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