For assistance with NCF related issues contact: rchelp [at] fas [dot] harvard [dot] edu or call (617) 299-9724 and leave a message. Please provide as much detail as possible so that the Helpdesk staff can address your problem quickly. In addition, Luis Silva from RC has office hours on Tuesday and Thursday, 1:00-3:00 PM in the mini cluster on the second floor of the Northwest building, east wing, by the kitchen.

Questions about network, desktop or laptop support should be directed to Harvard University IT support (HUIT) at ithelp [at] harvard [dot] edu or (617) 495-7777.

For questions about CBSCentral (XNAT) or the NRG tools (i.e. fcfast) contact the neuroinfomatics group at at cbssupport [at] neuroinfo [dot] org.

For questions about the scanning facility, including safety issues, contact Tammy at tmoran [at] fas [dot] harvard [dot] edu, and see here.

For questions about setting up scan parameters or MR physics questions, talk to Ross at rmair [at] fas [dot] harvard [dot] edu.

For questions about experimental paradigm design, data analysis issues, or comments/questions about anything on the FAQ page, contact Stephanie at smcmains [at] fas [dot] harvard [dot] edu.

What is the NCF?

The Neuroimaging Compute Facility (NCF) is a central enabling infrastructure for neuroimaging teaching and research whose mission is to provide high performance, high power, robust, reliable and secure computer systems and human expertise to meet the challenges of neuroimaging research and teaching. The NCF is a collaboration between the Center for Brain Science and the Life Sciences Division of Research Computing. It consists of a collection of workstations and a compute cluster.

Who may use the NCF?

The NCF is a resource for the Harvard Neuroimaging Community and their collaborators. To access, just sign up for a user account indicating your laboratory and Principal Investigator.

How do I use the NCF?

There are several main uses for the NCF. With modern technology and advanced analysis techniques, datasets can be very large and can often fill up a users’ personal computer quickly. Therefore, the NCF provides a safe and secure location to store data. In addition, the data is backed up automatically and regularly, providing peace of mind. Second, the NCF has several analysis packages that are maintained to help users analyze data. This is done in two main ways. First, the compute cluster can be used to run computationally intensive jobs via the command line that do not require user input or interactions with a GUI. Second, the workstations can be used for data analysis that requires interaction from the user or the use of a GUI interface. The fastest way to run programs like this, such as SPM, is to sit in front of a workstation. In addition, users can login remotely from their own machine via VPN and x11 forwarding. However, this can be slow depending on the program being used. Another possibility that some users have reported is faster than logging in remotely, is to set up a VNC session, a type of virtual desktop program, that allows you to ‘take over’ a workstation from your desktop. Importantly, this doesn’t prevent someone else from using the workstation.

How do I get an NCF User Account?

To request a new account, fill out the online Account Request form. Requests for new accounts will be verified with lab PIs, so please allow a few days. When your account is ready, you will be sent instructions for logging onto the system.

How do I set up my user environment/access software on the NCF?

If you are working in bash, which is the default on the NCF, you should have a file in your user directory called .bashrc. You can open/create this file using your favorite text editor, such as gedit. Copy and paste the lines from below. This will get you all the default programs, including the NRG tools (fcfast, procfast), and many brain analysis packages. Many of the defaults are very old versions, given that people often don't want these to be randomly changing on them. To see how to select a different version, go here.

# writen by Luis Silva 02/10/2012
# For assistance please contact rchelp [at] fas [dot] harvard [dot] edu
#
#################################
# NCF Base setup install script #
#################################
#

#default environment, by using 'current' it will be updated automatcially with new releases. This should not change the default versions of software without assuring backwards compatibility.

. /ncf/tools/current/code/bin/env_setup.sh

#this makes your history file larger and easier to read so RC can more easily help you
HISTFILESIZE=10000
HISTCONTROL=ignoreboth
HISTSIZE=10000

#This makes your command prompt pretty, including having the pathname to where you are

PS1='\[\033[0;36m\]\u\[\033[0;35m\]@\h:\[\033[0;36m\]\w\[\033[0;35m\]\n[\!]\[\033[0m\]';

#
##################################################################
# Insert additional configuration below this line, like module loading and alis setting #
##################################################################

If you have questions about setting up your environment, you can contact Stephanie (smcmains [at] fas [dot] harvard [dot] edu) or RC help (rchelp [at] fas [dot] harvard [dot] edu). See below for how to change versions of software via environment variables, or modules.

How do I set my permissions so that everything is readable and writable by my group?

Initially, your permissions on the cluster are set up so that new directories and files are readable and writable to you, and readable by your group, and by the world (in this case, everyone with access to our cluster). You can tell what the permissions of a file are by typing ls -l. You will see something like this:

For a file:

-rw-r--r-- 1 mcmains cnl 54 Oct 5 2012 file_name

For a directory:

drwxr-xr-x 1 mcmains cnl 54 Oct 5 2012 directory_name

For a script: -rwxr-xr-x 1 mcmains cnl 54 Oct 5 2012 script_name

The first slot is either - for a file or d for a directory. The next three slots designate the owner's permissions (r=readable, w=writable, x=executable). The next three are the permissions for the group, and the last three are everyone else. Following this is the user name of the owner (mcmains) and then the owner's group (cnl).

Often, you will share files with other people in your group. In this case, you might want other members of your group to be able to read and write (edit) your files. In addition, you may not want other's on the cluster to be able to read your files. The default permissions can be set by adding a line to your .bashrc file. What you add depends on the permissions you want.

The command is umask followed by three numbers that designate the permissions separately for the three designations (users, group, everyone else).

0=rwx 1=rw 3=r 7=nothing

So if you wanted to make your files readable, writable, and executable by you and your group, but no one else, you would add the line:

umask 007

to your .bashrc file. For more information on permissions, including how to change them for just a single file or directory of files, see: http://www.dartmouth.edu/~rc/help/faq/permissions.html

How do I access the NCF network remotely?

The latest Neuroimaging Compute Facility (NCF 2.0) uses two-factor authentication, which requires users to use their username and password as well as second factor, which is now (5/18/2012) an openauth token, in order to gain entry to NCF infrastructure.

You must first install the openauth software. The link below will provide instructions for how to install this on your smart phone and/or your computer. This software creates a token that is specific to you, so if you use a different computer, you will need to set it up again, or use the token from your phone. Therefore, if you plan on VPNing to the cluster from multiple locations it is highly recommended to install the phone app also. Just follow the instructions on the page below, until you get the java application installed, then continue on with these instructions to see how to VPN.

https://software.rc.fas.harvard.edu/openauth

Once you download the software click on the JAuth.jar file to launch the program. This will make a little black and green box appear with a 6 digit code that is updated every minute or so. This code will be needed to successfully VPN to the NCF.

Now that you have the openauth token generator, you will need the actual VPN client. These steps will only need to be followed once per machine you want to install it on, and this application is not specific to a user, so if you find it already installed on a machine you can use it if you have your own personal openauth token. To get the VPN client (if you don't already have it) go here. Again, you will only have to do this step once, as this will install the Cisco AnyConnect VPN Client onto your system.

Once you launch the VPN client, make sure the "Connect to" path name at the top is [see below for notes on how to set this if the correct path doesn't show up in the drop down list]:

vpn.rc.fas.harvard.edu

Next you will be prompted for your username: @ncf i.e. jsmith@ncf. Next you will be prompted for your password: The second password field is for the 6 digit passcode from your openauth app. Once you enter this information, you should be able to connect.

Occasionally, you may have to try logging in once or twice, particularly if the token is getting ready to expire right as you put it in. Once you are connected, you can use a SSH client, such as putty on a PC, or terminal on a MAC.

Open an SSH session:

ssh –YC username [at] ncfws12 [dot] rc [dot] fas [dot] harvard [dot] edu There are several workstations (other than ncfws12) you can log into, with a list and instructions here.

NOTE ON CHANGING Connect to ADDRESS IF NOT IN DROP DOWN MENU:

In order to make "Connect to" show the address you want (vpn.rc.fas.harvard.edu) on a MAC (PC will keep what you type automatically), you need to edit a file located in (or a path similar to this):

/opt/cisco/vpn/profile/RC-SSL-Client-Profile.xml

Somtimes you might not be albe to see /opt because you don't have permissions. In this case you can search for the name, and find it that way to edit. I recommend editing this with text wrangler, as it will handle the permissions correctly. Otherwise, you most likely won't be able to save the file. To solve this, you can save it to a temporary location like the desktop (make sure it doesn't change the extension on the file), and then drag and drop it where it should go. You should then be prompted for your password. You need to look for the lines below, which are towards the very end of the file:

<HostName>rcvpn.rc.fas.harvard.edu</HostName>
<HostAddress>rcvpn.rc.fas.harvard.edu</HostAddress>

Change them to:

<HostName>vpn.rc.fas.harvard.edu</HostName>
<HostAddress>vpn.rc.fas.harvard.edu</HostAddress>

Why do I have to use an NCF designated workstation and where can I find one?

