OSC timely installs new software versions on OSC systems, and periodically do coordinated software refresh (update the default versions to be more up-to-date and remove some versions that are quite out of date) on OSC systems. While we encourage everyone to use up-to-date software, the old defaults will still be available till the next software refresh, in case some users prefer to use the old defaults. The software refresh is usually made during the scheduled downtime, while we will send out notifications to all users ahead of time for any questions/suggestions/concerns.
Information about the old and new default versions, as well as all available versions of each software package will be included on the corresponding OSC software webpage. See https://www.osc.edu/supercomputing/software-list. If you would like OSC to install (and purchase, if necessary) software or update new version, or you have any questions, please contact OSC Help.
OSC is refreshing the software stack on Oakley on September 15, 2015 (during the scheduled downtime); something we have not done since Oakley entered service in 2012. During the software refresh, some default versions are updated to be more up-to-date and some older versions are removed. Information about the old and new default versions, as well as all available versions of each software package will be included on the corresponding OSC software webpage. See https://www.osc.edu/supercomputing/software-list.
If you compile and link your own software you need to be particularly aware of the changes in the default modules. You will probably need to either rebuild your software or explicitly load the compiler and MPI modules that you built your code with before you run the code.
module load modules/au2014
. This environment was the default environment at login on Oakley from 2012 to 9/15/2015. If your code is built with compilers other than Intel compiler, you can explicitly load the default module prior to 9/15/2015 using the command module load name
. Please refer to Compilers/MPI or the corresponding OSC software webpage (See https://www.osc.edu/supercomputing/software-list) for more information.The following table gives details about the upcoming changes to software applications. All version numbers refer to actual module names. Applications not listed here will remain unchanged.
Software | Current default | New default | To be removed | Notes | |
---|---|---|---|---|---|
ABAQUS | 6.11-2 | 6.14 | 6.8-4, 6.8-4-test, 6.11-1, 6.11-1-test | ||
AMBER | 11 | 14 | |||
ANSYS | 14.5.7 | 16.0 | 13, 15.0 | ansyspar licenses moving to Oakley | |
COMSOL | 43a-4.3.1.161 | 51 | 42a, 50 | ||
CUDA | 5.0.35 | 6.5.14 | 4.1.28, 4.2.9 | ||
FLUENT | 15.0.7 | 15.0.7 | 13, 13-ndem, 13-test | no change to default; ansyspar licenses moving to Oakley | |
Gaussian | g09c01 | g09d01 | |||
GROMACS | 4.5.5 | 4.6.3 | |||
LAMMPS | 12Feb12 | 5Sep14 | |||
LS-DYNA | LS-DYNA (smp solvers) | 971_d_5.1.1 | 971_d_7.1.1 | R5.0 | |
MPP-DYNA (mpp solvers) | 971_s_R5.1.1_ndem | 971_d_7.1.1 | R4.2.1, R5.0 | Dependent on IntelMPI | |
MATLAB | r2013a | r2014b | R2011b, R2012a, R2012b | ||
Python | 2.7.1 | 3.4.2 | 3.4.1 | Module only (misnamed) | |
Q-Chem | 4.0.1 | 4.3 | |||
STAR-CCM | 7.06.012 | 10.4.009 | 7.04 | ||
TotalView | 8.9.2-1 | 8.14.1-8 | |||
Turbomole | 6.3.1 | 6.5 | |||
TurboVNC | 1.1 | 1.2 |
The following table gives details about the default versions for compilers and MPI implementations . The versions refer to actual module names.
softwar | Current default | New default | To be removed | Notes |
---|---|---|---|---|
GNU Compilers | 4.4.7 | 4.8.4 | 4.4.5 (module only) | Module default version is not system default |
Intel Compilers | 12.1.4.319 | 15.0.3 | 12.1.0, 13.0.1.117, 13.1.2.183 | |
Intel MPI | 4.0.3 | 5.0.3 | Default depends on compiler version. | |
MVAPICH2 | 1.7 | 2.1 | 1.7-r5140, 1.8-r5668, 1.9a2, 1.9a, 1.9b, 1.9rc1, 2.0a, 2.0rc1, 2.0 | Default depends on compiler version |
PGI Compilers | 12.10 | 15.4 | 11.8, 12.5, 12.6, 12.9 |
The following libraries will be rebuilt for the new default compiler/mvapich2 versions.
