Allocating More Memory:
Use the -l mem resource list option in your PBS script, or in your command-line invocation of qsub; or, Gaussian users may employ the -m option to g98sub or g03sub, specifying the amount of memory, in MB (megabytes), MW (megawords), or GB (gigabytes). (Sweetgum has a word-size of 64 bits, or 8 bytes, so 8MB=1MW.) PBS will route your job to appropriate queue.
NOTE: The most privileged PBS queues, such the large memory queues, require a special, one-time validation for your account to access them. Email your request and research justification to firstname.lastname@example.org. For more information, see the PBS Queue Configuration.
NOTE to GAUSSIAN USERS: Any memory specifications in your Gaussian input file will override those you specify via PBS. To avoid problems of conflicting resource requests, you should either: 1. Remove any memory resource specifications from your Gaussian input file, or 2. Ensure that that you request enough memory in both your Gaussian input file, and your PBS script (or in the command line of your qsub/g98sub/g03sub invocation.)
PBS Script Examples:
#PBS -l mem=800MB
#PBS -l mem=100MW
#PBS -l mem=1GB
qsub -l mem=200MW myscript.pbs
g98sub -m 2GB myprogram.com
g03sub -m 100MB myprogram.com
- The -m option to this script has been disabled
- Amount of memory specified in the input file should be an amount equal to 90% * nprocs * 1GB (or just under 1 GB per processor requested) since this amount of memory from PBS will be available to use anyway.
Check on the status of my PBS job(s)
Use the qstat utility. See examples of PBS commands.
For more information, see the Unix man page for qstat.
Delete a running or queued PBS job
Use the qdel utility. First, use qstat to determine the numeric ID of your PBS job.
Then, run qdel to delete the job. For more information, see the Unix man page for qdel.
Run a job on specific Mimosa nodes
Mimosa is a Beowulf Cluster, and a file containing the description of all the nodes in the cluster is
/var/spool/PBS/server_priv/nodes on mimosa.
So, If a user wanted to make sure his/her Mimosa job was run only on dell computers (that's the vendor we bought them from),
in the pbs script for submitting the job the following option should be set:
#PBS -l nodes=8:dell
Or, if he/she wanted to run on 16 2800 MHz PCs, regardless of vendor, the option to set is:
#PBS -l nodes=16:MHz2800
Submit Gaussian jobs using PBS:
For computational chemistry users, there are two scripts in place for
using PBS: g98sub and g94sub
Usage: g98sub [-t time] [-m memory] [-f filesize] jobs
sweetgum 11% g98sub -t 3600 -m 100MW g98test3.com
Submitting files to nqs...
Input file g98test3.com found.
Submitting job g98test3 to res-gate.
Data file is /ptmp/chwang/g98test3.com.
G98 Output will be sent to g98test3.out.
NQS Output will be sent to g98test3.log.
Memory requested is 100MW.
Time requested is 3600.
g98 job g98test3 submitted.
<< Previous Next>>