Frequently asked questions

We are a group of theoretical and computational scientists using high performance computing as one of many tools in our daily research. The group does not have a designated system administrator, which means that the burden of maintaining the cluster is on already very busy group members. Therefore, if you have a question, before e-mailing us, we request you to take a glance at this page. A lot of answers are already here. Thanks!

Q: Can I get an account on TARDIS?

A: If you are a member or a collaborator of Olvera de la Cruz Group, of course you can! As a matter of fact, YOU SHOULD! If you are not a member of the group, unfortunately, the answer is NO. TARDIS cluster is intended exclusively for members and collaborators of the group. Sorry!

Q: How do I access TARDIS?

A: For a detailed set of instructions (with pretty pictures) please follow this link.

Q: How do I submit a job?

A: For a detailed set of instructions please visit the Usage page.

Q: Which software is installed?

A: Full list of installed software is given on this page. You can always check what is there by typing "module avail" (of course, without quotes).

Q: I have all bunch of PBS scripts. Why can't I use them? What is all that Sun Grid Engine business?

A: Unfortunately, you will need to modify your PBS scripts. Sun Grid Engine (SGE) and PBS have similar but not identical syntax for job submission scripts. You can find a few examples at the usage page.

Q: Why SGE?

A: Well, because it can do what we need it to do, that is seamlessly manage serial and parallel CPU and GPU jobs. Torque/Maui are simply not yet up to the task. A solution which is compatible with PBS scripts is not free.

Q: Compiler cannot find library "-lxyz"?

A: 1. Make sure the library is installed (for the list check this page)
2. Make sure the module is loaded (for instructions how to do this, please follow this link)

Q: Can you install this software, library, tool,...?

A: It depends! If it is something only you are going to use, we urge you to install and maintain it in your home directory. If it is a tool of general use for the group, we'll be happy to install it to the system. One warning, thou! The software has to be free. For example, we cannot install Intel Compilers as they are not free.

Q: How do I run LAMMPS, HOOMD,...?

A: Please refer to the documentation of the corresponding program/package. We can only help you with the issues related to the access, job submission and data retrieval. We cannot provide support for any software installed on the cluster. However, ask around the group. Most likely someone has already used that tool/package.

Q: I need to run this job for 3 month on 128 processors. Is this possible?

A: We have a question: Are you planing to track all atoms in our Solar system? :-) Joking aside, you can find out about scheduling policies at this page. In general, there is a time limit on every job that runs on TARDIS. The group is large and resources are limited. In order to make the system equaly accessible to everyone, some restrictions are neccessary. If you really need to run a 1000+ processors job, you might want to consider using Quest cluster.

Q: At my previous group the cluster had "this and that" really cool feature...

A: Fantastic! You are more than welcome to implement it. The group will greatly appreciate your effort!

Q: My code used to work on my old machine, but it does not work on TARDIS. Something must be wrong with the cluster!

A: While indeed there might be something wrong with the cluster, our experience tells us that there is a 99.99% chance that you have a very subtle bug in your code. So, please, make sure that your code is 100% correct before asking us to look into the problem with the system. Thanks!

Q: Can you help me with a bug in my code?

A: It depends on how busy we are. In general, we deal with the issues related to the proper operation of the system and have very little time for anything else.

Q: What are pointers? What is duck typing?...

A: Those are cool questions, but you won't find an answer here. Google might be a good place to start.

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