Software | New default | Notes |
---|---|---|
FFTW3 | 3.3.4 | |
HDF5 | 1.8.15 | Patch 1, serial & parallel |
Metis | 5.1.0 | |
MKL | 11.2.3 | interfaces |
NetCDF | 4.3.3.1 | serial & parallel, with Fortran & C++ interfaces |
ParMetis | 4.0.3 | |
ScaLAPACK | 2.0.2 | |
SPRNG | 2.0b | |
SuiteSparse | 4.4.4 | |
SuperLU_DIST | 4.0 | |
SuperLU_MT | 3.0 |
OSC is refreshing the software stack on Ruby on September 15, 2015 (during the scheduled downtime). During the software refresh, some default versions are updated to be more up-to-date. Information about the old and new default versions, as well as all available versions of each software package will be included on the corresponding OSC software webpage. See https://www.osc.edu/supercomputing/software-list.
module load mic
to set up the environment for programming for the Phi. For more details, see https://www.osc.edu/documentation/supercomputers/using_the_intel_xeon_phi_on_ruby. If you compile and link your own software you need to be particularly aware of the changes in the default modules. You will probably need to either rebuild your software or explicitly load the compiler and MPI modules that you built your code with before you run the code.
module load modules/au2014
. This environment was the default environment at login on Ruby prior to 9/15/2015. If your code is built with compilers other than Intel compiler, you can explicitly load the default module prior to 9/15/2015 using the command module load name
. Please refer to Compilers/MPI or the corresponding OSC software webpage (See https://www.osc.edu/supercomputing/software-list) for more information.The following table gives details about the upcoming changes to software applications. All version numbers refer to actual module names. Applications not listed here will remain unchanged.
Software | Current default | New default | |
---|---|---|---|
MATLAB | r2014a | r2014b |
The following table gives details about the default versions for compilers and MPI implementations . The versions refer to actual module names.
software | Current default | New default | Notes |
---|---|---|---|
GNU Compilers | 4.4.7 | 4.8.4 | Module default version is not system default |
Intel Compilers | 15.0.0 | 15.0.3 | |
MVAPICH2 | 2.1rc1 | 2.1 | Default depends on compiler version. |
PGI Compilers | 14.9 | 15.4 |
The following libraries will be rebuilt for the new default compiler/mvapich2 versions.
Software | New default | Notes |
---|---|---|
FFTW3 | 3.3.4 | |
HDF5 | 1.8.15 | Patch 1, serial & parallel |
MKL | 11.2.3 | interfaces |
NetCDF | 4.3.3.1 | serial & parallel, with Fortran & C++ interfaces |
ScaLAPACK | 2.0.2 |
OSC is refreshing the software stack for Oakley and Ruby on February 22, 2017 (during the scheduled downtime). During the software refresh, some default versions are updated to be more up-to-date and some older versions are removed. Information about the old and new default versions, as well as all available versions of each software package will be included on the corresponding OSC software webpage. See https://www.osc.edu/supercomputing/software-list.
If you compile and link your own software you need to be particularly aware of the changes in the default modules. You will probably need to either rebuild your software or explicitly load the compiler and MPI modules that you built your code with before you run the code.
module load modules/au2015
. This environment was the default environment at login on Oakley from 9/15/2015 to 2/22/2017. If your code is built with compilers other than Intel compiler, you can explicitly load the old default module using the command module load name/version
. Please refer to Compilers/MPI or the corresponding OSC software webpage (See https://www.osc.edu/supercomputing/software-list) for more information.The following table gives details about the default versions for compilers and MPI implementations . The versions refer to actual module names. Except where otherwise noted, the new default on Oakley and Ruby matches the current default on Owens, i.e., all clusters will have the same defaults.
