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software refresh (update the default versions to be more up-to-date and remove some versions that are quite out of date) on OSC systems.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

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: 

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: