setup.md

### **Setup**

#### Get permissions

Before setting up, you need permissions to access the codes and the input database. Email the following people to ask for the corresponding permissions.

```Note:: |:warning:| Currently, the codes are only accessible with an ETH account.
```

- Xuejiao Han (xuhan@eeh.ee.ethz.ch):
  - permission for the **DistIv** repository
  - access to the **PSL server** for the database (server name: itet-psl-s02)
- Jared Garrison (garrison@fen.ethz.ch):
  - permissions for the **eMark** repository
  - permissions for the **Shared** repository,
- Blazhe Gjorgiev (gblazhe@ethz.ch):
  - permission for the **Cascades** repository
  - permission for the **Run_Nexuse** repository
- Elena Raycheva (elena.raycheva@esc.ethz.ch):
  - permission for the **CentIv** repository
- Florian Landis  (landisf@ethz.ch):
  - permission for the **GemEl** repository
- Xuqian Yan (xuqian.yan@esc.ethz.ch):
  - permission for the overarching **Nexus-e** repository (<https://gitlab.ethz.ch/xyan/nexus-e.git>)

#### Local setup
Even though the current Nexus-e platform is **not** suitable to run locally because of high consumption of resources such as memory, we do recommend to at least get the codes and connect to the database locally in order to view, understand, and edit them easily.

Most the instructions below have been tested both on **Windows** and on **Mac**.

#####  1. Get the codes
Make sure you have installed [git](https://git-scm.com/).

The instructions here use **command lines**. If you have a GUI tool for git, you could use the corresponding operations in the GUI tool instead. An example using a GUI tool "GitKraken" can be found in section [Nexus-e repository instructions](nexuse_repo_instruction.html).

