wiki.snu.edu.in - User contributions [en]

Vasp5.4

2025-07-30T07:02:48Z

Snuadmin:

[[File:275px-vasp logo.1716182944939.png|left|frameless]]

'''The Vienna Ab initio Simulation Package (VASP)''' is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. VASP computes an approximate solution to the many-body Schrödinger equation, either within density functional theory (DFT), solving the Kohn-Sham equations, or within the Hartree-Fock (HF) approximation, solving the Roothaan equations. Hybrid functionals that mix the Hartree-Fock approach with density functional theory are implemented as well. Furthermore, Green's functions methods (GW quasiparticles, and ACFDT-RPA) and many-body perturbation theory (2nd-order Møller-Plesset) are available in VASP. In VASP, central quantities, like the one-electron orbitals, the electronic charge density, and the local potential are expressed in plane wave basis sets. The interactions between the electrons and ions are described using norm-conserving or ultrasoft pseudopotentials, or the projector-augmented-wave method.

 To determine the electronic groundstate, VASP makes use of efficient iterative matrix diagonalisation techniques, like the residual minimisation method with direct inversion of the iterative subspace (RMM-DIIS) or blocked Davidson algorithms. These are coupled to highly efficient Broyden and Pulay density mixing schemes to speed up the self-consistency cycle.

'''Introduction''' VASP is a complex package for performing ab-initio quantum-mechanical molecular dynamics (MD) simulations using pseudopotentials or the projector-augmented wave method and a plane wave basis set. The approach implemented in VASP is based on the (finite-temperature)local-density approximation with the free energy as variational quantity andan exact evaluation of the instantaneous electronic ground state at each MD time step. VASP uses efficient matrix diagonalisation schemesand an efficient Pulay/Broyden charge density mixing.These techniques avoid all problems possibly occurring in the original Car-Parrinello method,which is based on the simultaneous integration of electronic and ionicequations of motion.The interaction between ions and electrons is described by ultra-softVanderbilt pseudopotentials (US-PP) or by the projector-augmentedwave (PAW) method.US-PP (and the PAW method) allow for a considerablereduction of the number of plane-waves per atom fortransition metals and first row elements.Forces and the full stress tensor can be calculated with VASP and used to relaxatoms into their instantaneous ground-state. Vasp Manual

[[Vasp Manual|File:Vasp Manual.pdf]]

'''Environment Variables required for running VASP on Magus.'''

'''Job Submission script'''

{| class=" wikitable" style="height: 56px;" width="1066"
|-
||
Example can be copied from /data/jobscript/VASP

|}
'''Explanation is given below in braces.'''

{| class=" wikitable" style="height: 546px;" width="1039"
|-
||
#!/bin/bash

SBATCH --partition=medium # include the appropriate partition, node, ntasks, ntasks-pernode for the respective SLURM key

SBATCH --ntasks=128 #SBATCH --job-name=VASP ##SBATCH --mail-user= ##SBATCH --mail-type=all #SBATCH --output vasp.%J.out #SBATCH --error vasp.%J.err 

###Inputs###

<nowiki>###</nowiki> modify the appropriate version of the executable

export exec_name=/data/apps/VASP5.4/IntelMPI/5.4.4/bin/vasp_std

keep the input file on the local directory where this job is launched

ulimit -s unlimited module purge module load compiler/2022.0.2 mkl/2022.0.2 mpi/2021.2.0

export I_MPI_FABRICS=shm:ofi export UCX_TLS=sm,ud export UCX_NET_DEVICES=mlx5_0:1

 export FI_PROVIDER=mlx export UCX_UNIFIED_MODE=y export UCX_USE_MT_MUTEX=y

export OMP_NUM_THREADS=1

<nowiki>#</nowiki>Application Execution###

{ time mpiexec.hydra -np $SLURM_NPROCS ${exec_name}; } > vasp_${SLURM_JOB_ID}.std.out 2>&1 

|}

Vasp5.4

2025-07-30T06:54:53Z

Snuadmin:

[[File:275px-vasp logo.1716182944939.png|left|frameless]]

'''The Vienna Ab initio Simulation Package (VASP)''' is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. VASP computes an approximate solution to the many-body Schrödinger equation, either within density functional theory (DFT), solving the Kohn-Sham equations, or within the Hartree-Fock (HF) approximation, solving the Roothaan equations. Hybrid functionals that mix the Hartree-Fock approach with density functional theory are implemented as well. Furthermore, Green's functions methods (GW quasiparticles, and ACFDT-RPA) and many-body perturbation theory (2nd-order Møller-Plesset) are available in VASP. In VASP, central quantities, like the one-electron orbitals, the electronic charge density, and the local potential are expressed in plane wave basis sets. The interactions between the electrons and ions are described using norm-conserving or ultrasoft pseudopotentials, or the projector-augmented-wave method.

 To determine the electronic groundstate, VASP makes use of efficient iterative matrix diagonalisation techniques, like the residual minimisation method with direct inversion of the iterative subspace (RMM-DIIS) or blocked Davidson algorithms. These are coupled to highly efficient Broyden and Pulay density mixing schemes to speed up the self-consistency cycle.

'''Introduction''' VASP is a complex package for performing ab-initio quantum-mechanical molecular dynamics (MD) simulations using pseudopotentials or the projector-augmented wave method and a plane wave basis set. The approach implemented in VASP is based on the (finite-temperature)local-density approximation with the free energy as variational quantity andan exact evaluation of the instantaneous electronic ground state at each MD time step. VASP uses efficient matrix diagonalisation schemesand an efficient Pulay/Broyden charge density mixing.These techniques avoid all problems possibly occurring in the original Car-Parrinello method,which is based on the simultaneous integration of electronic and ionicequations of motion.The interaction between ions and electrons is described by ultra-softVanderbilt pseudopotentials (US-PP) or by the projector-augmentedwave (PAW) method.US-PP (and the PAW method) allow for a considerablereduction of the number of plane-waves per atom fortransition metals and first row elements.Forces and the full stress tensor can be calculated with VASP and used to relaxatoms into their instantaneous ground-state. Vasp Manual

[[Vasp Manual|File:Vasp Manual.pdf]]

'''Environment Variables required for running VASP on Magus.'''

'''Job Submission script'''

{| class=" wikitable" style="height: 56px;" width="1066"
|-
||
Example can be copied from /data/jobscript/VASP

|}
'''Explanation is given below in braces.'''

{| class=" wikitable" style="height: 546px;" width="1039"
|-
||
#!/bin/bash

SBATCH --partition=medium # include the appropriate partition, node, ntasks, ntasks-pernode for the respective SLURM key

SBATCH --ntasks=128 #SBATCH --job-name=VASP ##SBATCH --mail-user= ##SBATCH --mail-type=all #SBATCH --output vasp.%J.out #SBATCH --error vasp.%J.err Inputs###

modify the appropriate version of the executableexport exec_name=/data/apps/VASP5.4/IntelMPI/5.4.4/bin/vasp_std

keep the input file on the local directory where this job is launched

ulimit -s unlimited module purge module load compiler/2022.0.2 mkl/2022.0.2 mpi/2021.2.0

export I_MPI_FABRICS=shm:ofi export UCX_TLS=sm,ud export UCX_NET_DEVICES=mlx5_0:1

 export FI_PROVIDER=mlx export UCX_UNIFIED_MODE=y export UCX_USE_MT_MUTEX=y

export OMP_NUM_THREADS=1 

|}

Magus02

2025-07-30T06:28:32Z

Snuadmin:

====What is HPC?====
<div style="font-size: 0.875em;">High performance computing (HPC) is the ability to process data and perform complex calculations at high speeds. To put it into perspective, a laptop or desktop with a 3 GHz processor can perform around 3 billion calculations per second. While that is much faster than any human can achieve, it pales in comparison to HPC solutions that can perform quadrillions of calculations per second.</div>
HPC is specifically needed for these reasons:

* It paves the way for new innovations in science, technology, business and academia.
* It improves processing speeds, which can be critical for many kinds of computing operations, applications and workloads.
* It helps lay the foundation for a reliable, fast IT infrastructure that can store, process and analyze massive amounts of data for various applications.

'''Specification:'''

* Total Cores = 8064 (AMD)
* 238 Tflops
* 57 Compute Nodes
* 2 Login Nodes
* 2 Master Nodes
* 12 High memory nodes with local SSD
* Better performance of applications, which require high performance storage but do not scale well across nodes. E.g. Gaussian.

'''Memory'''

* 4 GB Per core for Compute Nodes, with a total memory = 29,184 GB
* 16 GB Per core for High Memory Nodes, with total memory = 12,288 GB

===='''Compute Specification:'''====
{| class=" wikitable" style="height: 49px;" width="1084"
|-
| width="115"|'''COMPUTE NODES'''
| width="162"|''' PROCESSOR'''
| width="86"|''' RAM'''
| width="79"|''' CORE'''
| width="86"|''' GPU '''
| width="91"|''' NO OF NODES'''
| width="81"|'''TOTAL RAM'''
| width="89"|'''TOTAL CORES'''
|}
{| class=" wikitable" style="height: 118px;" width="912"
|-
||Compute Node
||AMD EPYC 7763
||512 GB
||128
||-
||57
||29184GB
||7296
|-
||High Memory Node
||AMD EPYC 7543
||1024GB
||64
||-
||12
||12228GB
||768
|-
||GPU
||INTEL XEON PLATINUM 8358
||512GB
||64
||Tesla A100*4
||2
||1024GB
||128
|-
||Total
||
||
||
||
||
||42436
||8192
|-
||Storage
||750TB PFS
||
||
||
||
||
||
|}

===='''How to connect to Snu HPC ?'''====
 Enumerated here are the various types.

* '''SSH : '''Host magus02.snu.edu.in ( default port 22 )
* '''From Linux Machine : '''$ssh user@magus02.snu.edu.in
* '''From Windows Machine using ''''''putty.'''

===='''How to Reset Password on Magus02 ?'''====
 Step1. Login to magus02 account.

[[File:magus 02 pic 1.1716181911641.png|frameless|578x578px]]

Step2: Use Passwd Command.

[[File:magus 03 pic.1716182070345.png|frameless|558x558px]] 

==='''How to Connect to Magus from outside SNU Network ?'''===
To gain access to MEGUS from outside the SNU network, a VPN connection is mandatory. To acquire VPN access, kindly click on the [https://forms.office.com/Pages/ResponsePage.aspx?id=12YS_ftig0aFL0FyYUAqLN3tPd66H1xCnswYz1fby35UMkhBR0lMSlJLUlZGT0wwTzJTOUtLNEpZVy4u VPN Request Form] or utilize the option of accessing it by scanning the barcode provided below.

===='''How to Transfers data using WinSCP Windows (Client).'''====
Step1 : Open the WinSCP and fill all the details, After that click on the Login Button.

[[File:magus 04 pic.1716182129572.png|frameless|589x589px]]

Step 2 : Click Yes on Warning tab.

Step 3: Connected, Now you can transfer the data using Right click of key Panel.

[[File:magus o5 pic.1716182172254.png|left|frameless|530x530px]]

'''Applications on Megus'''

[[Vasp5.4|Vasp]], [[02HPC Quantum Espresso Magus02|Quantum espresso]], [[Gaussian16|Gaussian]], Siesta, [[Gromacs]], OpenFOAM.

==='''Queue Structure on Magus02.'''===
{| class="wikitable" style="background-color: #fafafa; height: 418px;" border="1" width="1523"
|-
| style="background-color:#bababa;" class="" width="60" |S.No.
| style="background-color:#bababa;" class="" width="115" |Processor Architecture
| style="background-color:#bababa;" class="" width="81" |Priority
| style="background-color:#bababa;" class="" width="147" |Queue Name
| style="background-color:#bababa;" class="" width="110" |Min no of Cores Required to submit job
| style="background-color:#bababa;" class="" width="99" |Max no of cores allowed per job
| style="background-color:#bababa;" class="" width="68" |No of nodes in the queue
| style="background-color:#bababa;" class="" width="92" |Wall Time
| style="background-color:#bababa;" class="" width="111" |MAX Cores User can Use in the Queue
| style="background-color:#bababa;" class="" width="111" |Max No. of Pending Jobs Per user
| style="background-color:#bababa;" class="" width="111" |Max No. of Running Jobs Per user
|-
| width="60" |'''1'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Medium

| width="110" |
32

| width="99" |
128

| width="68" |
17

| width="92" |
1 week

| width="111" |
512

| width="111" | 2
| width="111" | 2
|-
| width="60" |'''2'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
Small

| width="110" |
8

| width="99" |
32

| width="68" |
16

| width="92" |
1 Month

| width="111" |
128

| width="111" |2
| width="111" |4
|-
| width="60" |'''3'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
High_mem

| width="110" |
32

| width="99" |
256

| width="68" |
12

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''4'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Large

| width="110" |
64

| width="99" |
256

| width="68" |
24

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''5'''

| width="115" |
Intel Xeon Platinum 8358

| width="81" |
50

| width="147" |
GPU

| width="110" |
16

| width="99" |
16

| width="68" |
2

| width="92" |
1 week

| width="111" |
32

| width="111" |
| width="111" |2
|-
| width="60" |'''6'''

| width="115" |
AMD EPYC 7763

| width="81" |
Low

| width="147" |
Long

| width="110" |
32

| width="99" |
1024

| width="68" |
All lm nodes

| width="92" |
1 Month

| width="111" |
1024

| width="111" |
| width="111" |8
|}
====='''[[Slurm Command Reference:]]'''=====
'''[[index.php?title=Media:Linux Command Reference.pdf|Linux_Command_Reference.pdf]]'''

Main Page

2025-07-30T06:26:47Z

Snuadmin:

{| class="greyscale" style="width: 100%;" width="1334" data-mce-style="height: 26px ;background-color:#005197;"
| style="background-color:;font-family:Verdana, Arial, Helvetica, sans-serif;font-size:11px;border:1px dashed rgb(187, 187, 187);" class="col-white-bg" |
=== Information Technology Resource Centre : ===
'''<big>Configuration of Wi-Fi</big>''' [[File:down13.jpg|frameless|25x25px]]

