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, whether 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.

(Regardless of whether the server would be added into the cluster environment or remain a standalone machine, any purchases must be done through University's purchase contracts to ensure that legal aspects such as formal bidding contest are fulfilled properly.)

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.

- Terms for purchasing and using the scientific software at the university.
- Availability and licensing of mathematical software.

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 Type	Node Qty	Sockets x Core (HT) per Node	Node Memory	Where	How to Use	Notes
GPU, Tesla P100	2	2x 2.4GHz 14HT, 4xGPU	512GB	Kale	-p --gres:gpu=1	Academic Nvidia GPU Grant
GPU Tesla k80	1	2x 2.4GHz 12, 4xGPU		Kale	-p --gres:gpu=1	Academic Nvidia GPU Grant
Skylake	23	2x 20HT cores	384GB	Kale	--constraint=avx	AVX-512
Xeon E5	31	2x 2.4GHz 14HT cores	256GB	Ukko2	Default
Xeon E7	2	4x 2.2GHz 24HT cores	3TB	Ukko2	-p bigmem
Xeon	19	2x 2.4GHz 12 cores	129GB	Kale	--constraint=smem, Default
Xeon	13	2x 2.4GHz 12 cores	260GB	Kale	--constraint=mmem, Default
Xeon	1	4x 2.4GHz 12 cores	1.57TB	Kale	--constraint=bmem
GPU, V100	4	4x GPU	384GB	Kale		800GB NVMe SSD. 12GPU's with 32GB, 4GPU's with 16GB Academic Nvidia GPU Grant
Sandybridge	180	2x 2.66GHz 8HT (32 HT cores)	64GB	Vorna		About 6000 cores
Sandybridge	12	2x 2.66GHz 8 cores	64GB	Vorna		Service nodes
AMD Epyc	10			Carrington
AMD Epyc	16			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 Path	Nodes	Where	How to Access (examples)	Quota Limit	Notes
/home/$USER	NFS	ALL	Home directories	Very low
Data Lake	Ceph	ALL		N/A
/wrk/users/$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)	Turso	Temp directory		$WRKDIR Capacity: 750TB, non-redundant, ZFS backend
/proj/$USER	NFS	Turso, pangolin, melkki, melkinkari, desktops	User application directory for applications, source codes. pangolin, melkki and melkinkari: /home/ad/turso-proj/$USER	20GB	$USERAPPL
/appl/	NFS	Turso	Global software module repository (RHEL7, CentOS7)	N/A	Read Only
/proj/$USER	NFS	Turso, pangolin, 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.

Name	Where	How to Access	Licenses
Comsol	Turso	Installed as a module.
Intel C++ compiler	Turso, Cubbli Linux, Desktop	As a module in clusters, Check eligibility for a free license.	2
Intel Fortran	Turso, Cubbli Linux, Desktop	As a module in clusters, Check eligibility for a free license .	2
Intel MKL	Turso, Cubbli Linux, Desktop	As a module in clusters, Check eligibility for a free license .	2
Intel DAAL	Turso, Cubbli Linux, Desktop	As a module in clusters, Check eligibility for a free license .	2
Intel IPP	Turso, Cubbli Linux, Desktop	As a module in clusters, Check eligibility for a free license .	2
Intel Advisor	Turso, Cubbli Linux, Desktop	As a module in clusters, Check eligibility for a free license .	2
Intel Inspector	Turso, Cubbli Linux, Desktop	As a module in clusters, Check eligibility for a free license .	2
Intel MPI	Turso, Cubbli Linux, Desktop	As a module in clusters, Check eligibility for a free license .	2
Intel VTune Amplifier	Turso, Cubbli Linux, Desktop	As a module in clusters, Check eligibility for a free license .	2
Intel Trace Analyzer	Turso, Cubbli Linux, Desktop	As a module in clusters, Check eligibility for a free license .	2
Intel Distribution for Python	Turso, Cubbli Linux, Desktop	As a module in clusters, Check eligibility for a free license .	2
Intel Cluster Checker	Turso, Cubbli Linux, Desktop	As a module in clusters, Check eligibility for a free license .	2
Matlab	Turso, Cubbli Linux, Desktop	As a module in clusters.	TAC
IBM ILOC CPEX		Check eligibility for a free license
Mathematica	Cubbli	Software Distribution	Commercial?
ARCGIS		Software Distribution	Commercial?
IDRISI		Software Distribution	Commercial?
MAPINFO		Software Distribution	Commercial?

