Add CNS installation instructions #469

cvnoort · 2022-06-07T08:03:21Z

General instructions for installing/recompiling CNS for HADDOCK added to INSTALL.md.

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Added section to INSTALL.md that lists the basic steps for installing CNS.

For now, it links to the CNS routines to add on Dropbox. I would be happy to also add these to the repository and update the instructions accordingly, would just need to know where.

General instructions for installing/recompiling CNS for HADDOCK added to INSTALL.md.

amjjbonvin · 2022-06-07T08:12:08Z

I would suggest to create a separate document just for CNS and refer to it in the INSTALLATION.md file

amjjbonvin

This is a rather simple description. We need to extend to put some compiler requirements if needed and also make a separate document just for CNS.

amjjbonvin · 2022-06-07T08:14:05Z

docs/INSTALL.md

+
+#### Add HADDOCK routines
+
+HADDOCK requires some adjustments in CNS to function properly. Download the [set of routines to add](https://www.dropbox.com/s/wliubqovuusqdvr/cns.tgz?dl=0). Uncompress the archive and move all of its files into the CNS source directory (`PATH/TO/cns_solve_1.3/source/`).


Where is the code coming from? Is this something we are providing? If not, may-be we better create our own archive and provide it under SURF drive for example (I can handle that)

This is a link that was provided to a user under #329 , but can of course be replaced with anything more appropriate.

Is this the same as haddock2.4/cns1.3? Since these might be crucial for the proper work of cns and haddock3, would it not be better if we package it together with the repo?

I would be happy to also add these to the repository and update the instructions accordingly, would just need to know where.
Added a link to the CNS instructions at the beginning of INSTALL.md, but if/when we add these files to the haddock3 repository it should probably be moved down to a step after cloning.

amjjbonvin · 2022-06-07T08:14:45Z

docs/INSTALL.md

+
+HADDOCK requires some adjustments in CNS to function properly. Download the [set of routines to add](https://www.dropbox.com/s/wliubqovuusqdvr/cns.tgz?dl=0). Uncompress the archive and move all of its files into the CNS source directory (`PATH/TO/cns_solve_1.3/source/`).
+
+#### Recompile CNS


What about the compiler requirements? And any OS-specific instructions?

Will add more details once I've moved the CNS instructions to a separate file!

codecov-commenter · 2022-06-07T08:46:03Z

Codecov Report

Merging #469 (00e0e78) into main (3258755) will not change coverage.
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  Lines        6124     6124           
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  Hits         4435     4435           
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amjjbonvin · 2022-06-08T05:14:25Z

Should be indeed. A good idea to package it together I would say.

…

Is this the same as https://github.com/haddocking/haddock/tree/haddock2.4/cns1.3? Since these might be crucial for the proper work of cns and haddock3, would it not be better if we package it together with the repo

Moving CNS installation instructions from INSTALL.md to its own file (CNS.md).

…nto documentation

Expanded information on the compilation of CNS. More details to be added particularly about the Makefile and different compilers/systems.

Updated to link directly to the "Installation" page of the CNS website, rather than to the main menu.

Some information on Makefile headers with specific details for gfortran.

Replacing the link path for mac to show an example of a self-compiled executable instead of the precompiled UU-specific one. For both mac and linux, specify the name of the CNS_FOLDER (cns_solve_1.3).

joaomcteixeira

Great work @cvnoort! Left some some comments on the pertinent lines 👍

joaomcteixeira · 2022-06-20T08:19:10Z

docs/CNS.md

+source .cns_solve_env_sh
+```
+
+To avoid having to repeat this step each time you open a terminal window to run CNS/HADDOCK, you may want to add the relevant `source` line to your `~/.cshrc`, `~/.tcshrc`, `~/.bashrc`, or `~/.bash_profile`. When doing this, make sure to use the full path instead of only the file name.


I think this is not needed to run HADDOCK. At least, I don't have it in my .bashrc. It doesn't hurt, though ☺️

joaomcteixeira · 2022-06-20T08:21:15Z

docs/INSTALL.md


 # on linux
-ln -s /PATH/TO/CNS_FOLDER/intel-x86_64bit-linux/source/cns_solve-2002171359.exe bin/cns
+ln -s /PATH/TO/cns_solve_1.3/intel-x86_64bit-linux/source/cns_solve-2002171359.exe bin/cns


I suggest keeping the CNS_FOLDER instead of cns_solve_1.3 because it better explains the command, as it is more general.

joaomcteixeira · 2022-06-20T08:22:03Z

docs/CNS.md

+
+## 3 Compile CNS
+
+#### Start compilation


This head should have 3 # instead of 4.