The NCF system is a secure private network. Dedicated high-performance workstations are set up and maintained by NCF staff for data management and image analysis. You may access the system via one of the designated terminals located in the MRI suite area in Northwest B4, in the Northwest office suite 280-295 area, and at the Center for Brain Science Neuroimaging pod on the second floor of William James Hall. See here for a list of designated workstations.

How and where do I login remotely?

In order to login in remotely, you first need to have your VPN access setup and going. Before logging into a workstation, it is advisable to check the usage on the machines in order to pick a machine that is not being heavily used. This can be done via a website. The newest workstations are:

Hostname: ncfws12.rc.fas.harvard.edu IP: 10.242.38.130

Hostname: ncfws13.rc.fas.harvard.edu IP: 10.242.38.131

Hostname: ncfws14.rc.fas.harvard.edu IP: 10.242.38.132

Hostname: ncfws15.rc.fas.harvard.edu IP: 10.242.38.133

However, several older machines exist also:

ncfws03.rc.fas.harvard.edu 10.242.38.53

ncfws04.rc.fas.harvard.edu 10.242.38.54

ncfws05.rc.fas.harvard.edu 10.242.38.55

ncfws06.rc.fas.harvard.edu 10.242.38.56

ncfws08.rc.fas.harvard.edu 10.242.38.58

ncfws09.rc.fas.harvard.edu 10.242.38.59

ncfws16.rc.fas.harvard.edu 10.242.38.134

ncfws20.rc.fas.harvard.edu 10.242.38.57

Once you decide on a machine, you need to SSH. On a Mac, this can be done via the Terminal, which is located in the Applications folder, inside of Utilities. For a PC, see directions below.

At the Terminal prompt, type:

ssh –YC ncfusername@ncfws??.rc.fas.harvard.edu

Where the ?? would be replaced by the workstation number.

How do I connect remotely to the NCF from a PC?

On a PC you will have to download an X11 clienet, and a SSH client. The preferred X11 client is Xming, downloaded here. Next, you have to download the SSH client, PuTTY from here. To enable X11 forwarding in PuTTY you need to configure your settings.

Start up PuTTY. In the configuration box you need to give it the Host Name of a ncf workstation. A list of available numbers (to replace the ??) can be found here. You can also save these settings by giving your session a name in the Saved Sessions box and then click Save. You should save it again once you set the X11 forwarding.

Next, under the Connection Category, expand SSH (click where red arrow pointing) and choose X11. Click on the Enable X11 Forwarding checkbox (where red arrow pointing).

Then, click on the Session Category, and save your settings again. Next time when you open this program, you can Load the saved settings.

Finally, click on Open. You should then be prompted for your username and password. When you are done, make sure you end your SSH session by typing exit at the command prompt before you X out of the PuTTY program.

How do I get files back and forth between the NCF and my computer?

This can be done in two main ways. The first is via the command line via sftp.

1. Command line:

Start an sftp session from your laptop. To do this you will need to have a VPN session going, and a terminal window open:

sftp username@ncfws??.rc.fas.harvard.edu

Where the ?? is replaced by the number of the workstation you want to remotely login to. For choices, see here. You will be prompted for your password. It is important to note that it is easiest to start the sftp session from the directory that contains the files you want to put on the NCF or from the directory where you want files from the NCF to be placed, as the starting directory is the default directory and ‘tab completion’ doesn’t seem to work (at least not for me).

If you want to PUT files from your laptop to the NCF, go to the directory on the NCF where you want the files to end up and then type:

put <filename>

If you want to get files from the NCF, go to the directory where the files are (cd, ls, and most unix commands should work). Then:

get <filename>

You can put or get multiple files using the * character to select multiple files.

2. GUI based:

You can also use a program to link the NCF to your computer so that you can surf through the directory structures easily on both, and just drag and drop files or folders that you want. There are two free downloadable choices, Fugu (recommended by RC), and Cyberduck (recommended by Luis).