Software | Old default | new default | notes |
---|---|---|---|
intel | 15.0.3 | 16.0.3 | |
gnu | 4.8.4 | 4.8.5 | Module default is not system default |
pgi | 15.4 | 16.5 | |
mvapich2 | 2.1 | 2.2 | ***compiler-dependent |
intelmpi | 5.0.3 | 5.1.3 | Intel compiler only |
The following libraries will be rebuilt for the new default compiler/mvapich2 versions and also for gnu/6.3.0 with the default version of mvapich2.
software | new default | notes |
---|---|---|
boost | 1.63.0 | Intel and gnu compilers only, no mpi |
cairo | 1.14.2 | |
fftw3 | 3.3.5 | |
hdf5 | 1.8.17 | serial & parallel |
metis | 5.1.0 | |
mkl | 11.3.3 | Interfaces not built. Contact oschelp@osc.edu if you need them. |
netcdf | 4.3.3.1 | serial & parallel, with Fortran & C++ interfaces |
parmetis | 4.0.3 | |
scalapack | 2.0.2 | |
suitesparse | 4.5.3 |
The following table gives details about the upcoming changes to software applications. All version numbers refer to actual module names. Applications not listed here will remain unchanged.
Software | Old default | New default | Notes |
---|---|---|---|
MPP_DYNA | 971_d_R7.1.1 | 9.0.1 | |
NAMD | 2.11 | 2.12 | |
OPENFORM | 2.3.0 | 3.0.0 | |
WARP3D | 17.5.3 | 17.7.4 | |
CMAKE | 2.8.10.2 | 3.7.2 | |
PARAVIEW | 4.4.0 | ||
JAVA | 1.7.0_55 | 1.8.0_60 | |
BLAST | 2.2.26 | 2.6.0+ | |
TURBOMOLE | 6.5 | 7.0.1 | |
QCHEM | 4.3 | 4.4.1 | |
SCHRODINGER | 14 | 15 | |
ABAQUS | 6.14 | 2016 | |
FLUENT | 15.0.7 | 16.0 | |
LS-DYNA | 7.1.1 | 9.0.1 | |
COMSOL | 51 | 52 | |
CUDA | 6.5.14 |
7.5.18 (oakley) 8.0.44(ruby) |
|
STARCCM | 10.04.009 | 11.06.011 | |
TURBOVNC | 1.2 | 2.0.91 | |
MATLAB | r2014b | r2016b | |
GAUSSIAN | g09d01 | g09e01 |
OSC is refreshing the software stack for Owens and Ruby on September 4, 2018. This will be done by a rolling reboot. During the software refresh, some default versions are updated to be more up-to-date. Information about the old and new default versions, as well as all available versions of each software package will be included on the corresponding OSC software webpage. See https://www.osc.edu/supercomputing/software-list.
If you compile and link your own software you need to be particularly aware of the changes in the default modules. You will probably need to either rebuild your software or explicitly load the compiler and MPI modules that you built your code with before you run the code.
module load modules/au2016
. This environment was the default environment at login on Owens and Ruby until 9/4/2018. If your code is built with compilers other than Intel compiler, you can explicitly load the old default module using the command module load name/version
. Please refer to Compilers/MPI or the corresponding OSC software webpage (See https://www.osc.edu/supercomputing/software-list) for more information.The following table gives details about the default versions for compilers and MPI implementations . The versions refer to actual module names, except where otherwise noted. Intel 17.0.7 and gnu 4.8.5 is also available with mvapich2 2.3.
