Third-party software planZhengji Zhao
NERSC User [email protected]
NERSC User Group MeetingSeptember 19, 2007
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Third-party software
• Other than vendor-supplied applications, programming environment, libraries and tools – Compilers and Languages– Parallel Programming Libraries– Tools and Utilities– IO Libraries– Math Libraries– Application Software– Visualization Software
• Access to the third-party software is controlled via modules.
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Currently Available modules vendor-supplied vs third party applications
nid04107 z/zz217> module avail------------------------------- /opt/modulefiles ---------------------------------pgi, gcc, acml, mpich2 MPI, papi, Craypat, apprentice, torque/moab, …
--------------- /usr/common/usg/Modules/modulefiles -----------------ddt/2.1.3 idl/6.4(default) parmetis/3.1dfftpack/4.0(default) namd/2.6(default) subversion/1.3.1(default)ga/4.0.7(default) nco/3.1.6(default) szip/2.0(default)hdf/4.2r1(default) netcdf/3.6.1(default)hdf5/1.6.5(default) netcdf/3.6.2 vasp/4.6.28.pkent(default)hdf5_par/1.6.5(default) null zlib/1.2.1(default)
------------------ /usr/common/acts/Modules/modulefiles -------------aztec/2.1(default) petsc/2.3.3_O_complex superlu/3.0(default)petsc/2.3.3 petsc/2.3.3_g superlu_dist/2.0(default)petsc/2.3.3_O petsc/2.3.3_g_c++ tau/2.16.5(default)petsc/2.3.3_O_c++ petsc/2.3.3_g_complex
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Which software to install?
• Importance
• Budget
• Installation efforts
• CNL supported or not
• Users’ requests
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Compilers and Languages
• Vendor provided: – PGI Fortran77, PGI Fortran90, 95, PGI C, C++– GCC Fortran77, GCC C, C++, java (login nodes)– NAST
• Will install:– UPC (~late 2007)
• Possibly install:– PathScale
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IO Libraries
• Installed:– netCDF – HDF – HDF5 – HDF5 Parallel – NCO
• Will not install:– NCARU
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Parallel Programming Libraries
• Vendor provided:– MPICH2 MPI – Portals – SHMEM
• Installed:– Global Arrays
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Tools and Utilities
• Vendor supplied :– PAPI, CrayPat, Cray Apprentice, Shells, Modules, Perl,
Tcl/Tk, Python,GNU tools, GDB, CVS, RCS, Emacs, Vim, Gzip,
• Installed:– DDT– SubVersion– TAU
• Will install:– IPM end of 2007– nersc_utils end of 2007– Xemacs end of 2007?
• Will not install: – Totalview, Vast77to90, Crayconv, Sptools, Zerofault,
Assure, Vampir
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Math Libraries
• Vendor supplied:– ACML (LAPACK ), Libsci, FFTW
• Vendor will install:– BLACS, SCALAPACK, SuperLU, PETSc.
• Installed:– BLACS – SCALAPACK – SuperLU – PETSc
• Will install:– more ACTS (Osni’s talk)
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Math Libraries (cont)
• Possibly install:– PARPACK
• Will not install:– NAG serial, NAG parallel, NAG SMP – CERNLIB– IMSL– SPRNG – WSMP
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Application Software
• Installed:– NAMD (2.6)– VASP (4.6.28.pkent)
• Will install:– GAMESS when Cray version is available– NWChem when supported– CCSM when supported– CAM when supported– AMBER/PMEMD in ~1 month– MOLPRO in ~1 month– Q-Chem when supported
• Will not install:– GAUSSIAN – WIEN2k
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Visualization Software
• Installed:– IDL (6.4)
• Will install:– NCAR (4.4.2) soon
• Possibly install:– AVS/Express– Simple visualization tools, eg., Gnuplot
• Franklin is not really suitable for interactive graphics; suggest to use DaVinci for data analysis and visualization (analytics).