Fugu Instructions: Once installed, open the program up and choose SFTP from the file menu at the top, and select “Show SFTP Window”. Then enter the requested information as below. You can either login to one of the workstations, or for fast transfers you can use ncflogin3.

This will bring up something similar to the Finder (Mac) or Explore (PC). You can travel through the directory structures by double clicking. To go up a directory, hit the blue up arrow next to the ‘side’ you want to go up one level in.

Cyberduck Instructions: Once installed, open the program up and from the File menu at the top, select “Open Connection”, and select SFTP at the top of the box that pops up.

In the Server box select your favorite workstation, or if you are just transferring a few files you can use ncflogin3 (See here for a list). Leave the Port at 22, enter your username and password, and click “Connect”. This will bring up something similar to Explorer on the PC or Finder on the Mac.

How do I look at and/or edit a text file on the NCF or my computer?

There are several ways to ‘read’ files from a workstation.

1. If you just want a quick view of the contents without opening up the file you can use ‘more’:

more <filename>

Press the space bar to advance the document, and ‘q’ to quit.

2. If you want to open the file up for editing or easier viewing, one of the nice text editors installed on the workstations is gedit.

gedit <filename> &

This will open up a nice GUI based text editors that has all the bells and whistles like find/replace, go to line, and such. The & sign means to gedit in the background so that you can still type and do things in the terminal window you launched gedit from.

3. On your Mac, you also have several options. The one I recommend is Text Wrangler. Make sure to install the command line editor. You can use this to open any text file. From the Finder, by right clicking, selecting ‘Open With’, and then TextWrangler. The main reason I recommend textwrangler is because it has a powerful find/replace function, taking most unix commands. In addition, it has a command line tool, so that when you are in a terminal, you can open things right there, just like gedit on the workstation, via:

edit <filename>

It will also let you edit ‘protected’ files by prompting you for a username and password, where other programs like the default text editor will often just deny you permission.

How do I submit jobs to the compute cluster?

There are several ways you can submit a job.

1. You can submit from any workstation.

2. You can submit from any SSH session to an individual workstation

3. You can SSH to the NCF login node (ncflogin1, ncflogin2, or ncflogin3). Just keep in mind that the ncflogin node is only for submitting scripts. It should not be used for analyzing data or other computationally intensive jobs as it is a shared space. Those types of things should be done from individual workstations.

From any of locations you can submit a job via the bsub command.

bsub –q ncf <script_name>

When the job is finished, you will receive an email notification along with all the output that would have normally been written to the screen. Importantly, after submitting, you can close the terminal and logout, the script will still be running in the background. If the script you want to submit is not in your path, such as when you make your own script to run, you need to make sure you give the full pathname to the script and that it is executable (chmod u+x <filename>). If it is a standard script like procfast or recon-all this is not necessary. See here for how to submit a matlab script.

If the script takes arguments afterwards, such as recon-all, then enclose it in quotes:

bsub –q ncf “recon-all –all –subjid mysubject”

Other useful flags inlcude:

-J a_job_name (useful for giving your job a name that is easily identifiable)

-o output_filename (stores output of your script to a file, but will no longer email you when the script is done. To get an email still, add a -N flag. You will still get an email when the script is done but the output from the script will be stored in the file specified by -o)

-e error_filename (stores any error messages generated by system. Can be useful for RC to debug issues)

-m hostname (to choose an unbusy node to submit your work to. To choose a host look here)

-n number of processors (This is the number of processors your submit job will go to, the default is 1. Please be respectful of other users and don't hog the system. To see how busy the compute cluster is, go here.)

bsub –q ncf -J recon_s102 -0 s102_output -e s102_erroutput “recon-all –all –subjid mysubject”

Useful commands to work with submitted scripts (bsub tools).

Some useful commands:

bjobs

Displays all your jobs currently running.

bkill <job id>

This will kill a submitted job. You can find the job id by running bjobs, or it is given when you submit the job.

bpeek <job id>

This allows you to ‘peek’ at the output of your job while it is running, to see what would have thus far been normally printed to the screen. This will not work if you directed the output of your job to a file with the –o opition, in that case you can look at the output file.

bsub –q ncf –o <output_filename> <script_name>

The –o option will redirect the standard output, or what would have been normally written to the screen if not submitting the job, to the filename given. In this case, you won’t receive an email when the job is done.

How do I setup VNC, which allows GUI intensive programs from my laptop?

1. You need to install a VNC program on your laptop, such as Real VNC, or Chicken of the VNC, which is used in the example below.

2. Log into the workstation you want to open a VNC connection to, see here for a list of worstations.

ssh –Y username@ncfws??.rc.fas.harvard.edu

3. Set up a VNC server:

vncserver –geometry (usually the resolution of your personal computer, such as 1440x900, 1024x768, the default is 800x600 which might be lower then you want)

vncserver –geometry 1440x900

This will prompt you for a password, we recommend you use your NCF, but you can use what ever you want, just remember it because you need to enter it into the VNC software.

This will report your display number:

New ‘ncfws06.rc.fas.harvard.edu:1 (your_username)’ desktop is ncfws06.rc.fas.harvard.edu:1

4. Click on Chicken of the VNC icon on your laptop and enter the required information The host name (e.g. ncfws06.rc.fas.harvard.edu). The display number reported by vncserver (e.g. 1) Enter your password Choose “Full Screen” if you want it.

If you choose full screen, you can exit it by typing cntrl+command+alt+’

NOTE: Importantly, when you end your VNC process, you must kill the vncserver you started on the workstation. Alternatively, if you plan to always VNC from one particular workstation you can leave this running to ensure the display number is the same, but make sure not to start a whole bunch of these and leave them running everywhere. To kill a session, you need to ssh to the workstation you stared it on and type:

vncserver –kill :<display_num>

vncserver –kill :1

How do I change my password?

From a workstation:

kpasswd

This will prompt you to enter your original password and then enter your new password (twice).

From your personal computer:

Go here and login using your ncf account information. At the top right click on the settings button, then click on the change password button.

What if I want to VPN to the NCF from a different computer than usual?

The openauth token code required for the two-factor authentication is specific to your username. Therefore, if you want to VPN from a different machine, you will have to set this up again. An alternative is to get the openauth app for your iphone, blackberry, or android. The instructions for doing so are here.

What software is available?

Common tools for data analysis are available and updated regularly. Licenses and software packages for data analysis include AFNI, Analyze, FreeSurfer, FIV, FSL, MatLab, and SPM. Neuroinformatics tools including XNAT and Oasis are also available. In addition, a developing shared resource will house common processing scripts and tutorials for neuroimaging data analysis including merged atlases for analysis of older adults and children, as well as innovative procedures for high resolution data analysis and surface visualization.

How much space will I be allocated to process and store my data?

Work and data storage space are allocated to the Principal Investigator of each laboratory. Within a lab, the PI is responsible for dividing up space, so see your PI for space requests. In addition, each user will have 20 GB of space in their home directory. Please do not use the home directory for data storage - it will run out fast! And definitely don't run jobs from your home directory as it can slow everyone's account down. In that case your account could be deactivated.

How do I check how much space I have left?

From a workstation or an SSH session, type:

df –h <directory_you_want_to_check>

How do I compress my dicoms to save space?

From a workstation or an SSH session, go to the directory that contains all of your dicoms. Type:

tar -czvf name.tar.gz what_you_want_to_tar

For instance: tar -czvf mydicoms.tar.gz subjid* or tar -czvf mydicoms.tar.gz *.dcm

To uncompress them: tar -xzvf name.tar.gz

How do I use the internet during VPN?

NCF system users will have access the Internet while connected to the NCF 2.0 VPN, with any compatible web browser that will get an automated proxy configuration. For most browsers you should not have to do anything. You should also have access to your email. If this is not true please contact rchelp [at] fas [dot] harvard [dot] edu. There maybe some issues with the VPN if you have to access other remote secure networks simultaneously. In that case, please contact rchelp [at] fas [dot] harvard [dot] edu.

How do I use the internet from the workstations?

The NCF workstation computers require proxy settings to be configured for each browser. Make sure you are not setting proxy settings in your .bashrc file, or it might make it so you can't access CBSCentral.

Below are the instructions for firefox.

1) Open the Firefox Browser application, and under the top menu "Firefox" select "Preferences" on the drop down list.

2) In the pop up window, select the "Advanced" top menu icon to the far right, and then click on "Network"

3) In the Connection option, click on the "Settings" button.

