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1.0 Introduction

IT for Science group provides resources and consulting services for the research community. This document provides an compendium of the free resources available for the research community. In short, we provide following services: 

  • Cubbli Linux distribution
  • GPU capacity, up to 20 GPU's available for interactive and batch use.
  • High Performance Computational capacity in three facilities for interactive and batch use.
  • Fast I/O
  • Consulting services and best practices.

1.1 Can I buy my own servers?

You may be considering procuring computational resources, wether they are GPU machines for Deep Learning, regular servers for computing, servers for heavy duty database use, or storage capacity and have checked that your requirement is something we do not yet offer. We have a good news. We can house servers that are used for computational tasks and incorporate them gladly to the existing pool of resources. These can be for example: 

    • Dedicated to you alone, or...
    • Your research group could ask for pre-emption capability, or...
    • A standard addition to common pool without special privileges besides of becoming an Investor User.

You can always opt to increase the common pool of resources at any time. Even ones that have been dedicated before.

1.1.1 We offer benefits

    • Standard, centrally managed Centos7 Linux environment.
    • All the software modules listed later in this document.
    •  Very high throughput/low latency I/O ($WRKDIR).
    • Automated data migration from $WRKDIR to CEPH data lake - Planned 2019Q2.
    • Other resources in a same high-bandwidth interconnect fabric.
    • Resource Usage statistics.
    • You can utilize our procurement process and therefore get better deals.

1.2 If you still think you must choose yourself, we have something to say...

In exchange for above benefits, we have a few requirements for servers that are not bought by us:

    • Rack mountable server, or chassis solution
    • Infiniband nic (depending on the bandwidth requirement, this can be FDR (56Gb/s) and EDR (100Gb/s))
    • Associated IB cable

1.3 Because

1.3.1 Why should I become Investor User?

    • You will be granted higher percentage of the shares of the computational resources.
    • Being investor user is especially beneficial when your jobs are resource intensive.
    • Having more shares means that job priorities decay slower.

1.3.2 Why not to use dedicated servers?

    • A history has shown that dedicated resources are often ill utilized. Utilization of less than 20% is very common.
    • Larger pool of common resources enables greater availability for everyone.
    • When resources are not dedicated, you can scale immediately upwards whenever you have temporary need.
    • Pooled resources are immediately available for use.
    • We are flexible, and if you know in advance, we can create resource reservations in advance.

If you would need to have dedicated pool of $WRKDIR I/O resources which is only accessible by named research group, we can do this as well. In this case you should contact us and we will discuss the details.

You can find additional details about access, restrictions etc and other topics in the User Guides. 

1.4 Other topics

A brief information about general University wide terms and conditions can be found through the links listed below.

For any concerns, questions or comments you can reach us in person at Kumpula campus, or through the university helpdesk at  helpdesk (at) helsinki (dot) fi . Resource requests, and bug reports should be addressed through  helpdesk (at) helsinki (dot) fi .

2.0 Cubbli Linux

Cubbli Linux distribution is fully supported by IT4SciFi. Please see the Cubbli Linux  for additional information about availability and release notes. Cubbli Linux is available for servers, workstations and laptops.

Cubbli documentation also here (in Finnish).

3.0 HPC Environment

If, and when the demand of computational resources exceed the capabilities of ordinary workstation, we invite you to utilize our HPC resources. We offer significant GPU, CPU and I/O resources, and fairly comprehensive - and constantly updated library of scientific software, compilers and programming environments. Should you have specific resource need  not listed here, you can contact us through helpdesk (at) helsinki (dot) fi. If you know that your workload scales beyond our resources, you can take a look at the national supercomputing resources available at CSC.

Below you can find a list of hardware resources available on the high performance computing platform. 'How to access example' refers to the use of batch scheduler flags. Notes include special details of the components included. 'HT' indicates that CPU Hyperthreading is used on the nodes to increase the core count. 

Note that sometimes Vendors have grants for certain resources as indicated on the list. Do check if you are eligible.

Node TypeNode QtySockets x Core (HT) per NodeNode MemoryWhereHow to UseNotes
GPU, Tesla P10022x 2.4GHz 14HT, 4xGPU512GBKale-p --gres:gpu=1Academic Nvidia GPU Grant
GPU Tesla k8012x 2.4GHz 12, 4xGPU
Kale-p --gres:gpu=1Academic Nvidia GPU Grant
Skylake232x 20HT cores384GBKale--constraint=avxAVX-512
Xeon E5312x 2.4GHz 14HT cores256GBUkko2Default
Xeon E724x 2.2GHz 24HT cores3TBUkko2-p bigmem
Xeon192x 2.4GHz 12 cores129GBKale--constraint=smem, Default
Xeon132x 2.4GHz 12 cores260GB Kale --constraint=mmem, Default
Xeon14x 2.4GHz 12 cores1.57TBKale--constraint=bmem
GPU, V10044x GPU384GBKale

800GB NVMe SSD. 12GPU's with 32GB, 4GPU's with 16GB

Academic Nvidia GPU Grant

Sandybridge1802x 2.66GHz 8HT (32 HT cores)64GBVorna
About 6000 cores
Sandybridge122x 2.66GHz 8 cores64GBVorna
Service nodes
AMD Epyc10

Carrington

AMD Epyc16

ukko

4.0 Storage and I/O

List of available I/O resources for the users. If a I/O resource is missing from the list, or there are bugs/problems or other concerns, please do contact us through university helpdesk at helpdesk (at) helsinki (dot) fi.  We are investing on high performance I/O, and additional computational resources at the moment, and expect a fresh capability to be in production 1Q2019. 

