (for example `software`). Navigate to this directory, then uncompress and extract the archive:

```bash
cd ~/software/
gunzip cns_solve_1.3_all.tar.gz
tar -xvf cns_solve_1.3_all.tar
```

Go to the CNS directory:

```bash
cd cns_solve_1.3
```

If you are using csh/tcsh, edit `cns_solve_env` to point to the correct location (the current directory):

```
# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY

            setenv CNS_SOLVE /PATH/TO/cns_solve_1.3
```

If you are using sh/bash, edit `.cns_solve_env_sh`:

```
# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY

        CNS_SOLVE=/PATH/TO/cns_solve_1.3
```

## 2 Add HADDOCK routines

HADDOCK requires some adjustments in CNS to function properly.
The set of routines to add is provided in the haddock3 repository under [`varia/cns1.3/`](/varia/cns1.3/README.md).
Copy all of these files into the CNS source directory (`/PATH/TO/cns_solve_1.3/source/`), for example:

```bash
cp ~/software/haddock3/varia/cns1.3/* source/
```

## 3 Compile CNS

Make sure you are inside the main `cns_solve_1.3` directory.

If a suitable compiler is installed on your system, the following command should start the compilation of CNS:

```bash
make install
```

If needed, you can specify the compiler you want to use by adding the `compiler` option, for example:

```bash
make install compiler=gfortran
```

You should see the progress of the compilation, followed by a confirmation that an executable has been created. For example (with gfortran):

```
created executable file cns_solve-2206031450.exe
```

If this does not work, check the [troubleshooting section](#Troubleshooting) below.

## 4 Source CNS

Lastly, CNS needs to be loaded in the current shell before it can be used.

For csh/tcsh:

```bash
source cns_solve_env
```

For sh/bash:

```bash
source .cns_solve_env_sh
```

## 5 Check installation

To check that CNS has been installed, start the program with the following command:

```bash
cns
```

If the installation was successful, CNS will open in your terminal with a header including the following information:

```
============================================================
|                                                          |
|            Crystallography & NMR System (CNS)            |
|                         CNSsolve                         |
|                                                          |
============================================================
 Version: 1.3 at patch level U
 Status: Special UU release with Rg, paramagnetic
         and Z-restraints (A. Bonvin, UU 2013)
============================================================
```

The command to exit CNS is `STOP`.

You now have a suitable CNS executable to finish [installing HADDOCK3](INSTALL.md).

***

# Troubleshooting

## Compiler

If no suitable compiler is found, you will get an error message:

```
Error: no suitable compiler (ifort, pgf95, ifort_i4, ifort_mp or pgf95_mp) found
```

In this case, you will have to install a compiler. For more information, check the [CNS Installation page](http://cns-online.org/v1.3/installation/frame.html).
One Fortran compiler that is easy (and free) to install is `gfortran`. It is part of the GNU Compiler Collection (GCC), which can be installed with one command if you have homebrew:

```bash
brew install gcc
```

Alternatively, gfortran can be downloaded as a [separate binary](https://gcc.gnu.org/wiki/GFortranBinaries).

## Makefile

If a suitable compiler is installed but no corresponding `Makefile.header` is found, `make install` will give an error as well. For example (with gfortran):

```
Error: Makefile template for compiler gfortran is not available
```

Makefile headers for each supported system-compiler combination are provided in `instlib/machine/supported/` (for unsupported systems, see `instlib/machine/unsupported/`). If you already tried `make install`, the appropriate directory for your system (eg. `mac-intel-darwin`) will have been copied to the main `cns_solve_1.3` directory.
If this directory does not contain the desired file (eg. `Makefile.header.2.gfortran`), you can create one manually.

For example, for `gfortran`, create a new file named `Makefile.header.6.gfortran` inside the directory containing Makefile headers for your system. Save the following lines in this file:

```
# fortran options
F77 = gfortran
F77STD = -fdefault-integer-8 -w -fallow-argument-mismatch
F77OPT = -O3 $(CNS_MALIGN_I86) -funroll-loops -ffast-math -march=native -mtune=native -static
F77FLAGS = $(F77STD) $(F77OPT) $(EXT_F77FLAGS) $(F77BUG)

# C options
CC = gcc
CPP = g++
CCFLAGS = -O -DINTEGER='long int' -DCNS_ARCH_TYPE_$(CNS_ARCH_TYPE) $(EXT_CCFLAGS)

# link options
LD = gfortran
LDFLAGS = -w $(EXT_LDFLAGS)
```

Note the `-fallow-argument-mismatch` flag. From gfortran version 10 onward, type mismatches by default give an error rather than a warning. This flag returns warnings instead, so that CNS compilation can successfully complete. If a `Makefile.header.x.gfortran` is provided for your system but compilation fails with (many) `Error: Type mismatch`, you may need to add this flag to the provided file.