FAQs


In the following section, john is used as an example username, and 12345 is used as an example simulation ID. Be sure to replace these with the appropriate Michigan Tech ISO username and simulation ID respectively.

Contact Information Technology means the following:

Use the template in ServiceDesk Plus Portal. Log in with ISO credentials, if necessary. A brief but descriptive ISSUE TITLE, and including as much information as possible -- command sequence/work flow that is causing the issue, simulation ID, full path to the folder where the simulation was started from, as is error messages, screenshots, etc. -- will help diagnose and resolve the issue faster.




  1. When I try SSH into Portage, I get something like

    @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
    @  WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED!  @
    @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
    IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
    Someone could be eavesdropping on you right now
    (man-in-the-middle attack)!
    It is also possible that the RSA host key has just
    been changed. The fingerprint for the RSA key sent by
    the remote host is
    c6:90:98:f2:0b:a9:87:39:4c:a5:39:1e:0c:e9:6b:2b.
    Please contact your system administrator.
    Add correct host key in /home/john/.ssh/known_hosts to
    get rid of this message.
    Offending key in /home/john/.ssh/known_hosts:2
    RSA host key has changed and you have requested strict
    checking. Host key verification failed.
                        
    If the SSH public key on your local machine was re-created OR if Information Technology specifically informed you to expect such a message -- because Portage was re-built and/or your account on Portage was re-created, then

    1. Open /home/john/.ssh/known_hosts
    2. Search for portage.
    3. Delete the matching line(s).
    4. Save and close the file.

    If that wasn’t the case, then contact Information Technology with a clear description of this problem


  2. When I try SSH into Portage, I get something like

    Could not chdir to home directory /home/john:
      No such file or directory
    mkdir: cannot create directory `/home/john':
      No such file or directory
    
    It doesn't appear that you have set up your ssh key.
    This process will make the files:
         /home/john/.ssh/id_rsa.pub
         /home/john/.ssh/id_rsa
         /home/john/.ssh/authorized_keys
    
    Generating public/private rsa key pair.
    Enter file in which to save the key
      (/home/john/.ssh/id_rsa):
    Could not create directory '/home/john/.ssh'.
    Enter passphrase (empty for no passphrase):
    Enter same passphrase again:
    open /home/john/.ssh/id_rsa failed:
      No such file or directory.
    Saving the key failed: /home/john/.ssh/id_rsa.
    -bash: /home/john/.ssh/authorized_keys:
      No such file or directory
    chmod: cannot access `/home/john/.ssh/authorized_keys':
      No such file or directory
    chmod: cannot access `/home/john':
      No such file or directory
    
    -bash-3.2$
                        
    Contact Information Technology with a clear description of this problem


  3. I do not remember my password.

    All users of Portage that belong to Michigan Tech may use their ISO password. If you do not remember your Michigan Tech ISO password, follow normal procedures for having it reset. If you do not belong to Michigan Tech and/or are away from the university, contact Information Technology with a clear description and your password will be reset


  4. I cannot SSH into Portage and/or check its website from off-campus.

    Use VPN


  5. I tried the solution in above FAQ and I still cannot SSH into Portage. My account seems to be locked. Can I use some other user's credentials to log in?

    No. Sharing login credentials (username and password) with other and/or unauthorized users is a violation of Acceptable Use of Information Technologies. Using this infrastructure in a manner that violates the above and/or other provisions described in the aforementioned policy will lead to immediate suspension of account to protect the integrity of the system and curtail abuse. To the extent computer usage is believed to be a violation of federal, state, or local laws, Michigan Tech will turn the matter over to the appropriate authorities


  6. I cannot run any/some program(s)!

    It is likely that you edited the contents ${HOME}/.bashrc or ${HOME}/.bash_profile instead of doing so in ${HOME}/.bash_${USER} -- re-defining one (or more) of the variables already in use.

    If that wasn't the case, then contact Information Technology with a clear description of this problem (and name of the software)


  7. How do I know which variables are already in use?

    Run one of the the following commands

    set or env


  8. Can I re-alias commands/variables to meet my needs?

    Re-aliasing any of the variables (i.e., output of set or env commands) is bad idea. Doing so for any of the q* commands counts as a violation of Portage's protocols and will be grounds for removal of your account


  9. When I submit a simulation via qsub command, I get

    Unable to run simulation: denied: host "compute-M-N.local" is no submit host.
                        