Software | Old default | new default | notes |
---|---|---|---|
intel | 16.0.3 | 18.0.3 | |
gnu | 4.8.4 | 7.3.0 | Module default is not system default |
pgi | 16.5.0 | 18.4 | |
mvapich2 | 2.2 | 2.3 | ***compiler-dependent |
intelmpi | 5.1.3 | 2018.3 | Intel compiler only |
openmpi | 1.10-hpcx | 3.1.0-hpcx | Owens only |
The following libraries will be rebuilt for the new default compiler/mvapich2 versions and also for gnu/4.8.5 and intel/17.0.7 with the new version of mvapich2 2.3.
software | old default | new default | notes |
---|---|---|---|
boost | 1.63.0 | 1.67.0 | Intel and gnu compilers only, no mpi |
fftw3 | 3.3.5 | 3.3.8 | |
hdf5 | 1.8.17 | 1.10.2 | serial & parallel |
metis | 5.1.0 | 5.1.0 | |
mkl | 11.3.3 | 2018.0.3 | Interfaces not built. Contact oschelp@osc.edu if you need them. |
netcdf | 4.3.3.1 | 4.6.1 | serial & parallel, with Fortran & C++ interfaces |
parmetis | 4.0.3 | 4.0.3 | |
scalapack | 2.0.2 | 2.0.2 | |
ncarg | 6.3.0 | 6.5.0 | Intel and gnu compilers only. Ownes only. |
The following table gives details about the upcoming changes to software applications. All software names and version numbers refer to actual module names.
Software | Old default | New default | Notes |
---|---|---|---|
cmake | 3.7.2 | 3.11.4 | |
python | 3.6 | 3.6-conda5.2 | 2.7-conda5.2 is also available. |
git | 1.9.4 | 2.18.0 | |
cuda | 8.0.44 | 9.2.88 | |
R | 3.2.0 | 3.5.0 | Owens only |
arm-ddt | 7.0 | 18.2.1 | |
arm-map | 7.0 | 18.2.1 | |
arm-pr | 7.0 | 18.2.1 | |
virtualgl | 2.5 | 2.5.2 | |
darshan | 3.1.2 | 3.1.6 | Owens only |
siesta | 4.0 | 4.0.2 | Owens only |
siesta-par | 4.0 | 4.0.2 | Owens only |
lammps | 14May16 | ||
gromacs | 5.1.2 | 2018.2 | Owens only |
namd | 2.12 | ||
amber | 16 | ||
paraview | 4.4.0 | 5.5.2 | |
qchem | 4.4.1 | 5.1.1 | |
schrodinger | 16 | 2018.3 | Owens only |
abaqus | 2016 | 2018 | Owens only |
turbomole | 7.1 | 7.2.1 | Owens only |
ansys | 17.2 | 19.1 | Owens only |
comsol | 52a | 53a | Owens only |
starccm | 11.06.011 | 13.02.011 | Owens only |
turbovnc | 2.1.1 | 2.1.90 | |
matlab | r2016b | r2018a | |
gaussian | g09e01 | g16a03 | |
nwchem | 6.6 | 6.8 | Owens only |
turbovnc | 2.1.1 | 2.1.90 |
OSC will be refreshing the software stack for Owens and Pitzer on May 19, 2020. This will be done in a system-wide downtime. During the software refresh, some default versions will be changed to be more up-to-date. Information about the new default versions, as well as all available versions of each software package will be included on the corresponding OSC software webpage. See https://www.osc.edu/supercomputing/software-list.
If you compile and link your own software you need to be particularly aware of the changes in the default modules. You will probably need to either rebuild your software or explicitly load the compiler and MPI modules that you built your code with before you run the code.
module load modules/au2018
. This environment was the default environment at login on Owens and Pitzer until 5/19/2020. If your code is built with compilers other than Intel compiler, you can explicitly load the old default module using the command module load name/version
. Please refer to Compilers/MPI or the corresponding OSC software webpage (See https://www.osc.edu/supercomputing/software-list) for more information.Certain MPI-IO operations with intelmpi/2019.3 may crash, fail or proceed with errors on the home directory. We do not expect the same issue on our GPFS file system, such as the project space and the scratch space. The problem might be related to the known issue reported by HDF5 group. Please read the section "Problem Reading A Collectively Written Dataset in Parallel" from HDF5 Known Issues for more detail.
MPI-IO routines with intelmpi/2019.5 on our GPFS file systems may fail as a known issue from Intel MPI. You can set an environment variable, I_MPI_EXTRA_FILESYSTEM=0
for a workaround or simply use intelmpi/2019.3
, which is our new default version. Please read the section "Known Issues and Limitations, Intel MPI Library 2019 Update 5" from Intel MPI Known Issues for more detail.