* [[Configuration of Wifi for Students|<big>Configuration of Wifi for Students</big>]]

*[[Configuration of Wifi System for Guest|<big>Configuration of Wifi System for Guest</big>]]
*[[How to Approve Guest Wifi Request|<big>How to Approve Guest Wifi Request</big>]]
*[[How to connect Eduroam WIfi|<big>How to connect Eduroam WIfi</big>]] 

'''<big>Net ID Setup</big>''' [[File:download (5).png|frameless|21x21px]]

*[[Setting up your NetID Password|<big>Setting up your NetID Password</big>]] : <big>(First Time Setup, Forget Password, Change Password)</big> 

'''<big>Email ID Setup</big>''' [[File:download (8).1716959100424.jpg|frameless|25x25px]]

* <big>[[Setting up your University Email ID Password.]]</big>

'''<big>Microsoft Teams Setup</big>''' [[File:RE1Mu3b.1747285649387.png|link=https://wiki.snu.edu.in/File:RE1Mu3b.1747285649387.png|frameless|101x101px]]

* <big>[[Microsoft Teams Installation and Guide]]</big>
* <big>[[Manage attendee audio permissions]]</big>
* <big>[[Schedule Microsoft Teams meeting from Microsoft Outlook]]</big>
* <big>[[How to Join Microsoft Teams meeting from web client]]</big>
* <big>[[Create a Class in MS Teams]]</big>
* <big>[[Change Meeting Permissions for Attendees through MS Teams]]</big>

'''<big>Configuration of VPN</big>''' [[File:download (6).1716183181171.png|frameless|27x27px]]
*[[How to connect VPN-IVANTI (Students)|<big>How to connect VPN-IVANTI (Students)</big>]]

'''<big>Get Acquainted with HPC</big>''' [[File:images (2).png|frameless|42x42px]]
*<big>[[HPC]]</big>

*<big>[[Magus02]]</big>
*<big>[[Open FOAM]]</big>
*<big>[[Nanoelectronics Computation Laboratory - NCL]]</big> 

'''<big>Academia Installation</big>''' [[File:images.png|frameless|21x21px]]

*<big>[[Academia NativeApps Client Installation]]</big> 

<big>'''DIGII Campus Application'''</big> [[File:download5678.png|frameless|38x38px]]
*<big>[[How to create Request (For Night and Day Out Pass)]]</big>
*<big>[[How to download the Digii Campus Application]]</big>
*<big>[[How to login Collpoll Application- Parent's|How to login DigiiCampus Application- Parent's]]</big>
*<big>[[How to login in Digii (Formely Coll Poll)|How to login in DigiiCampus Application]] - '''For Students'''</big>
*[[Parental Approval Process|<big>Parental Approval Process</big>]] - <big>'''For Parent's'''</big> 

<big>'''Obtaining a Free Windows 11 Education License for Students'''</big> [[File:win11.1753764385890.jpg|frameless|38x38px]]
*<big>[[Active students at University are eligible to obtain a free Windows 11 Education license]]</big>

====='''<big>[[Get Informed: Frequently Asked Questions"]]</big>'''=====
|-
|
|}

Gromacs

2025-07-30T06:06:02Z

Snuadmin: Created page with "thumb <span lang="EN-IN" style="font-family:"Aptos",sans-serif;mso-ascii-theme-font:minor-latin; mso-fareast-font-family:Ap..."

[[File:Gromacs.1753854840524.png|center|thumb]]
<span lang="EN-IN" style="font-family:"Aptos",sans-serif;mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:Aptos;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
minor-latin;mso-bidi-font-family:Mangal;mso-bidi-theme-font:minor-bidi;
color:black;mso-color-alt:windowtext;mso-fareast-language:EN-US;mso-bidi-language:
AR-SA">GROMACS is a '''versatile package to perform molecular dynamics''', i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles and is a '''community-driven project'''. Contributions are welcome in many forms, including improvements to documentation, patches to fix bugs, advice on the forums, bug reports that let us reproduce the issue, and new functionality. See [https://www.gromacs.org/development.html <span style="font-family:"Aptos",sans-serif;
mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Aptos;mso-fareast-theme-font:
minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Mangal;
mso-bidi-theme-font:minor-bidi;color:black;mso-color-alt:windowtext;mso-fareast-language:
EN-US;mso-bidi-language:AR-SA;text-decoration:none;text-underline:none">Development] <span lang="EN-IN" style="font-family:"Aptos",sans-serif;mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:Aptos;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
minor-latin;mso-bidi-font-family:Mangal;mso-bidi-theme-font:minor-bidi;
color:black;mso-color-alt:windowtext;mso-fareast-language:EN-US;mso-bidi-language:
AR-SA">page and [https://www.gromacs.org/report_issue.html <span style="font-family:"Aptos",sans-serif;mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:Aptos;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
minor-latin;mso-bidi-font-family:Mangal;mso-bidi-theme-font:minor-bidi;
color:black;mso-color-alt:windowtext;mso-fareast-language:EN-US;mso-bidi-language:
AR-SA;text-decoration:none;text-underline:none">Report an issue]<span lang="EN-IN" style="font-family:"Aptos",sans-serif;mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:Aptos;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
minor-latin;mso-bidi-font-family:Mangal;mso-bidi-theme-font:minor-bidi;
color:black;mso-color-alt:windowtext;mso-fareast-language:EN-US;mso-bidi-language:
AR-SA">.

<span lang="EN-IN" style="font-family:"Aptos",sans-serif;mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:Aptos;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
minor-latin;mso-bidi-font-family:Mangal;mso-bidi-theme-font:minor-bidi;
color:black;mso-color-alt:windowtext;mso-fareast-language:EN-US;mso-bidi-language:
AR-SA">It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers and fluid dynamics.

<span lang="EN-IN" style="font-family:"Aptos",sans-serif;mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:Aptos;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
minor-latin;mso-bidi-font-family:Mangal;mso-bidi-theme-font:minor-bidi;
color:black;mso-color-alt:windowtext;mso-fareast-language:EN-US;mso-bidi-language:
AR-SA">GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, (check the online reference or manual for details), but there are also quite a few features that make it stand out from the competition:

•GROMACS provides extremely high performance compared to all other programs. A lot of algorithmic optimizations have been introduced in the code; we have for instance extracted the calculation of the virial from the innermost loops over pairwise interactions, and we use our own software routines to calculate the inverse square root. The compute kernels are written using SIMD intrinsics for CPUs and CUDA, OpenCL, and SYCL for GPUs. Thus the full potential of all modern CPU and GPUs can be exploited.

•GROMACS can make simultaneous use of both CPU and GPU available in a system. There are options to statically and dynamically balance the load between the different resources.

•GROMACS is user-friendly, with topologies and parameter files written in clear text format. There is a lot of consistency checking, and clear error messages are issued when something is wrong. Since a C-preprocessor is used, you can have conditional parts in your topologies and include other files. You can even compress most files and GROMACS will automatically pipe them through gzip upon reading.

•There is no scripting required - all programs use a simple interface with command line options for input and output files. You can always get help on the options by using the -h option, or use the extensive manuals provided free of charge in electronic or paper format. There is ongoing work on a Python API which enables scripting of simulation setup, running and analysis.

•Both run input files and trajectories are independent of hardware endian-ness, and can thus be read by any version GROMACS, even if it was compiled using a different floating-point precision.

•GROMACS can write coordinates using lossy compression, which provides a very compact way of storing trajectory data. The accuracy can be selected by the user.

•GROMACS comes with a large selection of flexible tools for trajectory analysis and the output formats are also supported by all major analysis and visualisation packages.

•GROMACS can be run in parallel, using either the standard MPI communication protocol, or via our own “Thread MPI” library for single-node workstations.

•GROMACS contains several state-of-the-art algorithms that make it possible to extend the time steps is simulations significantly, and thereby further enhance performance without sacrificing accuracy or detail.

•The package includes a fully automated topology builder for proteins, even multimeric structures. Building blocks are available for the 20 standard aminoacid residues as well as some modified ones, the 4 nucleotide and 4 deoxinucleotide resides, several sugars and lipids, and some special groups like hemes and several small molecules.

•GROMACS is extensible through with modules through the so-called MDModules interface. This currently provides a way for added extra forces and it continuously being extended with new functionality.

•GROMACS is a proper name. It is not an acronym for anything.

'''Binary Location:'''

/data/apps/Gromacs/IntelMPI/2020.4/bin/gmx_mpi_d
'''Binary Location:'''

'''Version:''' 2020.4

'''Job Script:'''

#!/bin/bash

#SBATCH --partition=medium # include the appropriate partition, node, ntasks, ntasks-pernode for the respective SLURM key

#SBATCH --ntasks=128

#SBATCH --cpus-per-task=1

#SBATCH --job-name=Gromacs

#SBATCH --output gromacs.%J.out

#SBATCH --error gromacs.%J.err

###Inputs###

### modify the appropriate version of the executable (e.g. single precision / double precision ) along with the complete path

export exec_name=/data/apps/Gromacs/IntelMPI/2020.4/bin/gmx_mpi_d

## modify the input file along with the complete path

export input_name=/data/home/lenovo/BMT/job/gromacs/inputs/benchPEP.tpr

ulimit -s unlimited

module purge

module load compiler/2022.0.2 mkl/2022.0.2 mpi/2021.2.0

export I_MPI_FABRICS=shm:ofi

export UCX_TLS=sm,ud

export UCX_NET_DEVICES=mlx5_0:1

export FI_PROVIDER=verbs

export OMP_NUM_THREADS=1

#export I_MPI_PIN_ORDER=bunch

#export I_MPI_PIN_DOMAIN=core

##Application Execution###

time mpiexec.hydra -np $SLURM_NPROCS ${exec_name} mdrun -notunepme -dlb yes -v -resethway -noconfout -s ${input_name} -cpi >> gromacs_${SLURM_JOB_ID}.md.log

File:Gromacs.1753854789629.png

2025-07-30T05:59:10Z

Snuadmin:

[[File:Gromacs.1753854840524.png|center|thumb]]

File:Gromacs.1753854840524.png

2025-07-30T05:53:44Z

Snuadmin:

File:Gromacs.1753854789629.png

2025-07-30T05:52:53Z

Snuadmin:

Magus02

2025-07-30T05:52:09Z

Snuadmin:

====What is HPC?====
<div style="font-size: 0.875em;">High performance computing (HPC) is the ability to process data and perform complex calculations at high speeds. To put it into perspective, a laptop or desktop with a 3 GHz processor can perform around 3 billion calculations per second. While that is much faster than any human can achieve, it pales in comparison to HPC solutions that can perform quadrillions of calculations per second.</div>
HPC is specifically needed for these reasons:

* It paves the way for new innovations in science, technology, business and academia.
* It improves processing speeds, which can be critical for many kinds of computing operations, applications and workloads.
* It helps lay the foundation for a reliable, fast IT infrastructure that can store, process and analyze massive amounts of data for various applications.

'''Specification:'''

* Total Cores = 8064 (AMD)
* 238 Tflops
* 57 Compute Nodes
* 2 Login Nodes
* 2 Master Nodes
* 12 High memory nodes with local SSD
* Better performance of applications, which require high performance storage but do not scale well across nodes. E.g. Gaussian.

'''Memory'''

* 4 GB Per core for Compute Nodes, with a total memory = 29,184 GB
* 16 GB Per core for High Memory Nodes, with total memory = 12,288 GB

===='''Compute Specification:'''====
{| class=" wikitable" style="height: 49px;" width="1084"
|-
| width="115"|'''COMPUTE NODES'''
| width="162"|''' PROCESSOR'''
| width="86"|''' RAM'''
| width="79"|''' CORE'''
| width="86"|''' GPU '''
| width="91"|''' NO OF NODES'''
| width="81"|'''TOTAL RAM'''
| width="89"|'''TOTAL CORES'''
|}
{| class=" wikitable" style="height: 118px;" width="912"
|-
||Compute Node
||AMD EPYC 7763
||512 GB
||128
||-
||57
||29184GB
||7296
|-
||High Memory Node
||AMD EPYC 7543
||1024GB
||64
||-
||12
||12228GB
||768
|-
||GPU
||INTEL XEON PLATINUM 8358
||512GB
||64
||Tesla A100*4
||2
||1024GB
||128
|-
||Total
||
||
||
||
||
||42436
||8192
|-
||Storage
||750TB PFS
||
||
||
||
||
||
|}

===='''How to connect to Snu HPC ?'''====
 Enumerated here are the various types.

* '''SSH : '''Host magus02.snu.edu.in ( default port 22 )
* '''From Linux Machine : '''$ssh user@magus02.snu.edu.in
* '''From Windows Machine using ''''''putty.'''

===='''How to Reset Password on Magus02 ?'''====
 Step1. Login to magus02 account.

[[File:magus 02 pic 1.1716181911641.png|frameless|578x578px]]

Step2: Use Passwd Command.

[[File:magus 03 pic.1716182070345.png|frameless|558x558px]] 

==='''How to Connect to Magus from outside SNU Network ?'''===
To gain access to MEGUS from outside the SNU network, a VPN connection is mandatory. To acquire VPN access, kindly click on the [https://forms.office.com/Pages/ResponsePage.aspx?id=12YS_ftig0aFL0FyYUAqLN3tPd66H1xCnswYz1fby35UMkhBR0lMSlJLUlZGT0wwTzJTOUtLNEpZVy4u VPN Request Form] or utilize the option of accessing it by scanning the barcode provided below.

===='''How to Transfers data using WinSCP Windows (Client).'''====
Step1 : Open the WinSCP and fill all the details, After that click on the Login Button.

[[File:magus 04 pic.1716182129572.png|frameless|589x589px]]

Step 2 : Click Yes on Warning tab.

Step 3: Connected, Now you can transfer the data using Right click of key Panel.

[[File:magus o5 pic.1716182172254.png|left|frameless|530x530px]]

'''Applications on Megus'''

[[Vasp5.4|Vasp]], [[02HPC Quantum Espresso Magus02|Quantum espresso]], BigDFT, [[Gaussian16|Gaussian]], Siesta, [[Gromacs]], OpenFOAM.

