TSCC CentOS 7 Upgrade

Background

TSCC will be upgraded to CentOS 7 the week of  Jan. 6 - Jan 12. In addition to the OS upgrade, we will be updating compilers , applications, and libraries. Users can run SDSC built applications (such as AMBER, NAMD, Python etc) as before by loading the available modules. For users with their own codes, we have set up a subset of nodes to allow building and testing in the new environment. Access and usage details are provided below. 

 

Important Changes

1. Obsolete modules: As part of the upgrade we have eliminated some of previously required modules.  Users are requested to modify their scripts and login environment to remove any parts that load any of the modules listed below:

        a. gnutools module:  (no longer needed)

2. Singlularity in the New environment

  •  Singularity configuration has been changed.   The /oasis  filesystems will no longer be automatically  mounted within Singluarity containers at runtime.  Users will need to manually --bind mount them at runtime.

Example:

tscc ~]$ singularity shell --bind /oasis  ....../pytorch/pytorch-cpu.simg ......
 

  •  User running  our exisiting GPU-accelerated Singularitity containers with the older drivers will need to use the —nv switch.  The —nv switch will import the host system drivers and override the ones in the container, allowing users to run with the containers they’ve been using.

 

Building and Testing environment

There are multiple hotel and condo nodes available for testing.  The nodes are accessible via ssh from login host tscc-login7.sdsc.edu.  Users can review the available nodes with the following command:

        tscc-login7.sdsc.edu ~]$ pbsnodes -a

List of upgraded condo nodes:

Nodes with CentOS7 available Group
tscc-10-15, tscc-10-17

bafna

tscc-10-23

behrou

tscc-11-42

borsa

tscc-11-43

cornuelle

tscc-11-44, tscc-11-45, tscc-gpu-10-8

cw3e

tscc-10-12

davidson

tscc-10-19

farley

tscc-11-38, tscc-11-41, tscc-4-28, tscc-4-40

feddersen

tscc-gpu-10-9

gerstoft

tscc-11-40

jensen moore

tscc-11-36

kuperman

tscc-10-21

lipomi

tscc-gpu-6-7

mccammon

tscc-gpu-7-6

mgilson

tscc-gpu-10-10, tscc-gpu-10-11

palermo

tscc-11-39

ricke

tscc-10.13

rusell

 

 

TSCC Application Software Versions (Updated 12/6/2019)

This table identifies the Status of TSCC Applications after the upgrade.  

Version Version

abinit

8.10.2

abyss

2.2.3

amber

18

apbs

1.5

atlas

3.10.3

bbcp

17.12.00.00.0

bbftp

3.2.1

beagle

3.1.2

beast

1.10.4, 1.8.0, 1.8.1, 1.8.2

beast2

2.5.2

bamtools

2.5.1

bcftools

1.9

bedtools

2.27.1

bioperl

1.7.2

biopython

1.72

bismark

0.20.0

blast

2.7.1

blat

35

boost

1.68.0

bowtie

1.2.2

bowtie2

2.3.4.3

bwa

0.7.17

canu

1.8

cilk

5.4.6

cmake

3.12.1

cpmd

4.3

cp2k

6.1

cufflinks

2.2.1

ddt

19.0.3

dendropy

4.4.0

diamond

0.9.22

edena

3.131028

eigen

3.3.5

emboss

6.5.7

fastqc

0.11.8

fastx

0.0.14

fftw

3.3.8

fsa

1.15.9

gamess

2019.06

gaussian

16.C.01

gcc

7.2.0

gdal

2.4.0

GenomeAnalysisTK

4.0.11.0, 3.5

geos

3.7.1

gmap_gsnap

20180704

gmp

6.0.0a

gromacs

2018.3

gsl

2.5, 1.16

guile

2.2.4

hdf4

2.14

hdf5

1.10.3

hmmer

3.2.1

htseq`

0.11.0

idl

8.4

intelmpi

2018.1.163

ipm

2.0.6

jasper

2.0.14

lammps

20180822

lapack

3.8.0

llvm

7.0.1

matt

1.00

miRDeep2

0.0.8

mono

5.18.0.268

mpc

1.0.3

mpfr

3.1.2

mpi4py

3.0.3

mvapich2

2.3.2

mxml

2.12

namd

2.9,  2.10,  2.13

ncl_ncarg

6.5.0

ncview

2.1.7

netcdf

4.6.1, 3.6.2

nwchem

6.8

octave

4.4.1

openmpi

3.1.4

papi

5.6.0

parmetis

4.0.3

pdt

3.25

petsc

3.10.2

pgi

18.10

picard

2.18.15

plink

1.9

polymake

3.1

proj

5.2.0

pysam

0.15.1

python

2.7.15, 3.6.9

qchem

5.2

qe

6.4.1

R

3.6.1

randfold

2.0

rapidminer

9.1.0

rseqc

3.0.1

samtools

1.9, 1.2

scalapack

2.0.2

scipy

2.7, 3.6

siesta

4.0.2

slepc

3.10.0

soapdenovo

240

SOAPsnp

1.03

spades

3.13.0

sprng

5

squid

1.9g

stacks

1.37

sundials

3.2.1

superlu

6.0.0

tau

2.28

trilinos

12.14.1

trimmomatic

0.36

trinity

2.8.4

upc

2019.4.4

vasp

5.4.4, 4.6

vcftools

0.1.16

velvet

1.2.10

ViennaRNA

2.4.10

vmd

1.9.4a38

vtk

6.1.0