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myhost$ ssh narwhal.sharcnet.ca bash -l -c \' sqsub -r 5h ./myjob \'
myhost$ ssh narwhal.sharcnet.ca bash -l -c \' sqsub -r 5h ./myjob \'
Most problems with these commands are related to the local shell interpreting things that you wish to pass through to the remote side (e.g., stripping out any unescaped quotes). Use <tt>-v</tt> with ssh and <tt>set -x</tt> with bash to see what command(s) ssh and bash are executing respectively
Most problems with these commands are related to the local shell interpreting things that you wish to pass through to the remote side (e.g., stripping out any unescaped quotes). Use <tt>-v</tt> with ssh and <tt>set -x</tt> with bash to see what command(s) ssh and bash are executing respectively.
myhost$ ssh -v narwhal.sharcnet.ca bash -l -c \' sqsub -r 5h ./myjob \'
myhost$ ssh -v narwhal.sharcnet.ca bash -l -c \' sqsub -r 5h ./myjob \'
Revision as of 12:58, 26 June 2009
- 1 About SHARCNET
- 1.1 What is SHARCNET?
- 1.2 Where is SHARCNET?
- 1.3 What does SHARCNET have?
- 1.4 What can I do with SHARCNET?
- 1.5 Who is running SHARCNET?
- 1.6 How do I contact SHARCNET?
- 1.7 My application runs on Windows, can I run it on SHARCNET?
- 1.8 My application runs on Windows 2000 clusters, can I run it on SHARCNET clusters?
- 2 Getting an Account with SHARCNET and Related Issues
- 2.1 What is required to obtain a SHARCNET account
- 2.2 How do I apply for an account?
- 2.3 Can I just have a cluster account without having a web portal account?
- 2.4 Can I E-mail or call to open an account?
- 2.5 OK, I've seen and heard the word "web portal" enough, what is it anyway?
- 2.6 I have opened an account at the web portal, do I need to apply for a cluster account?
- 2.7 In the account application form, what should I fill in the "sponsor" field?
- 2.8 My supervisor does not have an account, so my application can't go through, what should I do?
- 2.9 My supervisor forgot all about his/her username, so my application can't go through, what should I do?
- 2.10 My supervisor does not use SHARCNET, why is my supervisor asked to have an account anyway?
- 2.11 I am a faculty member. In the application for an account, what should I fill in the field "sponsor"?
- 2.12 I am a visiting scholar, in the application for an account, what should I fill in the field "sponsor" ?
- 2.13 I am changing supervisor or I am becoming faculty, and I already have a SHARCNET account. Should I apply for a new account?
- 2.14 Is there any charge for using SHARCNET?
- 2.15 I have an account at a SHARCNET site, do I automatically have an account at rest of the sites?
- 2.16 I forgot my password
- 2.17 I forgot my username
- 2.18 My account has been disabled (so i cannot login). What should I do ?
- 3 Loggin in to Systems, Transferring and Editing Files
- 3.1 How do I login to SHARCNET?
- 3.2 How can I access to SHARCNET machines from Windows PC?
- 3.3 What operating systems are supported?
- 3.4 What makes a cluster different than my UNIX workstation?
- 3.5 Which cluster should I use?
- 3.6 What programming languages are supported?
- 3.7 How do I organize my files?
- 3.8 How do I transfer my files to and from a cluster?
- 3.9 How do I transfer an entire directory to and from a cluster?
- 3.10 How to archive my data?
- 3.11 How can I check the hidden files in directory?
- 3.12 SSH tells me SOMEONE IS DOING SOMETHING NASTY!?
- 3.13 Ssh works, but scp doesn't!
- 3.14 Running commands remotely
- 3.15 How do I edit my program on a cluster?
- 4 Compiling and Running Programs
- 4.1 How do I compile my programs
- 4.2 How do I run a program?
- 4.3 What is the batch job scheduling environment SQ?
- 4.4 How do I show and control jobs under SQ?
- 4.5 How do I translate my LSF command to SQ?
- 4.6 How can I submit jobs that will run where ever there are free cpus?
- 4.7 Command 'top' gives me two different memory size (virt, res). What is the difference between 'virtual' and 'real' memory?
- 4.8 Can I use a script to compile and run programs?
- 4.9 I have a program that runs on my workstation, how can I have it run in parallel?
- 4.10 How can I have a quick test run of my program?
- 4.11 Which system should I choose?
- 4.12 Where can I find available resources?
- 4.13 Can I find my job submission history?
- 4.14 How are jobs scheduled?
- 5 Programming and Debugging
- 5.1 What is MPI?
- 5.2 What is OpenMP?
- 5.3 How do I run an OpenMP program with multiple threads?
- 5.4 What mathematics libraries are available?
- 5.5 How do I use mathematics libraries such as BLAS and LAPACK routines?
- 5.6 My code is written in C/C++, can I still use those libraries?
- 5.7 What packages are available?
- 5.8 What interconnects are used on SHARCNET clusters?
- 5.9 I would like to do some grid computing, how should I proceed?
- 5.10 Debugging serial and parallel programs
- 5.11 What does my error code mean ?
- 6 Getting Help
- 6.1 I have encountered a problem while using a SHARCNET system and need help, who should I talk to?
- 6.2 How do I use the problem ticket system?
- 6.3 How do I give other users access to my files ?
- 6.4 What do I need to specify in a ticket ?
- 6.5 How do I checkpoint/restart my program on a SHARCNET cluster ?
- 6.6 I am new to parallel programming, where can I find quick references at SHARCNET?
- 6.7 I am new to parallel programming, can you help me get started with my project?
- 6.8 Can you install a package on a cluster for me?
- 6.9 I am in a process of purchasing computer equipment for my research, would you be able to provide technical advice on that?
- 6.10 Does SHARCNET have a mailing list or user group?
- 6.11 Does SHARCNET provide any training on programming and using the systems?
- 7 Research at SHARCNET
- 7.1 Where can I find what other people do at SHARCNET?
- 7.2 I have a research project I would like to collaborate on with SHARCNET, who should I talk to?
- 7.3 How can I contribute compute resources to SHARCNET so that other researchers can share it?
- 7.4 I do not know much about computation, nor is it my research interest. But I am interested in getting my research done faster with the help of the high performance computing technology. In other words, I do not care about the process and mechanism, but only the final results. Can SHARCNET provide this type of help?
- 8 Fellowships at SHARCNET
- 9 Contacting SHARCNET
- 10 How to Acknowledge SHARCNET in Publications
- 11 What types of research programs / support are provided to the research community?
What is SHARCNET?
SHARCNET stands for Shared Hierarchical Academic Research Computing Network. Established in 2000, SHARCNET is the largest high performance computing consortium in Canada, involving eleven universities and colleges across southern Ontario.
SHARCNET also refers to a grid of high performance clusters of thousands of processors on a dedicated, private high speed wide area network with a throughput of 1 Gigabits per second. Powered by the Ontario Research Innovation Optical Network (ORION) and the state-of-the-art operating system environments, the grid of SHARCNET enables researchers to run a single parallel application across multiple clusters deployed at different institutions seamlessly.
Where is SHARCNET?
