Software Refresh - August/September 2018

OSC is refreshing the software stack for Owens and Ruby on September 3, 2018(The date may be subject to change). 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 (9/3/2018), use the command   module load modules/au2016   . This environment was the default environment at login on Owens and Ruby until 9/3/2018. 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.

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

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 version numbers refer to actual module names. Applications not listed here will remain unchanged, however the list will be modified as we update the software. Before the rolling reboot, a complete list will be posted.

Software Old default New default Notes
cmake 3.7.2 3.11.4  
python 3.6 3.6-conda5.2  
R 3.2.0    
virtualgl 2.5    
darshan 3.1.2 3.1.6 Owens only
siesta 4.0 4.0.2 Owens only
mpp-dyna R9.0.1    
ls-dyna R9.0.1    
lammps 14May16    
gromacs 5.1.2    
namd 2.12    
amber 16    
nwchem 6.6    
gamess 18Aug2019    
openfoam 4.1    
warp3d 17.7.4    
paraview 4.4.0 5.5.2  
qchem 4.4.1 5.1  
schrodinger 16    
       
       
       
       

 

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