Third-party software planZhengji Zhao

NERSC User ServicesZZhao@lbl.gov

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).