The main office of SHARCNET is located in the Western Science Centre at The University of Western Ontario. The SHARCNET high performance clusters are installed at each institution of the consortium and operated by SHARCNET staff across different sites.
What does SHARCNET have?
The infrastructure of SHARCNET consists of a group of 64-bit high performance Itanium2, Xeon and Opteron clusters along with a group of storage units deployed at a number of universities and colleges. Those high performance clusters are interconnected with each other through the Ontario Research Innovation Optical Network (ORION) with a private, dedicated connection currently running at 1 Gigabits per second. SHARCNET clusters run the Linux operating system.
What can I do with SHARCNET?
If you have a program that takes months to run on your PC, you could probably run it within a few hours using hundreds of processors on the SHARCNET grid, provided your program is inherently parallelisable. If you have hundreds or thousands of test cases to run through on your PC or computers in your lab, then with hundreds of processors running those cases independently will significantly reduce your test cycles .
If you have used beowulf clusters made of commodity PCs, you may notice a performance improvement on SHARCNET clusters which have high-speed Quadrics and Myrinet interconnect, as well as SHARCNET machines which have large amounts of memory. Also, SHARCNET clusters themselves are connected through a dedicated, private connection over the Ontario Research Innovation Optical Network (ORION).
If you have access to other super computing facilities at other places and you wish to share your ideas with us and SHARCNET users, please contact us. Together we can make SHARCNET better.
Who is running SHARCNET?
The daily operation and development of SHARCNET computational facilities is managed by a group of highly qualified system administrators. In addition, we have a team of high performance technical computing consultants, who are responsible for technical support on libraries, programming and application analysis.
How do I contact SHARCNET?
My application runs on Windows, can I run it on SHARCNET?
It depends. If your application is written in a high level language such as C, C++ and Fortran and is system independent (meaning it does not depend on any particular third party libraries that are available only for Windows), then you should be able to recompile and run your application on SHARCNET systems. However, if your application completely depends upon a special software for Windows, then you are out of luck. In general it is impossible to convert code at binary level between Windows and any of UNIX platforms.
My application runs on Windows 2000 clusters, can I run it on SHARCNET clusters?
If your application does not use any Windows specific APIs then it should be able to recompile and run on SHARCNET UNIX/Linux based clusters.
Getting an Account with SHARCNET and Related Issues
What is required to obtain a SHARCNET account
Anyone who would like to use SHARCNET may apply for an account, bearing in mind the following:
- There are no shared/group accounts: each person who uses SHARCNET requires their own account.
- Primary accounts are available to faculty at Canadian institutions; non-Canadian faculty may be approved by the Scientific Director. The primary account holder is responsible for providing SHARCNET with citations for publications aided by SHARCNET resources.
- Students, postdocs and research fellows must be "sponsored" by a faculty-level account-holder, and require the SHARCNET username of their sponsor when applying for an account.
- All applicants must have an institutional email account that we can use for contact purposes; commercial email accounts such as Yahoo or Hotmail are not acceptable.
- All SHARCNET users must read and follow the policies listed here.
How do I apply for an account?
Click here to register for a SHARCNET account.
Your application will be processed within 24 hours and you will receive an E-mail notification of whether your application is approved or declined.
Please do not send E-mail or call to request for an account, as the system has no way to process your request.
Can I just have a cluster account without having a web portal account?
No. The web portal account is a web interface to your account in our user database. It also provides you a way of managing your information and keeping track of problems you have, which will be useful for troubleshooting if you encounter the same type of problem.
Can I E-mail or call to open an account?
No. The system has no way to process your request. You must apply through the web portal.
OK, I've seen and heard the word "web portal" enough, what is it anyway?
A web portal is a web site that offers online services. Usually a web portal has a database at the backend, in which people can store and access personal information. At SHARCNET, registered users can login to the web portal, manage their profiles, apply for computer accounts at specific sites and submit and review programming and performance related problems.
I have opened an account at the web portal, do I need to apply for a cluster account?
For people who acquired an account after January 2004, an account on various SHARCNET systems are created automatically. For those who had an account prior to January 2004, applying for accounts on specific systems may be necessary.
In the account application form, what should I fill in the "sponsor" field?
If you are a faculty member, then leave the field "sponsor" blank. Otherwise, the sponsor field is the SHARCNET username of your supervisor or collaborator.
My supervisor does not have an account, so my application can't go through, what should I do?
If your supervisor does not have an account yet, please ask your supervisor to apply for an account first.
My supervisor forgot all about his/her username, so my application can't go through, what should I do?
Send an E-mail to firstname.lastname@example.org. If your supervisor does have an account, we will find it out for you.
My supervisor does not use SHARCNET, why is my supervisor asked to have an account anyway?
Your supervisor's account ID is used to identify which group your account belongs to. This is the way the user account management system is designed, therefore is mandatory.
I am a faculty member. In the application for an account, what should I fill in the field "sponsor"?
If you are a faculty member with one of the SHARCNET institutions, you should leave the field "sponsor" blank.
I am a visiting scholar, in the application for an account, what should I fill in the field "sponsor" ?
You should fill in the user name of the person who invites you.
I am changing supervisor or I am becoming faculty, and I already have a SHARCNET account. Should I apply for a new account?
No. Send all of the details to email@example.com, and we will update your account.
Is there any charge for using SHARCNET?
No, not at this time.
I have an account at a SHARCNET site, do I automatically have an account at rest of the sites?
For those who acquired account before January 1, 2004, you must apply for a cluster account on a specific cluster. Those who acquired account after January 1, 2004, will have accounts created at all sites automatically.
I forgot my password
If you forgot your password you can always get it reset by clicking the "Forget password" button on the login page, or click here.
I forgot my username
If you forget your username, please send an E-mail to firstname.lastname@example.org. Your username for the web portal and cluster account are the same.
My account has been disabled (so i cannot login). What should I do ?
Typically your account expiry date was not renewed by your sponsor before the "Account expiration" date as shown on your profile. To fix this, ask your sponsor to visit sponsored and click enable to renew your account. Note that when your acccount is disabled you will not be able to log into any SHARCNET cluster or the SHARCNET web portal!
Loggin in to Systems, Transferring and Editing Files
How do I login to SHARCNET?
There is no single point of entry at present. "Logging in to SHARCNET" means you login to one of the SHARCNET systems. A complete list of SHARCNET systems can be found on our facilities page.
To login to a system, you need to use Secure Shell (SSH) connection. If you are logging from a UNIX machine, make sure it has SSH client (ssh) installed. If you have the same login name on both your local system and SHARCNET, and you want to login to, say, bull, you may use the command
If your SHARCNET username is different from the username on your local systems, then you may use either of the following commands
ssh bull.sharcnet.ca -l username email@example.com
If you want to eastablish an X window connection so that you can use graphics applications such as gvim and xemacs, you can add an option -Y and the end of the command, e.g.
ssh bull.sharcnet.ca -l username -Y
There is no need to set X display on the host you login to.
If you are logging from a Windows or Mac machine, you need to have SSH client for Windows or Mac installed.
How can I access to SHARCNET machines from Windows PC?
There are basically two options. One is using the software Secure Shell (SSH) File Transfer Client, available at www.ssh.com. It allows you transfer files between your desktop and remote host by dragging them from one side to the other. There are also text based programs (e.g. putty, psfp, pscp)
Another tool you can use, which is recommended, is Cygwin/X (www.cygwin.com). It provides an all-in-one, UNIX like environment. It comes with SSH support as a package. The installation is straightforward. During the installation, you will need to select the *Net* package. By default, SSH is NOT installed. If you are familiar with UNIX, then you can work within Cygwin/X using UNIX commands as if you were on a Linux box.
What operating systems are supported?
UNIX in general. Currently, Linux is the only operating system used within SHARCNET.
What makes a cluster different than my UNIX workstation?
If you are familiar with UNIX, then using a cluster is not much different from using a workstation. When you login to a cluster, you in fact only log in to one of the cluster nodes. In most cases, each cluster node is a physical machine, usually a server class machine, with one or several CPUs, that is more or less the same as a workstation you are familiar with. The difference is that these nodes are interconnected with special interconnect devices and the way you run your program is slightly different. Across SHARCNET clusters, you are not expected to run your program interactively. You will have to run your program through a queueing system. That also means where and when your program gets to run is not decided by you, but by the queueing system.
Which cluster should I use?
Each of our clusters is designed for a particular type of job. Our cluster map shows which systems are suitable for various job types.
What programming languages are supported?
Those primary programming languages such as C, C++ and Fortran are supported. Other languages, such as Java, Pascal and Ada, are also supported, but with limited technical support from us. That means, if your program is written in any language other than C, C++ and Fortran, and you encounter a problem, we may or may not be able solve it within a short period of time.
How do I organize my files?
Our experience is that when large amounts of storage are available, it is too easy to lose track of files, let stale copies accumulate, etc. The number of files that one can truly manage is also fairly modest and does not scale over time, or with availability of storage. For these reasons, SHARCNET provides the following pools of storage:
|/home||200 MB||none||unified||sources, small config files|
|/work||200 GB||none||per-cluster||active data files|
|/scratch||none||36 days||per-cluster||temporary files, checkpoints|
|/tmp||none||2 days||per-node||node-local scratch|
|archive||none||none||unified command-access||long term data archive|
These distinctions reflect the fact that different kinds of files have very different properties, so are best implemented using different file systems, servers, RAID levels and backup policies.
Backups are in place for your home directory only. Scratch and work are not backed up. In general we store one version of each file for the previous 5 working days, one for each of the 4 previous weeks, and one version per month before that. Backups began in September 2006.
The access column represents our design for the new SHARCNET environment: it is not implemented on all clusters yet. /home is shown as unified - this means that when you login, regardless of cluster, you always see the same directory. since /home is remote on most clusters, it's important that you not have lots of jobs doing IO to it. That's what /work is for, and is why most clusters have their own /work directory.
/scratch has no quota limit - so you can put as much data in /scratch/<userid> as you want, until there is no more space. The important thing to note though, is that all files on /scratch that are over 36 days old will be automatically deleted.
Once a file is created in /scratch/<userid> reading it, renaming, changing the file's timestamps with 'touch', or copying it into another file are all irrelevant. The file will be expired 36 days after it was created.
Only files that have been modified (e.g. more information written to the file) will be safe from deletion.
If you'd like to reliably backup large volumes of data to archive storage, use the archive command rather than leaving it on the per-cluster /work filesystems. There have been instances where data was lost on /work and /scratch, so it is definitely a good idea to back up your data to archive if it is important. archive is provided by the "Archive Tools" with command-only access (ie. it is not possible for users to directly manipulate the filesystem). See the following FAQ entry for further details.
How do I transfer my files to and from a cluster?
To transfer files to and from a cluster on a UNIX machine, you may use scp or sftp. For example, if you want to upload file foo.f to cluster narwhal from your machine myhost, use the following command
myhost$ scp foo.f narwhal.sharcnet.ca:
assuming that your machine has scp installed. If you want to transfer a file from Windows or Mac, you need have scp or sftp for Windows or Mac installed.
If you transfer file foo.f between SHARCNET clusters, say from your home directory on narwhal to your scratch directory on requin, simply use the following command
[username@nar316 ~]$ scp foo.f requin:/scratch/username/
How do I transfer an entire directory to and from a cluster?
If you are transferring files between a UNIX machine and a cluster, you may use scp command with -r option. For instance, if you want to download the subdirectory foo in the directory project in your home directory on whale to your local UNIX machine, on your local machine, use command
myhost$ scp -rp whale.sharcnet.ca:project/foo .
Similarly, you can transfer the subdirectory between SHARCNET clusters. The following command
[username@nar316 ~]$ scp -rp requin:/scratch/username/foo .
will download subdirectory foo from your scratch directory on requin to your home directory on narwhal (note that the prompt indicates you are currently logged on to narwhal).
The use of -p option above will preserve the time stamp of each file. For Windows and Mac, you need to check the documentation of scp for features.
You may also tar and compress the entire directory and then use scp to same bandwidth. In the above example, first you login to narwhal, then do the following
[username@nar316 ~]$ cd project [username@nar316 ~]$ tar -cvf foo.tar foo [username@nar316 ~]$ gzip foo.tar
Then on your local machine myhost, use scp to copy the tar file
myhost$ scp narwhal.sharcnet.ca:project/foo.tar.gz .
Note for most Linux distributions, tar has an option -z that will compress the .tar file using gzip.
How to archive my data?
SHARCNET provides a small set of scripts (hereafter "Archive Tools") allowing users to move their data between clusters and our Archive (a long-term storage facility with 200 TB capacity). Please note that Archive is not directly mounted on any of our clusters, and can be accessed only through Archive Tools.
The only Archive Tools script directly used by users is archive. Executing this script without any parameters on any of our clusters will print a short description of the program:
[xxx@wha783 ~]$ archive Usage: archive [--get name-you-chose] [--put name-you-choose list-of-local-files-and-dirs] [--remove name-you-choose] [--list [directory/file-name]] Options: --put store into an archive of the given name (the name can include subdirectories). --get retrieve files of the given name (also works with subdirectories). --list show your archives or directories (or specific one). --remove remove an archive or an empty directory. -h or --help show usage (default option). --man show man page.
The Tools allow basic functionality, such as an ability to move a collection of local files and/or directories to Archive (option --put), to move the data back (--get), to list the user's archives (--list), and to delete an archive (--remove).
An example: you want to archive the contents of two directories (with all the subdirectories), DIR1 and DIR2, and two files, file1 and file2. First, come up with a good (descriptive) name for your archive - say, DIR1-2_file1-2 . Then, execute the following command:
archive --put DIR1-2.file1-2 DIR1 DIR2 file1 file2
It will create an (uncompressed) TAR file DIR1-2.file1-2 in Archive containing the data from DIR1, DIR2, file1, and file2. To better organize their archives, users can create directories and subdirectories in Archive during the execution of archive --put. For example,
archive --put Level1/Level2/name file1 file2
will first create nested directories Level1/Level2 in Archive, and then will copy file1 and file2 to the archive Level1/Level2/name. If the archive with such a name already exists in Archive, the command will fail.
