Difference between revisions of "Software and Libraries"

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All the software listed on this page is accessed using a [[GPC_Quickstart#Environment_Variables | modules]] system.   
 
All the software listed on this page is accessed using a [[GPC_Quickstart#Environment_Variables | modules]] system.   
  
−
To use particular software just load the module (the last column in the following table) as follows.
+
To use particular software, just load the module (the last column in the following table) as follows.
 
<pre>
 
<pre>
 
module load module_name_here
 
module load module_name_here
 
</pre>
 
</pre>
 +
It is recommended to load frequently used modules in the file .bashrc in your home directory.
  
 +
Modules that load libraries, define environment variables pointing to the location of library files and
 +
include files for use Makefiles. These environment variables follow the naming convention
 +
<pre>
 +
SCINET_[module-name]_{LIB,INC,BASE}
 +
</pre>
 +
So to compile and link the library, you will have to add <tt>-I$SCINET_[module-name]_INC</tt> and <tt>-L$SCINET_[module-name]_LIB</tt>, respectively, in addition to the usual <tt>-l[libname]</tt>.
  
 
For a full list of available software packages that may be accesses with the modules system, use the command
 
For a full list of available software packages that may be accesses with the modules system, use the command
Line 31: Line 38:
 
! Command/Library
 
! Command/Library
 
! Module Name
 
! Module Name
−
|-
+
|- style='background: lightgray'
 
|Intel Compiler
 
|Intel Compiler
 
| 11.1  
 
| 11.1  
Line 37: Line 44:
 
| <tt>icpc,icc,ifort, includes MKL library</tt>
 
| <tt>icpc,icc,ifort, includes MKL library</tt>
 
| <tt>intel</tt>
 
| <tt>intel</tt>
−
|-
+
|- style='background: lightgray'
 
| GCC Compiler
 
| GCC Compiler
 
| 4.4.0
 
| 4.4.0
Line 43: Line 50:
 
| <tt>gcc,g++,gfortran</tt>
 
| <tt>gcc,g++,gfortran</tt>
 
| <tt>gcc</tt>
 
| <tt>gcc</tt>
−
|-
+
|- style='background: lightgray'
 
| IntelMPI
 
| IntelMPI
 
| 3.2.2
 
| 3.2.2
Line 49: Line 56:
 
| <tt>mpicc,mpiCC,mpif77,mpif90</tt>
 
| <tt>mpicc,mpiCC,mpif77,mpif90</tt>
 
| <tt>intelmpi</tt>
 
| <tt>intelmpi</tt>
−
|-
+
|- style='background: lightgray'
 
| OpenMPI
 
| OpenMPI
 
| 1.4.1
 
| 1.4.1
Line 55: Line 62:
 
| <tt>mpicc,mpiCC,mpif77,mpif90</tt>
 
| <tt>mpicc,mpiCC,mpif77,mpif90</tt>
 
| <tt>openmpi</tt>
 
| <tt>openmpi</tt>
−
|-
+
|- style='background: white'
 
| Emacs
 
| Emacs
 
| 23.1
 
| 23.1
Line 61: Line 68:
 
| <tt>emacs</tt>
 
| <tt>emacs</tt>
 
| <tt>emacs</tt>
 
| <tt>emacs</tt>
−
|-
+
|- style='background: white'
 
| Git
 
| Git
 
| 1.6.3
 
| 1.6.3
Line 67: Line 74:
 
| <tt>git,gitk</tt>
 
| <tt>git,gitk</tt>
 
| <tt>git</tt>
 
| <tt>git</tt>
−
|-
+
|- style='background: white'
 
| Valgrind
 
| Valgrind
 
| 3.4.1
 
| 3.4.1
Line 73: Line 80:
 
| <tt>valgrind,cachegrind</tt>
 
| <tt>valgrind,cachegrind</tt>
 
| <tt>valgrind</tt>
 
| <tt>valgrind</tt>
−
|-
+
|- style='background: lightgray'
 
| grace
 
| grace
 
| 5.22.1
 
| 5.22.1
Line 79: Line 86:
 
| <tt>xmgrace</tt>
 
| <tt>xmgrace</tt>
 
| <tt>graphics</tt>
 
| <tt>graphics</tt>
−
|-
+
|- style='background: lightgray'
 
| Gnuplot
 
| Gnuplot
 
| 4.2.6
 
| 4.2.6
Line 85: Line 92:
 
| <tt>gnuplot</tt>
 
| <tt>gnuplot</tt>
 
| <tt>graphics</tt>
 
| <tt>graphics</tt>
−
|-
+
|- style='background: lightgray'
 
| VMD
 
| VMD
 
| 1.8.6
 
| 1.8.6
Line 91: Line 98:
 
| <tt>vmd</tt>
 
| <tt>vmd</tt>
 
| <tt>vmd</tt>
 
| <tt>vmd</tt>
−
|-
+
|- style='background: lightgray'
 
| ferret
 
| ferret
 
| 6.4
 
| 6.4
Line 97: Line 104:
 
| <tt>ferret</tt>
 
| <tt>ferret</tt>
 
| <tt>ferret</tt>
 
| <tt>ferret</tt>
−
|-
+
|- style='background: lightgray'
 +
| ncl/ncarg
 +
| 5.1.1
 +
| NCARG graphics and ncl utilities
 +
| <tt>ncl</tt>
 +
| <tt>ncl</tt>
 +
|- style='background: white'
 
| netCDF + udunits
 
| netCDF + udunits
 
| 4.0.1 + 2.1.8
 
| 4.0.1 + 2.1.8
Line 103: Line 116:
 
| <tt>ncdump,ncgen,libnetcdf,libudunits2</tt>
 
| <tt>ncdump,ncgen,libnetcdf,libudunits2</tt>
 
| <tt>netcdf</tt>
 
| <tt>netcdf</tt>
−
|-
+
|- style='background: white'
 
| NCO
 
| NCO
 
| 3.9.9
 
| 3.9.9
Line 109: Line 122:
 
| <tt>ncap, ncap2, ncatted, etc.</tt>
 
| <tt>ncap, ncap2, ncatted, etc.</tt>
 
| <tt>nco</tt>
 
| <tt>nco</tt>
−
|-
+
|- style='background: white'
 
| HDF4
 
| HDF4
 
| 4.2r4
 
| 4.2r4
Line 115: Line 128:
 
| <tt>h4fc,hdiff,...,libdf,libsz</tt>
 
| <tt>h4fc,hdiff,...,libdf,libsz</tt>
 
| <tt>hdf4</tt>
 
| <tt>hdf4</tt>
−
|-
+
|- style='background: white'
 
| HDF5
 
| HDF5
 
| 1.8.4-v18
 
| 1.8.4-v18
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| <tt>h5ls, h5diff, ..., libhdf5</tt>
 
| <tt>h5ls, h5diff, ..., libhdf5</tt>
 
| <tt>hdf5</tt>
 
| <tt>hdf5</tt>
−
|-
+
|- style='background: lightgray'
−
| gsl
 
−
| 1.13
 
−
| GNU Scientific Library
 
−
| <tt>libgsl, libgslcblas</tt>
 
−
| <tt>gsl</tt>
 
−
|-
 
−
| fftw
 
−
| 3.2.2
 
−
| fftw fast Fourier transform library
 
−
| <tt>libfftw3</tt>
 
−
| <tt>fftw</tt>
 
−
|-
 
 
| [[gamess|GAMESS (US)]]
 
| [[gamess|GAMESS (US)]]
 
| January 12, 2009 R3
 
| January 12, 2009 R3
Line 139: Line 140:
 
| <tt>rungms</tt>
 
| <tt>rungms</tt>
 
| <tt>gamess</tt>
 
| <tt>gamess</tt>
−
|-
+
|- style='background: lightgray'
 
| [http://blast.ncbi.nlm.nih.gov BLAST]
 
| [http://blast.ncbi.nlm.nih.gov BLAST]
 