- Create a folder where you want to put the codes

- cd to that folder

- Clone the overarching repository with this command:

  ```git clone --recursive https://gitlab.ethz.ch/xyan/nexus-e.git```

  You will be asked for your username and password for the repository and its submodules.

In the end, the folder will look like the screenshot below. Note: You might not see the hidden files whose names start with a dot, and the `Results` folder will be automatically generated when you run Nexus-e.

![](images/nexus-e-folder.png)


##### 2. Connect with the input database

- Find information to connect with the database in `UserDBInfo.txt` in the repository. The file contains four lines (for confidentiality the username and password is not written here, but can be found in the file):
```
itet-psl-s02
3306
DATABASE_USERNAME
DATABASE_PASSWORD
```

- View the database
  - Install MySQL and MySQL Workbench
  - Connect to ETH VPN
  - Connect to the database with MySQL Workbench
    - Add a new MySQL connection
    ![](images/mysql-workbench-1.png)
    - Input connection information
    ![](images/mysql-workbench-2.png)
    - Click the button `Test Connection`. You will be asked to input your database password. Then you will see a seccess message:
    ![](images/mysql-workbench-3.png)
    ```eval_rst
    |:warning:| By default, everyone has write permission to the database. Therefore, to be safe, always make a local copy of the database before playing with it - i.e., first “Dump” it to a local folder, then import it to your personal MySQL account. These can be done in this window:
    ```
    ![](images/mysql-workbench-dump.png)

- (Optional) Work with a local copy of the database

    - Create a new text file to substitute `UserDBInfo.txt`.  
    For example, if you have dumped the common database to your local hosted database with IP address `127.0.0.1`, you could create a new text file as the following:
    ```
    127.0.0.1
    3306
    YOUR_LOCAL_USERNAME (e.g. "root")
    YOUR_LOCAL_PASSWORD
    ```  
    - Name the new file as  `UserDBInfo_xxx.txt`  (e.g., `UserDBInfo_local.txt`). An underscore "_" after "UserDBInfo" is needed to not synchronize it on git (see the file `.gitignore`).
    - Place the new file in the same folder as `UserDBInfo.txt`.
    - Point to the new file in the script.
      - Make a copy of `user_example_conf.m` in the folder `Run_Nexuse`. Name the copy as `user_conf.m`. (Note: You should only work with the local copy, because the original `xxx_example_conf.m` will be synchronized to git and it shouldn't be changed.)
      - Uncomment and adapt the variable `DB_INFO_FILE` in `user_conf.m` to be the new file name (e.g., `DB_INFO_FILE = 'UserDBInfo_local.txt';`).

    You might encounter the following problems when you run Nexus-e with a local database, follow the link for possible solutions:
    (1) [Error: "Access denied for user 'your_username'@'your_host_address' ..."](faq.html#access-denied-to-access-database)
    (2) [Error: "The server time zone value 'xxx' is unrecognized ..."](faq.html#database-server-timezone-issue)
    (3) [Error: "The user specified as a definer ('xxx'@'%') does not exist ..."](faq.html#database-definer-missing)

##### 3. Prepare software & license
You could skip this section if you don't plan to run the whole Nexus-e platform locally.

- **Matlab** (R2018a or higher, Matlab R2020b is recomended)

  - Set up database connector

    - Download the **MySQL connector** from [here](https://dev.mysql.com/downloads/connector/j/).
    Or, if you have access to the Nexus-e polybox, use the `mysql-connector-java-8.0.18.zip` provided in the folder `02_Model/02_Model_Setup_Instruction` (**Unzip** the file before the next step).

    - Copy the MySQL connector folder (e.g. mysql-connector-java-8.0.18) into a folder at your preference.
    We recommend to put it into the **Matlab preferences folder**, which you can find by typing in Matlab Command Window ```prefdir```.

    - Create a **javaclasspath.txt** file in the **Matlab preferences folder**.

    - In the **javaclasspath.txt** file, write the path to the connector .jar file that you just copied.
    E.g., On Blazhe's Windows computer the path is `C:\Users\gblazhe\AppData\Roaming\MathWorks\MATLAB\R2018a\mysql-connector-java-8.0.18\mysql-connector-java-8.0.18.jar`.

    - Reload Matlab

    - Test whether a database connector is set up successfully. Write the following commands in Matlab (substitue `YOUR_USERNAME` and `YOUR_PASSWORD` with your credentials for the database). If the second command returns `1`, it means success.
    ```
    conn = database("sys", YOUR_USERNAME, YOUR_PASSWORD, 'Vendor', 'MySQL', 'Server', "YOUR_HOST");
    isopen(conn)
    ```

- **Python** (3.8.6 is recomended)
  ```eval_rst
  |:warning:| Note: we are now in the phase of transferring from python 2.x to python 3.x. Therefore, it is recommended to use python 3.x locally and identify potential issues for the transfer.

  ```
  - Python packages: install the required packages listed in `requirements.txt`.
  - Python path: If you use Mac or if you want to run Nexus-e in a python virtual environment, you need to configure Python path in Matlab. Otherwise, you could skip this step.
    - Make a copy of `user_example_conf.m` in the folder `Run_Nexuse`. Name the copy as `user_conf.m`. (Note: You should only work with the local copy, because the original `xxx_example_conf.m` will be synchronized to git and it shouldn't be changed.)
    - Find out your python path (it varies largely depending on your PC's operating system and how you installed python). Uncomment and adapt the variable `PATH_PYTHON` in `user_conf.m` accordingly.
    - If you have a python virtual environment, you could configure it following the instructions in `user_conf.m`.

- **GAMS** (32.2 is recomended)
  - Download from [here](https://www.gams.com/download/)
  - Set GAMS License
    - Use the `gamslice.txt` provided in polybox `02_Model/02_Model_Setup_Instruction`.
    - Install the license: [here](https://support.gams.com/installation:how_do_i_install_a_license_file) or [here](https://www.youtube.com/watch?v=vSe3YGkUVoc) or (for MacOS) [here](https://www.gams.com/latest/docs/UG_MAC_INSTALL.html).
  - GAMS path