TIP: It is strongly recommended to create a list of the files being archived during the execution of archive --put ..., by piping the standard output to a local file:
archive --put Level1/Level2/name file1 file2 >& name.list
This is especially important if you create large (many gigabytes) archives containing many files. Keep these list files in one location. This will significantly simplify the task of locating one particular file or directory in your archives.
The opposite command is --get. For the above examples, the files will be copied back from Archive after executing the following commands:
archive --get DIR1-2_file1-2 archive --get Level1/Level2/name
If the local directories or files with the same names already exist, they will not be overwritten, and the program will produce error messages.
Finally, individual files or empty directories can be removed from Archive by executing archive --remove. Each deletion has to be explicitly confirmed (by typing "yes"). For example, to delete Level1/Level2/name from Archive, one has to execute the following sequence of commands, confirming each deletion with "yes":
archive --remove Level1/Level2/name archive --remove Level1/Level2 archive --remove Level1
The "." at the beginning of the name means that the file means it is "hidden". You have to use the -a option with ls to see it. I.e. 'ls -a'
SSH tells me SOMEONE IS DOING SOMETHING NASTY!?
Suppose you attempt to login to SHARCNET, but instead get an alarming message like this:
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ @ 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 fe:65:ab:89:9a:23:34:5a:50:1e:05:d6:bf:ec:da:67. Please contact your system administrator. Add correct host key in /home/user/.ssh/known_hosts to get rid of this message. Offending key in /home/hahn/.ssh/known_hosts:42 RSA host key for requin has changed and you have requested strict checking. Host key verification failed.
SSH normally tries to verify that the host you're connecting to is authentic. It does this by caching the hosts's "hostkey" in your ~/.ssh/known_hosts file. At times, it may be necessary to legitimately change its hostkey; when this happens, you may see such a message. It's a good idea to verify this with us, but the normal answer is to simply remove the old hostkey from your known_hosts file. You can use your choice of editor if you're comfortable doing so (it's a plain text file, but has long lines). On a unix-compatible machine, you can also use the following very small script:
perl -pi -e 'undef $_ if (++$line == 42)' ~/.ssh/known_hosts
(Substitute the line(s) printed in the warning message for '42' here.)
Another solution is brute-force: remove the whole known_hosts file. This throws away any authentication checking, and your first subsequent connection to any machine will prompt you to accept a newly discovered host key. If you find this prompt annoying, you can avoid it by adding a text file named ~/.ssh/config on your machine with the following content:
Ssh works, but scp doesn't!
If you can ssh to a cluster successfully, but cannot scp to to it, the problem is likely that your login scripts print unexpected messages which confuse scp. scp is based on the same ssh protocol, but assumes that the connection is "clean": that is, that it does not produce any un-asked-for content. If you have something like:
echo "Hello, Master; I await your command..."
scp will be confused by the salutation. To avoid this, simply ensure that the message is only printed on an interactive login:
if [ -t 0 ]; then echo "Hello, Master; I await your command..." fi
or in csh/tcsh syntax:
if ( -t 0 ) then echo "Hello, Master; I await your command..." endif
Running commands remotely
It is also possible to specify a command to run on the end of a ssh command. A command like ssh narwhal.sharcnet.ca sqjobs, however, will not work because ssh does not setup a full environment by default. In order to get the same environment you get as when you login, it is necessary to run the command under bash in login mode.
myhost$ ssh narwhal.sharcnet.ca bash -l -c sqjobs
If you wish to specify a command longer than a single word, it is necessary to quote it as the bash -c only takes a single argument. In order to pass these quotes through to ssh, however, it is necessary to escape them. Otherwise the local shell will interpret them and strip them off. An example is
myhost$ ssh narwhal.sharcnet.ca bash -l -c \' sqsub -r 5h ./myjob \'
Most problems with these commands are related to the local shell interpreting things that you wish to pass through to the remote side (e.g., stripping out any unescaped quotes). Use -v with ssh and set -x with bash to see what command(s) ssh and bash are executing respectively.
myhost$ ssh -v narwhal.sharcnet.ca bash -l -c \' sqsub -r 5h ./myjob \' myhost$ ssh narwhal.sharcnet.ca bash -l -c \' set -x\; sqsub -r 5h ./myjob \'
How do I edit my program on a cluster?
We provide a variety of editors, such as the traditional text-mode emacs and vi (vim), as well as a simpler one called nano. If you have X on your desktop (and properly tunneled through SSH), you can use the GUI versions (xemacs, gvim).
Compiling and Running Programs
How do I compile my programs
To make it easier to compile across all SHARCNET clusters, we provide a generic set of commands:
cc, c++, f77, f90, f95
and for MPI,
mpicc, mpic++, mpiCC, mpif77, mpif90, mpif95
These commands provide several benefits:
- they select optimization appropriate to the cluster's CPUs.
- using -lmpi or the mpi-prefixed commands will select the necessary cluster-specific options for MPI.
- using -llapack link with the vendor-tuned LAPACK library.
- using -openmp will direct the compiler to use OpenMP.
Here are some basic examples:
cc foo.c -o foo cc -openmp foo.c -llapack -o foo f90 *.f90 -lmpi -o my_mpi_prog mpif90 *.f90 -o my_mpi_prog f90 -mpi -c a.f90; mpif90 -c b.f90; compile a.o b.o -lmpi -o my_mpi_prog
In the first example, the preferred compiler and optimization flags will be selected, but not much else happens. In the second case, the underlying compiler's OpenMP flag (which differs among compilers) is selected, as well as linking with a system-tuned LAPACK/Blas library. in the third example, an MPI program written in Fortran90 is compiled and linked with whatever cluster-specific MPI libraries are required. The fourth example is identical except that the mpi-prefixed command is used. In the fifth example, two files are separately compiled, then linked with MPI stuff; the point is simply that even for non-linking, you need to declare that you're using MPI by either an mpi-prefixed command or -mpi or -lmpi.
These command commands will invoke the underlying compilers such as Intel or PathScale compilers, whichever are available to the system you are using. For specific compiler options, please refer to the man pages.
You aren't required to use these commands, and may not want to if you have pre-existing Makefiles, for instance. You can always add -v to see what full commands are being generated. Here's a brief summary of compilers available on various systems:
|Opteron systems (requin, narwhal, whale, bull)||pathcc pgcc gcc|
|Xeon systems (saw, mako)||icc ifc ifort gcc|
|Itanium2 systems (silky)||icc ifc ifort|
On Intel Itanium 2 clusters in particular, you should always use the high performance Intel compilers icc and ifort for C/C++ and Fortran code respectively, if available. They give much better performance than the generic GNU compilers on this chip.
How do I run a program?
In general, users are expected to run their jobs in "batch mode". That is, one submits a job -- the application problem -- to a queue through a batch queue command, the scheduler schedules the job to run at a later time and sends the results back once the program is finished.
In particular, one will use SQ command (see What is the batch job scheduling environment SQ? below) to launch a serial job foo
sqsub -o foo.log -r 5h ./foo
This means to submit the command foo as a job with a 5 hour runtime limit and put its standard output into a file foo.log (note that it is important to not put too tight of a runtime limit on your job as it may sometimes run slower than expected due to interference from other jobs).
If your program takes command line arguments, place the arguments after your program name just as when you run the program interactively
sqsub -o foo.log -r 5h ./foo arg1 arg2...
For example, suppose your program takes command line options -i input and -o output for input and output files respectively, they will be treated as the arguments of your program, not the options of sqsub
sqsub -o foo.log -i input.dat -o output.dat -r 5h ./foo
To launch a parallel job foo_p
sqsub -q mpi -n num_cpus -o foo_p.log -r 5h ./foo_p
The basic queues on SHARCNET are:
|serial||for serial jobs|
|mpi||for parallel jobs using the MPI library|
|threaded||for threaded jobs using OpenMP or POSIX threads|
To see the status of submitted jobs, use command sqjobs.
What is the batch job scheduling environment SQ?
SQ is a unified frontend for running jobs on SHARCNET, intended to hide unnecessary differences in how the clusters are configured. On clusters which are based on RMS, LSF+RMS, or Torque+Maui, SQ is just a thin shell of scripting over the native commands. On Wobbie, the native queuing system is called SQ.
To run a job, you use sqrun:
sqrun -n 16 -q mpi -r 5h ./foo
This runs foo as an MPI command on 16 processors with a 5 hour runtime limit (make sure to be somewhat conservative with the runtime limit as a job may run for longer than expected due to interference from other jobs). You can control input, output and error output using these flags:
sqrun -o outfile -i infile -e errfile -r 5h ./foo
this will run foo with its input coming from a file named infile, its standard output going to a file named outfile, and its error output going to a file named errfile. Note that using these flags is preferred over shell redirection, since the flags permit your program to do IO directly to the file, rather than having the IO transported over sockets, then to a file.
Often, especially with IO redirection as above, it is convenient to submit a job, and not wait for it to run. To do this, simply add a --bg switch to sqrun, or equivalently use sqsub. It makes no difference to the scheduler whether you run (wait to complete) or submit (batch mode).
For threaded applications (which use Pthreads, OpenMP, or fork-based parallelism), do this:
sqsub -q threaded -n 2 -r 5h ./foo
Serial jobs require no flags beyond the runtime
sqrun -r 5h ./foo
but you can provide IO redirection flags if you wish.
How do I show and control jobs under SQ?
To show your jobs, use "sqjobs". by default, it will show you only your own jobs. with "-a" or "-u all", it will show all users. similarly, "-u someuser" will show jobs only for this particular user.
To kill, suspend or resume your jobs, use sqkill/suspend/resume with the job ID as shown by sqjobs.
Note also that providing the -v switch to sqrun/sqsub will print the jobid at submission time.
How do I translate my LSF command to SQ?
SQ very strongly resembles LSF commands such as bsub. For instance, here are two versions, the first assuming LSF, the second using SQ:
bsub -q mpi -n 16 -o term.out ./ParTISUN sqsub -q mpi -n 16 -o term.out ./ParTISUN
There are some differences:
- SQ doesn't have static queues like LSF. Instead, the "-q" simply describes the kind of job - MPI(parallel), threaded or serial.
- SQ doesn't use the extra "prun" in there - it knows that parallel jobs always need the prun.
- sqjobs is quite similar to bjobs.
- sqkill/suspend/resume is quite similar to bkill/suspend/resume.
How can I submit jobs that will run where ever there are free cpus?
SHARCNET clusters differ in several ways: access to particular storage and cluster node properties. For instance, if you submit a job which refers to files in /work or /scratch, it may currently only run on that particular cluster. Similarly, a job may require, for instance, a very large amount of memory per processor, only available on Bull. But some jobs which do little IO, and which are serial and use modest amounts of memory may be run using the "global jobs" facility.
To submit a global job, just add --global to the sqsub command:
sqsub --global -o my.log ./program sqjobs --global
Again, this currently only applies to jobs which can run in your /home tree (which is very limited in size and speed), and which are serial.
Command 'top' gives me two different memory size (virt, res). What is the difference between 'virtual' and 'real' memory?
'virt' refers to the total virtual address space of the process, including virtual space that has been allocated but never actually instantiated, including memory which was instantiated but has been swapped out, and memory which may be shared. 'res' is memory which is actually resident - that is, instantiated with real ram pages. resident memory is normally the more meaningful value, since it may be judged relative to the memory available on the node. (recognizing, of course, that the memory on a node must be divided among the resident pages for all the processes, so an individual thread must always strive to keep its working set a little smaller than the node's total memory divided by the number of processors.)
there are two cases where the virtual address space size is significant. one is when the process is thrashing - that is, has a working set size bigger than available memory. such a process will spend a lot of time in 'D' state, since it's waiting for pages to be swapped in or out. a node on which this is happening will have a substantial paging rate expressed in the 'si' column of output from vmstat (the 'so' column is normally less significant, since si/so do not necessarily balance.)
the second condition where virtual size matters is that the kernel does not implement RLIMIT_RSS, but does enforce RLIMIT_AS (virtual size). we intend to enforce a sanity-check RLIMIT_AS, and in some cases do. the goal is to avoid a node becoming unusable or crashing when a job uses too much memory. current settings are very conservative, though - 150% of physical memory.
in this particular case, the huge V size relative to R is almost certainly due to the way Silky implements MPI using shared memory. such memory is counted as part of every process involved, but obviously does not mean that N * 26.2 GB of ram is in use.
in this case, the real memory footprint of the MPI rank is 1.2 GB - if you ran the same code on another cluster which didn't have numalink shared memory, both resident and virtual sizes would be about that much. since most of our clusters have at least 2GB per core, this code could run comfortably on other clusters.
Can I use a script to compile and run programs?
Yes. For instance, suppose you have a number of source files main.f, sub1.f, sub2.f, ..., subN.f, to compile these source code to generate an executable myprog, it's likely that you will type the following command
f77 -o myprog main.f sub1.f sub2.f ... sub N.f -llapack
Here, the -o option specifies the executable name myprog rather than the default a.out and the option -llapack at the end tells the compiler to link your program against the LAPACK library, if LAPACK routines are called in your program. If you have long list of files, typing the above command every time can be really annoying. You can instead put the command in a file, say, mycomp, then make mycomp executable by typing the following command
chmod +x mycomp
Then you can just type
at the command line to compile your program.
This is the simplest way to deal with multiple source files. However, this is not the efficient way. The most efficient way to compile multiple files and use different libraries is to use make.
I have a program that runs on my workstation, how can I have it run in parallel?
If the the program was written without parallelism in mind, then there is very little that you can do to run it automatically in parallel. Some compilers are able to translate some serial portion of a program , such as loops, into equivalent parallel code, which allows you to explore the potential architecture found mostly in symmetric multiprocessing (SMP) systems. Also, some libraries are able to use parallelism internally, without any change in the user's program. For this to work, your program needs to spend most of its time in the library, of course - the parallel library doesn't speed up your program itself. Examples of this include threaded linear algebra and FFT libraries.