==='''Queue Structure on Magus02.'''===
{| class="wikitable" style="background-color: #fafafa; height: 418px;" border="1" width="1523"
|-
| style="background-color:#bababa;" class="" width="60" |S.No.
| style="background-color:#bababa;" class="" width="115" |Processor Architecture
| style="background-color:#bababa;" class="" width="81" |Priority
| style="background-color:#bababa;" class="" width="147" |Queue Name
| style="background-color:#bababa;" class="" width="110" |Min no of Cores Required to submit job
| style="background-color:#bababa;" class="" width="99" |Max no of cores allowed per job
| style="background-color:#bababa;" class="" width="68" |No of nodes in the queue
| style="background-color:#bababa;" class="" width="92" |Wall Time
| style="background-color:#bababa;" class="" width="111" |MAX Cores User can Use in the Queue
| style="background-color:#bababa;" class="" width="111" |Max No. of Pending Jobs Per user
| style="background-color:#bababa;" class="" width="111" |Max No. of Running Jobs Per user
|-
| width="60" |'''1'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Medium

| width="110" |
32

| width="99" |
128

| width="68" |
17

| width="92" |
1 week

| width="111" |
512

| width="111" | 2
| width="111" | 2
|-
| width="60" |'''2'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
Small

| width="110" |
8

| width="99" |
32

| width="68" |
16

| width="92" |
1 Month

| width="111" |
128

| width="111" |2
| width="111" |4
|-
| width="60" |'''3'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
High_mem

| width="110" |
32

| width="99" |
256

| width="68" |
12

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''4'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Large

| width="110" |
64

| width="99" |
256

| width="68" |
24

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''5'''

| width="115" |
Intel Xeon Platinum 8358

| width="81" |
50

| width="147" |
GPU

| width="110" |
16

| width="99" |
16

| width="68" |
2

| width="92" |
1 week

| width="111" |
32

| width="111" |
| width="111" |2
|-
| width="60" |'''6'''

| width="115" |
AMD EPYC 7763

| width="81" |
Low

| width="147" |
Long

| width="110" |
32

| width="99" |
1024

| width="68" |
All lm nodes

| width="92" |
1 Month

| width="111" |
1024

| width="111" |
| width="111" |8
|}
====='''[[Slurm Command Reference:]]'''=====
'''[[index.php?title=Media:Linux Command Reference.pdf|Linux_Command_Reference.pdf]]'''

Magus02

2025-07-30T05:47:02Z

Snuadmin:

====What is HPC?====
<div style="font-size: 0.875em;">High performance computing (HPC) is the ability to process data and perform complex calculations at high speeds. To put it into perspective, a laptop or desktop with a 3 GHz processor can perform around 3 billion calculations per second. While that is much faster than any human can achieve, it pales in comparison to HPC solutions that can perform quadrillions of calculations per second.</div>
HPC is specifically needed for these reasons:

* It paves the way for new innovations in science, technology, business and academia.
* It improves processing speeds, which can be critical for many kinds of computing operations, applications and workloads.
* It helps lay the foundation for a reliable, fast IT infrastructure that can store, process and analyze massive amounts of data for various applications.

'''Specification:'''

* Total Cores = 8064 (AMD)
* 238 Tflops
* 57 Compute Nodes
* 2 Login Nodes
* 2 Master Nodes
* 12 High memory nodes with local SSD
* Better performance of applications, which require high performance storage but do not scale well across nodes. E.g. Gaussian.

'''Memory'''

* 4 GB Per core for Compute Nodes, with a total memory = 29,184 GB
* 16 GB Per core for High Memory Nodes, with total memory = 12,288 GB

===='''Compute Specification:'''====
{| class=" wikitable" style="height: 49px;" width="1084"
|-
| width="115"|'''COMPUTE NODES'''
| width="162"|''' PROCESSOR'''
| width="86"|''' RAM'''
| width="79"|''' CORE'''
| width="86"|''' GPU '''
| width="91"|''' NO OF NODES'''
| width="81"|'''TOTAL RAM'''
| width="89"|'''TOTAL CORES'''
|}
{| class=" wikitable" style="height: 118px;" width="912"
|-
||Compute Node
||AMD EPYC 7763
||512 GB
||128
||-
||57
||29184GB
||7296
|-
||High Memory Node
||AMD EPYC 7543
||1024GB
||64
||-
||12
||12228GB
||768
|-
||GPU
||INTEL XEON PLATINUM 8358
||512GB
||64
||Tesla A100*4
||2
||1024GB
||128
|-
||Total
||
||
||
||
||
||42436
||8192
|-
||Storage
||750TB PFS
||
||
||
||
||
||
|}

===='''How to connect to Snu HPC ?'''====
 Enumerated here are the various types.

* '''SSH : '''Host magus02.snu.edu.in ( default port 22 )
* '''From Linux Machine : '''$ssh user@magus02.snu.edu.in
* '''From Windows Machine using ''''''putty.'''

===='''How to Reset Password on Magus02 ?'''====
 Step1. Login to magus02 account.

[[File:magus 02 pic 1.1716181911641.png|frameless|578x578px]]

Step2: Use Passwd Command.

[[File:magus 03 pic.1716182070345.png|frameless|558x558px]] 

==='''How to Connect to Magus from outside SNU Network ?'''===
To gain access to MEGUS from outside the SNU network, a VPN connection is mandatory. To acquire VPN access, kindly click on the [https://forms.office.com/Pages/ResponsePage.aspx?id=12YS_ftig0aFL0FyYUAqLN3tPd66H1xCnswYz1fby35UMkhBR0lMSlJLUlZGT0wwTzJTOUtLNEpZVy4u VPN Request Form] or utilize the option of accessing it by scanning the barcode provided below.

===='''How to Transfers data using WinSCP Windows (Client).'''====
Step1 : Open the WinSCP and fill all the details, After that click on the Login Button.

[[File:magus 04 pic.1716182129572.png|frameless|589x589px]]

Step 2 : Click Yes on Warning tab.

Step 3: Connected, Now you can transfer the data using Right click of key Panel.

[[File:magus o5 pic.1716182172254.png|left|frameless|530x530px]]

'''Applications on Megus'''

[[Vasp5.4|Vasp]], [[02HPC Quantum Espresso Magus02|Quantum espresso]], BigDFT, [[Gaussian16|Gaussian]], Siesta, Gromacs, OpenFOAM.

==='''Queue Structure on Magus02.'''===
{| class="wikitable" style="background-color: #fafafa; height: 418px;" border="1" width="1523"
|-
| style="background-color:#bababa;" class="" width="60" |S.No.
| style="background-color:#bababa;" class="" width="115" |Processor Architecture
| style="background-color:#bababa;" class="" width="81" |Priority
| style="background-color:#bababa;" class="" width="147" |Queue Name
| style="background-color:#bababa;" class="" width="110" |Min no of Cores Required to submit job
| style="background-color:#bababa;" class="" width="99" |Max no of cores allowed per job
| style="background-color:#bababa;" class="" width="68" |No of nodes in the queue
| style="background-color:#bababa;" class="" width="92" |Wall Time
| style="background-color:#bababa;" class="" width="111" |MAX Cores User can Use in the Queue
| style="background-color:#bababa;" class="" width="111" |Max No. of Pending Jobs Per user
| style="background-color:#bababa;" class="" width="111" |Max No. of Running Jobs Per user
|-
| width="60" |'''1'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Medium

| width="110" |
32

| width="99" |
128

| width="68" |
17

| width="92" |
1 week

| width="111" |
512

| width="111" | 2
| width="111" | 2
|-
| width="60" |'''2'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
Small

| width="110" |
8

| width="99" |
32

| width="68" |
16

| width="92" |
1 Month

| width="111" |
128

| width="111" |2
| width="111" |4
|-
| width="60" |'''3'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
High_mem

| width="110" |
32

| width="99" |
256

| width="68" |
12

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''4'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Large

| width="110" |
64

| width="99" |
256

| width="68" |
24

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''5'''

| width="115" |
Intel Xeon Platinum 8358

| width="81" |
50

| width="147" |
GPU

| width="110" |
16

| width="99" |
16

| width="68" |
2

| width="92" |
1 week

| width="111" |
32

| width="111" |
| width="111" |2
|-
| width="60" |'''6'''

| width="115" |
AMD EPYC 7763

| width="81" |
Low

| width="147" |
Long

| width="110" |
32

| width="99" |
1024

| width="68" |
All lm nodes

| width="92" |
1 Month

| width="111" |
1024

| width="111" |
| width="111" |8
|}
====='''[[Slurm Command Reference:]]'''=====
'''[[index.php?title=Media:Linux Command Reference.pdf|Linux_Command_Reference.pdf]]'''

Magus02

2025-07-30T05:45:14Z

Snuadmin:

====What is HPC?====
<div style="font-size: 0.875em;">High performance computing (HPC) is the ability to process data and perform complex calculations at high speeds. To put it into perspective, a laptop or desktop with a 3 GHz processor can perform around 3 billion calculations per second. While that is much faster than any human can achieve, it pales in comparison to HPC solutions that can perform quadrillions of calculations per second.</div>
HPC is specifically needed for these reasons:

* It paves the way for new innovations in science, technology, business and academia.
* It improves processing speeds, which can be critical for many kinds of computing operations, applications and workloads.
* It helps lay the foundation for a reliable, fast IT infrastructure that can store, process and analyze massive amounts of data for various applications.

'''Specification:'''

* Total Cores = 8064 (AMD)
* 238 Tflops
* 57 Compute Nodes
* 2 Login Nodes
* 2 Master Nodes
* 12 High memory nodes with local SSD
* Better performance of applications, which require high performance storage but do not scale well across nodes. E.g. Gaussian.

'''Memory'''

* 4 GB Per core for Compute Nodes, with a total memory = 29,184 GB
* 16 GB Per core for High Memory Nodes, with total memory = 12,288 GB

===='''Compute Specification:'''====
{| class=" wikitable" style="height: 49px;" width="1084"
|-
| width="115"|'''COMPUTE NODES'''
| width="162"|''' PROCESSOR'''
| width="86"|''' RAM'''
| width="79"|''' CORE'''
| width="86"|''' GPU '''
| width="91"|''' NO OF NODES'''
| width="81"|'''TOTAL RAM'''
| width="89"|'''TOTAL CORES'''
|}
{| class=" wikitable" style="height: 118px;" width="912"
|-
||Compute Node
||AMD EPYC 7763
||512 GB
||128
||-
||57
||29184GB
||7296
|-
||High Memory Node
||AMD EPYC 7543
||1024GB
||64
||-
||12
||12228GB
||768
|-
||GPU
||INTEL XEON PLATINUM 8358
||512GB
||64
||Tesla A100*4
||2
||1024GB
||128
|-
||Total
||
||
||
||
||
||42436
||8192
|-
||Storage
||750TB PFS
||
||
||
||
||
||
|}

===='''How to connect to Snu HPC ?'''====
 Enumerated here are the various types.

* '''SSH : '''Host magus02.snu.edu.in ( default port 22 )
* '''From Linux Machine : '''$ssh user@magus02.snu.edu.in
* '''From Windows Machine using ''''''putty.'''

===='''How to Reset Password on Magus02 ?'''====
 Step1. Login to magus02 account.

[[File:magus 02 pic 1.1716181911641.png|frameless|578x578px]]

Step2: Use Passwd Command.

[[File:magus 03 pic.1716182070345.png|frameless|558x558px]] 

==='''How to Connect to Magus from outside SNU Network ?'''===
To gain access to MEGUS from outside the SNU network, a VPN connection is mandatory. To acquire VPN access, kindly click on the [https://forms.office.com/Pages/ResponsePage.aspx?id=12YS_ftig0aFL0FyYUAqLN3tPd66H1xCnswYz1fby35UMkhBR0lMSlJLUlZGT0wwTzJTOUtLNEpZVy4u VPN Request Form] or utilize the option of accessing it by scanning the barcode provided below.

===='''How to Transfers data using WinSCP Windows (Client).'''====
Step1 : Open the WinSCP and fill all the details, After that click on the Login Button.

[[File:magus 04 pic.1716182129572.png|frameless|589x589px]]

Step 2 : Click Yes on Warning tab.

Step 3: Connected, Now you can transfer the data using Right click of key Panel.

[[File:magus o5 pic.1716182172254.png|left|frameless|530x530px]]

'''Applications on Megus'''

[[:File:Vasp5.4|Vasp]], [[02HPC Quantum Espresso Magus02|Quantum espresso]], BigDFT, [[Gaussian16|Gaussian]], Siesta, Gromacs, OpenFOAM.

==='''Queue Structure on Magus02.'''===
{| class="wikitable" style="background-color: #fafafa; height: 418px;" border="1" width="1523"
|-
| style="background-color:#bababa;" class="" width="60" |S.No.
| style="background-color:#bababa;" class="" width="115" |Processor Architecture
| style="background-color:#bababa;" class="" width="81" |Priority
| style="background-color:#bababa;" class="" width="147" |Queue Name
| style="background-color:#bababa;" class="" width="110" |Min no of Cores Required to submit job
| style="background-color:#bababa;" class="" width="99" |Max no of cores allowed per job
| style="background-color:#bababa;" class="" width="68" |No of nodes in the queue
| style="background-color:#bababa;" class="" width="92" |Wall Time
| style="background-color:#bababa;" class="" width="111" |MAX Cores User can Use in the Queue
| style="background-color:#bababa;" class="" width="111" |Max No. of Pending Jobs Per user
| style="background-color:#bababa;" class="" width="111" |Max No. of Running Jobs Per user
|-
| width="60" |'''1'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Medium

| width="110" |
32

| width="99" |
128

| width="68" |
17

| width="92" |
1 week

| width="111" |
512

| width="111" | 2
| width="111" | 2
|-
| width="60" |'''2'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
Small

| width="110" |
8

| width="99" |
32

| width="68" |
16

| width="92" |
1 Month

| width="111" |
128

| width="111" |2
| width="111" |4
|-
| width="60" |'''3'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
High_mem

| width="110" |
32

| width="99" |
256

| width="68" |
12

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''4'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Large

| width="110" |
64

| width="99" |
256

| width="68" |
24

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''5'''

| width="115" |
Intel Xeon Platinum 8358

| width="81" |
50

| width="147" |
GPU

| width="110" |
16

| width="99" |
16

| width="68" |
2

| width="92" |
1 week

| width="111" |
32

| width="111" |
| width="111" |2
|-
| width="60" |'''6'''

| width="115" |
AMD EPYC 7763

| width="81" |
Low

| width="147" |
Long

| width="110" |
32

| width="99" |
1024

| width="68" |
All lm nodes

| width="92" |
1 Month

| width="111" |
1024

| width="111" |
| width="111" |8
|}
====='''[[Slurm Command Reference:]]'''=====
'''[[index.php?title=Media:Linux Command Reference.pdf|Linux_Command_Reference.pdf]]'''

Magus02

2025-07-30T05:42:02Z

Snuadmin:

====What is HPC?====
<div style="font-size: 0.875em;">High performance computing (HPC) is the ability to process data and perform complex calculations at high speeds. To put it into perspective, a laptop or desktop with a 3 GHz processor can perform around 3 billion calculations per second. While that is much faster than any human can achieve, it pales in comparison to HPC solutions that can perform quadrillions of calculations per second.</div>
HPC is specifically needed for these reasons:

* It paves the way for new innovations in science, technology, business and academia.
* It improves processing speeds, which can be critical for many kinds of computing operations, applications and workloads.
* It helps lay the foundation for a reliable, fast IT infrastructure that can store, process and analyze massive amounts of data for various applications.

