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FAQs/Howto / General |
After I submit a job I get the following error back ?
-bash: /var/spool/PBS/mom_priv/jobs/35102.fusion.SC: /bin/bash^M: bad interpreter: No such file or directory
Association: General - Posted on: 2006-02-21
To solve this problem do not use windows notepad or wordpad to create the file and then transfer it to the cluster. Extra characters are added by these programs.
Use vi or other editors on the cluster.
How do I log into the system ?
Association: General - Posted on: 2009-08-21
You can log into the system using ssh. This is the only method by which you can log into the system. For linux users the following command will log you into the system.
ssh user_name@firefox.bioinfo.ittc.ku.edu or ssh user_name@explorer.bioinfo.ittc.ku.edu
For windows users, you will need to use a ssh client. A freely downloaded version called PUTTY can be found here. If you are using a machine setup by ittc there should be a ssh client already installed on the system, it is called SSH Secure Shell Client.
How do I compile a stand alone program?
Association: General - Posted on: 2005-07-12
You have two choice for compiling stand alone programs. Both gcc (GNU compilers) and PGI (Portland Group Compilers) are in your path. These compilers are in your path and can be envoked by the following commands.
GCC:
gcc -> C compiler/linker
g++ -> C++ compiler/linker
f77 -> Fortran 77 compiler/linker
Example:
gcc program_name.c -> will compile program using gcc, the binary will be called a.out
PGI:
pgcc -> C compiler/linker
pgCC -> C++ compiler/linker
pgf77 -> Fortran 77 compiler/linker
pgf90 -> Fortran 90 compiler/linker
Example:
pgcc program_name.c -> will compile program using the Portland Compilers, the binary will be called a.out
More information on the pgi compilers can be found in the software section of these webpages.
How do I transfer files to and from the cluster ?
Association: General - Posted on: 2008-02-21
To transfer files to or from the cluster you need to use scp (Secure Copy). From a unix/linux machine this is done as follows:
scp
scp
This will copy the files from your current working directory on the machine you are logged into and transfer them to fusion and put it in your home directory. If you want to put the files someplese other then your home directory, and you have write access to those directories use the following command:
scp
user_name@explorer.bioinfo.ittc.ku.edu:/path/directory
For windows users, you will need to get a program called winscp to transfer your files. You can find this program here. You will want to download the newest Standalone Package. This package will give you a windows browser interface where you can drag and drop your files.
How do I check the status of the cluster?
Association: General - Posted on: 2005-06-10
There are many tools to check the status of the cluster. After logging into the system the fastest way to check is to run a cluster-fork and request the hostname of all the systems.
cluster-fork hostname
This should return the hostname of all the machines, if that machine is up. It should look something like this:
[ahock@fusion ~]$ cluster-fork hostname
compute-0-0:
compute-0-0.local
compute-0-1:
compute-0-1.local
compute-0-2:
compute-0-2.local
compute-0-3:
compute-0-3.local
compute-0-4:
compute-0-4.local
.
.
.
For a graphical representation of the cluster status click on the link "Cluster Status" found on this webpage or click here
Why am I not able to log into firefox or explorer but was able to log into fusion ?
Association: General - Posted on: 2006-06-21
When we migrated the user accounts from fusion to LDAP (for purposes of centralized authentication), we tried to move as much information as we could including passwords. But with all migrations some times not everything goes correctly. If you have this problem one of two things has happened.
1. We did not get your password migrated correctly. Please send a message to biohelp@ittc.ku.edu, and we will try and get your password changed.
2. If you have an ITTC account use that password instead of your cluster password.
Why am I not able to access any of the nodes through ssh ?
Association: General - Posted on: 2009-03-06
This is done by choice on our part. It allows us to have finer grained control over where jobs are ran and how to allocate resources. With an interactive queue you should not need to ssh to any of the nodes on the cluster. If you do need to access a specific node for your research, please contact help@ittc.ku.edu and we will see about getting another method setup to accomplish your task(s).
Some of my applications do not work any more when I try to compile and/or run them ?
Association: General - Posted on: 2006-06-21
For the most part everything should be exactly the same as on fusion. If by chance you having problems make sure all the paths are correct in your code, re-run configure (if the application has this). If you are still having problems please contact biohelp@ittc.ku.edu.
What InfiniBand networks are available?
Association: General - Posted on: 2009-08-26
In the Bioinformatics cluster, racks 4,5, 6, 7, and 8 each have InfiniBand switches. Jobs can be run using a single rack which has 16 nodes and a total of 128 cores.
Why do I want to use InfiniBand?
Association: General - Posted on: 2009-04-27
InfiniBand is a low-latency, high-speed switching fabric. It provides faster message passing and improves the scalability of parallel programs.
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