However, to gain the true parallelism and scalability, you will need to either rewrite the code using the message passing interface (MPI) library or annotate your program using OpenMP directives. We will be happy to help you parallelize your code if you wish. (Note that OpenMP is inherently limited by the size of a single node or SMP machine - most SHARCNET resources
Also, the preceding answer pertains only to the idea of running a single program faster using parallelism. Often, you might want to run many different configurations of your program, differing only in a set of input parameters. This is common when doing Monte Carlo simulation, for instance. It's usually best to start out doing this as a series of independent serial jobs. It is possible to implement this kind of loosely-coupled parallelism using MPI, but often less efficient and more difficult.
How can I have a quick test run of my program?
Sometimes you may experience long waiting time before your program in the queue starts running. To allow users to test their programs, a "test queue" is provided, which enables users to launch their programs quickly.
To have a test run, use sqsub option --test. For example, if you have an MPI program mytest that uses 8 processors, you may use the following command
sqsub --test -q mpi -n 8 -o mytest.log ./mytest
The only difference here is the "--test". The scheduler will normally start such test jobs within a few seconds.
The main purpose of the test queue is quickly test the startup of a changed job - just to verify that for a real, production run, it won't hit a bug shortly after starting (for instance, due to missing parameters.)
The "test queue" only allows one to run test program for a very short period of time, therefore you must make sure that your test run will not take hours to finish. In addition, the system monitors the user submissions and decreases the priority of submitted jobs over time within an internally defined time window. Hence if you keep submitting jobs as test runs, the waiting time before those jobs get started will be getting longer, or you will not be able to submit test jobs any more.
Which system should I choose?
There are many clusters, many of them specialized in some way. We provide an interactive map of SHARCNET systems on the web portal which visually presents a variety of criteria as a decision making aid. In brief however, depending on the nature of your jobs, there may be a clear preference for which cluster is most appropriate:
- is your job serial?
- Whale is probably the right choice, since it has a very large number of processors, and consequently has high throughput. Your job will probably run soonest if you submit it here.
- do you use a lot of memory?
- Bull or Hound is probably the right choice.
- does your MPI program utilize a lot of communication?
- Requin and Bull have the fastest networks, but it's worth trying Narwhal or Saw if you aren't familiar with the specific differences between Quadrics, Myrinet and Infiniband.
- does your job (or set of jobs) do a lot of disk IO?
- you probably want to stick to one of the major clusters (Bull/Narwhal/Requin/Saw/Whale) which have bigger and much faster (parallel) filesystems.
Where can I find available resources?
The change of status of each system, such as down time, power outage, etc is announced through the following three different channels:
- Web links under systems. You need to check the web site from time to time in order to catch such public announcements.
- System notice mailing list. This is the passive way of being informed. You receive the notices in e-mail as soon as they are announced. But some people might feel it is annoying to be informed. Also, such notices may be buried in dozens or hundreds of other e-mail messages in your mail box, hence are easily ignored.
- SHARCNET RSS broadcasting. A good analogy of RSS is like traffic information on the radio. When you are on a road trip and you want to know what the traffic conditions are ahead, you turn on the car radio, tune-in to a traffic news station and listen to updates periodically. Similarly, if you want to know the status of SHARCNET systems or the latest SHARCNET news, events and workshops, you can turn to RSS feeds on your desktop computer.
The term RSS may stand for Really Simple Syndication, RDF Site Summary, or Rich Site Summary depending on the version. Written in the format of XML, RSS feeds are used by websites to syndicate their content. RSS feeds allow you to read through the news you want, at your own convenience. The messages will show up on your desktop, e.g. using Mozilla Thunderbird, an integrated mail client software, as soon as there is an update.
Can I find my job submission history?
Yes. Your every single job submission is recorded in a database. Each record contains the command, the submission time, the start time, the completion time, exit status of your program (i.e. succeeded or failed), number of CPUs used, system, and so on.
You may review the history by logging in to your web account.
How are jobs scheduled?
Job scheduling is the mechanism which selects waiting jobs ("queued") to be started ("dispatched") on nodes in the cluster. In all cases, production SHARCNET clusters are "exclusively" scheduled, so that a job will have complete access to the CPUs its currently running on. Jobs may, however, sometimes be preempted (put into a suspended state) if some other, higher-priority job must be started. Normally, preemption happens only for "test" jobs, which are fairly short (always less than 1 hour). After being preempted, a job is resumed (and the intervening period is not counted as usage.)
In practice, if there are enough free processors to run your job, and no else has any jobs queued, then you should expect your jobs to start immediately. Once there are more jobs queued than available resources, the scheduler will attempt to arbitrate between the CPU demands of all queued jobs. This arbitration happens in the following order: Dedicated Resource jobs first, then "test" jobs (which may also preempt normal jobs), and finally normal jobs. Within the set of pending normal jobs, the scheduler will prefer jobs belonging to groups which have high "fairshare" priority.
Fairshare is based on a measure of recent (currently, past 2 months) resource usage. All user groups are ranked into 5 priority levels, with the heaviest users given lowest priority. You can examine your group's recent usage and priority here: Research Group's Usage and Priority
For information on expected queue wait times, users can check the Recent Cluster Statistics table in the web portal.
Some specific scheduling idiosyncrasies:
One problem with cluster scheduling is that for a typical mix of job types (serial, threaded, various-sized MPI), the scheduler will rarely accumulate enough free CPUs at once to start any larger job. When an job completes, it frees N cpus. If there's an N-cpu job queued (and of appropriate priority), it'll be run. Frequently, jobs smaller than N will start instead. This may still give 100% utilization, but each of those jobs will complete, probably at different times, effectively fragmenting the N into several smaller sets. Only a period of idleness (lack of queued smaller jobs) will allow enough cpus to collect to let larger jobs run.
Narwhal uses a form of reservation scheduling to address this: for a fixed period of time, the scheduler will accumulate idle cpus in an attempt to run the currently highest-priority job. If it takes too long, other jobs will be started, and the accumulation will begin again. The accumulation period is chosen to optimize the chances of running jobs of a target size (around 32 cpus).
Requin is intended to enable "capability", or very large jobs. Rather than eliminating the ability to run more modest job sizes, Requin is configured with a weekly cycle: every Monday at noon, all previously running jobs will have finished and large queued jobs can start. One implication of this is that no job over 1 week can be run (and a 1-week job will only have one chance per week to start). Shorter jobs can be started at any time, but only a 1-day job can be started on Sunday, for instance.
Note that both Requin and Narwhal now enforce runtime limits - if the job is still running at the end of the stated limit, it will be terminated. (Before December 1 2008, only Narwhal would enforce runtime limits.)
Gaussian jobs on Bull are also scheduled somewhat differently: they are given a separate queue, which provides slightly higher priority to groups who have bought into the SHARCNET Gaussian license.
Finally, when running DDT or OPT (debugger and profiler), it's normal to use the test queue. If you need to run such jobs longer than 1 hour, and find the wait times too high when using the normal queues, let us know (open a ticket). It may be that we need to provide a special queue for these uses - possibly preemptive like the test queue.
Programming and Debugging
What is MPI?