'''Specification:'''

* Total Cores = 8064 (AMD)
* 238 Tflops
* 57 Compute Nodes
* 2 Login Nodes
* 2 Master Nodes
* 12 High memory nodes with local SSD
* Better performance of applications, which require high performance storage but do not scale well across nodes. E.g. Gaussian.

'''Memory'''

* 4 GB Per core for Compute Nodes, with a total memory = 29,184 GB
* 16 GB Per core for High Memory Nodes, with total memory = 12,288 GB

===='''Compute Specification:'''====
{| class=" wikitable" style="height: 49px;" width="1084"
|-
| width="115"|'''COMPUTE NODES'''
| width="162"|''' PROCESSOR'''
| width="86"|''' RAM'''
| width="79"|''' CORE'''
| width="86"|''' GPU '''
| width="91"|''' NO OF NODES'''
| width="81"|'''TOTAL RAM'''
| width="89"|'''TOTAL CORES'''
|}
{| class=" wikitable" style="height: 118px;" width="912"
|-
||Compute Node
||AMD EPYC 7763
||512 GB
||128
||-
||57
||29184GB
||7296
|-
||High Memory Node
||AMD EPYC 7543
||1024GB
||64
||-
||12
||12228GB
||768
|-
||GPU
||INTEL XEON PLATINUM 8358
||512GB
||64
||Tesla A100*4
||2
||1024GB
||128
|-
||Total
||
||
||
||
||
||42436
||8192
|-
||Storage
||750TB PFS
||
||
||
||
||
||
|}

===='''How to connect to Snu HPC ?'''====
 Enumerated here are the various types.

* '''SSH : '''Host magus02.snu.edu.in ( default port 22 )
* '''From Linux Machine : '''$ssh user@magus02.snu.edu.in
* '''From Windows Machine using ''''''putty.'''

===='''How to Reset Password on Magus02 ?'''====
 Step1. Login to magus02 account.

[[File:magus 02 pic 1.1716181911641.png|frameless|578x578px]]

Step2: Use Passwd Command.

[[File:magus 03 pic.1716182070345.png|frameless|558x558px]] 

==='''How to Connect to Magus from outside SNU Network ?'''===
To gain access to MEGUS from outside the SNU network, a VPN connection is mandatory. To acquire VPN access, kindly click on the [https://forms.office.com/Pages/ResponsePage.aspx?id=12YS_ftig0aFL0FyYUAqLN3tPd66H1xCnswYz1fby35UMkhBR0lMSlJLUlZGT0wwTzJTOUtLNEpZVy4u VPN Request Form] or utilize the option of accessing it by scanning the barcode provided below.

===='''How to Transfers data using WinSCP Windows (Client).'''====
Step1 : Open the WinSCP and fill all the details, After that click on the Login Button.

[[File:magus 04 pic.1716182129572.png|frameless|589x589px]]

Step 2 : Click Yes on Warning tab.

Step 3: Connected, Now you can transfer the data using Right click of key Panel.

[[File:magus o5 pic.1716182172254.png|left|frameless|530x530px]]

'''Applications on Megus'''

[[Vasp]], [[02HPC Quantum Espresso Magus02|Quantum espresso]], BigDFT, [[Gaussian16|Gaussian]], Siesta, Gromacs, OpenFOAM.

==='''Queue Structure on Magus02.'''===
{| class="wikitable" style="background-color: #fafafa; height: 418px;" border="1" width="1523"
|-
| style="background-color:#bababa;" class="" width="60" |S.No.
| style="background-color:#bababa;" class="" width="115" |Processor Architecture
| style="background-color:#bababa;" class="" width="81" |Priority
| style="background-color:#bababa;" class="" width="147" |Queue Name
| style="background-color:#bababa;" class="" width="110" |Min no of Cores Required to submit job
| style="background-color:#bababa;" class="" width="99" |Max no of cores allowed per job
| style="background-color:#bababa;" class="" width="68" |No of nodes in the queue
| style="background-color:#bababa;" class="" width="92" |Wall Time
| style="background-color:#bababa;" class="" width="111" |MAX Cores User can Use in the Queue
| style="background-color:#bababa;" class="" width="111" |Max No. of Pending Jobs Per user
| style="background-color:#bababa;" class="" width="111" |Max No. of Running Jobs Per user
|-
| width="60" |'''1'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Medium

| width="110" |
32

| width="99" |
128

| width="68" |
17

| width="92" |
1 week

| width="111" |
512

| width="111" | 2
| width="111" | 2
|-
| width="60" |'''2'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
Small

| width="110" |
8

| width="99" |
32

| width="68" |
16

| width="92" |
1 Month

| width="111" |
128

| width="111" |2
| width="111" |4
|-
| width="60" |'''3'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
High_mem

| width="110" |
32

| width="99" |
256

| width="68" |
12

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''4'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Large

| width="110" |
64

| width="99" |
256

| width="68" |
24

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''5'''

| width="115" |
Intel Xeon Platinum 8358

| width="81" |
50

| width="147" |
GPU

| width="110" |
16

| width="99" |
16

| width="68" |
2

| width="92" |
1 week

| width="111" |
32

| width="111" |
| width="111" |2
|-
| width="60" |'''6'''

| width="115" |
AMD EPYC 7763

| width="81" |
Low

| width="147" |
Long

| width="110" |
32

| width="99" |
1024

| width="68" |
All lm nodes

| width="92" |
1 Month

| width="111" |
1024

| width="111" |
| width="111" |8
|}
====='''[[Slurm Command Reference:]]'''=====
'''[[index.php?title=Media:Linux Command Reference.pdf|Linux_Command_Reference.pdf]]'''

Gaussian16

2025-07-30T05:38:04Z

Snuadmin: Created page with "* frame Gaussian 16 is the latest version of the Gaussian series of electronic structure programs, used by chemists, chemical engin..."

* [[File:gaussian.1753853181823.jpg|center|frame]]

Gaussian 16 is the latest version of the Gaussian series of electronic structure programs, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Gaussian 16 provides a wide-ranging suite of the most advanced modeling capabilities available. You can use it to investigate the real-world chemical problems that interest you, in all of their complexity, even on modest computer hardware.

'''What Sets Gaussian 16 Apart from Other Software?'''

•Gaussian 16 produces accurate, reliable and complete models without cutting corners.

•A wide variety of methods makes Gaussian 16 applicable to a broad range of chemical conditions, problem sizes and compounds.

•Gaussian 16 provides state-of-the-art performance in single CPU, multiprocessor and multicore, cluster/network and GPU computing environments.

•Setting up calculations is simple and straightforward, and even complex techniques are fully automated. The flexible, easy-to-use options give you complete control over calculation details when needed.

•Calculation results are presented in natural and intuitive graphical form by GaussView 6.

'''Fundamental Capabilities'''

Starting from the fundamental laws of quantum mechanics, Gaussian 16 predicts the energies, molecular structures, vibrational frequencies and molecular properties of compounds and reactions in a wide variety of chemical environments. Gaussian 16’s models can be applied to both stable species and compounds which are difficult or impossible to observe experimentally, whether due to their nature (e.g., toxicity, combustibility, radioactivity) or their inherent fleeting nature (e.g., short-lived intermediates and transition structures).

With Gaussian 16, you can thoroughly investigate the chemical problems that interest you. For example, not only can you minimize molecular structures rapidly and reliably, you can also predict the structures of transition states, and verify that the predicted stationary points are in fact minima or transition structure (as appropriate). You can go on to compute the reaction path by following the intrinsic reaction coordinate (IRC) and determine which reactants and products are connected by a given transition structure. Once you have a complete picture of the potential energy surface, reaction energies and barriers can be accurately predicted. You can also predict a wide variety of chemical properties.

Gaussian 16 offers a wide range of methods for modeling compounds and chemical processes, including:

'''Molecular Properties in Gaussian 16'''

Antiferromagnetic coupling

Atomic charges

ΔG of solvation

Dipole moment

Electron affinities

Electron density

Electronic circular dichroism (ECD)

Electrostatic potential

Electrostatic potential-derived charges

Electronic transition band shape

High accuracy energies

Hyperfine coupling constants (anisotropic)

Hyperfine spectra tensors (including g tensors)

Ionization potentials

IR and Raman spectra*

Pre-resonance Raman spectra*

Resonance Raman spectra

Molecular orbitals

Multipole moments

NMR shielding and chemical shifts

NMR spin-spin coupling constants

Optical rotations (ORD)

Polarizabilities/hyperpolarizabilities

Raman optical activity (ROA)*

Thermochemical analysis

UV/Visible spectra

Vibration-rotation coupling

Vibrational circular dichroism (VCD)*

Vibronic (absorption and emission) spectra

<nowiki>*</nowiki>Harmonic approx. and including anharmonic effects

•Molecular mechanicsEGF: Amber, UFF, Dreiding

•Semi-empirical methodsEGF†: AM1, PM6, PM7, DFTB, among others

•Hartree-FockEGF

•Density functional (DFT) methodsEGF, with support for a plethora of published functionals; long-range and empirical dispersion corrections are available where defined

•Complete active space self-consistent field (CASSCF)EGF, including RAS support and conical intersection optimizations

•Møller-Plesset perturbation theory: MP2EGF, MP3EG, MP4(SDQ)EG, MP4(SDTQ)E, MP5E

•Coupled cluster: CCDEG, CCSDEG, CCSD(T)E

•Brueckner doubles: BDEG, BD(T)E

•Outer Valence Green’s Function (OVGF): ionization potentials and electron affinities

•High accuracy energy models: G1-G4, CBS series and W1 series, all with variants

•Excited state methods: TD-DFTEGF, EOM-CCSDEG and SAC-CIEG

EEnergies; GAnalytic gradients; FAnalytic frequencies; F†Reimplemented with analytic frequencies.

A wide range of Gaussian results can be examined with GaussView’s visualization capabilities:

•Molecule annotations and/or property-specific coloring: e.g., atomic charges, bond orders, NMR chemical shifts

•Plots, including NMR, vibrational and vibronic spectra

•Surfaces or contours: e.g., molecular orbitals, electron density, spin density. Properties such as the electrostatic potential can be visualized as a colorized density surface.

•Animations: e.g., normal modes, IRC paths, geometry optimizations

'''Binary Location''':

/data/apps/Gaussian/g09

Version: Gaussian16

'''Job Script''':

<nowiki>#</nowiki>!/bin/bash

<nowiki>#</nowiki>SBATCH --partition=long # include the appropriate partition, node, ntasks, ntasks-pernode for the respective SLURM key

<nowiki>#</nowiki>SBATCH --ntasks=32

<nowiki>#</nowiki>SBATCH --cpus-per-task=1

<nowiki>#</nowiki>SBATCH --job-name=Gaussian

<nowiki>#</nowiki>SBATCH --output Gaussian.%J.out

<nowiki>#</nowiki>SBATCH --error Gaussian.%J.err

ulimit -s unlimited

export g16root=/data/apps

export GAUSS_SCRDIR=/scratch/$USER

. $g16root/g16/bsd/g16.profile

<nowiki>#</nowiki>Name of your input file ie H_SPE1.gjf

JobFile=force

<nowiki>#</nowiki> This creates a list of nodes that you job received to run on

LindaList=./nodes_linda.$SLURM_JOBID

touch $LindaList

<nowiki>#</nowiki> This creates a job file

JobName=./${JobFile}${SLURM_JOBID}.com

touch $JobName

<nowiki>#</nowiki> Create a list of hostnames and save it to the LindaList machine file

srun hostname -s | sort -u > $LindaList

<nowiki>#</nowiki> Tell linda to use ssh

export GAUSS_LFLAGS=' -opt "Tsnet.Node.lindarsharg: ssh"'

<nowiki>#</nowiki> Read the contents of the machine file and put it in the job file

workers="%LindaWorkers="$(cat $LindaList | tr "\n" "," | sed "s/,$//")

<nowiki>#</nowiki> Write that out to the job file

cat <(echo "${workers}") ./$JobFile.com > $JobName

g16 < ${JobFile}${SLURM_JOBID}.com > ${JobFile}.log

echo "Job Complete"

File:gaussian.1753853181823.jpg

2025-07-30T05:26:06Z

Snuadmin:

Magus02

2025-07-30T04:37:51Z

Snuadmin:

====What is HPC?====
<div style="font-size: 0.875em;">High performance computing (HPC) is the ability to process data and perform complex calculations at high speeds. To put it into perspective, a laptop or desktop with a 3 GHz processor can perform around 3 billion calculations per second. While that is much faster than any human can achieve, it pales in comparison to HPC solutions that can perform quadrillions of calculations per second.</div>
HPC is specifically needed for these reasons:

* It paves the way for new innovations in science, technology, business and academia.
* It improves processing speeds, which can be critical for many kinds of computing operations, applications and workloads.
* It helps lay the foundation for a reliable, fast IT infrastructure that can store, process and analyze massive amounts of data for various applications.

