User Guides
Software Introduction
Publications
Literature Citation
Service Newsletters
I have forgotten my password, who should I contact to reset it?
I have accidentally deleted my files, can they be recovered?
What is the citation when publishing and presenting results obtained using the NSCCS resources?
Users are advised to read the NSCCS User Guide prior to accessing/using the NSCCS machines and its software.
I cannot log onto the machine, where can I get help?
Please refer to the NSCCS user guide (2.2 How to Log in) on how to log onto the machine.
Make sure you have a Secure Shell Client on your local computer to connect to Magellan. Please also type carefully when you enter your password as it is case sensitive.
If you still cannot log onto the machine, please contact columbus@hpc-support.rl.ac.uk for help.
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You can change your password simply by typing passwd at the Unix prompt and you will be prompted to enter your old password in order to set up a new one. Users are advised to change their password immediately after they first log onto the machine.
I have forgotten my password, who should I contact to reset it?
Please contact columbus@hpc-support.rl.ac.uk for assistance.
How to run a job/access software?
Runscripts (e.g. runadf, rung03) are available for all the chemistry software packages on Magellan. These are installed in the directory $CHEM on Magellan. Runscripts are shell scripts written for executing each software package. Each runscript has a man page and users are strongly advised to read this before running jobs. The man pages can be viewed by typing man followed by the name of the runscript. For example, to view the man page for Gaussian 09, type the following at the Unix prompt:
man rung09
Click here for a full list of runscripts available.
Which queue should I submit my job to?
Magellan has a number of queues with different configurations. Please refer to the NSCCS user guide (7. Batch Jobs) for details.
How can I check my job status?
The command to check the status of LSF jobs is bjobs. On its own, bjobs will return a list of all your jobs and whether they are queued or executing. Useful options are:
bjobs -u all - to see the jobs of all users
bjobs -q queue_name - to restrict the output to a single queue
bjobs -l jobid - to see more detailed information about a particular job
where jobid is the numeric identifier given to the job by LSF and is displayed as one of the fields in the bjobs command.
Users can also check the status of the queues by using the command qstat -a, which displays information such as how many jobs are currently running and pending on the queues.
How can I check how much time is left on my project?
To check your current usage and allocations, type:
acct qusage chemxxx
where xxx should be replaced by the number of your subproject.
e.g. acct qusage chem123
Please note the account information is only updated overnight, so the amount of CPU used during the current day will not appear until the following day.
How to check how much CPU time has been used for my job(s)?
The CPU times are reported in both the output files and the batchout files but they may be incorrect for some parallel applications. Although there is currently no way to accurately record the CPU time used by some of these jobs, the correct amount of time will be charged for.
Users can also view the following file to find out the exact time used for each of their jobs.
/var/log/chemuse.log
An example of what is printed in the chemuse.log file is given below.
Mar 14 09:38:17 6R:magellan ht3: /usr/local/Chem-Apps/nwchem5.0/bin/nwchem et=2.461 ut=0.596 st=0.372 mrKb=0 adMb=0 asMb=0 bi=0 bo=0 LSF=5670.a2
The date and time of the job completed, the machine the job was running on (e.g. magellan), the userid (e.g. ht3), the location of the program's executable (e.g. NWChem) are given. The CPU time for the job is the sum of the usage time (ut) and the system time (st) (e.g. CPU=0.596(ut) + 0.372(st)=0.968). All times are reported in seconds. Each of these jobs is identified by the LSF batch request ID number (e.g. 5670) and the name of the queue the job was submitted to (e.g. a2).
Older log files (e.g. chemuse.20101101), are available in the /usr/local/locallog/chemusage directory.
I have accidentally deleted my files, can they be recovered?
If your files were created today, then they would not have been backed up so we are unable to recover them for you. If the files were created the day before and the scheduled overnight back up has saved them, you can then to send a request to Columbus Support (email columbus@hpc-support.rl.ac.uk) quoting your userid, and information relating to your file(s). i.e. file name, file(s) location, when youve last accessed it(them).
What is the citation when publishing and presenting results obtained using the NSCCS resources?
Users must acknowledge the use of the NSCCS and any contributions from its staff in all publications, presentations, papers and seminars that arise from their project.
Click here for the official wordings for literature citations.