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Using Lab Computers

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Support for Laptops

What is supported

We can provide as much support as possible for laptops that have been purchased with funds from your lab. This support includes:

  • Connectivity to your local lab infrastructure and SBGrid's services.
  • Local installations of the SBGrid programs tree.
  • Basic troubleshooting.

 

What is not supported

SBGrid does not provide any support for personally purchased laptops, or machines that you do not use for work.

In addition, SBGrid is NOT responsible for (on any laptop):

  • Repairing laptop hardware.
    • Please contact the institution which you have purchased the laptop from.
  • Obtaining proprietary software licenses.
    • Non-free software is not available from SBGrid. Please contact your institution for purchasing software and obtaining installation media.
  • Software Installation (Other than the SBGrid Tree)
  • Providing backups for your laptop.
Submitting A Help Ticket

When you submit a help ticket, please try to include as much information as possible. The following is a list of information that should be useful in any ticket that you submit:
 

  • State the problem as best you can. Explain what is happening, and explain what you expect to happen when the issue is not present.
  • Include the name of the computer you are using. If you are not sure, run the `hostname` command from a Terminal.
  • Indicate whether the problem is isolated to a single machine, or if it affects all machines in your lab.
  • Include the operating system where applicable (Mac OS X/Linux).
  • If the issue is related to a piece of software, include the name of the software and version number.
  • If an error message is present, copy and paste the exact error message.

 

To submit a help request, you have two options:
 
 

It is important that you submit a help request for any SBGrid or IT related issue that you may be having, even if you have easy access to speak with SBGrid personnel.

Understanding Your Network Account

Changing Your Password

If you would like to change your password, you can do so by using the passwd command in a Terminal while logged into your network account.

Please note the following restrictions. Your new password must:

  • Differ from your account name
  • Contain at least one letter
  • Contain at least one number
  • Contain at least 8 characters

If you have forgotten your password, or are otherwise unable to log in, please submit a ticket by emailing help@sbgrid.org.

Network Account Creation and Deletion

Account Creation
 
Requests for user accounts must come from a PI or from someone a PI has authorized to perform requests of this nature. In order for SBGrid to create your account, please have your PI send the request to help@sbgrid.org with the following information:
 
  • Your first and last name.
  • Your primary email address

 

Account Deletion

  The PI must email help@sbgrid.org to notify us when a user leaves the lab. At termination, any SSH access is disabled. You may request 90-day extension prior to expiration by email (we'll CC: PI). You must set up forwarding email address if account is extended

Troubleshooting Firefox on a Network Account

The popular Firefox web Browser isn't written for concurrency within a user profile. That means that you can have only one open instance of the program per user. If your account is not local to your machine, you must close all previous instances before trying to start a new browsing session. On occassion, Firefox will not start, because previous sessions were not closed properly (because of a crash or network interruption.)

On Mac OS X

To fix this issue on OS X, please log out, and log back in.

You may also need to delete your parentlock file, located at ~/Library/Application Support/Firefox/Profiles/*.default/.parentlock

On Linux

Before attempting the following steps, please make sure that you are currently logged into only one computer.

Here are some steps to use Firefox, if it becomes locked by mistake:

  • Remove any application lock files. Typically, these lock files are found in the browser home directory. Just run the following to delete the locks:

    rm -f ~/.mozilla/firefox/*.default/.parentlock

    After you do so, try to run firefox one more time.

  • In the worst case scenario, you could do this: mv ~/.mozilla/firefox ~/.mozilla/firefox_hold

    (Note: this will completely reset Firefox.) Then start your browser, which will create a new profile. After you do this, you may wish to restore your bookmarks. You can do this via the Firefox menu path Bookmarks/Organize Bookmarks/File/Import (your old bookmarks would be in ~/.mozilla/firefox_hold/…)

Using the Linux Workstations

Installing Programs Without Root Access

~/bin

If you need to install a program that is not already available on your linux workstation, you can compile the program from source and install it into your home directory. This does not require root access, and if you need to work on another workstation of the same architecture, programs in your home directory will also be available to you there.

First, create a folder called bin in your home directory if it does not already exist. In this folder, you can place pre-compiled binaries of many Linux applications, such as Firefox. If the program you need is not available as a precompiled binary, you may be able to compile it yourself. Just download the source archive of your desired program, extract the source of the application, and cd into the resulting directory. Then, run the following:

./configure --prefix=$HOME
make
make install

If you would like to run the resulting program from a terminal, you can run it directly from it's containing directory, or add the path of your ~/bin folder to your unix $PATH variable.

Please note that SBGrid is not responsible for resolving dependencies or supporting applications that you build yourself. If you need a program for work that you cannot compile and you feel would be a valuable addition to the SBGrid software tree, please use the New Software Request form.

Firefox Plugins

If you need to install a plugin for Firefox, such as Adobe Flash, you can put the plugin .so file into your Mozilla plugins folder, located at ~/.mozilla/plugins

After you install your desired plugin, restart Firefox, and then enter about:plugins into the address bar, and look for the plugin in the list to verify its installation.

Using Email

Lab Mailing Lists

Editing Preferences

 
You can view and edit your mailing list subscription options by logging into the Sympa mailing list manager at https://cmcd.hms.harvard.edu/sympa.
 

