Single Particle LLC

Before Booting Up

• Recommended installation environment: 15°C to 30°C (59°F to 86°F) ambient temperature with ventilation cooling or air conditioning equipment to ensure good heat dissipation.

• Connect the power supply of the workstation to the electric outlet by power cord. Please note that the workstation may have several power supplies, and all the power supplies need to be connected to the electrical outlets.

• Connect the HDMI port on the workstation to the corresponding port on the monitor by HDMI cable. 

• Connect the ethernet port on the workstation to the corresponding ethernet port in the lab.

Booting Up

1. Power on

  Please remove all the USB devices, and then power on the workstation. If you are using an HDMI monitor, you need to connect the HDMI monitor first.

2. Login

  The default account/password will be sent through email. This account has sudo privilege. For your data safety, please change the default password to your preferred password.

3. DO NOT Upgrade the OS

  Please DO NOT upgrade the OS by yourself. It may lead to Cryo-EM software error. We will help our customers to upgrade the OS after we finish the compatibility validation.

4. Check Hardware Info

  Please check the hardware information by using the following command line:

  If you can’t see the detailed GPU information by using the last command line, please use the one below:

  If there is any difference between the hardware list in PO and the delivered hardware, please contact us ASAP.

Installed Software

• The installed software packages are all inside the path /spshared/apps/, where /spshared/apps/bin is for small independent tools and softlinks such as Gctf, Gautomatch and etc.

• Large software platforms such as Relion, EMAN2 and etc, would have their own directories in /spshared/apps/.

• If you need to install new software, please contact us via ticket. And if you need to install the software yourself, install the software in the /spshared/apps directory.

• Plus, the corresponding tarballs or installation binaries are located at /home/install.

Relion Version Switch

1. Open a terminal

2. Check the available environmental module by the following command line:

Normally you will see all available modules: such as relion/gpu/3.1.4relion/gpu/4.0, etc.

3. Load the environmental module you prefer. For example, you’d like to use Relion4, so you need to load the environmental module relion/gpu/4.0  by the following command line.

Now if you run Relion in the Terminal by the following command line, the version of Relion is 2.1.0 (see the upper-left corner of Relion GUI).

4. If you’d like to switch the version from Relion4 to Relion3, please close the GUI of Relion2.1 first, and then load the environmental module relion/gpu/3.1.4  by the following command line.

Now if you run Relion in the Terminal by the following command line, the version of Relion is 3.0.5 (see the upper-left corner of Relion GUI).

5. Please note that the environment module relies on the Terminal. When you open a new Terminal, you need to load the environment module again. 

Storage Suggestion

1. A raid system of SSDs (normally raid0) is mounted at /ssd in order for data scratch when running Relion, cryosparc and etc.

2. A raid system of HDDs (normally raid5) is mounted at /data in order for cryoEM data storage. User can make their own directory in it. 

3. We suggest to use /ssd to store the data in process. After finishing the processing, please move the data to /data.

Tips: All experimental data is stored in the /data directory and not in the account's home directory. 

Service

We have a ticket system to help you solve the software and hardware problem (https://singleparticle.freshdesk.com/a/dashboard/default). If you haven’t received the account and password of the ticket system, please contact our sales for help (sales@singleparticle.com).

  For software problem, in order to improve our response efficiency, please provide the following information when you submit a ticket:

• Teamview ID/Password or Hamachi ID
• Detailed description of the problem
• The work directory of the wrong job
• Is that ok to reboot the workstation?

Teamview ID/Password or Hamachi ID can be checked by the following command lines:

  Please note that don’t run teamviewer with sudo. After running teamviewer, there will be a GUI which displays the teamviewer ID/Password.

Notes

• For Ubuntu, we haven’t preset the password for root. For CentOS, we set the default password. For your data safety, please change the default password to your preferred password.
• Please DO NOT delete the account called spadm.This account is used for the remote service.