IT infrastructure¶
Private Cluster¶
The NBD Linux Cluster consists of 6 computing nodes with 2 GPUS NVIDIA GeForceTM GTX 1080 and 1 xeon Gold Processors, for a total of 156 cores (312 HT threads). Includes 2 GPUs for offloading calculations.
- Folders:
/shared/scratch: To compute
/shared/work: Large storage
/shared/home-nbdcalc01/: What used to be the office machine (28 cpus)
/shared/data-nbdcalc01/: Libraries of compounds (ZINC, fragments…)
/shared/data-ndbdata01/users/user/: Individual storage
/shared/data-nbddata01/common/: Shared storaged & Project management
To connect: ssh -X username@10.10.0.6
Queue system¶
The cluster uses Slurm workload manager to schedule jobs and allocate resources. It is fairly simple to use, you only have to learn a handful of commands:
sbatch run.sl # to submit a file to the queue
squeue # to see all jobs on the queue
scancel job_id # to cancel a job with specific ID, e.g. scancel 10240
If you want to dive in deeper, check out the official Slurm documentation.
You can also run programs in interactive mode, e.g.
interactive -n 20 # launch interactive with 20 CPUs available
module load module_name # to load a specific module, e.g. module load Python/3.7.0-foss-2018a
RES¶
The RES grant allows us to use MN4 to run our in house ModTox project. (MD&PELE for academic purposes/publications)
To connect: You need to ask for an account. Please, contact with it@nostrumbiodiscovery.com
Backup¶
A daily backup is done from /shared/home-nbdcalc01/ and /shared/data-nbdcalc01/ to NAS Synology.
A daily backup is done /shared/data-nbddata01/ to NAS Synology
The backup is automatically done at 00:00 sending a daily report to support
The backup keeps:
A daily backup for the last 14 days
A weekly backup for the last 8 weeks
A monthly backup for the last 12 months
A yearly backup for all years
This means that we have daily granularity up to 2 weeks, weekly granulatiry up to 2 month, month granularity up to 1 year and year granularuty for past years.
In order to get backed up files contact with HPCNow support