Development modules update
A quick update listing modules that have been moved from the development environment to production, or deprecated.
Welcome to the QMUL HPC blog¶
Short queue
In addition to the primary queue, there is a queue designed to minimise waiting times for short jobs and interactive sessions, in response to users who requested the ability to quickly obtain qlogin sessions for quick tests and debugging. This short queue runs on a wider selection of nodes and is automatically selected if your runtime request is 1 hour or less.
Deprecated modules
We removed some problematic module files. Please check your job scripts for use of these modules:
- Python: Due to a number of issues with the module installs of python,
older versions below
2.7.14and3.6.3are being removed from Apocrita (python/2.7.13,python/2.7.13-1,python/2.7.13-3,python/3.6.1,python/3.6.2,python/3.6.2-2). - Java: version
java/1.8.0_121-oraclecauses problems with mass thread spawning on the cluster and will be removed.java/1.8.0_152-oraclewill remain the default version loaded.
Home and Group Directories
During the summer, home directories were migrated to the new storage platform. This means that quotas have grown slightly as the underlying block size has increased.
The qmquota command will tell you how much space you are using,
and that quotas are applied on size as well as the number of files.
Each Research group gets a free 1Tb of storage space on the cluster; if your
group has not got one then please contact us and we can organise it for your
group.
Tier 2 Announcement
QMUL have access to powerful Tier 2 (formerly known as Regional) HPC resources, predominantly for EPSRC researchers. If you run multi-node parallel code (using MPI, for example), you will likely benefit from using the Tier2 clusters.
Deprecated openmpi 2.0.2-gcc module
We identified a problem with the openmpi/2.0.2-gcc module and have removed
it as the correct interface was not being used for the MPI communication
between nodes. This resulted in potentially much slower communication and
consequently jobs taking longer to run.
Programs should be rebuilt against the other available openmpi modules which correctly select the Infiniband interconnect as default for communication. Recent users of this module have been contacted directly.
New cluster announcement
We are pleased to announce that the new cluster is available for general use. This has been a large project, involving the following:
Python performance in containers
Singularity (now Apptainer) is a container solution designed for HPC. Due to the secure and simple design, it can be easily used to provide applications for use with HPC clusters where other containers, such as Docker would not be suitable.
1PB added storage
We recently added an additional petabyte of storage, it is necessary to move all files to the new storage to benefit from improved performance.