MPI stands for Message Passing Interface, a standard for writing portable parallel programs which is well-accepted in the scientific computing community. MPI is implemented as a library of subroutines which is layered on top of a network interface. The MPI standard has provided both C/C++ and Fortran interfaces so all of these languages can use MPI. There are several MPI implementations, including OpenMPI and MPICH. Specific high-performance interconnect vendors also provide their own libraries - usually a version of MPICH layered on an interconnect-specific hardware library. For SHARCNET Alpha clusters, the interconnect is Quadrics, which provides MPI and a low-level library called "elan". for Myrinet, the low-level library is MX or GM.
In addition to C/C++ and Fortran versions of MPI, there exist other language bindings as well. If you have any special needs, please contact us.
What is OpenMP?
OpenMP is a standard for programming shared memory systems using threads with compiler directives instrumented in the source code. It provides a higher-level approach to utilizing multiple processors within a single machine while keeping the structure of the source code as close to the conventional form as possible. OpenMP is much easier to use than the alternative (Pthreads) and thus is suitable for adding modest amounts of parallelism to pre-exiting code. Because OpenMP is a set of programs, your code can still be compiled by a serial compiler and should still behave the same.
OpenMP for C/C++ and Fortran are supported by many compilers, including the PathScale and PGI for Opterons, and the Intel compilers for IA32 and IA64 (such as SGI's Altix.). OpenMP support has been provided in the GNU compiler suite since v4.2 (OpenMP 2.5), and starting with v4.4 supports the OpenMP 3.0 standard.
How do I run an OpenMP program with multiple threads?
An OpenMP program uses a single process with multiple threads rather than multiple processes. On SMP systems, threads will be scheduled on available processors, thus run concurrently. In order for each thread to run on one processor, one needs to request the same number of CPUs as the number of threads to use. This is done differently on different systems at SHARCNET where queueing systems are used. For instance, on Tru64 Alpha clusters, to run an OpenMP program foo that uses four threads with sqrun command, use the following
sqrun -q threaded -n 4 ./foo
The option -n 4 specifies to reserve 4 CPUs per process. The same command applies to all systems which support sqrun (SQ).
What mathematics libraries are available?
Every system has the basic linear algebra libraries BLAS and LAPACK installed. Normally, these interfaces are contained in vendor-tuned libraries. On Intel-based (Xeon, Itanium2) clusters, users have the access to Intel math kernel library. On Opteron-based clusters, AMD's ACML library is available.
One may also find the GNU scientific library (GSL) useful to some point for their particular needs. The GNU scientific library is an optional package, available on any machine.
For a detailed list of libraries on each clusters, please check the documentation on the corresponding SHARCNET satellite web sites
How do I use mathematics libraries such as BLAS and LAPACK routines?
First you need to know which subroutine you want to use. You need to check the references to find what routines meet your needs. Then place calls to those routines you want in your program and compile your program to use the particular libraries that have those routines. For instance, if you want compute the eigenvalues, and optionally the eigenvectors, of an N by N real non symmetric matrix in double precision, you find the LAPACK routine DGEEV will do that. All you need to do is to have a call to DGEEV, with required parameters as specified in the LAPACK document, and compile your program to link against the LAPACK library.
f77 -o myprog main.f sub1.f sub2.f ... sub13.f -llapack
The option -llapack tells the compiler to use library liblapack.a.
If the system you are using has vendor supplied libraries that have optimized LAPACK routines, such as Intel's math kernel library MKL (libmkl.a) or AMD's ACML library (libacml.a), then use those libraries with options -lmkl or -lacml instead, as they will give you better performance. The installation directories of those vendor libraries may vary from site to site. If such a library is not installed in the standard directory /lib, /usr/lib or /usr/local/lib, then chances are you would have to specify the lookup path for the compiler. For instance, on the Itanium2 cluster Spinner, the Intel version of LAPACK in the math kernel library mkl is located in /opt/intel/mkl/lib/64, in the above example, one will use command
ifort -o myprog main.f sub1.f sub2.f ... sub13.f -L/opt/intel/mkl/lib/64 -lmkl_lapack
where ifort is the Intel Fortran compiler, the option -L/opt/intel/mkl/lib/64 -lmkl_lapack specifies the library path. Please check the local documentation at each site for details.
You should never need to copy or use the individual source code of those library routines and compile them together with your program.
My code is written in C/C++, can I still use those libraries?
Yes. Most of the libraries have C interfaces. If you are not sure about the C interface or you need assistance in using those libraries written in Fortran, we can help you out on a case to case basis.
What packages are available?
Various packages have been installed on SHARCNET clusters at users' requests. Custom installed packages include, for example, Gaussian, PETSc, R, Featflow, Gamess, Tinker, Rasmol, and Maple. Please check the SHARCNET web portal for the software packages installed and related usage information.
What interconnects are used on SHARCNET clusters?
I would like to do some grid computing, how should I proceed?
Depends on what you mean by "grid computing". If you simply mean you want to queue up a bunch of jobs (MPI, threaded or serial) and have them run without further attention, then great! SHARCNET's model is exactly that kind of grid. However, we do not attempt to hide differences between clusters, such as file systems that are remote, different types of CPUs or interconnect. We do not currently attempt to provide a single queue which feeds jobs to all of the clusters. Such a unified grid would require you to ensure that your program was compiled and configured to run under Alpha Linux, Alpha Tru64, IA32 Linux, IA64 Linux, AMD64 Linux. It would also have to assume nothing about shared file systems, and it would have to be aware of the 5000x difference in latency when sending messages within a cluster versus between clusters, as well as either rely on least-common-denominator networking (ethernet) or else explicitly manage the differences between Quadrics, Myrinet, Infiniband and ethernet.
If, however, you would like to try something "unusual" that requires much more freedom than the current resource management system can handle, then, you would need to discuss the details of your plan with us for special arrangement.
Debugging serial and parallel programs
Debugger is a program which helps to identify mistakes ("bugs") in programs - either run-time, or "post-mortem" (by analyzing the core file produced by a crashed program). Debuggers can be either command-line, or GUI (graphical user interface) based. Before a program can be debugged, it needs to be (re-)compiled with a switch, -g, which tells the compiler to include symbolic information into the executable.
SHARCNET provides a few debuggers. gdb (installed on all clusters, type "man gdb" to get a list of options), pathdb (Optron clusters), and idb (Silky) are the command-line-based ones. The idb debugger also has a GUI (run "idb -gui"). For a brief introduction on common programming bugs and how to use gdb at SHARCNET please see the Common Bugs and Debugging with gdb online tutorial.
The above debuggers can only be used for serial programs. For parallel codes (either MPI or threads based), one can use the commercial debugger DDT which is installed on most of our Optron clusters (requin, narwhal, bull, and the PoP clusters). DDT has an advanced GUI, and can also be used for debugging serial programs. The short description of DDT can be found on our Software page. You can also refer to the detailed Parallel Debugging with DDT online tutorial.
What does my error code mean ?
When your program returns an error code it means something went wrong. You can findout the meaning of the error code by typing following command:
man 7 signal
However, if you want to fix the problem then you should use a debugger (e.g. gdb or DDT) to locate the instructions that are causing the problem. For a brief introduction on how to use gdb see the Common Bugs and Debugging with gdb online tutorial.
