Comet CentOS 7 Upgrade

Background

Comet will be upgraded to CentOS 7 on Dec 3, 2019. In addition to the OS upgrade, we will be updating compilers (Intel, PGI, GNU), applications, and libraries. Users can run SDSC built applications (such as AMBER, NAMD, MrBayes 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)

        b. singularity module:   (Binary included in the default path )

2. Singlularity in the New environment

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

Example:

comet-14-04 ~]$ singularity shell --bind /oasis,/scratch /share/apps/compute/singularity/images/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.

 

Comet Application Software Versions (Updates)

This table identifies the Status of Comet Applications after the upgrade.  Please note that in some cases there is a

[1] New default version  ( * indicates that the version is still available)

[2] Multiple versions available

[3] Older versions, or software packages have been removed, and are no longer available.  See notes column for explanation

[4] Software has been replaced

[5] No change

Pre-Upgrade(default) Post-Upgrade(default)

Notes & List of Additional Version(s) available
*abaqus/6.14-1

abaqus/6.14-1

 I6.11-2

abinit/8.4.2

abinit/8.10.2

 

 abyss/2.0.2

abyss/2.2.3

 

amber/16 

amber/18

*apbs/1.5

 apbs/1.5

 

atlas3.10.2

atlas/3.10.3

 

bamtools/2.4.0

bamtools/2.5.1

 

bbcp/14.09.02.00.0

bbcp/17.12.00.00.0

 

*bbftp/3.2.1

 bbftp/3.2.1

 

bcftools/1.3

bcftools/1.9

 

beagle/2.1

beagle/3.1.2

 

*beast/1.8.2

beast/1.10.4

beast/1.8.0, beast/1.8.1, beast/1.8.2

beast2/2.1.3

beast2/2.5.2

bedtools/2.25.0

bedtools/2.27.1

bioperl/1.007002

bioperl/1.7.2

biopython/1.66

biopython/1.72

bismark/0.15.0

bismark/0.20.0

blast/2.3.0

blast/2.7.1

*blat/35

 blat/35

boost/1.55.0

boost/1.68.0

bowtie/1.1.2

bowtie/1.2.2

bowtie2/2.2.7

bowtie/2.3.4.3

bwa/0.7.13

bwa/0.7.17

bx-python/0.8.1

bx-python/0.8.2

clera/8.3rc2

canu/1.8

 application replaced with canu/1.8

cmake/3.9.1

cmake/3.12.1

cp2k/4.1

cp2k6.1

cpmd/3.17.1

cpmd/4.3

cuda7.0

cuda/10.1

 cuda/7.5,cuda/8.0, cuda/9.2

*cufflinks/2.2.1

 cufflinks/2.2.1

ddt/19.0.2

ddt/19.0.3

dendropy/4.0.3

dendropy/4.4.0

diamond/0.7.12

diamond/0.9.22

edena/3.131028

 edena/3.131028

eigen/3.2.7

eigen/3.3.5

eman2/2.1

eman2/2.22

emboss/6.5.7

 emboss/6.5.7

fastqc/0.11.4

fastqc/0.11.8

fasttree/2.1.8

fasttree/2.1.10

*fastx/0.0.14

 fastx/0.0.14

fftw/3.3.4

fftw/3.3.8

 fftw2.1.5

*frealign/9.11

 frealign/9.11

fsa/1.15.9

 fsa/1.15.9

gamess/2017.04

gamess/2019.06

*garli/2.01

 garli/2.01

 

gateway-usage-reporting/2.1

 

gaussian/0.9.D.01 

gaussian/16.C.01

gdal/2.2.0

gdal/2.4.0

GenomeAnalysisTK/4.0.4.0

GenomeAnalysisTK/4.0.11.0

 GenomeAnalysisTK/3.5

geos/3.6.1

geos/3.7.1

globus/5.2.5

globus/6.0

gmap_gsnap/20151231

gmap_gsnap/20180704

gmp/6.0.0a

 gmp/6.0.0a

gnu/4.9.2

gnu/7.2.0

gnubase

--

 removed application(gnuebase/2.69)

gnutools 

--

 removed application (gnutools/2.69)

