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Software



System software


The cluster is running Centos 7.  There is a base of software available from that.  Many compilers and libraries are available directly from the base OS.  Many of the software packages IMSS has installed are built off of the base image.

User software

Users are welcome to install whatever software they need into their home directories or available space in your group directory.  Some groups like to maintain their own domain specific software or software that may be in a fast development cycle.  Some groups may want to add a software directory to their group directory in which to keep the software.  This is also a good place to install software that is licensed only for the group to ensure that you are following the licensing terms.

IMSS installed software

There are large numbers of packages that are helpful to all users, but not available from the base system. For these types of packages, IMSS will compile and install them and make then available via "modules" which can be loaded to add them to your environment. These include things like MPI, compilers, libraries, and other applications.

If there is something that you think should be made available to all users in this manner, email help-hpc@caltech.edu and we can see about installing it for you.  To see what is already installed, you can run "module avail" to get a current list. If you think something is miscategorized, please let us know.

Module Installed software as of November 1, 2018:

Biology: 

bcftools/1.8

bwa/0.1.17

cistem/1.0.0b

ctfind/4.1.10

eman2/2.22

gangstr/1.4

gatk/4.0.7.0

gdc-client/1.3

hipstr/hipstr

htslib/1.8

igv/igv2414

imod/4.10.13

imod/4.9.8

peet/1.12.0

picard/2.18.11

samtools/1.8


Chemistry: 

gromacs/2018_ompi212_cuda91

gromacs/2018_ompi300_cuda91

lammps/16Mar18

lammps/20160725

libxc/3.0.1

libxc/4.0.4

orca/orca_4_0_1_2_linux_x86-64_openmpi202


Compilers: 

clang/7.0.0

gcc/6.4.0

gcc/7.3.0

intel/17.1

intel/18.1

intel/19.1


Data: 

hdf5/1.10.1-opmi300

hdf5/1.10.2

mongodb/3.6.5

netcdf-c/4.6.1

netcdf-cxx/4.3.0

netcdf-fortran/4.4.4


Development: 

bazel/0.13.1

googletest/20180320

mpe2/2.4.9b_intel-18.1

swig/3.0.12

valgrind/3.13.0


Geology: 

gdal/2.3.1


Languages: 

java/1.8.0_172

python/2.7.14

python/2.7.15

python/2.7.15-tf

python3/3.6.4

python3/3.7.0

R/3.5.0


Libraries: 

arpack-ng/3.6.2

blas/3.8.0

cuda/8.0

cuda/9.0

cuda/9.1

fftw/3.3.7

fftw/3.3.8

fftw/3.3.8-ompi300

gsl/2.4

lapack/3.8.0

libctl/4.1.2

mkl/18.1

ntl/11.3.1

openblas/0.2.20

scalapack/2.0.2


MPI Libraries/Tools: 

mpich/3.2.1

mpich2/1.1.1p1

mvapich2/2.3rc1

openmpi/1.10.7

openmpi/2.1.2

openmpi/3.0.0

openmpi/3.1.2

openmpi/3.1.2_gcc-7.3.0

openmpi/3.1.2_intel-18.1


Tools: 

abinit/8.6.3

activetcl/8.5.18

armadillo/8.400.0

bcl2fastq2/2.20

boost/1_60_0

boost/1_66_0

boost/1_68_0-gcc730

bowtie/2.3.4.1

cmake/3.10.2

debyer/0.4

dmtcp/2.5.2

dynamo/1.1.333-intel

eigen/eigen

fdtd/8.19.1541-CHICgroup

fdtd/8.19.1541-greergroup

fdtd/8.19.1584-CHICgroup

fdtd/8.19.1584-greergroup

ffmpeg/4.0

gctf/1.06

gctf/1.18

ior/3.0.2

iozone3/471

mathematica/11.1

matlab/r2016b

matlab/r2017b

matlab/r2018b

mosh/1.3.2

motioncor2/1.0.5

motioncor2/1.1.0

mpb/1.6.1

mpb/1.6.1-ompi300

novactf/1.0

opencv/3.4.0

opensees/2.4.2-MP

opensees/2.4.2-SP

parallel/20180222

petsc/3.8.4

petsc/3.8.4-debug

petsc/3.8.4-intel

petsc/3.8.4-intel-debug

relion/2.1.0

relion/2.1.0-benchmarking

singularity/2.5.1

singularity/2.6.0

singularity/old/2.4.2

singularity/old/2.4.5

star/2.5.3a

stressapptest/1.0.9

visit/2.13.1


Visualization:

ovito/2.9.0

vmd/1.9.2

vmd/1.9.3


Testing:

mpptest/ompi300

openmpi/3.0.1_intel-18.1


Cloud: 

awscli/1.15.27