'''Specification:'''

* Total Cores = 8064 (AMD)
* 238 Tflops
* 57 Compute Nodes
* 2 Login Nodes
* 2 Master Nodes
* 12 High memory nodes with local SSD
* Better performance of applications, which require high performance storage but do not scale well across nodes. E.g. Gaussian.

'''Memory'''

* 4 GB Per core for Compute Nodes, with a total memory = 29,184 GB
* 16 GB Per core for High Memory Nodes, with total memory = 12,288 GB

===='''Compute Specification:'''====
{| class=" wikitable" style="height: 49px;" width="1084"
|-
| width="115"|'''COMPUTE NODES'''
| width="162"|''' PROCESSOR'''
| width="86"|''' RAM'''
| width="79"|''' CORE'''
| width="86"|''' GPU '''
| width="91"|''' NO OF NODES'''
| width="81"|'''TOTAL RAM'''
| width="89"|'''TOTAL CORES'''
|}
{| class=" wikitable" style="height: 118px;" width="912"
|-
||Compute Node
||AMD EPYC 7763
||512 GB
||128
||-
||57
||29184GB
||7296
|-
||High Memory Node
||AMD EPYC 7543
||1024GB
||64
||-
||12
||12228GB
||768
|-
||GPU
||INTEL XEON PLATINUM 8358
||512GB
||64
||Tesla A100*4
||2
||1024GB
||128
|-
||Total
||
||
||
||
||
||42436
||8192
|-
||Storage
||750TB PFS
||
||
||
||
||
||
|}

===='''How to connect to Snu HPC ?'''====
 Enumerated here are the various types.

* '''SSH : '''Host magus02.snu.edu.in ( default port 22 )
* '''From Linux Machine : '''$ssh user@magus02.snu.edu.in
* '''From Windows Machine using ''''''putty.'''

===='''How to Reset Password on Magus02 ?'''====
 Step1. Login to magus02 account.

[[File:magus 02 pic 1.1716181911641.png|frameless|578x578px]]

Step2: Use Passwd Command.

[[File:magus 03 pic.1716182070345.png|frameless|558x558px]] 

==='''How to Connect to Magus from outside SNU Network ?'''===
To gain access to MEGUS from outside the SNU network, a VPN connection is mandatory. To acquire VPN access, kindly click on the [https://forms.office.com/Pages/ResponsePage.aspx?id=12YS_ftig0aFL0FyYUAqLN3tPd66H1xCnswYz1fby35UMkhBR0lMSlJLUlZGT0wwTzJTOUtLNEpZVy4u VPN Request Form] or utilize the option of accessing it by scanning the barcode provided below.

===='''How to Transfers data using WinSCP Windows (Client).'''====
Step1 : Open the WinSCP and fill all the details, After that click on the Login Button.

[[File:magus 04 pic.1716182129572.png|frameless|589x589px]]

Step 2 : Click Yes on Warning tab.

Step 3: Connected, Now you can transfer the data using Right click of key Panel.

[[File:magus o5 pic.1716182172254.png|left|frameless|530x530px]]

'''Applications on Megus'''

[[Vasp]], [[02HPC Quantum Espresso Magus02|Quantum espresso]], BigDFT, Gaussian, Siesta, Gromacs, OpenFOAM.

==='''Queue Structure on Magus02.'''===
{| class="wikitable" style="background-color: #fafafa; height: 418px;" border="1" width="1523"
|-
| style="background-color:#bababa;" class="" width="60" |S.No.
| style="background-color:#bababa;" class="" width="115" |Processor Architecture
| style="background-color:#bababa;" class="" width="81" |Priority
| style="background-color:#bababa;" class="" width="147" |Queue Name
| style="background-color:#bababa;" class="" width="110" |Min no of Cores Required to submit job
| style="background-color:#bababa;" class="" width="99" |Max no of cores allowed per job
| style="background-color:#bababa;" class="" width="68" |No of nodes in the queue
| style="background-color:#bababa;" class="" width="92" |Wall Time
| style="background-color:#bababa;" class="" width="111" |MAX Cores User can Use in the Queue
| style="background-color:#bababa;" class="" width="111" |Max No. of Pending Jobs Per user
| style="background-color:#bababa;" class="" width="111" |Max No. of Running Jobs Per user
|-
| width="60" |'''1'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Medium

| width="110" |
32

| width="99" |
128

| width="68" |
17

| width="92" |
1 week

| width="111" |
512

| width="111" | 2
| width="111" | 2
|-
| width="60" |'''2'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
Small

| width="110" |
8

| width="99" |
32

| width="68" |
16

| width="92" |
1 Month

| width="111" |
128

| width="111" |2
| width="111" |4
|-
| width="60" |'''3'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
High_mem

| width="110" |
32

| width="99" |
256

| width="68" |
12

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''4'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Large

| width="110" |
64

| width="99" |
256

| width="68" |
24

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''5'''

| width="115" |
Intel Xeon Platinum 8358

| width="81" |
50

| width="147" |
GPU

| width="110" |
16

| width="99" |
16

| width="68" |
2

| width="92" |
1 week

| width="111" |
32

| width="111" |
| width="111" |2
|-
| width="60" |'''6'''

| width="115" |
AMD EPYC 7763

| width="81" |
Low

| width="147" |
Long

| width="110" |
32

| width="99" |
1024

| width="68" |
All lm nodes

| width="92" |
1 Month

| width="111" |
1024

| width="111" |
| width="111" |8
|}
====='''[[Slurm Command Reference:]]'''=====
'''[[index.php?title=Media:Linux Command Reference.pdf|Linux_Command_Reference.pdf]]'''

Magus02

2025-07-30T04:37:16Z

Snuadmin:

====What is HPC?====
<div style="font-size: 0.875em;">High performance computing (HPC) is the ability to process data and perform complex calculations at high speeds. To put it into perspective, a laptop or desktop with a 3 GHz processor can perform around 3 billion calculations per second. While that is much faster than any human can achieve, it pales in comparison to HPC solutions that can perform quadrillions of calculations per second.</div>
HPC is specifically needed for these reasons:

* It paves the way for new innovations in science, technology, business and academia.
* It improves processing speeds, which can be critical for many kinds of computing operations, applications and workloads.
* It helps lay the foundation for a reliable, fast IT infrastructure that can store, process and analyze massive amounts of data for various applications.

'''Specification:'''

* Total Cores = 8064 (AMD)
* 238 Tflops
* 57 Compute Nodes
* 2 Login Nodes
* 2 Master Nodes
* 12 High memory nodes with local SSD
* Better performance of applications, which require high performance storage but do not scale well across nodes. E.g. Gaussian.

'''Memory'''

* 4 GB Per core for Compute Nodes, with a total memory = 29,184 GB
* 16 GB Per core for High Memory Nodes, with total memory = 12,288 GB

===='''Compute Specification:'''====
{| class=" wikitable" style="height: 49px;" width="1084"
|-
| width="115"|'''COMPUTE NODES'''
| width="162"|''' PROCESSOR'''
| width="86"|''' RAM'''
| width="79"|''' CORE'''
| width="86"|''' GPU '''
| width="91"|''' NO OF NODES'''
| width="81"|'''TOTAL RAM'''
| width="89"|'''TOTAL CORES'''
|}
{| class=" wikitable" style="height: 118px;" width="912"
|-
||Compute Node
||AMD EPYC 7763
||512 GB
||128
||-
||57
||29184GB
||7296
|-
||High Memory Node
||AMD EPYC 7543
||1024GB
||64
||-
||12
||12228GB
||768
|-
||GPU
||INTEL XEON PLATINUM 8358
||512GB
||64
||Tesla A100*4
||2
||1024GB
||128
|-
||Total
||
||
||
||
||
||42436
||8192
|-
||Storage
||750TB PFS
||
||
||
||
||
||
|}

===='''How to connect to Snu HPC ?'''====
 Enumerated here are the various types.

* '''SSH : '''Host magus02.snu.edu.in ( default port 22 )
* '''From Linux Machine : '''$ssh user@magus02.snu.edu.in
* '''From Windows Machine using ''''''putty.'''

===='''How to Reset Password on Magus02 ?'''====
 Step1. Login to magus02 account.

[[File:magus 02 pic 1.1716181911641.png|frameless|578x578px]]

Step2: Use Passwd Command.

[[File:magus 03 pic.1716182070345.png|frameless|558x558px]] 

==='''How to Connect to Magus from outside SNU Network ?'''===
To gain access to MEGUS from outside the SNU network, a VPN connection is mandatory. To acquire VPN access, kindly click on the [https://forms.office.com/Pages/ResponsePage.aspx?id=12YS_ftig0aFL0FyYUAqLN3tPd66H1xCnswYz1fby35UMkhBR0lMSlJLUlZGT0wwTzJTOUtLNEpZVy4u VPN Request Form] or utilize the option of accessing it by scanning the barcode provided below.

===='''How to Transfers data using WinSCP Windows (Client).'''====
Step1 : Open the WinSCP and fill all the details, After that click on the Login Button.

[[File:magus 04 pic.1716182129572.png|frameless|589x589px]]

Step 2 : Click Yes on Warning tab.

Step 3: Connected, Now you can transfer the data using Right click of key Panel.

[[File:magus o5 pic.1716182172254.png|left|frameless|530x530px]]

'''Applications on Megus'''

[[Vasp]], [[02HPC Quantum Espresso Magus02|Quantum espresso]], BigDFT, Gaussian, Siesta, Gromacs, OpenFOAM.

==='''Queue Structure on Magus02.'''===
{| class="wikitable" style="background-color: #fafafa; height: 418px;" border="1" width="1523"
|-
| style="background-color:#bababa;" class="" width="60" |S.No.
| style="background-color:#bababa;" class="" width="115" |Processor Architecture
| style="background-color:#bababa;" class="" width="81" |Priority
| style="background-color:#bababa;" class="" width="147" |Queue Name
| style="background-color:#bababa;" class="" width="110" |Min no of Cores Required to submit job
| style="background-color:#bababa;" class="" width="99" |Max no of cores allowed per job
| style="background-color:#bababa;" class="" width="68" |No of nodes in the queue
| style="background-color:#bababa;" class="" width="92" |Wall Time
| style="background-color:#bababa;" class="" width="111" |MAX Cores User can Use in the Queue
| style="background-color:#bababa;" class="" width="111" |Max No. of Pending Jobs Per user
| style="background-color:#bababa;" class="" width="111" |Max No. of Running Jobs Per user
|-
| width="60" |'''1'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Medium

| width="110" |
32

| width="99" |
128

| width="68" |
17

| width="92" |
1 week

| width="111" |
512

| width="111" | 2
| width="111" | 2
|-
| width="60" |'''2'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
Small

| width="110" |
8

| width="99" |
32

| width="68" |
16

| width="92" |
1 Month

| width="111" |
128

| width="111" |2
| width="111" |4
|-
| width="60" |'''3'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
High_mem

| width="110" |
32

| width="99" |
256

| width="68" |
12

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''4'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Large

| width="110" |
64

| width="99" |
256

| width="68" |
24

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''5'''

| width="115" |
Intel Xeon Platinum 8358

| width="81" |
50

| width="147" |
GPU

| width="110" |
16

| width="99" |
16

| width="68" |
2

| width="92" |
1 week

| width="111" |
32

| width="111" |
| width="111" |2
|-
| width="60" |'''6'''

| width="115" |
AMD EPYC 7763

| width="81" |
Low

| width="147" |
Long

| width="110" |
32

| width="99" |
1024

| width="68" |
All lm nodes

| width="92" |
1 Month

| width="111" |
1024

| width="111" |
| width="111" |8
|}
====='''[[Slurm Command Reference:]]'''=====
'''[[index.php?title=Media:Linux Command Reference.pdf|Linux_Command_Reference.pdf]]'''

Magus02

2025-07-30T04:36:15Z

Snuadmin:

====What is HPC?====
<div style="font-size: 0.875em;">High performance computing (HPC) is the ability to process data and perform complex calculations at high speeds. To put it into perspective, a laptop or desktop with a 3 GHz processor can perform around 3 billion calculations per second. While that is much faster than any human can achieve, it pales in comparison to HPC solutions that can perform quadrillions of calculations per second.</div>
HPC is specifically needed for these reasons:

* It paves the way for new innovations in science, technology, business and academia.
* It improves processing speeds, which can be critical for many kinds of computing operations, applications and workloads.
* It helps lay the foundation for a reliable, fast IT infrastructure that can store, process and analyze massive amounts of data for various applications.

'''Specification:'''

* Total Cores = 8064 (AMD)
* 238 Tflops
* 57 Compute Nodes
* 2 Login Nodes
* 2 Master Nodes
* 12 High memory nodes with local SSD
* Better performance of applications, which require high performance storage but do not scale well across nodes. E.g. Gaussian.

'''Memory'''

* 4 GB Per core for Compute Nodes, with a total memory = 29,184 GB
* 16 GB Per core for High Memory Nodes, with total memory = 12,288 GB

===='''Compute Specification:'''====
{| class=" wikitable" style="height: 49px;" width="1084"
|-
| width="115"|'''COMPUTE NODES'''
| width="162"|''' PROCESSOR'''
| width="86"|''' RAM'''
| width="79"|''' CORE'''
| width="86"|''' GPU '''
| width="91"|''' NO OF NODES'''
| width="81"|'''TOTAL RAM'''
| width="89"|'''TOTAL CORES'''
|}
{| class=" wikitable" style="height: 118px;" width="912"
|-
||Compute Node
||AMD EPYC 7763
||512 GB
||128
||-
||57
||29184GB
||7296
|-
||High Memory Node
||AMD EPYC 7543
||1024GB
||64
||-
||12
||12228GB
||768
|-
||GPU
||INTEL XEON PLATINUM 8358
||512GB
||64
||Tesla A100*4
||2
||1024GB
||128
|-
||Total
||
||
||
||
||
||42436
||8192
|-
||Storage
||750TB PFS
||
||
||
||
||
||
|}

===='''How to connect to Snu HPC ?'''====
 Enumerated here are the various types.

