Running a simple MC simulation
(please see click for Yang lab website)
Connecting to HPCC
A simple command from your local Cygwin (or Mac) terminal will let you connect to HPCC,
ssh -l yourCaseID hpc1.case.edu
Or, if X11 is desired, you can try
ssh -X -l yourCaseID hpc1.case.eduWhen prompted,
<use the same password associated with your case ID>
By now, you are not working on your own laptop any more, but a remote computer (or a cluster of computers). In this case, the frontend of this computer cluster has a hostname called hpclogin.case.edu. Once you are logged in, we can do a lot of things from now on.
This should work if you are using the campus CaseWireless wireless network. However, if you login from off-campus or from the campus CaseGuest wireless network, a VPN client may be required from CWRU.
All the UNIX/Linux commands are available. For example, you can try
showing the current working directory. Or
showing all current running processes, including which Unix shell that is running.
Get your own computer node to play with
Generally, it is a good idea to run computing jobs at the login-node simply because it can slow down the entire cluster system. So, it is recommended to get yourself on one of so-called computing nodes by
If a large amount of resource, say a large memory node, is required, you can get via
qsub -I -l mem=8gb
Now you are transferred from the login node to a computing node. You can find out which node you are at by
Some basic of MATLAB
A lot of good examples can be found at the MATLAB website. It has both a graphic and non-graphic/text interface. For this example, we are going to use the text mode by
Some simple uses are like:
a = [1 2]; b = [3 4] c = a + b
A realistic MC code for a two-state conformational change
We are going through this example when we meet. There are three/four files we will use. You can copy them to your own folder (at your current dir) by
cp -r /home/sxy227/class2015/bmc .
Now, let us take a closer look ...