4) Select the bottom option "Automatic proxy configuration URL: and type the following in the field:

http://forefront-prd.rc.fas.harvard.edu/wpad.dat

Please close all current Firefox Sessions, and open a new session and you should now be able to access the Internet.

*** some older browsers may not work with the automatic proxy configuration file. In this case you may manually set your proxy settings by selecting manual proxy settings and enter the url as forefront-prd.rc.fas.harvard.edu and the port as 8080.

How do I change my version of Freesurfer, Afni, FSL or other brain analysis software packages?

Thanks to Tim O'Keefe from the Neuroinfomatics group, we have a simple script to change between most of the major brain analysis software packages. If there is a version you want not listed below, contact Tim (timothy_okeefe [at] harvard [dot] edu) and CBS help (cbssupport [at] neuroinfo [dot] org) for support.

For the following 'loader' scripts to work, you must be using the default enviornment (see here).

To get a list of availabe versions, type:

list_loaders

This should give you something that looks like the list below. Which has the software package name followed by the available versions. To select one, type the command (load_??) followed by the version:

load_fsl 4.1.7

load_freesurfer 5.1.0

IMPORTANT: If you want this change to be permenant, you need to add it to your .bashrc file (located in your home directory). Add it below the area saying "Insert additional configuration below this line".

Changing SPM is a little more compliated, because your matlab path must be updated. See here.

load_afni: 2011_05_26_1457

load_caret: 5.0

load_dcmtk: 3.6

load_freesurfer: 4.0.2 4.5.0

load_fsl: 4.0.3 4.1.6 4.1.7

load_java: 1.5 1.5.0_22 1.6 1.6.0_21_64 1.6.0_24

load_matlab: 7.11 7.4 7.7 7.8 7.9

load_mricron: 2009_12

load_nit: 1.0 1.0.1 1.0.2 1.1 1.2 1.2.1 1.2.2 1.3.2 1.3.3 1.3.4 1.4 1.4.1 1.5.0b dev

load_php: 5.3.10

load_python: 2.7.0 2.7.2

load_sd: 1.5.1

load_spm: 2.0 5.0 8.0 8.1 8.4667

load_xjview: 8.4

How do I set or change my SPM version?

You can change your SPM version similar to any other brain analysis software using the tools described above. However, you also need to add the SPM version to your matlab path. You can do this by using one of the variables set in the default unix enviornment (see here) and the load_spm function, $_HVD_SPM_DIR. To check what that variable is set to, type:

echo $_HVD_SPM_DIR

If the variable doesn't exist then you are not using the correct enviornment. If it is not the version you want, see how to change it via load_spm above. Remember, if you want to use a different version of SPM on future logins and in different terminals, you must add it to your .bashrc file. Once you have the SPM you want you can add this variable to your ~/matlab/startup.m file (See here for editing files).

addpath(getenv('_HVD_SPM_DIR'));

This will prepend SPM and its subdirectories to your matlab path, which means it will supersede any version you had previously set in your path. You should be aware that if you make changes to your path in matlab and then save it, this version of spm will become part of your 'permanent' path, as it was added on the fly at startup, but then you just saved the whole current thing. This can become a problem if you are swiches versions back and forth. This is also true of Freesurfer, who likes to add things to your matlab path, so make sure to check this occasionally and make sure mutliple things aren't added (via file - set path in matlab).

How do I change my matlab version?

While your matlab version can be changed via the package loader scripts above, it is better to use the modules made by research computing which provide a dynamic way to choose different packages. First, search for available matlab versions:

module keyword –i matlab

Then load the version:

module load math/matlab-R2011b

To unload a module:

module unload math/matlab-R2011b

If you use a package frequently, you can choose it automatically by adding it to your .basrc file: This is required if you want to use the selected software for jobs submitted to the cluster.

module load math/matlab-R2011b

What are modules on the NCF and how do I use them to select software versions?

Modules provide a dynamic modification of a users’ environment in order to individually select software versions. They will modify environment variables as needed, such as PATH. They can be loaded dynamically and in most popular shells. For a list of all modules, go here. You can use any of these, but if you want to see ones specifically made for the NCF, you can type:

module avail ncf

You can also search for a program using the module tools:

module keyword –i matlab

This looks for any packages that included the key word matlab, –i means to ignore case.