* '''SSH : '''Host magus02.snu.edu.in ( default port 22 )
* '''From Linux Machine : '''$ssh user@magus02.snu.edu.in
* '''From Windows Machine using ''''''putty.'''

===='''How to Reset Password on Magus02 ?'''====
 Step1. Login to magus02 account.

[[File:magus 02 pic 1.1716181911641.png|frameless|578x578px]]

Step2: Use Passwd Command.

[[File:magus 03 pic.1716182070345.png|frameless|558x558px]] 

==='''How to Connect to Magus from outside SNU Network ?'''===
To gain access to MEGUS from outside the SNU network, a VPN connection is mandatory. To acquire VPN access, kindly click on the [https://forms.office.com/Pages/ResponsePage.aspx?id=12YS_ftig0aFL0FyYUAqLN3tPd66H1xCnswYz1fby35UMkhBR0lMSlJLUlZGT0wwTzJTOUtLNEpZVy4u VPN Request Form] or utilize the option of accessing it by scanning the barcode provided below.

===='''How to Transfers data using WinSCP Windows (Client).'''====
Step1 : Open the WinSCP and fill all the details, After that click on the Login Button.

[[File:magus 04 pic.1716182129572.png|frameless|589x589px]]

Step 2 : Click Yes on Warning tab.

Step 3: Connected, Now you can transfer the data using Right click of key Panel.

[[File:magus o5 pic.1716182172254.png|left|frameless|516x516px]]

'''Applications on Megus'''

[[Vasp]], [[02HPC Quantum Espresso Magus02|Quantum espresso]], BigDFT, Gaussian, Siesta, Gromacs, OpenFOAM.

==='''Queue Structure on Magus02.'''===
{| class="wikitable" style="background-color: #fafafa; height: 418px;" border="1" width="1523"
|-
| style="background-color:#bababa;" class="" width="60" |S.No.
| style="background-color:#bababa;" class="" width="115" |Processor Architecture
| style="background-color:#bababa;" class="" width="81" |Priority
| style="background-color:#bababa;" class="" width="147" |Queue Name
| style="background-color:#bababa;" class="" width="110" |Min no of Cores Required to submit job
| style="background-color:#bababa;" class="" width="99" |Max no of cores allowed per job
| style="background-color:#bababa;" class="" width="68" |No of nodes in the queue
| style="background-color:#bababa;" class="" width="92" |Wall Time
| style="background-color:#bababa;" class="" width="111" |MAX Cores User can Use in the Queue
| style="background-color:#bababa;" class="" width="111" |Max No. of Pending Jobs Per user
| style="background-color:#bababa;" class="" width="111" |Max No. of Running Jobs Per user
|-
| width="60" |'''1'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Medium

| width="110" |
32

| width="99" |
128

| width="68" |
17

| width="92" |
1 week

| width="111" |
512

| width="111" | 2
| width="111" | 2
|-
| width="60" |'''2'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
Small

| width="110" |
8

| width="99" |
32

| width="68" |
16

| width="92" |
1 Month

| width="111" |
128

| width="111" |2
| width="111" |4
|-
| width="60" |'''3'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
High_mem

| width="110" |
32

| width="99" |
256

| width="68" |
12

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''4'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Large

| width="110" |
64

| width="99" |
256

| width="68" |
24

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''5'''

| width="115" |
Intel Xeon Platinum 8358

| width="81" |
50

| width="147" |
GPU

| width="110" |
16

| width="99" |
16

| width="68" |
2

| width="92" |
1 week

| width="111" |
32

| width="111" |
| width="111" |2
|-
| width="60" |'''6'''

| width="115" |
AMD EPYC 7763

| width="81" |
Low

| width="147" |
Long

| width="110" |
32

| width="99" |
1024

| width="68" |
All lm nodes

| width="92" |
1 Month

| width="111" |
1024

| width="111" |
| width="111" |8
|}
====='''[[Slurm Command Reference:]]'''=====
'''[[index.php?title=Media:Linux Command Reference.pdf|Linux_Command_Reference.pdf]]'''

How to login Collpoll Application- Parent's

2025-07-29T09:25:20Z

Snuadmin:

{{DISPLAYTITLE:How to login DigiiCampus Application- Parent's}}

===Please follow the steps below to log in to the Coll Poll application:===
Please enter ''''SNU' in the URL section''', then proceed to enter your '''ID and Password'''. Finally, click the ''''Sign In'''' button.

[[File:2.1753770899609.jpg|frame|alt=|center]]

'''Note :You will receive the ID and Password on your registered Email ID.'''

How to login in Digii (Formely Coll Poll)

2025-07-29T09:23:42Z

Snuadmin:

{{DISPLAYTITLE:How to login in DigiiCampus Application}}

===Please follow the steps below to log in to the CollPoll Application.===
 1.Please enter '''"SNU"''' in the URL path and click on '''"Sign in with Microsoft option."'''

("''Please do not enter email ID and password" use Net ID and Password after clicking the Sign in With Microsoft Option.'')

[[File:Login student 1.jpg|left|frame]]

 2.Please enter your '''Net ID''' and P'''assword,''' and '''Accept''' the required permissions.

[[File:Login student 2.jpg|left|frame]]

How to login in Digii (Formely Coll Poll)

2025-07-29T09:21:08Z

Snuadmin:

{{DISPLAYTITLE:How to login in DigiiCampus}}

===Please follow the steps below to log in to the CollPoll Application.===
 1.Please enter '''"SNU"''' in the URL path and click on '''"Sign in with Microsoft option."'''

("''Please do not enter email ID and password" use Net ID and Password after clicking the Sign in With Microsoft Option.'')

[[File:Login student 1.jpg|left|frame]]

 2.Please enter your '''Net ID''' and P'''assword,''' and '''Accept''' the required permissions.

[[File:Login student 2.jpg|left|frame]]

Main Page

2025-07-29T08:42:35Z

Snuadmin:

{| class="greyscale" style="width: 100%;" width="1334" data-mce-style="height: 26px ;background-color:#005197;"
| style="background-color:;font-family:Verdana, Arial, Helvetica, sans-serif;font-size:11px;border:1px dashed rgb(187, 187, 187);" class="col-white-bg" |
=== Information Technology Resource Centre : ===
'''<big>Configuration of Wi-Fi</big>''' [[File:down13.jpg|frameless|25x25px]]

* [[Configuration of Wifi for Students|<big>Configuration of Wifi for Students</big>]]

*[[Configuration of Wifi System for Guest|<big>Configuration of Wifi System for Guest</big>]]
*[[How to Approve Guest Wifi Request|<big>How to Approve Guest Wifi Request</big>]]
*[[How to connect Eduroam WIfi|<big>How to connect Eduroam WIfi</big>]] 

'''<big>Net ID Setup</big>''' [[File:download (5).png|frameless|21x21px]]

*[[Setting up your NetID Password|<big>Setting up your NetID Password</big>]] : <big>(First Time Setup, Forget Password, Change Password)</big> 

'''<big>Email ID Setup</big>''' [[File:download (8).1716959100424.jpg|frameless|25x25px]]

* <big>[[Setting up your University Email ID Password.]]</big>

'''<big>Microsoft Teams Setup</big>''' [[File:RE1Mu3b.1747285649387.png|link=https://wiki.snu.edu.in/File:RE1Mu3b.1747285649387.png|frameless|101x101px]]

* <big>[[Microsoft Teams Installation and Guide]]</big>
* <big>[[Manage attendee audio permissions]]</big>
* <big>[[Schedule Microsoft Teams meeting from Microsoft Outlook]]</big>
* <big>[[How to Join Microsoft Teams meeting from web client]]</big>
* <big>[[Create a Class in MS Teams]]</big>
* <big>[[Change Meeting Permissions for Attendees through MS Teams]]</big>

'''<big>Configuration of VPN</big>''' [[File:download (6).1716183181171.png|frameless|27x27px]]
*[[How to connect VPN-IVANTI (Students)|<big>How to connect VPN-IVANTI (Students)</big>]]

'''<big>Get Acquainted with HPC</big>''' [[File:images (2).png|frameless|42x42px]]
*<big>[[HPC]]</big>

*<big>[[Magus02]]</big>
*<big>[[Open FOAM]]</big>
*<big>[[Nanoelectronics Computation Laboratory - NCL]]</big>
*<big>[[Vasp5.4]]</big>
*<big>[[Vasp5.5]]</big> 

'''<big>Academia Installation</big>''' [[File:images.png|frameless|21x21px]]

*<big>[[Academia NativeApps Client Installation]]</big> 

<big>'''DIGII Campus Application'''</big> [[File:download5678.png|frameless|38x38px]]
*<big>[[How to create Request (For Night and Day Out Pass)]]</big>
*<big>[[How to download the Digii(Formerly CollPoll) Application|How to download the DigiiCampus Application]]</big>
*<big>[[How to login Collpoll Application- Parent's|How to login DigiiCampus Application- Parent's]]</big>
*<big>[[How to login in Digii (Formely Coll Poll)|How to login in DigiiCampus Application]] - '''For Students'''</big>
*[[Parental Approval Process|<big>Parental Approval Process</big>]] - <big>'''For Parent's'''</big> 

<big>'''Obtaining a Free Windows 11 Education License for Students'''</big> [[File:win11.1753764385890.jpg|frameless|38x38px]]
*<big>[[Active students are eligible to obtain a free Windows 11 Education product key]]</big>

====='''<big>[[Get Informed: Frequently Asked Questions"]]</big>'''=====
|-
|
|}

Main Page

2025-07-29T08:39:21Z

Snuadmin:

{| class="greyscale" style="width: 100%;" width="1334" data-mce-style="height: 26px ;background-color:#005197;"
| style="background-color:;font-family:Verdana, Arial, Helvetica, sans-serif;font-size:11px;border:1px dashed rgb(187, 187, 187);" class="col-white-bg" |
=== Information Technology Resource Centre : ===
'''<big>Configuration of Wi-Fi</big>''' [[File:down13.jpg|frameless|25x25px]]

* [[Configuration of Wifi for Students|<big>Configuration of Wifi for Students</big>]]

*[[Configuration of Wifi System for Guest|<big>Configuration of Wifi System for Guest</big>]]
*[[How to Approve Guest Wifi Request|<big>How to Approve Guest Wifi Request</big>]]
*[[How to connect Eduroam WIfi|<big>How to connect Eduroam WIfi</big>]] 

'''<big>Net ID Setup</big>''' [[File:download (5).png|frameless|21x21px]]

*[[Setting up your NetID Password|<big>Setting up your NetID Password</big>]] : <big>(First Time Setup, Forget Password, Change Password)</big> 

'''<big>Email ID Setup</big>''' [[File:download (8).1716959100424.jpg|frameless|25x25px]]

* <big>[[Setting up your University Email ID Password.]]</big>

'''<big>Microsoft Teams Setup</big>''' [[File:RE1Mu3b.1747285649387.png|link=https://wiki.snu.edu.in/File:RE1Mu3b.1747285649387.png|frameless|101x101px]]

* <big>[[Microsoft Teams Installation and Guide]]</big>
* <big>[[Manage attendee audio permissions]]</big>
* <big>[[Schedule Microsoft Teams meeting from Microsoft Outlook]]</big>
* <big>[[How to Join Microsoft Teams meeting from web client]]</big>
* <big>[[Create a Class in MS Teams]]</big>
* <big>[[Change Meeting Permissions for Attendees through MS Teams]]</big>

'''<big>Configuration of VPN</big>''' [[File:download (6).1716183181171.png|frameless|27x27px]]
*[[How to connect VPN-IVANTI (Students)|<big>How to connect VPN-IVANTI (Students)</big>]]

'''<big>Get Acquainted with HPC</big>''' [[File:images (2).png|frameless|42x42px]]
*<big>[[HPC]]</big>

*<big>[[Magus02]]</big>
*<big>[[Open FOAM]]</big>
*<big>[[Nanoelectronics Computation Laboratory - NCL]]</big>
*<big>[[Vasp5.4]]</big>
*<big>[[Vasp5.5]]</big> 

'''<big>Academia Installation</big>''' [[File:images.png|frameless|21x21px]]

*<big>[[Academia NativeApps Client Installation]]</big> 

<big>'''DIGII Campus Application'''</big> [[File:download5678.png|frameless|38x38px]]
*<big>[[How to create Request (For Night and Day Out Pass)]]</big>
*<big>[[How to download the Digii(Formerly CollPoll) Application|How to download the DigiiCampus Application]]</big>
*<big>[[How to login Collpoll Application- Parent's]]</big>
*<big>[[How to login in Digii (Formely Coll Poll)]] - '''For Students'''</big>
*[[Parental Approval Process|<big>Parental Approval Process</big>]] - <big>'''For Parent's'''</big> 

<big>'''Obtaining a Free Windows 11 Education License for Students'''</big> [[File:win11.1753764385890.jpg|frameless|38x38px]]
*<big>[[Active students are eligible to obtain a free Windows 11 Education product key]]</big>

====='''<big>[[Get Informed: Frequently Asked Questions"]]</big>'''=====
|-
|
|}

How to Join Microsoft Teams meeting from web client

2025-05-15T06:08:33Z

Snuadmin:

'''How to Join Microsoft Teams meeting from web client'''

Step 1: Please click on the meeting invite link received in the email.

[[File:How to Join Microsoft Teams meeting from web client 1747203760443.png|none|alt=|thumb|518x518px]]

Step 2: click on “'''join on the web instead'''”

[[File:How to Join Microsoft Teams meeting from web client 1747203876847.png|none|alt=|frame]]

Step 3: Enter your name and click on '''Join now'''

[[File:How to Join Microsoft Teams meeting from web client 1747203942770.png|none|alt=|frame]]

Step 4: You have joined the meeting successfully.