Actual PathNodesWhereHow to Access (examples)Quota LimitNotes
/home/$USERNFSALLHome directoriesVery low
Data Lake Ceph ALL
N/A
/wrk/users/$USER

Lustre

(Vakka)

Turso, pangolin, melkki, melkinkari, desktops


User Guide

#SBATCH --workdir=/wrk/users/<username>

Samba desktops: ukko2-smb.cs.helsinki.fi

pangolin, melkki and melkinkari: /home/ad/ukko2-wrk/$USER

User quota limit 50T

$WRKDIR

Capacity: 1.2PB, redundant ZFS backend

/wrk/users/$USER

Lustre

(Kappa)

TursoTemp directory

$WRKDIR

Capacity: 750TB, non-redundant, ZFS backend

/proj/$USERNFS

Turso, pangolin, melkki, melkinkari, desktops

User application directory for applications, source codes.

pangolin, melkki and melkinkari: /home/ad/turso-proj/$USER

20GB$USERAPPL
/appl/NFSTursoGlobal software module repository (RHEL7, CentOS7)N/ARead Only
/proj/$USERNFS

Tursopangolin, melkki, melkinkari, desktops

Longer term storage for datasets and results.

pangolin, melkki and melkinkari: /home/ad/turso-proj/$USER

20GB$PROJ

5.0 Licensed Software

We provide licensed software, some which are available also for free for certain users, or user groups. It is advisable to check if you qualify for a free license, if the product information so implies. If the licensed program is not present and you would like it to be included, please do not hesitate to contact us through university helpdesk at helpdesk (at) helsinki (dot) fi.  

NameWhereHow to AccessLicenses

Comsol

TursoInstalled as a module.
Intel C++ compiler Turso, Cubbli Linux, DesktopAs a module in clusters, Check eligibility for a free license.2
Intel FortranTurso, Cubbli Linux, DesktopAs a module in clusters, Check eligibility for a free license .

2

Intel MKLTurso, Cubbli Linux, DesktopAs a module in clusters, Check eligibility for a free license .2
Intel DAALTurso, Cubbli Linux, DesktopAs a module in clusters, Check eligibility for a free license .2
Intel IPPTurso, Cubbli Linux, DesktopAs a module in clusters, Check eligibility for a free license .2
Intel AdvisorTurso, Cubbli Linux, DesktopAs a module in clusters, Check eligibility for a free license .2
Intel InspectorTurso, Cubbli Linux, DesktopAs a module in clusters, Check eligibility for a free license .2
Intel MPITurso, Cubbli Linux, DesktopAs a module in clusters, Check eligibility for a free license .2
Intel VTune AmplifierTurso, Cubbli Linux, DesktopAs a module in clusters, Check eligibility for a free license .2
Intel Trace AnalyzerTurso, Cubbli Linux, DesktopAs a module in clusters, Check eligibility for a free license .2
Intel Distribution for PythonTurso, Cubbli Linux, DesktopAs a module in clusters, Check eligibility for a free license .2
Intel Cluster CheckerTurso, Cubbli Linux, DesktopAs a module in clusters, Check eligibility for a free license .2
MatlabTurso, Cubbli Linux, DesktopAs a module in clusters.TAC
IBM ILOC CPEX
Check eligibility for a free license
MathematicaCubbliSoftware DistributionCommercial?
ARCGIS
Software DistributionCommercial?
IDRISI
Software DistributionCommercial?
MAPINFO
Software DistributionCommercial?

6.0 Open Source Software & Libraries

This list includes most of the special scientific software packages, tools and specialized libraries made available by IT4SciFi. Items on this list have multiple versions available on the clusters and different versions cam be managed with Modules. If the utility, tool, library or program, or specific version is not present and you would like it to be included, please do not hesitate to contact us through university helpdesk at helpdesk (at) helsinki (dot) fi

You can also create modules for of your own software and then share it conveniently within the research group if you like. We have brief instructions here.

All system and development libraries are present on the computational environment by default, and therefore not included in the list - except where tools are installed as modules in the HPC environment. 