Or via a RC made script for searching:

/n/sw/rc/bin/modulesearch matlab

You can see that a lot of the matlab versions are within the group math. This group may have other useful software which can be checked via:

module avail math

To use a module that you see:

module load math/matlab-R2011b

To unload a module:

module unload math/matlab-R2011b

If you use a package frequently, you can choose it automatically by adding it to your .basrc file:

module load math/matlab-R2011b

To list your currently loaded modules:

module list

Firefox won’t open because it thinks it is already running.

The reason this happens is because Firefox uses one profile by default, and this profile gets “locked” when in use. To resolve this issues, when logged into workstation, open a terminal session and type in the command line:

firefox -profilemanager

A “Firefox – Choose your profile ” dialogue box will come up. Click on “Profile” -> “next” -> fill in a description, such as “second”, then click “finish” Then highlight the new profile, by clicking on it once with the mouse, and click on “Start firefox” Firefox should start up now, but you will now need to configure the Proxy Server information (All workstations are inside the NCF, and must use a proxy server for Internet).

Once on the NCF, I can’t start applications such as Firefox or Matlab.

There are a few possibilities:

1) Please make sure that you are either typing the full path, or that the application is in your path. To check if an application is in your path, type:

which <program_or_script_name>

If that returns a path for the application, then you shouldn’t need the whole path, see other possibilities below.

2) Please verify that your home directory has not reached it’s max quota. Go here for instructions on checking your space.

3) If you are remotely logged in, the problem could involve X11 forwarding. On the Mac, make sure that you used the –X or –Y flag when sshing (example). On the PC if you are using Putty, there should be an option to check ‘Enable X11 Forwarding).

4) Make sure you are sourcing the default environment that includes most packages and sets your path. Go here to see what it should look like.

4) If you are still having issues, email rchelp [at] fas [dot] harvard [dot] edu.

I tried to ssh to a workstation and it gave me a scary message about the token or IP address changing, what should I do?

The error message looks something like:

@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ @ WARNING: POSSIBLE DNS SPOOFING DETECTED! @ @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ The RSA host key for ncfws01.rc.fas.harvard.edu has changed, and the key for the corresponding IP address 10.242.38.51 has a different value. This could either mean that DNS SPOOFING is happening or the IP address for the host and its host key have changed at the same time. Offending key for IP in /Users/stephanie/.ssh/known_hosts:8 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ @ 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 ee:bf:41:7d:3f:00:29:1a:8f:05:99:b2:51:28:a0:93. Please contact your system administrator. Add correct host key in /Users/stephanie/.ssh/known_hosts to get rid of this message. Offending key in /Users/stephanie/.ssh/known_hosts:16 RSA host key for ncfws01.rc.fas.harvard.edu has changed and you have requested strict checking. Host key verification failed.

To fix it, you need to edit the file it tells you: /Users/username/.ssh/known_hosts.

For instance, if you got this message when trying to ssh to ncfws01.rs.fas.harvard.edu, you would open up the requested file and delete the line containing information for that workstation (highlighted in gray below).

FAQ

How can I get help?

What is the NCF?

Who may use the NCF?

How do I use the NCF?

How do I get an NCF User Account?

How do I set up my user environment/access software on the NCF?

How do I set my permissions so that everything is readable and writable by my group?

How do I access the NCF network remotely?

Why do I have to use an NCF designated workstation and where can I find one?

How and where do I login remotely?

How do I connect remotely to the NCF from a PC?

How do I get files back and forth between the NCF and my computer?

How do I look at and/or edit a text file on the NCF or my computer?

How do I submit jobs to the compute cluster?

Useful commands to work with submitted scripts (bsub tools).

How do I setup VNC, which allows GUI intensive programs from my laptop?

How do I change my password?

What if I want to VPN to the NCF from a different computer than usual?

What software is available?

How much space will I be allocated to process and store my data?

How do I check how much space I have left?

How do I compress my dicoms to save space?

How do I use the internet during VPN?

How do I use the internet from the workstations?

How do I change my version of Freesurfer, Afni, FSL or other brain analysis software packages?

What are modules on the NCF and how do I use them to select software versions?

Firefox won’t open because it thinks it is already running.

Once on the NCF, I can’t start applications such as Firefox or Matlab.

I tried to ssh to a workstation and it gave me a scary message about the token or IP address changing, what should I do?

Science

Community

Science

Resources

About this Site