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

Name	Where Available	How to Access	Tutorials & Use Cases
AOCC	Turso	As a module in clusters.	AMD Compiler Suite
TensorFlow	Turso	Through Python Virtualenv	Basic Tutorials
Keras	Turso	Through Python Virtualenv	Tutorial Keras model into Tensorflow Practical use case
CUDA	Turso, Cubbli	As a module in clusters. Cubbli default	GPU Tutorials
CudNN	Turso	As a module in clusters.	Convolutions tutorial
AMBER	Turso	As a module in clusters.	Molecular simulation toolkit
GROMACS	Turso	As a module in clusters.	G romacs tutorials, GROMACS/2018.3-fosscuda-2018b with GPU support.
OpenBLAS	Turso	As a module in clusters.
OpenMPI	Turso	As a module in clusters.	Tutorial Tutorial
OpenFOAM	Turso	As a module in clusters.	Tutorial
Python	Turso	As a module in clusters.
GCC	Turso, Cubbli	As a module in clusters. Cubbli default	GNU Compiler Collection
Java	Turso, Cubbli	As a module in clusters. Cubbli default
Bison	Turso	As a module in clusters.
Dalton	Turso	As a module in clusters.
MVAPICH	Turso	As a module in clusters.	MVAPICH tutorials
Molden	Turso	As a module in clusters.	Molecular Structure Analysis
ORCA	Turso	As a module in clusters.	Quantum Chemistry
Perl	Turso, Cubbli	As a module in clusters. Cubbli default
ScaLAPACK	Turso	As a module in clusters.
GMP	Turso	As a module in clusters.
NASM	Turso	As a module in clusters.
Mesa	Turso	As a module in clusters.
Mako	Turso	As a module in clusters.
R	Turso	As a module in clusters.	R Tutorials
R-Studio	Cubbli	Cubbli default
GNU Octave	Cubbli	Cubbli default
FreeSurfer	Cubbli	Software Distribution	MRI Imaging
NoMachine client	Cubbli	Software Distribution
VMD	Cubbli	Software Distribution	Molecular Dynamics
PCRE	Turso	As a module in clusters.
OpenPGM	Turso	As a module in clusters.
PyZMQ	Turso	As a module in clusters.
IPython	Turso	As a module in clusters.	Jupyter Notebook
ZeroMQ	Turso	As a module in clusters.
XZ	Turso	As a module in clusters.
Valgrind	Turso	System Package	Small tutorial
Valgrind-openmpi	Turso	System Package	Resources for OpenMPI debugging
v8	Turso	System Package	v8 Development Library
LLVM	Turso	As a module in clusters.
NLopt	Turso	As a module in clusters.
M4	Turso	As a module in clusters.
GDAL	Turso	As a module in clusters.	Geospatial Data Abstraction Library
HDF5	Turso	As a module in clusters.
H5py	Turso	As a module in clusters.
FFTW	Turso	As a module in clusters.	C subroutine library for discrete Fourier transform
Spark	Turso	As a module in clusters.	HY User Guide
Fortran	Turso	As a module in clusters.
Julia	Cubbli	Cubbli default	Data science tutorial Julia on HPC environment
Haskell	Cubbli	Cubbli default
Oracle JDK	Cubbli	Cubbli default
Tcl/tk	Turso	As a module in clusters.
SHRiMP	Turso	As a module in clusters.
GPAW	Turso	As a module in clusters.
BLAST+	Turso	As a module in clusters.
ASE	Turso	As a module in clusters.
LAMMPS	Turso	As a module in clusters.
Geant4	Turso	As a module in clusters.
SQLite	Turso	As a module in clusters.
NumPy	Turso	As a module in clusters.	Julia vs. Python performance
Scilab	Cubbli?	Software Distribution	Commercial?
Cernlib	Cubbli ?	Software Distribution
GSL	Cubbli ?, Mutteri, Turso	Software Distribution
SLATEC	Cubbli ?	Software Distribution	Commercial?
Maple	Cubbli ?	Software Distribution	Commercial?
Singularity	Turso	System package on a compute nodes	Container 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.

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