setup.md 13.1 KB
Newer Older
1
2
3
4
### **Setup**

#### Get permissions

5
6
Before setting up, you need permissions to access the codes and the input database. Email the following people to ask for the corresponding permissions.

Xuqian Yan's avatar
Xuqian Yan committed
7
```Note:: |:warning:| Currently, the codes are only accessible with an ETH account.
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
```

- 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):
Xuqian Yan's avatar
Xuqian Yan committed
24
  - permission for the overarching **Nexus-e** repository (<https://gitlab.ethz.ch/xyan/nexus-e.git>)
25

26
#### Local setup
27
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.
28

Xuqian Yan's avatar
Xuqian Yan committed
29
30
31
Most the instructions below have been tested both on **Windows** and on **Mac**.

#####  1. Get the codes
Xuqian Yan's avatar
Xuqian Yan committed
32
Make sure you have installed [git](https://git-scm.com/).  
Xuqian Yan's avatar
Xuqian Yan committed
33

34
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).
Xuqian Yan's avatar
Xuqian Yan committed
35
36
37
38
39
40
41
42
43

- 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```

Xuqian Yan's avatar
Xuqian Yan committed
44
  You will be asked for your username and password for the repository and its submodules.
Xuqian Yan's avatar
Xuqian Yan committed
45

Xuqian Yan's avatar
Xuqian Yan committed
46
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.
Xuqian Yan's avatar
Xuqian Yan committed
47
48
49
50
51
52

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


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

Xuqian Yan's avatar
Xuqian Yan committed
53
- 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):
54
55
56
```
itet-psl-s02
3306
Xuqian Yan's avatar
Xuqian Yan committed
57
58
DATABASE_USERNAME
DATABASE_PASSWORD
59
60
61
62
63
64
65
66
67
68
69
70
71
```

- 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
Xuqian Yan's avatar
Xuqian Yan committed
72
    |: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:  
73
    ```  
Xuqian Yan's avatar
Xuqian Yan committed
74
75
76
    ![](images/mysql-workbench-dump.png)
    
- (Optional) Work with a local copy of the database  
77

Xuqian Yan's avatar
Xuqian Yan committed
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
    - 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  (e.g., named as `UserDBInfo_local.txt`) as the following:
    ```
    127.0.0.1
    3306
    YOUR_LOCAL_USERNAME (e.g. "root")
    YOUR_LOCAL_PASSWORD
    ```
    - 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)
Xuqian Yan's avatar
Xuqian Yan committed
95
96

##### 3. Prepare software & license
97
You could skip this section if you don't plan to run the whole Nexus-e platform locally.
Xuqian Yan's avatar
Xuqian Yan committed
98

Xuqian Yan's avatar
Xuqian Yan committed
99
- **Matlab** (2018a or higher)
Xuqian Yan's avatar
Xuqian Yan committed
100
101
102
103

  - Set up database connector

    - Download the **MySQL connector** from [here](https://dev.mysql.com/downloads/connector/j/).  
104
    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).
Xuqian Yan's avatar
Xuqian Yan committed
105
106
107
108
109
110

    - 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**.

111
    - In the **javaclasspath.txt** file, write the path to the connector .jar file that you just copied.  
Xuqian Yan's avatar
Xuqian Yan committed
112
113
114
115
116
117
    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.  
    ```
Xuqian Yan's avatar
Xuqian Yan committed
118
    conn = database("sys", YOUR_USERNAME, YOUR_PASSWORD, 'Vendor', 'MySQL', 'Server', "YOUR_HOST");
Xuqian Yan's avatar
Xuqian Yan committed
119
120
    isopen(conn)
    ```
Xuqian Yan's avatar
Xuqian Yan committed
121
122
123
124
125
126
127
  
- **Python** (3.x)  
  ```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`.
128
  - Gurobi (9.x): Download gurobi and set up a free Gurobi academic license <https://www.gurobi.com/academia/academic-program-and-licenses>
Xuqian Yan's avatar
Xuqian Yan committed
129
  - 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. 
Xuqian Yan's avatar
Xuqian Yan committed
130
131
132
    - 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`.
Xuqian Yan's avatar
Xuqian Yan committed
133
134
135
136
137
138
139

- **GAMS**
  - 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
Xuqian Yan's avatar
Xuqian Yan committed
140
141
    - 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.
Xuqian Yan's avatar
Xuqian Yan committed
142
143
144


##### 4. Run Nexus-e
145

Xuqian Yan's avatar
Xuqian Yan committed
146
147
148
149
150
151
- Connect to ETH VPN (in order to connect with the database)
- Open Matlab
- Run the script `run_Nexuse.m` in the `Run_Nexuse` folder
  - 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.

152
#### Euler setup
153
154
155
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
156
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`.
157
158

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”.
Xuqian Yan's avatar
Xuqian Yan committed
159
160

##### 2. Get the codes
161

Xuqian Yan's avatar
Xuqian Yan committed
162
163
164
165
166
- 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.
167

Xuqian Yan's avatar
Xuqian Yan committed
168
169
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)
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226

##### 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
  ```

Xuqian Yan's avatar
Xuqian Yan committed
227
##### 5. Run Nexus-e
228
229
230
231
232
233
234
235
236
237
238
239
240
- cd to the `Run_Nexuse` folder
- 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.