I have encountered a problem while using a SHARCNET system and need help, who should I talk to?
If you have access to the Internet, we encourage you to use the problem ticketing system through the web portal. As this is the most efficient way of reporting a problem and receiving quick responses. You are also welcome to contact system administrators and/or high performance technical computing consultants at any time. You may find the contact information on the directory page.
How do I use the problem ticket system?
We have a simple problem ticket system that you can find by logging into our website and clicking on "Help" then "Problems". It allows you to submit and track your problem tickets. If you are searching for a solution, one thing you can do is type keywords into the "Search" field in the upper right hand corner of the SHARCNET web page, and this will perform a search of current and past problem tickets. Someone else may have already submitted a problem ticket on the same issue. Once you find a ticket that concerns you, you can add a comment or click "watch" to get email updates.
How do I give other users access to my files ?
To give other users access to your files follow following procedure:
In the instructions below instead of <your-subdirectory> type the name of the subdirectory where the files you want to give access to are located:
(1) Go to your home directory by typing:
(2) Authorize access to the home directory by typing command:
chmod go+rX .
(3) Authorize access to subdirectory <your-subdirectory> by typing command:
chmod -R go+rX <your-subdirectory>
What do I need to specify in a ticket ?
If you do not find any tickets that deal with you current problem, then you should logging into our website and click on "Help" then "Problems" then "Submit and supply detailed information on your problem. In the Comments box enter information on how you execute the program (i.e. specify the commands you use to run the job).
If this is a program that uses source files to compile your program then indicate where the source files are located and give read access to your files and directories (starting from the home directory up to the subdirecory where the source files are). See previous FAQ: How do I give other users access to my files
How do I checkpoint/restart my program on a SHARCNET cluster ?
Assuming it is a serial or multi-threaded program (i.e. *not* MPI), you can make use of Berkeley Labs Checkpoint Restart software that is provided on the clusters. Documentation and usage instructions can be found on SHARCNET's BLCR software page.
I am new to parallel programming, where can I find quick references at SHARCNET?
SHARCNET has a number of training modules on parallel programming using MPI, OpenMP, pthreads and other frameworks. Each of these modules has working examples that are designed to be easy to understand while illustrating basic concepts. You may find these along with copies of slides from related presentations and links to external resources on the Main Page of this training/help site.
I am new to parallel programming, can you help me get started with my project?
Absolutely. We will be glad to help you from planning the project, architecting your application programs with appropriate algorithms and choosing efficient tools to solve associated numerical problems to debugging and analyzing your code. We will do our best to help you speed up research.
Can you install a package on a cluster for me?
I am in a process of purchasing computer equipment for my research, would you be able to provide technical advice on that?
If you tell us what you want, we may be able to help you out.
Does SHARCNET have a mailing list or user group?
Yes. You may subscribe to one or more mailing lists on the email list page available once you log into the web portal.
Does SHARCNET provide any training on programming and using the systems?
Yes. SHARCNET provides workshops on specific topics from time to time and offers courses at some sites. Every June, SHARCNET holds an annual summer school with a variety of in-depth, hands-on workshops. All materials from past workshops/presentations can be found on the SHARCNET web portal.
Research at SHARCNET
Where can I find what other people do at SHARCNET?
I have a research project I would like to collaborate on with SHARCNET, who should I talk to?
You may contact SHARCNET head office or contact members of the SHARCNET technical staff.
Most people's research is "bursty" - there are usually sparse periods of time when some computation is urgently needed, and other periods when there is less demand. One problem with this is that if you purchase the equipment you need to meet your "burst" needs, it'll probably sit, underutilized, during other times.
An alternative is to donate control of this equipment to SHARCNET, and let us arrange for other users to use it when you are not. We prefer to be involved in the selection and configuration of such equipment. Some of SHARCNET's most useful clusters were created this way — Goblin and Wobbie were purchased with user contributions. Our promise to contributors is that as much as possible, they should obtain as much benefit from the cluster as if it were not shared. Owners get preferential access. Naturally, owners are also able to burst to higher peak usage, since their equipment has been pooled with other contributions. (Technically, SHARCNET cannot itself own such equipment — it remains owned by the institution in question, and will be returned to the contributor upon request.) If you think this model will also work for you and you would like to contribute your computational resource to help the research community at SHARCNET, you can contact us for such arrangement.
I do not know much about computation, nor is it my research interest. But I am interested in getting my research done faster with the help of the high performance computing technology. In other words, I do not care about the process and mechanism, but only the final results. Can SHARCNET provide this type of help?
We will be happy to bring the technology of high performance computing to you to accelerate your research, if at all possible. If you would like to discuss your plan with us, please feel free to contact our high performance computing specialists. They will be happy to listen to your needs and are ready to provide appropriate suggestions and assistance.
Fellowships at SHARCNET
I heard SHARCNET offers fellowships, where can I get more information?
I would like to do some research at SHARCNET as a visiting scholar, how should I apply?
In general, you will need to find a hosting department or a person affiliated with one of the SHARCNET institutions. You may also contact us directly for more specific information.
I would like to send my students to SHARCNET to do some work for me. How should I proceed?
How do I contact SHARCNET for research, academic exchanges, and technical issues?
Please contact our Scientific Director or check for your specific issue in this FAQ.
How do I contact SHARCNET for business development, education and other issues?
Please contact SHARCNET head office.
How to Acknowledge SHARCNET in Publications
How do I acknowledge SHARCNET in my publications?
We recommend the following:
This work was made possible by the facilities of the Shared Hierarchical Academic Research Computing Network (SHARCNET:www.sharcnet.ca).
I've seen different spellings of the name, what is the standard spelling of SHARCNET?
We suggest the spelling SHARCNET, all in upper case.
What types of research programs / support are provided to the research community?
Our overall intent is to provide support that can both respond to the range of needs that the user community presents and help to increase the sophistication of the community and enable new and larger-in-scope applications making use of SHARCNET's HPC facilities. The range of support can perhaps best be understood in terms of a pyramid:
At the apex of the pyramid, SHARCNET supports a small number of projects with dedicated programmer support. The intent is to enable projects that will have a lasting impact and may lead to a "step change" in the way research is done at SHARCNET. Inter-disciplinary and inter-institutional projects are particularly welcomed. Projects can expect to receive support at the level of 2 to 6 months direct support per year for one to two years. Programming time is allocated through a competitive process. See the guidelines.
The middle layers of support are provided through a number of initiatives.
- Programming support of more modest duration (several days to one month engagement, usually part time)
- Training on a variety of topics through workshops, seminars and online training materials
- Consultation. This may include user-initiated interactions on particular programs, algorithms, techniques, debugging, optimization etc., as well as unsolicited help to ensure effective use of SHARCNET systems
- Site Leaders play an important role in working with the community to help researchers connect with SHARCNET staff and to obtain appropriate help and support.
The base level of the pyramid handles the very large number of small requests that are essential to keeping the user community working effectively with the infrastructure on a day-to-day basis. Several of these can be answered by this FAQ; many of the issues are presented through the ticketing system. The support is largely problem oriented with each problem being time limited.