    - If you haven't done so, make a copy of `user_example_conf.m` in the folder `Run_Nexuse`. Name the copy as `user_conf.m`. (Note: You should only work with the local copy, because the original `xxx_example_conf.m` will be synchronized to git and it shouldn't be changed.)
    - Find out your GAMS path (it varies largely depending on your PC's operating system and the version of GAMS). Uncomment and adapt the variable `PATH_GAMS` in `user_conf.m` accordingly.
    
- **Gurobi**(9.0 is recomended)  
    - Download Gurobi and set up a free Gurobi academic license <https://www.gurobi.com/academia/academic-program-and-licenses>. 
    - Connect Gurobi with Matlab following [this instruction](https://www.gurobi.com/documentation/9.0/quickstart_mac/matlab_setting_up_grb_for_.html).

##### 4. Run Nexus-e

- Connect to ETH VPN (in order to connect with the database)
- Open Matlab
- Before running `run_Nexuse.m` for the first time, you need to run `bench_Nexuse.m`.
  It is recommended to repeat this step after major changes to the modules eMark and CentIv.
- Run the script `run_Nexuse.m` in the `Run_Nexuse` folder. Note, make sure you are into the `Run_Nexuse` folder before runing the `run_Nexuse.m` script.
  - You could change the variables `scen`, `tpRes`, and `limDifference` as instructed in the script
  - Consult Blazhe Gjorgiev (gblazhe@ethz.ch) if you want to run other scripts in the `Run_Nexuse` folder.

#### Software for interacting with Euler from local machine ####

In our experience, it is usefull to have two tools available for
- transferring files between Euler and your local machine and
- interacting with the command prompt on Euler.

**GUIs for file transfer**

For transferring files between Euler and your personal computer, a graphical user interface (GUI) is useful.
We suggest [FileZilla](https://filezilla-project.org/) since it is available for "all" platforms.
The scicomp wiki also has [information](https://scicomp.ethz.ch/wiki/Getting_started_with_clusters#Graphical_tools) on this.

**Command prompts for secure shell connections**

Unix systems (Linux/Mac) come with shells (command prompts) from which useful interactions with Euler are possible.
E.g., type `ssh <username>@euler.ethz.ch` to make a "secure shell" connection to Euler and issue commands to the Euler command prompt.
Windows users are less fortunate and have to install additional software to achieve this functionality.
Examples are
- putty.exe and
- [MobaXterm](https://mobaxterm.mobatek.net/).

We can highly recommend MobaXTerm.

<!-- ##### Install: putty.exe (not needed for Mac) ##### -->

<!-- Putty is command promt like interface from which you run your scripts on the cluster. -->
<!-- Use the commands below to run everything through putty. -->

<!-- ##### Install: WinSCP.exe/or Filezilla (for Mac) ##### -->

<!-- WinSCP is your GUI with your folder on the cluster, there you put your scripts and receive your results. -->
<!-- Results must be saved with a command in your script: -->
<!-- save (‘results’,’Var1’,’Var2’…). Var1, Var2, … denote the variables you want to save, while results denote the name of the file crated by Matlab (this is wat you see in WinSCP). -->

<!-- Remember to type in port 22 (default might be different) -->

**Login**

- Log-in with `ssh` on Unix-based operating systems:

  `ssh <ethz-username>@euler.ethz.ch`

  Lacking SSH keys, ssh will ask you for your ETH (LDAP) password and after that your following commands are issued to Euler.
  See [scicomp wiki](https://scicomp.ethz.ch/wiki/Getting_started_with_clusters#SSH) for instructions for setting up SSH keys if desired.
- File transfers between local and Euler in FileZilla can be made through `sftp` (secure file transfer protocol).
  For this, enter `sftp://euler.ethz.ch` in the 'server' field and your ETH-user name and password in the respective fields, then hit 'connect'.
- Access to Euler: since May 2020, first time access to Euler is only granted upon request. ETH account holders just write an email to	cluster-support@id.ethz.ch;
   If you used the Euler cluster before the 15. May 2020, then you
   would need to change
   your LDAP password to get again access to the Euler cluster
   (wait for 1 day until the change takes effect).
   (see https://scicomp.ethz.ch/wiki/Getting_started_with_clusters
   for more info).

<!-- #### Starting steps #### -->

<!--  - login on putty (Hostname: euler.ethz.ch; than ethz username and pasword) -->
<!--  - login on the WinSCP (Hostname: euler.ethz.ch; than ethz username and	password) -->
<!--  - -->

<!-- NOTE: You can use windows Command Prompt to run your jobs on Euler instead of Putty. In this case, you can connect by typing: ssh username@euler.ethz.ch -->

<!-- #### Alternative to Putty #### -->

<!-- MobaXterm https://mobaxterm.mobatek.net/ -->

<!-- It offers more options and better interface looks then Putty.  In the same time, it can replace WinSCP. Strongly recommended. However for copying/transferring files from/to Euler -->
<!-- folders is slow. For this purpose WinSCP is better. [FileZilla](https://filezilla-project.org/) does the job well, too. -->

#### Euler setup
In order to run the full Nexus-e platform efficiently, we use [Euler](https://scicomp.ethz.ch/wiki/Euler), an ETH cluster for High Performance Computing. To set up the Nexus-e platform on Euler, you first need to access Euler. Instructions on accessing Euler and commands for Euler can be found [here](https://scicomp.ethz.ch/wiki/Getting_started_with_clusters#Euler).

##### 1. Join the Nexus-e user group
We have a user group for access to Nexus-e specific licenses (e.g. GAMS) and the Euler pre-paid share. The user group is called: **MAVT-esc-nexus-e**, and is set and maintained by D-MAVT IT. To join the user group, ask Blazhe Gjorgiev (gblazhe@ethz.ch) to send an email to `servicedesk@mavt.ethz.ch`.

To check whether you are added to the user group, use command line ssh to Euler (type `ssh username@euler.ethz.ch`), then type `groups` to show a list of groups that your user account is linked to, which should contain “MAVT-esc-nexus-e”.

##### 2. Get the codes

- Create a folder where you want to put the codes
- cd to that folder
- Clone the overarching repository with this command:
  ```git clone --recursive https://gitlab.ethz.ch/xyan/nexus-e.git```
  You will be asked for your username and password for the repository and its submodules.