PGI compilers later than version 19.1 use a LLVM-based back-end for code generation. OSC's previous default PGI compiler was pgi/18.4, and it used a non-LLVM back-end. For more detail, please read our PGI compiler page.
You may have a warning message when you run a MPI job with pgi/20.1 and mvapich2/2.3.3:
WARNING: Error in initializing MVAPICH2 ptmalloc library.Continuing without InfiniBand registration cache support.
Please read about the impact of disabling memory registration cache on application performance in the Mvapich2 2.3.3 user guide
The following table gives details about the default versions for compilers and MPI implementations . The versions refer to actual module names, except where otherwise noted.
Software | Old default | new default | notes |
---|---|---|---|
intel | 18.0.3 | 19.0.5 | |
gnu | 7.3.0 | 9.1.0 | |
pgi | 18.4 | 20.1 | |
mvapich2 | 2.3.2 | 2.3.3 | available with intel, gnu, pgi compiler |
intelmpi | 2018.3 | 2019.3 | Intel compiler only |
openmpi | 3.1.0-hpcx | 4.0.3-hpcx | Intel and gnu compiler |
The following libraries will be built for the new default compiler/MPI versions.
software | old default | new default | notes |
---|---|---|---|
boost | 1.67.0 | 1.72.0 | |
fftw3 | 3.3.8 | 3.3.8 | |
hdf5 | 1.10.2 | 1.12.0 |
serial & parallel. There is API compatibility issue on the new version, 1.12.0. Please read this page for more detail. |
metis | 5.1.0 | 5.1.0 | |
mkl | 2018.0.3 | 2019.0.5 | Only modules not built. |
netcdf | 4.6.1 | 4.7.4 | serial & parallel, with C, Fortran and C++ interfaces |
parmetis | 4.0.3 | 4.0.3 | |
scalapack | 2.0.2 | 2.1.0 | |
ncarg | 6.5.0 | 6.6.2 |
software/module | versions | notes |
---|---|---|
lapack | 3.8.0, owens and pitzer | We recommand to use mkl instead. |
The following table gives details about the upcoming changes to software applications. All software names and version numbers refer to the actual module names.
Software | Old default | New default | Notes |
---|---|---|---|
amber | 18 | 19 | 20 coming |
darshan | 3.1.6 | 3.1.8 | |
espresso | 6.3 | 6.5 | |
gromacs | 2018.2 | 2020.2 | |
lammps | 22Aug18 | 3Mar20 | |
mpp-dyna | 971_d_10.1.0.lua | 971_s_11.0.0 | Owens only |
namd | 2.12 | 2.13 | |
nwchem | 6.8 | 7.0.0 | |
openfoam | 5.0 | 7.0 | |
bedtools | 2.25.0 | 2.29.2 | Owens only |
rosetta | 3.10 | 3.12 | |
abaqus | 2018 | 2020 | Owens only |
arm-ddt/arm-map/arm-pr | 18.2.1 | 20.0.3 | |
bowtie2 | 2.2.9 | 2.4.1 | |
cmake | 3.11.4 | 3.17.2 | |
comsol | 53a | 5.5 | Owens only |
cuda | 9.2.88 | 10.2.89 | See the software page for GNU compiler support |
desmond | 2018.2 | 2019.1 | Owens only |
gatk | 3.5 | 4.1.2.0 | |
gaussian | g16a03 | g16c01 | |
hyperworks | 2017.1 | 2019.2 | Owens only |
ls-dyna | 971_s_9.0.1 | 971_s_11.0.0 | Owens only |
matlab | r2018b | r2020a | |
paraview | 5.5.2 | 5.8.0 | |
samtools | 1.3.1 | 1.10 | |
schrodinger | 2018.3 | 2020.1 | Owens only |
sratoolkit | 2.9.0 | 2.9.6 | |
starccm | 13.02.011 | 15.02.007 | Owens only |
vcftools | 0.1.14 | 0.1.16 |