Software Refresh

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coordinated software refresh (update the default versions to be more up-to-date and remove some versions that are quite out of date) on OSC systems.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. (link sends e-mail)

Supercomputer: 
Service: 

Updates to Oakley Application Software - September 2015

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.

Summary of Changes

  • New versions of the compilers and MPI have been installed and will become the defaults. Libraries will be rebuilt with the new default compilers and MPI. The newest stable version of each library will be used in most cases.
  • For software applications, the latest installed version will become the default in most cases, but the current default version will be kept and can be requested explicitly. New versions of some applications will be installed (which is done by request). Some old versions will be deleted (but not the current default version). Details are given in the tables below.
  • Licenses that are currently restricted to Glenn, specifically ansyspar licenses (parallel Ansys/Fluent/CFX), will be moved to Oakley in preparation for retirement of the Glenn cluster.
  • Some behind-the-scenes changes will be made to the module system. These changes won’t affect most users. Contact OSC Help if you experience problems.

Impact on User-Built Software

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.

To load the default environment at login on Oakley prior to the downtime (9/15/2015), use the command   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.

Details

Software Applicationso

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    

 

Compilers/MPI

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  

Libraries

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  

 

Service: 

Updates to Ruby Application Software - September 2015

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.

Summary of Changes

  • New versions of the compilers and MPI have been installed and will become the defaults. Libraries will be rebuilt with the new default compilers and MPI. The newest stable version of each library will be used in most cases.
  • For software applications, the latest installed version will become the default in most cases, but the current default version will be kept and can be requested explicitly. Details are given in the tables below.
  • The mic functionality has been merged into the intel modules and will be loaded automatically at login. There is no need to use 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

Impact on User-Built Software

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.

To load the default environment at login on Ruby prior to the downtime (9/15/2015), use the command   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.

Details

Software Applications

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

Compilers/MPI

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  

Libraries

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  
Service: 

Software Refresh - February 2017

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.

Summary of Changes

  • New versions of the compilers and MPI have been installed and will become the defaults. Libraries will be rebuilt with the new default compilers and MPI. The newest stable version of each library will be used in most cases.
  • For software applications, the latest installed version will become the default in most cases, but the current default version will be kept and can be requested explicitly. New versions of some applications will be installed (which is done by request).

Impact on User-Built Software

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.

To load the default environment at login on Oakley or Ruby prior to the downtime (2/22/2017), use the command   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.

Details

Compilers/MPI

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

Libraries

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  

Applications

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  

 

Service: 

Software Refresh - August/September 2018

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.

Summary of Changes

  • New versions of the compilers and MPI have been installed and will become the defaults. Libraries will be rebuilt with the new default compilers and MPI. The newest stable version of each library will be used in most cases.
  • For software applications, the latest installed version will become the default in most cases, but the current default version will be kept and can be requested explicitly. New versions of some applications will be installed (which is done by request).

Impact on User-Built Software

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.

To load the default environment at login on Owens or Ruby prior to the rolling reboot (9/4/2018), use the command   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.
Libraries for intel/18.0.3 and intel/17.0.7 are not compatible with cxx17. Intel compilers need gnu library to support 2017 ISO C++ standard, and cxx17 is the module to load the gnu environment for the intel compilers. You could have errors when you try to compile with the libraries with the default intel environment. Currently, we are fixing the issue. For the update, please see the Known Issue page for more information.

Details

Compilers/MPI

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

Libraries

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.

Applications

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  

 

Service: 

Software Refresh - May 2020

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.

Summary of Changes

  • New versions of the compilers and MPI have been installed and will become the defaults. Libraries will be rebuilt with the new default compilers and MPI. The newest stable version of each library will be used in most cases.
  • For software applications, the latest installed version will become the default in most cases, but the current default version will be kept and can be requested explicitly. New versions of some applications will be installed.

Impact on User-Built Software

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.

After the refresh on May 19, 2020, to load the previous default environment at login on Owens or Pitzer, use the command   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.

Known issues and changes

intelmpi/2019.3: MPI-IO issues on home directories

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.

intelmpi/2019.5: MPI-IO issues on GPFS file system

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/20.1: LLVM back-end for code generation as default

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.

pgi/20.1: disabling memory registration

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

Details

 

Compilers/MPI

 

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

 

Libraries

 

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 to be removed

 

software/module versions notes
lapack 3.8.0, owens and pitzer We recommand to use mkl instead.

 

Applications

 

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  

 

 

 

Supercomputer: 
Service: