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Checking the Limits an application is imposed during run

If you wish to look at a specific application limits during run, you can do the following

pgrep fortcom
12345

* I used for fortcom, but it could be any application you wish to take a look.

cat /proc/12345/limits
Limit Soft Limit Hard Limit Units
Max cpu time unlimited unlimited seconds
Max file size unlimited unlimited bytes
Max data size unlimited unlimited bytes
Max stack size 8388608 unlimited bytes
Max core file size 0 unlimited bytes
Max resident set unlimited unlimited bytes
Max processes 4096 2190327 processes
Max open files 1024 4096 files
Max locked memory unlimited unlimited bytes
Max address space unlimited unlimited bytes
Max file locks unlimited unlimited locks
Max pending signals 2190327 2190327 signals
Max msgqueue size 819200 819200 bytes
Max nice priority 0 0
Max realtime priority 0 0
Max realtime timeout unlimited unlimited us

* You can take a look that there is no limits to Max locked Memory and Max file locks are unlimited.

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Compiling Gromacs-2019.3 with Intel MKL and CUDA

Prerequisites

GCC-6.5 Compilers and associates libraries
m4-1.4.18
mpfr-3.1.4
cmake-3.15.1
gmp-6.1.0
mpc-1.0.3

Intel Compilers and Prerequisites

source /usr/local/intel/2018u3/bin/compilervars.sh intel64
source /usr/local/intel/2018u3/impi/2018.3.222/bin64/mpivars.sh intel64
source /usr/local/intel/2018u3/mkl/bin/mklvars.sh intel64
source /usr/local/intel/2018u3/parallel_studio_xe_2018/bin/psxevars.sh intel64
MKLROOT=/usr/local/intel/2018u3/mkl

Create a setup file

touch gromacs_cpu.sh

Put the following into the gromacs_cpu.sh

CC=mpicc CXX=mpicxx cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=on -DGMX_FFT_LIBRARY=mkl
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2019.3_intel18_mkl -DREGRESSIONTEST_DOWNLOAD=ON
-DCMAKE_C_FLAGS:STRING="-cc=icc -O3 -xHost -ip"
-DCMAKE_CXX_FLAGS:STRING="-cxx=icpc -O3 -xHost -ip" 
-DGMX_GPU=off -DCMAKE_BUILD_TYPE=Release
./gromacs_cpu.sh
make
make install

Testing and Verification

$ source /your/installation/prefix/here/bin/GMXRC
./gmxtest.pl all -np 2
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Compiling Gromacs-2019.3 with Intel 2018 and MKL

Prerequisites

GCC-6.5 Compilers and associates libraries
m4-1.4.18
mpfr-3.1.4
cmake-3.15.1
gmp-6.1.0
mpc-1.0.3

Intel Compilers and Prerequisites

source /usr/local/intel/2018u3/bin/compilervars.sh intel64
source /usr/local/intel/2018u3/impi/2018.3.222/bin64/mpivars.sh intel64
source /usr/local/intel/2018u3/mkl/bin/mklvars.sh intel64
source /usr/local/intel/2018u3/parallel_studio_xe_2018/bin/psxevars.sh intel64
MKLROOT=/usr/local/intel/2018u3/mkl

Create a setup file

touch gromacs_cpu.sh

Put the following into the gromacs_cpu.sh

CC=mpicc CXX=mpicxx cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx
-DGMX_MPI=on -DGMX_FFT_LIBRARY=mkl -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2019.3_intel18_mkl 
-DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_FLAGS:STRING="-cc=icc -O3 -xHost -ip" 
-DCMAKE_CXX_FLAGS:STRING="-cxx=icpc -O3 -xHost -ip" -DGMX_GPU=off -DCMAKE_BUILD_TYPE=Release
./gromacs_cpu.sh
make
make install

Testing and Verification

$ source /your/installation/prefix/here/bin/GMXRC
./gmxtest.pl all -np 2
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Compiling OpenMPI-3.1.6 with GCC-6.5

We assumed that you have installed GNU 6.5 and isl-0.15

Download the latest OpenMPI 3.1.6 package from OpenMPI site

./configure --prefix=/usr/local/gnu/openmpi-3.1.6 --with-tm=/opt/pbs --enable-orterun-prefix-by-default --enable-mpi-cxx --enable-openib-rdmacm-ibaddr

–enable-orterun-prefix-by-default (Configure OMPI –enable-orterun-prefix-by-default and so that you do not need to add the prefix option)
–enable-openib-rdmacm-ibaddr (To enable routing over IB)
–enable-mpi-cxx (C++ bindings are no more built by default)

make all install | tee install.log
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Another way to calculate shared memory swapping

Using ipcs utlities to find out information on shared memory utilisation which can be useful for analysing the performance of the system. Let’s says you want to measure how much memory has been swapped.

ipcs -mu
------ Shared Memory Status --------
segments allocated 55
pages allocated 6655333
pages resident  5661034
pages swapped   947522
Swap performance: 0 attempts     0 successes

where
-m is “information about active shared memory segments”
-u is “Show status summary”

You would need PAGE Memory

getconf PAGESIZE
4096

To provide us with the information in MB

echo "$((947522*4096/1024/1024)) MB"
3701 MB

 

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Cultural Data Sculpting

SPEAKER: Sarah Kenderdine | Digital Museology, Digital Humanities Institute |
Lead: Laboratory for Experimental Museology (eM+) | Director: ArtLab | EPFL Lausanne Switzerland

TITLE: Cultural data sculpting

DATE&TIME: Thursday, June 11, 2020 at 4:00 PM CEST

ABSTRACT:
In 1889 the curator G. B. Goode of the Smithsonian Institute delivered an anticipatory lecture entitled ‘The Future of the Museum’ in which he said this future museum would stand side by side with the library and the laboratory.’
Convergence in collecting organisations propelled by the liquidity of digital data now sees them reconciled as information providers in a networked world.
The media theorist Lev Manovich described this world-order as “database logic,” whereby users transform the physical assets of cultural organisations into digital assets to be—uploaded, downloaded, visualized, shared, users who treat institutions not as storehouses of physical objects, but rather as datasets to be manipulated. This presentation explores how such a mechanistic description can replaced by ways in which computation has become ‘experiential, spatial and materialized; embedded and embodied’. It was at the birth of the Information Age in the 1950s that the prominent designer Gyorgy Kepes of MIT said “information abundance” should be a “landscapes of the senses” that organizes both perception and practice. “This ‘felt order’ he said should be “a source of beauty, data transformed from its measured quantities and recreated as sensed forms exhibiting properties of harmony, rhythm and proportion.”

Archives call for the creation of new prosthetic architectures for the production and sharing of archival resources. At the intersection of immersive visualisation technologies, visual analytics, aesthetics and cultural (big) data, this presentation explores diverse digital cultural heritage experiences of diverse archives from scientific, artistic and humanistic perspectives.
Exploiting a series of experimental and embodied platforms, the discussion argues for a reformulation of engagement with digital archives at the intersection of the tangible and intangible and as a convergence across domains. The performative interfaces and repertoires described demonstrate opportunities to reformulate narrative in a digital context and they ways they support personal affective engagement with cultural memory.

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Addressing The Challenges In Higher ED and Research

Date: Wednesday, June 17, 2020
Time: 11:00am – 12:00am SGT
Duration: 1 hour

Universities are undergoing an unprecedented challenge to provide staff to work from home, remote teaching and learning , and still provide high value learning to students and cutting edge tools and services to faculty and researchers. While remote learning is not a new phenomenon, providing quality service at scale is now a requirement, along with a new set of challenges that span user experience, mobility, effective management of a distributed deployment.

Solutions that enable remote learning and research, such as NVIDIA virtual GPU (vGPU) technology, enable you to meet these new requirements across various workloads with cost-effective solutions for existing on-premise infrastructure assets and in the cloud.

By attending this webinar, you’ll learn:
How NVIDIA vGPU technology solutions enable remote work and learning
How vGPU solutions are helping universities, across both education and research
How to get started with vGPU and vComputeServer to accelerate VDI and computational workloads in your institution

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ISC High Performance 2020 Digital (Free Registration)

Welcome to ISC 2020 Digital, the inaugural online event that focuses on bringing the most critical developments and trends in high performance computing, machine learning and data analytics for the benefit of the global HPC community.

As the largest online HPC event this year, we anticipate registration numbers to match our live Frankfurt event, which is 3,700 registrations.

The event takes place over four days, from Monday, June 22 – Thursday, June 25, and is free of registration fees. All talks are exclusively available for registered participants for 14 days.

https://www.isc-hpc.com/