Installing GROMACS to Bridges-2

One reminder: Alec cannot fix logon issues. If the system is closing the connection, and you're entering the correct password, go to portal.xsede.org and submit a helpdesk ticket. You may also need to set your password at PSC's website if you have not done so already.

Necessary Downloads

1. GROMACS 2020.4. Use either link on that webpage to download the file (either will work fine).

2. GCC 8.4.0.

3. gcc.slu and build_gromacs.slu.

Steps for Installation

1. Log on to sftp by entering sftp yourusernamehere@data.bridges2.psc.edu. When prompted, enter your password.

2. You will need to change your local directory to your Downloads folder. If you are on a Mac or Linux machine, that command will be lcd ~/Downloads. For Windows, you'll need to find the file path for your Downloads folder and enter that after lcd instead.

3. Use put build_gromacs.slu to upload that file to Bridges-2. Since it is a small text file, this process should be quick.

4. Continue to use sftp's put command to upload gcc-8.4.0.tar.gz, gcc.slu, and gromacs-2020.4.tar.gz to your home directory on Bridges-2.

5. When the uploads have been completed, close your Terminal, then log on to Bridges-2 using ssh. Enter your password when prompted.

6. Enter sbatch gcc.slu. This will compile and install gcc-8.4.0 and and g++-8.4.0 (at ~/opt/gcc-8.4.0/bin/) and may take 40-60 minutes. You will receive an email when this process is complete.

7. Enter sbatch build_gromacs.slu. This will compile and install GROMACS. Again, you will receive an email when this process is complete.