| 2.2.23+
 
| 2.2.23+
Line 145: Line 146:
 
| <tt>blastn,blastp,blastx,psiblast,tblastn...</tt>
 
| <tt>blastn,blastp,blastx,psiblast,tblastn...</tt>
 
| <tt>blast</tt>
 
| <tt>blast</tt>
−
|-
+
|- style='background: lightgray'
 
| [[amber|AMBER 10]]
 
| [[amber|AMBER 10]]
 
| Amber 10 + Amber Tools 1.3
 
| Amber 10 + Amber Tools 1.3
Line 151: Line 152:
 
| <tt>sander, sander.MPI</tt>
 
| <tt>sander, sander.MPI</tt>
 
| <tt>amber10</tt>
 
| <tt>amber10</tt>
−
|-
+
|- style='background: lightgray'
−
| ncl/ncarg
+
| [http://www.gdal.org/ GDAL]
−
| 5.1.1
+
| 1.7.1
−
| NCARG graphics and ncl utilities
+
| Geospatial Data Abstraction Library
−
| <tt>ncl</tt>
+
| <tt>gdal_contour,gdal_rasterize,gdal_grid, libgdal</tt>
−
| <tt>ncl</tt>
+
| <tt>gdal</tt>
−
|-
+
|- style='background: lightgray'
 
| [http://www.mcs.anl.gov/petsc/petsc-as/  PETSc ]
 
| [http://www.mcs.anl.gov/petsc/petsc-as/  PETSc ]
 
|  
 
|  
Line 163: Line 164:
 
| <tt>libpetsc, etc.. </tt>
 
| <tt>libpetsc, etc.. </tt>
 
| <tt>petsc</tt>
 
| <tt>petsc</tt>
−
|-
+
|- style='background: lightgray'
 +
| Matlab/IDL/Commercial software
 +
|
 +
| Little to none.  See [[FAQ#How_can_I_run_Matlab_.2F_IDL_.2F_my_favourite_commercial_software_on_SciNet.3F | the FAQ]]
 +
|
 +
|
 +
|- style='background: white'
 +
| gsl
 +
| 1.13
 +
| GNU Scientific Library
 +
| <tt>libgsl, libgslcblas</tt>
 +
| <tt>gsl</tt>
 +
|- style='background: white'
 +
| fftw
 +
| 3.2.2
 +
| fftw fast Fourier transform library
 +
| <tt>libfftw3</tt>
 +
| <tt>fftw</tt>
 +
|- style='background: white'
 
| extras
 
| extras
 
|   
 
|   
Line 169: Line 188:
 
| <tt>libXaw,...,libjpeg</tt>
 
| <tt>libXaw,...,libjpeg</tt>
 
| <tt>extras</tt>
 
| <tt>extras</tt>
−
|-
 
−
| [http://www.gdal.org/ GDAL]
 
−
| 1.7.1
 
−
| Geospatial Data Abstraction Library
 
−
| <tt>gdal_contour,gdal_rasterize,gdal_grid, libgdal</tt>
 
−
| <tt>gdal</tt>
 
−
|-
 
−
| Matlab/IDL/Commercial software
 
−
|
 
−
| Little to none.  See [[FAQ#How_can_I_run_Matlab_.2F_IDL_.2F_my_favourite_commercial_software_on_SciNet.3F | the FAQ]]
 
−
|
 
−
|
 
 
|}
 
|}
  

Revision as of 23:22, 27 April 2010

GPC Software

All the software listed on this page is accessed using a modules system.

To use particular software, just load the module (the last column in the following table) as follows. 

module load module_name_here

It is recommended to load frequently used modules in the file .bashrc in your home directory.

Modules that load libraries, define environment variables pointing to the location of library files and include files for use Makefiles. These environment variables follow the naming convention 

SCINET_[module-name]_{LIB,INC,BASE}

So to compile and link the library, you will have to add -I$SCINET_[module-name]_INC and -L$SCINET_[module-name]_LIB, respectively, in addition to the usual -l[libname].