    All simulations need to be submitted to the queue from the login node (also known as submission host) The error message appears when a simulation is submitted to the queue from a compute node (also known as an execution host), from within a qlogin session


  10. Will my data be backed up?

    No. Users are responsible for their own data


  11. Can I run programs in the Front End/Login Node(s)?

    No. Front End [in the absence of Login Node(s)] is intended for submitting simulations to the queuing system. Running simulations in Front End/Login Node(s) will slow the system down. All such simulations will be terminated without prior notice. Continued violation, after a warning, will lead to blocking/removal of account


  12. Where can I compile my code/software?

    Use qlogin and it will log you into a compute node to which you have access to. Standard set of compilers, tools and utilities will be available in that node, and you can compile your code. module command may be used to load/unload packages as necessary


  13. When I run screen command in a qlogin session, I get

    Cannot open your terminal '/dev/pts/0' - please check.
                        
    Once in a qlogin session, run

    script /dev/null

    and then run the screen


  14. There is no simulation running on a particular compute node. Can I log in and submit my simulation?

    No. All simulations must ONLY be submitted via their respective submission scripts from the Front End/Login Node(s) to the queuing system


  15. I submitted a simulation but can't find it now. There is (are) no output file(s) either. What happened to my simulation?

    Suppose that the script used to submit the simulation is called projectX.sh. Check the contents of projectX.sh.o12345 for any additional information. If the simulation was aborted/suspended, you will have received an email from the root to that effect


  16. When I submit a simulation, the compute node asks for my password.

    This probably means you are attempting run your calculation outside of the queuing system. If that isn't the case, then contact Information Technology with a clear description of this problem (and name of the software)


  17. Some commands do not work the way they should!

    Read the man page for that command. Meaning of a certain optional argument for the command might be different from the version/distribution of linux you use(d) elsewhere


  18. When trying to save files, vi says

    E138: Can't write viminfo file /${HOME}/.viminfo!
                        
    The following command should resolve this problem rm -f ~/.viminf?.tmp

    If that did not solve the problem, then contact Information Technology with a clear description of this problem


  19. When running COMSOL (with or without MATLAB LiveLink), username and/or password prompt appears.

    The following command, to be run just once, should resolve this problem (be sure to choose a password different than your Michigan Tech ISO credentials)

    /research/apps/comsol/VERSION/bin/comsol server

    This is applicable only for authorized users of COMSOL


  20. Is peer-to-peer file sharing allowed?

    No, if it is for personal and/or (non) commercial purposes. Yes, if and only if it is for academic and research purposes. However, distribution of such material is governed by the Digital Millennial Copyright Act. Michigan Tech's compliance with the Higher Education Opportunity Act and consequences of illegal file sharing are described here.

    Information Technology will disable accounts of users found employing peer-to-peer file sharing for personal, non-academic, non-research and/or (non) commercial purposes in this computing infrastructure, and take additional action as necessary


  21. There seem to be a number of unused CPU cycles. Can I use them for mining BitCoins?

    Yes, if and only if it is for academic and research purposes as indicated by your (or your advisor's) proposal/project - and has been granted explicit permission.

    No, if it is for personal, non-academic, non-research and/or (non) commercial purposes. Information Technology will treat any such instance of BitCoin mining (and/or any derivative thereof and/or similar to) as a violation of Information Security Compliance Policy.

    Any University employee, student or non-university individual with access to University data who engages in unauthorized use, disclosure, alteration, or destruction of data is in violation of this plan and will be subject to appropriate disciplinary action, including possible dismissal and/or legal action


  22. Can I run visualization programs - for e.g., Jmol, MolDen, XCrySDen, etc.?

    Yes and no. When explicitly permitted to do so, all such visualization programs must be run from within a qlogin session.


  23. Portage's performance does not match my expectation and/or that of some other cluster.

    If you believe you have done everything you can to optimize your code (using the appropriate version of dependencies, relevant compilation flags, and variables in your script) and still cannot get the performance you expect and/or you are used to getting in some other cluster, it is requested that you

    1. provide Information Technology with information about
      1. name of and source code for your software as well as a complete list of its dependents (and their version)
      2. your methods of compilation - compiler and compilation flags used
      3. your methods of running the software
      4. metrics (specifically tCPU and tWall) from Portage and that other cluster
      5. specifications (hardware, software, compilers, network, etc.) of that other cluster

    2. put Information Technology in touch with administrators of that other cluster so that attempts can be to rebuild/customize the cluster in as much the same way as possible

    Information Technology is also more than willing to compile (and possibly optimize) your code. While every effort will be made to get this done as quickly as possible, owing to the very nature of compilation process and limited availability of resources, Information Technology cannot guarantee a set deadline


  24. My problem does not seem to be listed. What should I do?

    Read other FAQs to make sure that your problem is not a variant of some other problem. Results from a Google search often provide a quick solution. If these do not help, then contact Information Technology with a clear description of the problem and Information Technology will work with you to diagnose/resolve the issue as soon as possible