[[File:How to Join Microsoft Teams meeting from web client 1747203984504.png|none|alt=|frame]]

Step 5: You can manage your Camera & Mic from below icon

[[index.php%3Ftitle=File:How_to_Join_Microsoft_Teams_meeting_from_web_client_1747204042907.png|alt=|frameless]]

Turn camera on/off

[[index.php%3Ftitle=File:How_to_Join_Microsoft_Teams_meeting_from_web_client_1747204138470.png|alt=|frameless]]

<big>Unmute/mute</big> 

[[index.php%3Ftitle=File:How_to_Join_Microsoft_Teams_meeting_from_web_client_1747204180571.png|alt=|frameless]]

<span lang="EN-US" style="font-size:
11.0pt;font-family:"Calibri",sans-serif;mso-fareast-font-family:Calibri;
letter-spacing:-.1pt;mso-ansi-language:EN-US;mso-fareast-language:EN-US;
mso-bidi-language:AR-SA"><big>Share</big>

[[index.php%3Ftitle=File:How_to_Join_Microsoft_Teams_meeting_from_web_client_1747204213657.png|alt=|frameless]]

Show Conversation

[[File:How to Join Microsoft Teams meeting from web client 1747204289178.png|none|thumb]]
Show Participants

[[index.php%3Ftitle=File:How_to_Join_Microsoft_Teams_meeting_from_web_client_1747204324007.png|alt=|frameless]]

<big>Hang up</big>

File:Microsoft Office Teams (2018–present).svg.1746683872563.png

2025-05-08T05:57:53Z

Snuadmin:

File:Microsoft Office Teams (2018–present).svg.1746683769797.png

2025-05-08T05:56:10Z

Snuadmin:

Slurm Command Reference:

2025-03-27T09:58:09Z

Snuadmin: Created page with "slurm command reference..1739949741392.pdf"

[[Media:slurm command reference..1739949741392.pdf|slurm command reference..1739949741392.pdf]]

Index.php?title=Media:Linux Command Reference.pdf

2025-03-27T09:57:14Z

Snuadmin: Blanked the page

Index.php?title=Media:Linux Command Reference.pdf

2025-02-19T07:22:41Z

Snuadmin: Created page with "slurm command reference..1739949741392.pdf"

[[Media:slurm command reference..1739949741392.pdf|slurm command reference..1739949741392.pdf]]

File:slurm command reference..1739949741392.pdf

2025-02-19T07:22:21Z

Snuadmin:

Main Page

2024-10-17T10:32:01Z

Snuadmin:

{| class="greyscale" style="width: 100%;" width="1334" data-mce-style="height: 26px ;background-color:#005197;"
| style="background-color:;font-family:Verdana, Arial, Helvetica, sans-serif;font-size:11px;border:1px dashed rgb(187, 187, 187);" class="col-white-bg" |
=== Information Technology Resource Centre : ===
'''<big>Configuration of Wi-Fi</big>''' [[File:down13.jpg|frameless|25x25px]]

* [[Configuration of Wifi for Students|<big>Configuration of Wifi for Students</big>]]

*[[Configuration of Wifi System for Guest|<big>Configuration of Wifi System for Guest</big>]]
*[[How to Approve Guest Wifi Request|<big>How to Approve Guest Wifi Request</big>]]
*[[How to connect Eduroam WIfi|<big>How to connect Eduroam WIfi</big>]] 

'''<big>Net ID Setup</big>''' [[File:download (5).png|frameless|21x21px]]

*[[Setting up your NetID Password|<big>Setting up your NetID Password</big>]] : <big>(First Time Setup, Forget Password, Change Password)</big> 

'''<big>Email ID Setup</big>''' [[File:download (8).1716959100424.jpg|frameless|25x25px]]

* <big>[[Setting up your University Email ID Password.]]</big>

'''<big>Configuration of VPN</big>''' [[File:download (6).1716183181171.png|frameless|27x27px]]
*[[How to connect VPN-IVANTI (Students)|<big>How to connect VPN-IVANTI (Students)</big>]]

'''<big>Get Acquainted with HPC</big>''' [[File:images (2).png|frameless|42x42px]]
* <big>[[HPC]]</big>

*<big>[[Magus02]]</big>
*<big>[[Open FOAM]]</big>
*<big>[[Nanoelectronics Computation Laboratory - NCL]]</big>
*<big>[[Vasp5.4]]</big>
*<big>[[Vasp5.5]]</big> 

'''<big>Academia Installation</big>''' [[File:images.png|frameless|21x21px]]

*<big>[[Academia NativeApps Client Installation]]</big> 

<big>'''DIGII (formerly Collpoll)'''</big> [[File:download5678.png|frameless|38x38px]]
*<big>[[How to create Request (For Night and Day Out Pass)]]</big>
*<big>[[How to download the Digii(Formerly CollPoll) Application]]</big>
*<big>[[How to login Collpoll Application- Parent's]]</big>
*<big>[[How to login in Digii (Formely Coll Poll)]] - '''For Students'''</big>
*[[Parental Approval Process|<big>Parental Approval Process</big>]] - <big>'''For Parent's'''</big> 
===== '''<big>[[Get Informed: Frequently Asked Questions"]]</big>''' =====
|-
|
|}

Main Page

2024-10-17T10:25:18Z

Snuadmin:

{| class="greyscale" style="width: 100%;" width="1334" data-mce-style="height: 26px ;background-color:#005197;"
| style="background-color:;font-family:Verdana, Arial, Helvetica, sans-serif;font-size:11px;border:1px dashed rgb(187, 187, 187);" class="col-white-bg" |
=== Information Technology Resource Centre : ===
'''<big>Configuration of Wi-Fi</big>''' [[File:down13.jpg|frameless|25x25px]]

* [[Configuration of Wifi for Students|<big>Configuration of Wifi for Students</big>]]

*[[Configuration of Wifi System for Guest|<big>Configuration of Wifi System for Guest</big>]]
*[[How to Approve Guest Wifi Request|<big>How to Approve Guest Wifi Request</big>]]
*[[How to connect Eduroam WIfi|<big>How to connect Eduroam WIfi</big>]] 

'''<big>Net ID Setup</big>''' [[File:download (5).png|frameless|21x21px]]

*[[Setting up your NetID Password|<big>Setting up your NetID Password</big>]] : <big>(First Time Setup, Forget Password, Change Password)</big> 

'''<big>Email ID Setup</big>''' [[File:download (8).1716959100424.jpg|frameless|25x25px]]

* <big>[[Setting up your University Email ID Password.]]</big>

'''<big>Configuration of VPN</big>''' [[File:download (6).1716183181171.png|frameless|27x27px]]
*[[How to connect VPN-IVANTI (Students)|<big>How to connect VPN-IVANTI (Students)</big>]]

'''<big>Get Acquainted with HPC</big>''' [[File:images (2).png|frameless|42x42px]]
* <big>[[HPC]]</big>

*<big>[[Magus02]]</big>
*<big>[[Magus Queues]]</big>
*<big>[[Open FOAM]]</big>
*<big>[[Nanoelectronics Computation Laboratory - NCL]]</big>
*<big>[[Vasp5.4]]</big>
*<big>[[Vasp5.5]]</big> 

'''<big>Academia Installation</big>''' [[File:images.png|frameless|21x21px]]

*<big>[[Academia NativeApps Client Installation]]</big> 

<big>'''DIGII (formerly Collpoll)'''</big> [[File:download5678.png|frameless|38x38px]]
*<big>[[How to create Request (For Night and Day Out Pass)]]</big>
*<big>[[How to download the Digii(Formerly CollPoll) Application]]</big>
*<big>[[How to login Collpoll Application- Parent's]]</big>
*<big>[[How to login in Digii (Formely Coll Poll)]] - '''For Students'''</big>
*[[Parental Approval Process|<big>Parental Approval Process</big>]] - <big>'''For Parent's'''</big> 
===== '''<big>[[Get Informed: Frequently Asked Questions"]]</big>''' =====

|}

Magus02

2024-08-22T04:30:13Z

Snuadmin:

====What is HPC?====
<div style="font-size: 0.875em;">High performance computing (HPC) is the ability to process data and perform complex calculations at high speeds. To put it into perspective, a laptop or desktop with a 3 GHz processor can perform around 3 billion calculations per second. While that is much faster than any human can achieve, it pales in comparison to HPC solutions that can perform quadrillions of calculations per second.</div>
HPC is specifically needed for these reasons:

* It paves the way for new innovations in science, technology, business and academia.
* It improves processing speeds, which can be critical for many kinds of computing operations, applications and workloads.
* It helps lay the foundation for a reliable, fast IT infrastructure that can store, process and analyze massive amounts of data for various applications.

'''Specification:'''

* Total Cores = 8064 (AMD)
* 238 Tflops
* 57 Compute Nodes
* 2 Login Nodes
* 2 Master Nodes
* 12 High memory nodes with local SSD
* Better performance of applications, which require high performance storage but do not scale well across nodes. E.g. Gaussian.

'''Memory'''

* 4 GB Per core for Compute Nodes, with a total memory = 29,184 GB
* 16 GB Per core for High Memory Nodes, with total memory = 12,288 GB

===='''Compute Specification:'''====
{| class=" wikitable" style="height: 49px;" width="1084"
|-
| width="115"|'''COMPUTE NODES'''
| width="162"|''' PROCESSOR'''
| width="86"|''' RAM'''
| width="79"|''' CORE'''
| width="86"|''' GPU '''
| width="91"|''' NO OF NODES'''
| width="81"|'''TOTAL RAM'''
| width="89"|'''TOTAL CORES'''
|}
{| class=" wikitable" style="height: 118px;" width="912"
|-
||Compute Node
||AMD EPYC 7763
||512 GB
||128
||-
||57
||29184GB
||7296
|-
||High Memory Node
||AMD EPYC 7543
||1024GB
||64
||-
||12
||12228GB
||768
|-
||GPU
||INTEL XEON PLATINUM 8358
||512GB
||64
||Tesla A100*4
||2
||1024GB
||128
|-
||Total
||
||
||
||
||
||42436
||8192
|-
||Storage
||750TB PFS
||
||
||
||
||
||
|}

===='''How to connect to Snu HPC ?'''====
 Enumerated here are the various types.

* '''SSH : '''Host magus02.snu.edu.in ( default port 22 )
* '''From Linux Machine : '''$ssh user@magus02.snu.edu.in
* '''From Windows Machine using ''''''putty.'''

===='''How to Reset Password on Magus02 ?'''====
 Step1. Login to magus02 account.

[[File:magus 02 pic 1.1716181911641.png|frameless|578x578px]]

Step2: Use Passwd Command.

[[File:magus 03 pic.1716182070345.png|frameless|558x558px]] 

==='''How to Connect to Magus from outside SNU Network ?'''===
To gain access to MEGUS from outside the SNU network, a VPN connection is mandatory. To acquire VPN access, kindly click on the [https://forms.office.com/Pages/ResponsePage.aspx?id=12YS_ftig0aFL0FyYUAqLN3tPd66H1xCnswYz1fby35UMkhBR0lMSlJLUlZGT0wwTzJTOUtLNEpZVy4u VPN Request Form] or utilize the option of accessing it by scanning the barcode provided below.

===='''How to Transfers data using WinSCP Windows (Client).'''====
Step1 : Open the WinSCP and fill all the details, After that click on the Login Button.

[[File:magus 04 pic.1716182129572.png|frameless|589x589px]]

Step 2 : Click Yes on Warning tab.

Step 3: Connected, Now you can transfer the data using Right click of key Panel.

[[File:magus o5 pic.1716182172254.png|left|frameless|534x534px]]

'''Applications on Megus'''

[[Vasp]], [[02HPC Quantum Espresso Magus02|Quantum espresso]], BigDFT, Gaussian, Siesta, Gromacs, OpenFOAM.

==='''Queue Structure on Magus02.'''===
{| class="wikitable" style="background-color: #fafafa; height: 418px;" border="1" width="1523"
|-
| style="background-color:#bababa;" class="" width="60" |S.No.
| style="background-color:#bababa;" class="" width="115" |Processor Architecture
| style="background-color:#bababa;" class="" width="81" |Priority
| style="background-color:#bababa;" class="" width="147" |Queue Name
| style="background-color:#bababa;" class="" width="110" |Min no of Cores Required to submit job
| style="background-color:#bababa;" class="" width="99" |Max no of cores allowed per job
| style="background-color:#bababa;" class="" width="68" |No of nodes in the queue
| style="background-color:#bababa;" class="" width="92" |Wall Time
| style="background-color:#bababa;" class="" width="111" |MAX Cores User can Use in the Queue
| style="background-color:#bababa;" class="" width="111" |Max No. of Pending Jobs Per user
| style="background-color:#bababa;" class="" width="111" |Max No. of Running Jobs Per user
|-
| width="60" |'''1'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Medium

| width="110" |
32

| width="99" |
128

| width="68" |
17

| width="92" |
1 week

| width="111" |
512

| width="111" | 2
| width="111" | 2
|-
| width="60" |'''2'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
Small

| width="110" |
8

| width="99" |
32

| width="68" |
16

| width="92" |
1 Month

| width="111" |
128

| width="111" |2
| width="111" |4
|-
| width="60" |'''3'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
High_mem

| width="110" |
32

| width="99" |
256

| width="68" |
12

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''4'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Large

| width="110" |
64

| width="99" |
256

| width="68" |
24

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''5'''

| width="115" |
Intel Xeon Platinum 8358

| width="81" |
50

| width="147" |
GPU

| width="110" |
16

| width="99" |
16

| width="68" |
2

| width="92" |
1 week

| width="111" |
32

| width="111" |
| width="111" |2
|-
| width="60" |'''6'''

| width="115" |
AMD EPYC 7763

| width="81" |
Low

| width="147" |
Long

| width="110" |
32

| width="99" |
1024

| width="68" |
All lm nodes

| width="92" |
1 Month

| width="111" |
1024

| width="111" |
| width="111" |8
|}
====='''[[Slurm Command Reference:]]'''=====
'''[[index.php?title=Media:Linux Command Reference.pdf|Linux_Command_Reference.pdf]]'''

Magus02

2024-08-13T04:15:30Z

Snuadmin:

====What is HPC?====
<div style="font-size: 0.875em;">High performance computing (HPC) is the ability to process data and perform complex calculations at high speeds. To put it into perspective, a laptop or desktop with a 3 GHz processor can perform around 3 billion calculations per second. While that is much faster than any human can achieve, it pales in comparison to HPC solutions that can perform quadrillions of calculations per second.</div>
HPC is specifically needed for these reasons:

* It paves the way for new innovations in science, technology, business and academia.
* It improves processing speeds, which can be critical for many kinds of computing operations, applications and workloads.
* It helps lay the foundation for a reliable, fast IT infrastructure that can store, process and analyze massive amounts of data for various applications.