### Start compilation

joaomcteixeira · 2022-06-20T08:23:04Z

docs/CNS.md

+
+If this worked, you can continue to the [next step](#4-Source-CNS).
+
+#### Install a compiler


I suggest moving this section and the next one to a Troubleshooting section at the end of the file. Like that, we can continue adding examples and solutions to possible future problems without perturbing the reading flow.

This sounds great to me, I was thinking something similar to prevent confusing users with too much information when everything runs smoothly for them.

Moving some compilation details to a separate Troubleshooting section at the bottom of the file.

Brief statement about importance of CNS and extra link to INSTALL.md to make sure repository (eventually with the additional CNS routines) is cloned before CNS installation.

Update of the CNS instructions to point to the custom CNS routines that are now provided in the haddock3 repository, instead of a Dropbox link.

Point users to the CNS installation instructions after cloning the haddock3 repository.

Add CNS installation instructions

c8f532c

General instructions for installing/recompiling CNS for HADDOCK added to INSTALL.md.

amjjbonvin requested review from amjjbonvin and rvhonorato June 7, 2022 08:11

amjjbonvin reviewed Jun 7, 2022

View reviewed changes

Merge branch 'haddocking:main' into documentation

33105c8

rvhonorato assigned cvnoort Jun 8, 2022

rvhonorato added documentation Improve docs CNS Improvements in the CNS engine labels Jun 8, 2022

cvnoort added 9 commits June 8, 2022 22:36

Merge branch 'haddocking:main' into documentation

a4c694a

Separate CNS instructions

56ea021

Moving CNS installation instructions from INSTALL.md to its own file (CNS.md).

Merge branch 'documentation' of https://github.com/cvnoort/haddock3 i…

32cebe2

…nto documentation

Add compilation info

8dc47d2

Expanded information on the compilation of CNS. More details to be added particularly about the Makefile and different compilers/systems.

Change CNS installation page link

a9ab926

Updated to link directly to the "Installation" page of the CNS website, rather than to the main menu.

Merge branch 'haddocking:main' into documentation

7c47b13

Add Makefile and gfortran info

b81faf3

Some information on Makefile headers with specific details for gfortran.

Merge branch 'haddocking:main' into documentation

289a9d4

Change CNS paths in INSTALL.md

00e0e78

Replacing the link path for mac to show an example of a self-compiled executable instead of the precompiled UU-specific one. For both mac and linux, specify the name of the CNS_FOLDER (cns_solve_1.3).

joaomcteixeira reviewed Jun 20, 2022

View reviewed changes

cvnoort added 3 commits June 20, 2022 11:07

Merge branch 'haddocking:main' into documentation

1279e38

Add CNS troubleshooting section

af5e6e0

Moving some compilation details to a separate Troubleshooting section at the bottom of the file.

Add CNS intro

7b828c7

Brief statement about importance of CNS and extra link to INSTALL.md to make sure repository (eventually with the additional CNS routines) is cloned before CNS installation.

rvhonorato approved these changes Oct 6, 2022

View reviewed changes

cvnoort added 4 commits November 17, 2022 12:56

Merge branch 'haddocking:main' into documentation

334f5af

Merge branch 'haddocking:main' into documentation

6e21226

Update location of CNS files

c117c9a

Update of the CNS instructions to point to the custom CNS routines that are now provided in the haddock3 repository, instead of a Dropbox link.

Update INSTALL reference to CNS instructions

fbf56b5

Point users to the CNS installation instructions after cloning the haddock3 repository.

cvnoort marked this pull request as ready for review November 17, 2022 15:54

amjjbonvin merged commit d0bca1c into haddocking:main Nov 22, 2022

This was referenced Jun 1, 2023

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Add CNS installation instructions #469

Add CNS installation instructions #469

cvnoort commented Jun 7, 2022 •

edited by amjjbonvin

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cvnoort Jun 20, 2022


		#### Add HADDOCK routines

		HADDOCK requires some adjustments in CNS to function properly. Download the [set of routines to add](https://www.dropbox.com/s/wliubqovuusqdvr/cns.tgz?dl=0). Uncompress the archive and move all of its files into the CNS source directory (`PATH/TO/cns_solve_1.3/source/`).


		HADDOCK requires some adjustments in CNS to function properly. Download the [set of routines to add](https://www.dropbox.com/s/wliubqovuusqdvr/cns.tgz?dl=0). Uncompress the archive and move all of its files into the CNS source directory (`PATH/TO/cns_solve_1.3/source/`).

		#### Recompile CNS


		If this worked, you can continue to the [next step](#4-Source-CNS).

		#### Install a compiler

Add CNS installation instructions #469

Add CNS installation instructions #469

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cvnoort commented Jun 7, 2022 • edited by amjjbonvin Loading

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cvnoort commented Jun 7, 2022 •

edited by amjjbonvin

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