Aalto software modules

You are also eligible to use software module from Aalto univerisity. However these are not defaulted because the module list would be very long. To have Aalto modules included, please add modules:

module use /cvmfs/fgi.csc.fi/apps/el7/aalto/spack/lmod/linux-centos7-x86_64/all
module use /cvmfs/fgi.csc.fi/apps/el7/aalto/spack/lmod/linux-centos7-westmere/all/

Local software modules

NameWhere AvailableHow to AccessTutorials & Use Cases
AOCCTursoAs a module in clusters.AMD Compiler Suite
TensorFlow TursoThrough Python Virtualenv

Basic Tutorials

KerasTursoThrough Python Virtualenv

Tutorial

Keras model into Tensorflow

Practical use case

CUDATursoCubbli

As a module in clusters.

Cubbli default

GPU Tutorials

CudNNTurso

As a module in clusters.

Convolutions tutorial

AMBERTursoAs a module in clusters.Molecular simulation toolkit
GROMACSTursoAs a module in clusters.G romacs tutorials, GROMACS/2018.3-fosscuda-2018b with GPU support.
OpenBLASTursoAs a module in clusters.
OpenMPITursoAs a module in clusters.

Tutorial

Tutorial

OpenFOAMTursoAs a module in clusters.Tutorial
PythonTursoAs a module in clusters.
GCCTursoCubbli

As a module in clusters.

Cubbli default

GNU Compiler Collection
JavaTursoCubbli

As a module in clusters.

Cubbli default


BisonTursoAs a module in clusters.
DaltonTursoAs a module in clusters.
MVAPICHTursoAs a module in clusters.

MVAPICH tutorials

MoldenTursoAs a module in clusters.Molecular Structure Analysis
ORCATursoAs a module in clusters.Quantum Chemistry
PerlTurso, Cubbli

As a module in clusters.

Cubbli default


ScaLAPACKTursoAs a module in clusters.
GMPTursoAs a module in clusters.
NASMTursoAs a module in clusters.
MesaTurso
As a module in clusters.
MakoTursoAs a module in clusters.
RTursoAs a module in clusters.

R Tutorials

R-StudioCubbliCubbli default
GNU OctaveCubbliCubbli default
FreeSurferCubbliSoftware DistributionMRI Imaging
NoMachine clientCubbliSoftware Distribution
VMDCubbliSoftware DistributionMolecular Dynamics
PCRETursoAs a module in clusters.
OpenPGMTursoAs a module in clusters.
PyZMQTursoAs a module in clusters.
IPythonTursoAs a module in clusters.Jupyter Notebook
ZeroMQTurso
As a module in clusters.
XZTursoAs a module in clusters.
ValgrindTursoSystem PackageSmall tutorial
Valgrind-openmpiTursoSystem PackageResources for OpenMPI debugging
v8Turso
System Packagev8 Development Library
LLVMTursoAs a module in clusters.
NLoptTurso
As a module in clusters.
M4TursoAs a module in clusters.
GDALTursoAs a module in clusters.Geospatial Data Abstraction Library
HDF5TursoAs a module in clusters.
H5pyTursoAs a module in clusters.
FFTWTursoAs a module in clusters.C subroutine library for discrete Fourier transform
SparkTursoAs a module in clusters.

HY User Guide

FortranTursoAs a module in clusters.
JuliaCubbliCubbli default

Data science tutorial

Julia on HPC environment

HaskellCubbliCubbli default
Oracle JDKCubbliCubbli default
Tcl/tkTursoAs a module in clusters.
SHRiMPTursoAs a module in clusters.
GPAWTursoAs a module in clusters.
BLAST+TursoAs a module in clusters.
ASETursoAs a module in clusters.
LAMMPSTursoAs a module in clusters.
Geant4TursoAs a module in clusters.
SQLiteTursoAs a module in clusters.
NumPyTursoAs a module in clusters.Julia vs. Python performance
ScilabCubbli?Software DistributionCommercial?
CernlibCubbli ?Software Distribution
GSLCubbli ?, MutteriTursoSoftware Distribution
SLATECCubbli ?Software DistributionCommercial?
MapleCubbli ?Software DistributionCommercial?
SingularityTursoSystem package on a compute nodesContainer system

7.0 VDI

Please see the Cubbli and VDI for additional information.

Note: that VDI is not an environment to be used for computationally intensive tasks, such as Tensorflow over GPU. You will get far better performance if you use these resources instead.

8.0 GitLab Server

IT4SciFi offers and manages GitLab server at version.helsinki.fi. Please see the User Guide for further details and usage policies.

9.0 Infrastructure

9.1 Geoinformatics

The university of Helsinki uses the  CSC GIS services  as a central source for GIS data.

9.2 VMWare Virtual Servers

What to say?

10.0 Consulting Services

IT4SciFi offers consulting services. Wether the question is about virtual machines, hardware, software or computational, or storage etc. resource requirements, project servers or any other topic, feel free to contact us through university helpdesk at helpdesk (at) helsinki (dot) fi.

11.0 ePouta

 A cloud computing environment designed for processing and / or storing sensitive data. Service provided by csc but server administration handled by IT department. Request resources via helpdesk@helsinki.fi. See https://research.csc.fi/epouta for further details.