For a full list of available software packages that may be accesses with the modules system, use the command 

module avail

For a list of the currently loaded modules in your shell, use the command 

module list

For a description of a particular module, use the command 

module help module_name_here


Software Version Comments Command/Library Module Name
Intel Compiler 11.1 icpc,icc,ifort, includes MKL library intel
GCC Compiler 4.4.0 gcc,g++,gfortran gcc
IntelMPI 3.2.2 mpicc,mpiCC,mpif77,mpif90 intelmpi
OpenMPI 1.4.1 mpicc,mpiCC,mpif77,mpif90 openmpi
Emacs 23.1 New version of popular text editor emacs emacs
Git 1.6.3 Revision control system git,gitk git
Valgrind 3.4.1 Memory checking utility valgrind,cachegrind valgrind
grace 5.22.1 Plotting utility xmgrace graphics
Gnuplot 4.2.6 Plotting utility gnuplot graphics
VMD 1.8.6 Visualization and analysis utility vmd vmd
ferret 6.4 Plotting utility ferret ferret
ncl/ncarg 5.1.1 NCARG graphics and ncl utilities ncl ncl
netCDF + udunits 4.0.1 + 2.1.8 Scientific data storage and retrieval ncdump,ncgen,libnetcdf,libudunits2 netcdf
NCO 3.9.9 NCO utilities to manipulate netCDF files ncap, ncap2, ncatted, etc. nco
HDF4 4.2r4 Scientific data storage and retrieval h4fc,hdiff,...,libdf,libsz hdf4
HDF5 1.8.4-v18 Scientific data storage and retrieval, parallel I/O h5ls, h5diff, ..., libhdf5 hdf5
GAMESS (US) January 12, 2009 R3 General Atomic and Molecular Electronic Structure System rungms gamess
BLAST 2.2.23+ Basic Local Alignment Search Tool blastn,blastp,blastx,psiblast,tblastn... blast
AMBER 10 Amber 10 + Amber Tools 1.3 Amber Molecular Dynamics Package sander, sander.MPI amber10
GDAL 1.7.1 Geospatial Data Abstraction Library gdal_contour,gdal_rasterize,gdal_grid, libgdal gdal
PETSc Portable, Extensible Tolkit for Scientific Computation (PETSc) libpetsc, etc.. petsc
Matlab/IDL/Commercial software Little to none. See the FAQ
gsl 1.13 GNU Scientific Library libgsl, libgslcblas gsl
fftw 3.2.2 fftw fast Fourier transform library libfftw3 fftw
extras Full set of X11 libraries and others not installed on compute nodes libXaw,...,libjpeg extras

TCS Software

The software listed below uses the same module system as described above for the GPC.

Software Version Comments Command/Library Module Name
antlr 2.7.7 ANother Tool for Language Recognition antlr, antlr-config
libantlr, antlr.jar, antlr.py 		antlr
gsl 1.13 GNU Scientific Library libgsl,libgslcblas gsl
HDF4 4.2.5 Scientific data storage and retrieval h4fc,hdiff,...,libdf,libsz hdf4
mpe 2 1.0.6 Performance Visualization for Parallel Programs -lmpe mpe
netCDF + ncview 4.0.1 Scientific data storage and retrieval ncdump,ncgen,libnetcdf, ncview netcdf
NCL 5.1.1 NCAR Command Language ncl
libncl, ... 		ncl
NCO 3.9.6 NCO utilities to manipulate netCDF files ncap, ncap2, ncatted, etc. nco
parallel netCDF 1.1.0 Scientific data storage and retrieval using MPI-IO libpnetcdf.a parallel-netcdf
scalasca 1.2 SCalable performance Analysis of LArge SCale Applications scalasca, ... scalasca
upc 1.2 Unified Parallel C xlupc upc
extras Adds paths to a fuller set of libraries to your user environment
compile with -I$SCINET_EXTRAS_INC
link with -L$SCINET_EXTRAS_LIB 		libfftw, libfftw_mpi, libfftw3, libhdf5, liblapack, ... extras
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