In the end, the folder will look like the screenshot below. Note: tThe `Results` folder will be automatically generated when you run Nexus-e.
![](images/euler-nexus-e-folder.png)

##### 3. Connect with the input database
- Download the **MySQL connector** from [here](https://dev.mysql.com/downloads/connector/j/).
Or, if you have access to the Nexus-e polybox, use the `mysql-connector-java-8.0.18.zip` provided in the folder `02_Model/02_Model_Setup_Instruction` (**Unzip** the file before the next step).

- Copy the MySQL folder in the hidden .matlab folder (e.g., .matlab/2019b)

- Create a **javaclasspath.txt** file in the same folder as above.

- In the **javaclasspath.txt** file, write the path to the connector .jar file that you just copied.
E.g., On Blazhe's Euler account the path is `/cluster/home/gblazhe/.matlab/R2018a/mysql-connector-java-8.0.18/mysql-connector-java-8.0.18.jar`.

- Logoff and re-login to Euler

##### 4. Prepare dependencies
Unlike setting up Nexue-s locally, we don't need to download any software or license on Euler. Instead, they are all prepared for all users in the user group **MAVT-esc-nexus-e**. You should already be a member of the group if you have followed the [first step](#join-the-nexus-e-user-group).

But still, we need to explicitely load all the dependencies, including modules (an Euler term for "software") and python packages.

- Load modules

  **Option 1**: Manually load modules every time before running Nexus-e

  Copy the following commands into Euler:
  ```
  module load new
  module load gams/28.2
  module load gurobi/8.1.1
  module load matlab/R2018a
  module load gcc/4.8.2
  module load python/3.7.1
  ```
    ```eval_rst
    |:warning:| Note: We used to load python/2.7.14. But we are now in the phase of transferring from python 2.x to python 3.x. Therefore, it is recommended to use python 3.x and identify potential issues for the transfer.
    ```
    Your Euler window should look similar to this:
    ```eval_rst
    .. image:: images/euler-module-load.png
      :width: 300px
    ```

  **Option 2**: Edit `.bash_profile` so that the modules are automatically loaded upon log in to Euler

  Write the same commands at the end of `.bash_profile`. This is a hidden file in your Euler's home directory. After adding these commands, your `.bash_profile` should look similar to this:
  ![](images/euler-bash-profile.png)

  **Test**: To test whether the modules have been successfully loaded, type `module list` in the commaand line. It should then list all loaded modules.

- Install python packages

  This you only need to do it **once**, i.e. you don't need to do it everytime when you run Nexus-e.

  In command line under your home directory, type
  ```
  pip install --user -r nexus-e/requirements.txt
  ```

##### 5. Run Nexus-e
- cd to the `Run_Nexuse` folder
- Before running `run_Nexuse.m` for the first time, you need to run `bench_Nexuse.m`.
  It is recommended to repeat this step after major changes to the modules eMark and CentIv.
- Submit the job with a command such as
```
bsub -n 36 -R "model==XeonGold_6150" -R "rusage[mem=5180]" -W "10:00" matlab -r run_Nexuse
```
The parameters in this command can be costomized. Details can be found [here](https://scicomp.ethz.ch/wiki/Getting_started_with_clusters).

Here we give a short explanation to the example command above:
![](images/euler-job-submission.png)

After submission, Euler will respond by telling you what the jobID is.