grace/5.1.25

 grace/5.1.25

gromacs/2016.3

 gromacs/2018.3

gsl/2.1

 gsl/2.5 gsl/1.16
guile/2.0.11 guile/2.2.4 *missing
hadoop2.6.0 hadoop/1.2.1
*hdf-serial/1.10.3 hdf-serial/1.10.3
hdf4/2.11 hdf4/2.14
hdf5/1.8.14 hdf5/1.10.3 hdf5/1.8.21
hmmer/3.1b2 hmmer/3.2.1
htseq/0.6.1p1 htseq/0.11.0
*idba-ud/1.1.1 idba-ud/1.1.1
*idl/8.4 idl/8.4
intel/2013_sp1.2.144 (removed) intel/2018.1.163 removed versions: intel/2013_sp1.2.144, intel/2015.2.164
intelmpi/2016.3.210 (removed) intelmpi/2018.1.163
ipm/2.0.3 ipm/2.0.6
jags/4.2.0
jasper/1.900.1 jasper/2.0.14
julia/0.6.0 julia/1.1.0 missing
knime/2.9.2
lammps/20170331 lammps/20180822
lapack/3.6.0 lapack/3.8.0
llvm/3.6.2 llvm/7.0.1 missing
mafft/7.187 mafft/7.427
matlab/2018a matlab/2018a
matt/1.00 matt/1.00
miRDeep2/0.0.7 miRDeep2/0.0.8
migrate/3.6.11 migrate/2.6.11 migrate/3.6.8
miso/0.5.3 -- removed application: no longer maintained and not compatible with python3 (required numpy)
mkl/11.1.2.144  mkl/2018.1.163 removed versions: mkl/11.1.2.144, mkl/11.2.2.164
molden/5.0.7 molden/5.9
mono/3.12.0 mono/5.18.0.268 missing
mopac/2016
mpc/1.0.3 mpc/1.0.3
mpfr/3.1.2 mpfr/3.1.2
mpi4py/1.3.1 mpi4py/3.0.0
mpiblast/1.6.0  -- revmoved application: mpiblast/1.6.0
mrbayes/3.2.4 mrbayes/3.2.7a mrbayes/3.2.3
mvapich2_grr/2.1 mvapich2_gdr/2.3.2 mvapich2/2.2
mvapich_ib/2.1 mvapich2_ib/2.3.2
mxml/2.9 mxml/2.12
namd/2.10 namd/2.13 namd/2.9,namd/2.10
ncl_ncarg/6.2.1 ncl_ncarg/6.5.0
ncview/2.1.7
netcdf-serial/4.6.1
netcdf/4.3.2 netcdf/4.6.1 netcdf/3.6.2
NucleoATAC/0.3.1
-- removed application: no longer maintained, incompatible eith python3
neuron/7.3
nwchem/6.6 nwchem/6.8
octave/4.2.1 octave/4.4.1
openbabel/2.3.2 openbabel/2.4.1
openmpi_ib/1.8.4 openmpi_ib/3.1.4
p3dfft/2.7.4 p3dfft/2.7.7
papi/5.4.1 papi/5.6.0
parmetis/4.0.3
pdt/3.20 pdt/3.25
petsc/3.6.3 petsc/3.10.2
pgi/17.5 pgi/18.10
phylobayes/1.5.a
picard/2.3.0 picard/2.18.15
plink/1.9
polymake/2.14 polymake/3.1
proj/4.9.3 proj/5.2.0
pysam/0.8.4 pysam/0.15.1
python/2.7.10 python/2.7.15
qchem/5.1.2 qchem/5.2
qe/6.3 qe/6.4.1
R/3.4.0 R/3.6.1
*randfold/2.0 randfold/2.0
rapidminer/7.1.0 rapidminer/9.1.0
raxml/8.2.3 raxml/8.2.12 raxml/8.1.24
relion/1.4 relion/2.1
rseqc/2.6.4 rseqc/3.0.1
samtools/1.3 samtools/1.9 samtools/1.2
*scalapack/2.0.2 scalapack/2.0.2
*scipy/2.7 scipy/2.7 scipy/3.6
siesta/4.0 siesta/4.0.2
singluarity/2.6.1 singlularity/3.1
slepc/3.6.2 slepc/3.10.0
*soapdenovo/240 soupdenovo/240
*SOAPsnp/1.03 SOAPsnp/1.03
spades/3.9.0 spades/3.13.0
spark/1.5.2 spark/1.2.0
sprng/2.0b sprng/5
*squid/1.9g squid/19.g
*stacks/1.37 stacks/1.37
sundials/2.6.2 sundials/3.2.1
superlu/4.2 superlu/6.0.0
swiftclient/3.4.0
tau/2.23 tau/2.28
tophat/2.1.1  -- application removed:  no longer maintained and not compatible with python3
trilinos/11.12.1 trilinos/12.14.1
trimmomatic/0.35 trimmomatic/0.36
trinity/2.1.1 trinity/2,8.4
*vasp/5.4.4 vasp/5.4.4 vasp/4.6
vctools/0.1.14 vctools/0.1.16
*velvet/1.2.10 velvet/1.2.10
ViennaRNA/2.2.4 ViennaRNA/2.4.10
Visit/2.9.1 Visit/3.0.2 /share/apps/compute/visit/3.0.2/linux-x86_64
vmd/1.9.3 vmd/....... In progress
vtk/6.1.0
weka/3.7.12 weka/3.8.3