Unsubscribing

 
There is currently no way to completely unsubscribe from the lab mailing lists, but it is possible to disable receiving mail in your sympa preferences. To do this, log in via the link above, select the mailing list on the left, and then click "Subscriber Options". In the 'Receiving Mode' dropdown list, select 'no mail'.
 

Sending Mail

 
In order to send an email to your lab, just send an email to the mailing list address, which you can find by clicking on the mailing list name in the menu on the left of the page. The address will be listed in the top-center of the page after clicking that link. Sending an email to that address will send an email to everyone in your lab's group (i.e. the sch address will send mail to everyone in the sche group, with a [SCH] prefix).
 
Note: Replies to the 'SCHE' list do not send to the entire list, but only the sender of the originating message.

Using SBGrid Programs

Running GUI Programs Remotely

It is currently possible to run programs remotely over SSH through a process called X-forwarding. To accomplish this, you may simply use the -Y flag in your SSH command, like so:

[user@host ~]$ ssh -Y user@remote-host

If you have to access your machine through a gateway (i.e., ssh to crystal.harvard.edu, then to a workstation), you can use a command such as:

[user@host ~]$ ssh -t -Y user@remote-host ssh -Y internal-host

After logging in to the remote host, you may launch programs by running the command name in a Terminal. With X-forwarding enabled, programs will launch their user interfaces on your computer, much like they would if you ran the program locally.

NOTE: On Mac OS X, you may need to change your display output in order for certain programs to run correctly. You can do this by opening the X11 preferences, clicking the output tab, and selecting a different option from the 'Colors:' dropdown (the default is "From Display"). 256 Colors will emulate an 8-bit color scheme for running applications such as WEB.

If you need to download a newer version of X11 for OS X, you can find the binaries here: http://xquartz.macosforge.org/trac/wiki

Running SBGrid Programs

Running programs from the SBGrid software tree should be as simple as opening a Terminal and typing the name of the application you would like to run. You may see a list of available software packages at: http://sbgrid.org/software.php
If you are unable to run programs in this manner, you'll need to add the appropriate lines to your shell configuration. Run echo $SHELL in a terminal to determine which file you should edit.

/bin/tcsh

Edit your ~/.cshrc file to contain:

if ( -e /programs/sbgrid.cshrc ) then
    source /programs/sbgrid.cshrc
endif

/bin/bash

Edit your ~/.bashrc file to contain:

if [ -f /programs/sbgrid.shrc ]; then
    . /programs/sbgrid.shrc
fi

You may also need to create a .bash_profile with the following contents:

if [ -f $HOME/.bashrc ]; then
  . $HOME/.bashrc
fi

 

Software Overrides

Most of the software titles installed in the SBGrid Suite have several versions available. Typically, we try to provide at least three versions of each software package, although very old or very new applications may have fewer versions. To override the default version, follow the instructions posted to the SBGrid Consortium website.


Network File Storage and Backups

Copying Data Between Sites

If you need to transfer data from a remote location (such as a synchrotron site), you can take advantage of the UNIX command line to do so.  In order to do this, you will need SSH access to your lab. This is not enabled by default at all research sites. If you need SSH access, please submit a ticket to help@sbgrid.org. The recommended way that you transfer your data is by using the rsync command.

EXAMPLE

rsync -av /path/to/folder remote-host:/path/to/data/folder

This example shows how to copy a whole folder from your local computer, to the remote computer. The local and remote filepaths may be reversed in order to copy a file from a remote host to your local computer.

If you are uncomfortable using the command line for moving files, you can also do so with a desktop SFTP (SSH File Transfer Protocol) Application. For OS X, a recommended SFTP client is Cyberduck (http://cyberduck.ch/). For Windows, you can download WinSCP (http://winscp.net/eng/index.php). Both applications are free.

 

Like with rsync, You will need SSH access enabled. To connect to your lab, just enter your server's fully qualified domain name (i.e. lab.university.edu) in the server field and use your network account username and password to log in.

Using the Mac Workstations

Installing non-free software

It is common for lab workstations to contain proprietary, or "non-free", software such as the Adobe Creative Suite, Microsoft Office, or MATLAB.  If you need a program installed that isn't free, you need to make sure that a copy of that software is purchased or accounted for before requesting installation.

In many cases, your organization may contain a site license for some of these software titles that legally covers your work computer to run the software.  You are responsible for determining the presence of a site-license. You must consult with your PI or institutional IT department to check if a license needs to be purchased before contacting SBGrid to install the software. 

SBGrid does not participate in software piracy, and following these steps will ensure that we are appropriately abiding by the commercial software license agreements.
Installing Applications Without Admin Priviledges

If you would like to install an application on your mac that is not included by default, you may do so by placing the application file in your User account Applications folder, located at /Users/<username>/Applications (you may create this folder if it does not already exist). Note that this location is unique from the system Applications folder, which is located at /Applications.

At /Users/<username>/Applications, you are the owner of the folder and have write permissions and can install simple application files, such as Firefox.app, via drag and drop.

Some applications include installers which ask for the Administrator password. If this is the case, the installer is either modifying the system Applications folder, or needs to modify important system files to fully install itself.  If an application you need to install requires an Administrator password, please send an email to help@sbgrid.org.