1. How to ask a question

Since HPC is a research cluster, it is in perpetual flux as hardware, apps, libraries, and modules are added, updated, and/or modified so often a bug will creep in where none existed before. When you find something missing or a behavior that seems odd, please let us know. You can email the HPC admins here.

Note that it will help considerably if you tell us more than It doesn’t work, or I can’t log in. If you want quick resolution of the problem, please send us as much relevant info as possible, including a description of what triggered the misbehavior. For us to help you, we have to be able to re-create the problem, so include the commandline you used, including all the options, the input and output file paths and preferably the command prompt which should include the node from which it was issued, and the time.

If the misbehavior involves an error message, doing a Google search on that error message will often produce the answer. (see Fix IT yourself with Google.

While many of you are not programmers, you’re dealing with programs, and if we are to have any hope of debugging the process that caused the failure, the more info the better (usually). PLEASE READ How to Report Bugs Effectively before you report a failure. At least glance at it.

If you’re going to spend a lot of time with computers, you should also read Eric Raymond’s encyclopedic How To Ask Questions The Smart Way. It will be of use thru your life, not only for computers, but in many other domains as well.

2. Access to HPC

Access to HPC is blocked from off-campus for security reasons. From off-campus, you have to use a Virtual Private Network connection. See UCI’s VPN Web page for more information and to download the required VPN client software. Or you can first ssh to an unblocked machine that’s on the UCI network, THEN connect to HPC.

3. Local Computer Support

Note that many such login problems are due to your local hardware and software configurations. If you have a local computer support person, s/he may be able to help you faster than we can. Here is a list of such Computer Support People.

4. The minimum information we need

4.1. Consider using mayday

I’ve written a script (mayday) that captures a lot of the background info we need and allows you fill in the rest. Just cd to working dir (often that’s the one in which you’ve typically cd’ed to anyway.)

Then just type mayday.

Described in more detail in the matching doc

4.2. If it’s a login problem:

  • where are you trying to log in FROM (from campus? from UHills? from Kansas? from Uganda?). If from offcampus, see above.

  • what kind of computer and Operating System you’re connecting from is often useful, especially for connection-related problems.

  • what software are you using to connect and which version?

  • what command did you use (exactly)?

  • what was the error message (exactly)?

  • what did you find when you searched Google with that error message?

4.3. If the error occurred on HPC:

Please include this information:

  • your UCINETID. Many of you do not use a UCNETID@uci.edu address, so we can’t tell what your user ID is without backtracking thru a variety of old email, LDAP lookups, etc. Just include your alphabetic user ID (aka UCINETID).

  • the directory in which you’re working (pwd, if it’s not in your prompt (see below))

  • if you’re running from your login dir (your HOME), how many GBs you’re currently using (type: "cd; du -shc *" (without the "s) and include the entire output).

  • the FULL PATH of files that you reference. HPC has a huge file search space, even for a single user.

  • the machine or node you’re working on (hostname, if it’s not in your prompt')

  • the modules you’ve loaded (module list)

  • the version of the software can also be useful.

  • the command you used (exactly) or if it was caused by a script, the full path to the script.

  • Break long commands into readable length with the use of the continuation character "\". ie: instead of one continuous line which will cause line breaks randomly:

# this is hard to read:
 $ make_2d_plots.py -i wetdry_cr/beta_diveuclidean/beta_div_euclideancoords.txt -m wetdry_cr/mapping_files/merged_mapping_data.txt -b 'Elevation' -o wetdry_cr/2dplots/elevation
  • format it like this, which shows how the arguments are called, with the matching filenames:

# so much easier to read
 $ make_2d_plots.py \
   -i wetdry_cr/beta_diveuclidean/beta_div_euclideancoords.txt \
   -m wetdry_cr/mapping_files/merged_mapping_data.txt \
   -b 'Elevation' \
   -o wetdry_cr/2dplots/elevation
  • include the error that it caused (exactly), including the full path to the error files if they were generated. SGE will drop error files in your $HOME dir named ' "<SGE_NAME>.e<JOBID>"'. You might also examine the contents of those files before you call for help.

  • If the error was more than a few lines, copy/paste them into pastebin (or an alternative and include the link generated rather than the pages of output. (Obviously, don’t include sensitive information in public pastes.)

  • you can also use the termbin service to capture output direct from STDOUT on HPC to provide a short-lived paste service:

$ ls -l | nc termbin.com 9999
http://termbin.com/oxi8h    # < include this in your email
  • copy the TEXT of the command and output if possible. DO NOT send us a screenshot of the commands unless you’re using a graphics program and the problem is more succinctly described with a screenshot (reason: it’s harder to copy text from a screenshot.

  • much of this info can be automatically generated by a decent prompt and it also helps YOU by letting YOU know where you are (on what machine, in what dir).

4.4. Make your prompt useful

If you add one of the following PS1 lines to your ~/.bashrc, it will speed things up because you can just copy your prompt to supply a lot of the needed info:

# the colorless short version that creates a prompt like this:

# Thu Mar 20 14:48:47 hjm@stunted:~/Downloads
# 522 $

PS1="\n\d \t \u@\h:\w\n \! \$ "

# the colorful longer version that creates a prompt like this:

# Thu Mar 20 12:08:38 [0.68 0.70 0.64]  hjm@stunted:~/nacs
# 556 $

PS1="\n\[\033[01;34m\]\d \t \[\033[00;33m\][\$(cat /proc/loadavg | cut -f1,2,3 -d' ')] \
 \[\033[01;32m\]\u@\[\033[01;31m\]\h:\[\033[01;35m\]\w\n\! \$ \[\033[00m\]"

The above looks like this on a black background: long color bash prompt
where the numbers in the brackets indicate the [1m, 5m, & 10m] system load average, which is also useful for debugging problems.

5. Make sure that …

  • You’re on the right machine. This is why we want the information about which machine you’re on.

  • the files you’re using have not been corrupted during transfer. This is frequently the problem when transferring files from Windows machines with applications that do not do automatic newline conversion. Use the file command to check whether there are DOS newlines.

6. Frequent mistakes

6.1. Outside UCI

Most of the login problems, especially from new users, result from trying to log into HPC from outside UCI, whether that be from nearby housing (including UHills). If you’re not on the main UCI Campus, you won’t be able to log into HPC directly since we only allow logins from UCI addresses. Therefore you will have to either:

  • use a VPN connection to log in. You can get the necessary software here.

  • or first ssh to an intermediate machine on the campus, such as your lab server, if it allows external connections.

6.2. Wrong machine

People new to HPC often confuse which machine they are working on, especially if they are using a Mac. This is why we want the information about which machine shows up in your prompt. See above.

6.3. DOS newlines

Check that your input files don’t have DOS newlines. Use the file utility to examine the files.

$ file /path/to/suspect_file.txt
/path/to/suspect_file.txt : ASCII text, with CRLF line terminators

# If output contains the phrase above:  ^^^^^^^^^^^^^^^^^^^^^^^^^^
# then it needs to be converted to Linux newlines with 'dos2unix'

$ dos2unix /path/to/suspect.txt
$ file /path/to/suspect.txt
/path/to/suspect.txt: ASCII text

6.4. Forgetting module load

All applications in the module system have to be set up by requesting HPC’s module system do so so. So if you wanted to run R, version 3.2.1, you would have to enter the module command:

module load R/3.2.1

At that point the environment for that version of R is set up and you can start R in the usual way:


Note that omitting the version number will load the numerically highest version available which is often NOT the latest version since many versioning schemes use non-numerically increasing series. It’s safest to be explicit which version you want.