'''Specification:'''

* Total Cores = 8064 (AMD)
* 238 Tflops
* 57 Compute Nodes
* 2 Login Nodes
* 2 Master Nodes
* 12 High memory nodes with local SSD
* Better performance of applications, which require high performance storage but do not scale well across nodes. E.g. Gaussian.

'''Memory'''

* 4 GB Per core for Compute Nodes, with a total memory = 29,184 GB
* 16 GB Per core for High Memory Nodes, with total memory = 12,288 GB

===='''Compute Specification:'''====
{| class=" wikitable" style="height: 49px;" width="1084"
|-
| width="115"|'''COMPUTE NODES'''
| width="162"|''' PROCESSOR'''
| width="86"|''' RAM'''
| width="79"|''' CORE'''
| width="86"|''' GPU '''
| width="91"|''' NO OF NODES'''
| width="81"|'''TOTAL RAM'''
| width="89"|'''TOTAL CORES'''
|}
{| class=" wikitable" style="height: 118px;" width="912"
|-
||Compute Node
||AMD EPYC 7763
||512 GB
||128
||-
||57
||29184GB
||7296
|-
||High Memory Node
||AMD EPYC 7543
||1024GB
||64
||-
||12
||12228GB
||768
|-
||GPU
||INTEL XEON PLATINUM 8358
||512GB
||64
||Tesla A100*4
||2
||1024GB
||128
|-
||Total
||
||
||
||
||
||42436
||8192
|-
||Storage
||750TB PFS
||
||
||
||
||
||
|}

===='''How to connect to Snu HPC ?'''====
 Enumerated here are the various types.

* '''SSH : '''Host magus02.snu.edu.in ( default port 22 )
* '''From Linux Machine : '''$ssh user@magus02.snu.edu.in
* '''From Windows Machine using ''''''putty.'''

===='''How to Reset Password on Magus02 ?'''====
 Step1. Login to magus02 account.

[[File:magus 02 pic 1.1716181911641.png|frameless|578x578px]]

Step2: Use Passwd Command.

[[File:magus 03 pic.1716182070345.png|frameless|558x558px]] 

==='''How to Connect to Magus from outside SNU Network ?'''===
To gain access to MEGUS from outside the SNU network, a VPN connection is mandatory. To acquire VPN access, kindly click on the [https://forms.office.com/Pages/ResponsePage.aspx?id=12YS_ftig0aFL0FyYUAqLN3tPd66H1xCnswYz1fby35UMkhBR0lMSlJLUlZGT0wwTzJTOUtLNEpZVy4u VPN Request Form] or utilize the option of accessing it by scanning the barcode provided below.

===='''How to Transfers data using WinSCP Windows (Client).'''====
Step1 : Open the WinSCP and fill all the details, After that click on the Login Button.

[[File:magus 04 pic.1716182129572.png|frameless|589x589px]]

Step 2 : Click Yes on Warning tab.

Step 3: Connected, Now you can transfer the data using Right click of key Panel.

[[File:magus o5 pic.1716182172254.png|left|frameless|534x534px]]

'''Applications on Megus'''

[[Vasp]], [[02HPC Quantum Espresso Magus02|Quantum espresso]], BigDFT, Gaussian, Siesta, Gromacs, OpenFOAM.

==='''Queue Structure on Magus02.'''===
{| class="wikitable" style="background-color: #fafafa; height: 418px;" border="1" width="1523"
|-
| style="background-color:#bababa;" class="" width="60" |S.No.
| style="background-color:#bababa;" class="" width="115" |Processor Architecture
| style="background-color:#bababa;" class="" width="81" |Priority
| style="background-color:#bababa;" class="" width="147" |Queue Name
| style="background-color:#bababa;" class="" width="110" |Min no of Cores Required to submit job
| style="background-color:#bababa;" class="" width="99" |Max no of cores allowed per job
| style="background-color:#bababa;" class="" width="68" |No of nodes in the queue
| style="background-color:#bababa;" class="" width="92" |Wall Time
| style="background-color:#bababa;" class="" width="111" |MAX Cores User can Use in the Queue
| style="background-color:#bababa;" class="" width="111" |Max No. of Pending Jobs Per user
| style="background-color:#bababa;" class="" width="111" |Max No. of Running Jobs Per user
|-
| width="60" |'''1'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Medium

| width="110" |
32

| width="99" |
128

| width="68" |
17

| width="92" |
1 week

| width="111" |
512

| width="111" | 2
| width="111" | 2
|-
| width="60" |'''2'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
Small

| width="110" |
8

| width="99" |
32

| width="68" |
16

| width="92" |
1 week

| width="111" |
128

| width="111" |2
| width="111" |2
|-
| width="60" |'''3'''

| width="115" |
AMD EPYC 7543

| width="81" |
50

| width="147" |
High_mem

| width="110" |
32

| width="99" |
256

| width="68" |
12

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''4'''

| width="115" |
AMD EPYC 7763

| width="81" |
50

| width="147" |
Large

| width="110" |
64

| width="99" |
256

| width="68" |
24

| width="92" |
2 weeks

| width="111" |
1024

| width="111" |2
| width="111" |2
|-
| width="60" |'''5'''

| width="115" |
Intel Xeon Platinum 8358

| width="81" |
50

| width="147" |
GPU

| width="110" |
16

| width="99" |
16

| width="68" |
2

| width="92" |
1 week

| width="111" |
32

| width="111" |
| width="111" |2
|-
| width="60" |'''6'''

| width="115" |
AMD EPYC 7763

| width="81" |
Low

| width="147" |
Long

| width="110" |
32

| width="99" |
1024

| width="68" |
All lm nodes

| width="92" |
1 Month

| width="111" |
1024

| width="111" |
| width="111" |8
|}
====='''[[Slurm Command Reference:]]'''=====
'''[[index.php?title=Media:Linux Command Reference.pdf|Linux_Command_Reference.pdf]]'''

MediaWiki:Sidebar

2024-05-29T09:41:59Z

Snuadmin:

* navigation
** bs-sandbox-page|bs-sandbox

Configuration of Wifi for Students

2024-05-17T09:32:17Z

Snuadmin:

= How to connect to Wi-Fi - Android Phone =
'''Step 1''' – Make sure Wi-Fi is switched on. Select “Student” SSID.
[[File:wifi android 1.1715937061239.jpg|left|frameless]]

'''Step 2''' – Enter the following information and Click on '''Connect'''.

'''EAP method:''' PEAP

'''Phase 2 authentication''': MSCHAPV2

'''CA certificate''': Use system certificates

'''Online certificate status:''' Don’t validate.

'''Domain:''' snu.in

'''Identity''': Your Net ID username (e.g.: ab123)

'''Password''': Your Net ID password

'''MAC address type''': Phone Mac

'''Note:''' Turn off the Private DNS.

[[File:wifi android 2.1715937102490.jpg|left|frameless]]

Your mobile device is now connected to Student Network.

Below link for detailed setup instructions

'''https://wiki.snu.edu.in/index.php/Wifi'''

= How to connect to Wi-Fi – Apple/iOS Device =
Step 1 - Go to Settings and select Wi-Fi. Turn it on as shown in screenshot below:
[[File:wifi apple 1.1715937135643.png|left|frameless]]

Step 2 - Select '''Student''' from the list of Networks available
[[File:wifi apple 2.1715937157916.jpg|left|frameless]]

Step 3 – Select the '''Student''' Network. You will be prompted to enter the Username and Password.

Please enter your '''NetID and Password''' and click on '''join.'''
[[File:wifi apple 3.1715937187497.jpg|left|frameless]]

Step 4 - Click on '''Join.''' Pop-up window will appear. Click on '''Trust''' to Accept the Certificate.
[[File:wifi apple 4.1715937265978.jpg|left|frameless]]

Step 5 - Once you Click '''Trust''', you will be connected with Wi-Fi.
[[File:wifi apple 5.1715937303478.jpg|left|frameless]]

Step 6 – Open the browser (Safari) and enter your NetID and Password to get Internet access.

= How to connect to Wi-Fi – Apple Macbook =
Step 1 - Click the AirPort icon in the upper-right corner of the desktop. The AirPort icon looks like a series of circular waves. This will display a pull-down menu

Step – 2 Click "Turn AirPort on." If this option is not displayed, your MacBook's AirPort adapter is already enabled. While the AirPort adapter is on, the MacBook automatically scans periodically for broadcasts from nearby Wi-Fi access points. The pull-down menu displays the names of all access points discovered.

Step 3 - Click the name of the '''Student''' Wi-Fi access point
[[File:wifi mac 1.1715937367339.jpg|left|frameless]]

Step 4 – A pop-up box will appear. Enter your NetID credentials and click on '''join'''.
[[File:wifi mac 2.1715937405265.jpg|left|frameless]]

Step 5 – Open the browser (Safari) and enter your NetID and password to get Internet access.
[[File:wifi mac 3.1715937436264.jpg|left|frameless]]

= Steps to connect Wi-Fi in Windows 7/8/8.1/10 =
Step 1 - Bring your mouse pointer to extreme right of the screen and click on Wi-Fi connection icon

Step 2 – Right click on that icon select the second option '''“Open Network and Sharing Center”'''

Step 3 – A new window will open. Click on “'''Set up a new connection or network”'''
[[File:network setting 1.1715937558794.jpg|left|frameless]]

Step 4 – Select third option '''“Manually connect to a wireless network”'''
[[File:network setting 2.1715937592253.jpg|left|frameless]]

Step 5 – Enter the Network Name '''“Student”'''

Step 6 – Select the security type '''“WPA-2Enterprise”''' and click on '''Next'''
[[File:network setting 3.1715937633886.jpg|left|frameless]]

Step 7 – Click on '''“Change connection settings”'''
[[File:network setting 4.1715937677322.jpg|left|frameless]]

Step 8 – Select Second Tab “'''Security”''' of wireless network properties

Step 9 – Click on network authentication Method Settings
[[File:network setting 5.1715937712682.jpg|left|frameless]]

Step 10 – Uncheck '''“Verify the server’s identity by validating the certificate”''' and click on '''"configure of Select Authentication Method"'''
[[File:network setting 6.1715937830152.jpg|left|frameless]]

Step 11 – Uncheck '''“Automatically use my windows logon name and password”''' and click OK

Step 12 – Click on Advance Setting of wireless network properties
[[File:network setting 7.1715937861767.png|left|frameless]]

Step 13 – Check the box – '''“Specify authentication mode”''' and select User Authentication. Click on '''Save Credentials'''
[[File:network setting 8.1715937901422.jpg|left|frameless]]

Step 14 – In the Save Credentials window, enter your '''NETID''' and '''password'''
[[File:network setting 9.1715937931084.jpg|left|frameless]]

Step 15 – Right click on Wi-Fi icon and connect to Student connection
[[File:wifi laptop setting 1.1715938005751.jpg|left|frameless]]

Step 16 – The browser window will automatically open. Enter your NetID and password to get Internet access

(In case the browser window does not pop-up, you can open if manually)
[[File:wifi laptop setting 2.1715938038846.jpg|left|frameless]]

= How to connect Wi-Fi in Ubuntu =
Step 1 - Click on Wi-Fi Icon on the top slide bar and select '''Student''' connection.
[[File:wifi ubuntu laptop setting 1.1715938123767.png|left|frameless]]

Following screen will appear
[[File:wifi ubuntu laptop setting 2.1715938158886.png|left|frameless]]

Step 2 - Set Authentication to '''Protected EAP (PEAP).'''
[[File:wifi ubuntu laptop setting 3.1715938191005.png|left|frameless]]

Step 3 - Enter Your NETID and password and Click on '''Connect'''
[[File:wifi ubuntu laptop setting 4.1715938221436.png|left|frameless]]

Step 4 - The following pop-up screen will appear. Select '''“Don’t warn me again”''' check box and Click '''Ignore'''.
[[File:wifi ubuntu laptop setting 5.1715938252811.png|left|frameless]]

Now Click on Wi-Fi Icon to check whether you have successfully connected to the '''Student''' connection.
[[File:wifi ubuntu laptop setting 6.1715938290528.png|left|frameless]]

Step 5 – Open the browser window and enter your NetID and password to get Internet access

.

File:wifi ubuntu laptop setting 6.1715938290528.png

2024-05-17T09:31:29Z

Snuadmin:

File:wifi ubuntu laptop setting 5.1715938252811.png

2024-05-17T09:30:51Z

Snuadmin:

File:wifi ubuntu laptop setting 4.1715938221436.png

2024-05-17T09:30:20Z

Snuadmin:

File:wifi ubuntu laptop setting 3.1715938191005.png

2024-05-17T09:29:49Z

Snuadmin:

File:wifi ubuntu laptop setting 2.1715938158886.png

2024-05-17T09:29:17Z

Snuadmin:

File:wifi ubuntu laptop setting 1.1715938123767.png

2024-05-17T09:28:42Z

Snuadmin:

File:wifi laptop setting 2.1715938038846.jpg

2024-05-17T09:27:17Z

Snuadmin:

File:wifi laptop setting 1.1715938005751.jpg

2024-05-17T09:26:44Z

Snuadmin:

File:network setting 9.1715937931084.jpg

2024-05-17T09:25:29Z

Snuadmin:

File:network setting 8.1715937901422.jpg

2024-05-17T09:24:59Z

Snuadmin:

File:network setting 7.1715937861767.png

2024-05-17T09:24:20Z

Snuadmin:

File:network setting 6.1715937830152.jpg

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Snuadmin:

File:network setting 5.1715937712682.jpg

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Snuadmin:

File:network setting 4.1715937677322.jpg

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Snuadmin:

File:network setting 3.1715937633886.jpg

2024-05-17T09:20:32Z

Snuadmin: