Difference between revisions of "Software:Frontenac"

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|}
 
|}
  
−
Please note that all commands are ''case-sensitive''.
+
Please note that all commands are ''case-sensitive''. For an extremely comprehensive set of documenation on using the module system (such as how to write your own modules), you can refer to the official Lmod documentation here: [http://lmod.readthedocs.io/en/latest/ http://lmod.readthedocs.io/en/latest/]
−
 
+
−
For an extremely comprehensive set of documenation on using the module system (such as how to write your own modules), you can refer to the official Lmod documentation here: [http://lmod.readthedocs.io/en/latest/ http://lmod.readthedocs.io/en/latest/]
+
  
 
= Local vs. Compute Canada software =  
 
= Local vs. Compute Canada software =  
  
−
Software on the Frontenac cluster can come from two locations: locally or from Compute Canada's centralized software stack. The Compute Canada software stack is standardized, and contains a set of software that is identically compiled and setup across every cluster it is installed on. This is a fantastic tool for reproducibility and scaling your work across multiple clusters: the same software will work the same way, regardless of where you are using it. There is also a large amount of locally installed software as well. This is how most software requiring licensing or other special local considerations is installed. Using both sets of software is identical- just run <code>module load softwareName<code>.
+
Software on the Frontenac cluster can come from two locations: locally or from Compute Canada's centralized software stack. The Compute Canada software stack is standardized, and contains a set of software that is identically compiled and setup across every cluster it is installed on. This is a fantastic tool for reproducibility and scaling your work across multiple clusters: the same software will work the same way, regardless of where you are using it. There is also a large amount of locally installed software as well. This is how most software requiring licensing or other special local considerations is installed. Using both sets of software is identical- just run <code>module load softwareName</code>.
  
−
Please note that if you are the first user to use a software package, or it
+
Please note that if you are the first user to use a Compute Canada software package on a node (or it has not been used in some time), the software may initially appear to "hang" and do nothing for several seconds on launch. This is normal - the software is being re-downloaded and cached on the local system. To tell if a piece of software being used is coming from this centralized stack, you can run <code>which <some_command></code>. If the output begins with <code>/cvmfs</code>, it is part of the Compute Canada software stack.
  
 
= List of all installed software =  
 
= List of all installed software =  
Line 43: Line 41:
  
 
{| class="wikitable" style="text-align: left;  
 
{| class="wikitable" style="text-align: left;  
−
! Software Name !! Version !! Package Name !! Usage Notes  
+
! Software Name !! Package Name / version !! Usage Notes  
 +
|-
 +
| ABINIT || abinit/8.2.2 ||
 +
|-
 +
| ABySS || abyss/1.9.0 ||
 +
|-
 +
| AGOUTI || agouti/v0.3.3 ||
 +
|-
 +
| ALLPATHS-LG || allpaths-lg/52488 ||
 +
|-
 +
| rowspan=2 | Anaconda Python distribution || anaconda/2.7.13 || rowspan=2 |
 +
|-
 +
| anaconda/3.5.3
 +
|-
 +
| ARPACK || arpack-ng/3.4.0 ||
 +
|-
 +
| BamTools || bamtools/2.4.1 ||
 +
|-
 +
| BCFtools || bcftools/1.4 ||
 +
|-
 +
| beagle-lib || beagle-lib/2.1.2 ||
 +
|-
 +
| BEAST || beast/2.4.0 ||
 +
|-
 +
| BEDTools || bedtools/2.26.0 ||
 +
|-
 +
| Bioperl || bioperl/1.7.1 ||
 +
|-
 +
| BLAST || blast+/2.6.0 ||
 +
|-
 +
| BLAT || blat/3.5 ||
 +
|-
 +
| Boost || boost/1.60.0 ||
 +
|-
 +
| Boost MPI libraries || boost-mpi/1.60.0 ||
 +
|-
 +
| Bowtie || bowtie/1.1.2 ||
 +
|-
 +
| Bowtie2 || bowtie2/2.3.0 ||
 +
|-
 +
| BWA || bwa/0.7.15 ||
 +
|-
 +
| CLHEP || clhep/2.3.1.1 ||
 +
|-
 +
| Cufflinks || cufflinks/2.1.1 ||
 +
|-
 +
| Eclipse || eclipse/4.6.0 ||
 +
|-
 +
| Eigen || eigen/3.3.2 ||
 +
|-
 +
| FastQC || fastqc/0.11.5 ||
 +
|-
 +
| FFTW || fftw/3.3.5 ||
 +
|-
 +
| rowspan=2 | Gaussian || gaussian/g09e1_sse4 || rowspan=2 |
 +
|-
 +
| gaussian/g16a3_sse4
 +
|-
 +
| rowspan=2 | GCC || gcc/4.8.5 || rowspan=2 |
 +
|-
 +
| gcc/5.4.0
 +
|-
 +
| GDAL || gdal/2.1.3 ||
 +
|-
 +
| Geant4 || geant4/10.02.p03 ||
 +
|-
 +
| GEOS || geos/3.6.1 ||
 +
|-
 +
| GLPK || glpk/4.61 ||
 +
|-
 +
| GMAP + GSNAP || gmap-gsnap/2017-04-13
 +
|-
 +
| rowspan=4 | GROMACS || gromacs/4.6.7 || rowspan=4 |
 +
|-
 +
| gromacs/5.0.7
 +
|-
 +
| gromacs/5.1.4
 +
|-
 +
| gromacs/2016.3
 +
|-
 +
| GSL || gsl/2.2.1 ||
 +
|-
 +
| HDF5 || hdf5/1.8.18 ||
 +
|-
 +
| HDF5 MPI libraries || hdf5-mpi/1.8.18 ||
 +
|-
 +
| HPL || hpl/2.2 ||
 +
|-
 +
| htslib || htslib/1.4 ||
 +
|-
 +
| igraph || igraph/0.7.1 ||
 +
|-
 +
| IMPUTE2 || impute2/2.3.2 ||
 +
|-
 +
| rowspan=2 | Intel Math Kernel Library (MKL) || imkl/11.3.4.258 || rowspan=2 |
 +
|-
 +
| imkl/2017.1.132
 +
|-
 +
| Intel Compiler Suite (local version) || ics/2017u1 ||
 +
|-
 +
| rowspan=2 | Intel Compiler Suite (CC version) || intel/2016.4 || rowspan=2 |
 +
|-
 +
| intel/2017.1
 +
|-
 +
| InterProScan || interproscan/5.23-62.0 ||
 +
|-
 +
| JAGS || jags/4.2.0 ||
 +
|-
 +
| JasPer || jasper/1.900.1 ||
 +
|-
 +
| Java 8 || java/1.8.0_121 ||
 +
|-
 +
| Jellyfish || jellyfish/2.2.6 ||
 +
|-
 +
| Julia || julia/0.5.1 ||
 +
|-
 +
| Libxc || libxc/3.0.0 ||
 +
|-
 +
| MACH || mach/1.0.18 ||
 +
|-
 +
| MATLAB || matlab/R2017a ||
 +
|-
 +
| rowspan=7 | MATLAB Compiler Runtime || mcr/R2013a || rowspan=7 |
 +
|-
 +
| mcr/R2014a
 +
|-
 +
| mcr/R2014b
 +
|-
 +
| mcr/R2015a
 +
|-
 +
| mcr/R2015b
 +
|-
 +
| mcr/R2016a
 +
|-
 +
| mcr/R2016b
 +
|-
 +
| rowspan=2 | METIS || metis/4.0.3 || rowspan=2 |
 +
|-
 +
| metis/5.1.0
 +
|-
 +
| Minimac2 || minimac2/2014.9.15 ||
 +
|-
 +
| Minimac3 || minimac3/2.0.1 ||
 +
|-
 +
| Mothur || mothur/1.39.4 ||
 +
|-
 +
| MrBayes || mrbayes/3.2.6 ||
 +
|-
 +
| NetCDF || netcdf/4.4.1.1 ||
 +
|-
 +
| NetCDF MPI libraries || netcdf-mpi/4.4.1.1 ||
 +
|-
 +
| NetCDF C++ || netcdf-c++/4.2 ||
 +
|-
 +
| NetCDF C++ MPI libraries || netcdf-c++-mpi/4.2 ||
 +
|-
 +
| NetCDF C++4 MPI libraries || netcdf-c++4-mpi/4.3.0 ||
 +
|-
 +
| NetCDF Fortran MPI libraries || netcdf-fortran-mpi/4.4.4 ||
 +
|-
 +
| Octave || octave/4.2.1 ||
 +
|-
 +
| OpenMPI || openmpi/2.0.2 ||
 +
|-
 +
| ParaView || paraview/5.3.0 ||
 +
|-
 +
| ParaView Offscreen support || paraview-offscreen/5.3.0
 +
|-
 +
| Perl 5 || perl/5.22.2 ||
 +
|-
 +
| rowspan=2 | PETSc || petsc/3.7.5 || rowspan=2 |
 +
|-
 +
| petsc-64bits
 +
|-
 +
| PGI compilers || pgi/17.3 ||
 +
|-
 +
| Picard Tools || picard/2.1.1 ||
 +
|-
 +
| rowspan=2 | Python || python/2.7.13 || rowspan=2 |
 +
|-
 +
| python/3.5.2
 +
|-
 +
| Python 2 Scipy Stack || python27-scipy-stack/2017a ||
 +
|-
 +
| Qhull || qhull/2015.2 ||
 +
|-
 +
| qrupdate || qrupdate/1.1.2 ||
 +
|-
 +
| rowspan=2 | Qt GUI toolkit || qt/4.8.7 || rowspan=2 |
 +
|-
 +
| qt/5.6.1
 +
|-
 +
| Quantum ESPRESSO || quantumespresso/6.0 ||
 +
|-
 +
| R || r/3.3.3 ||
 +
|-
 +
| Ray || ray/2.3.1 ||
 +
|-
 +
| Redundans || redundans/a6621dc ||
 +
|-
 +
| Repast for High Performance Computing || repasthpc/2.2.0 ||
 +
|-
 +
| rowspan=2 | SAMTools || samtools/0.1.20 ||  rowspan=2 |
 +
|-
 +
| samtools/1.3.1
 +
|-
 +
| SIESTA || siesta/4.0
 +
|-
 +
| Apache Spark || spark/2.1.0 ||
 +
|-
 +
| Stacks || stacks/1.45 ||
 +
|-
 +
| SuiteSparse || suitesparse/4.5.4 ||
 +
|-
 +
| SuperLU || superlu/5.1.1 ||
 +
|-
 +
| Intel Threading Building Blocks (TBB) || tbb/2017.2.132 ||
 +
|-
 +
| TopHat 2 || tophat/2.1.1 ||
 +
|-
 +
| TransDecoder || transdecoder/3.0.1 ||
 +
|-
 +
| Trimmomatic || trimmomatic/0.36 ||
 +
|-
 +
| Trinity || trinity/2.4.0 ||
 +
|-
 +
| rowspan=2 | WPS || wps/3.8.0 || rowspan=2 |
 
|-
 
|-
−
| rowspan=1 | Abaqus || default || abaqus || rowspan=1 | [[Software:abaqus|Info]]; restricted to Queen's University.
+
| wps/3.8.1
 +
|-
 +
| rowspan=2 | WRF || wrf/3.8.0 || rowspan=2 |
 
|-
 
|-
−
| tophat || 2.1.1 || tophat/2.1.1 ||
+
| wrf/3.8.1
 
|-
 
|-
 
|}
 
|}

Revision as of 16:09, 10 May 2017

The Frontenac cluster includes a wide variety of software and compilers. There are several new ways of accessing and using software, which are documented here. For a list of software available on the SW cluster, please see our SW software page.

The "module" system

Frontenac uses a new method of loading software compared to the SW cluster, the Lmod modules system. We have switched to this system to ensure consistency with other Compute Canada systems and provide a better user interface to our software. The modules system uses more or less the same concepts as the "use" system in use on the SW cluster.

On a large compute cluster, it is impossible to have all sets of software loaded all the time by default. Some software has multiple versions, some packages conflict with each other, and some pieces of software need to be configured separately for different use cases. Environment modules are designed to solve this problem, by treating each software package and all of its associated files as a distinct package to be loaded on demand. Modules also handle the loading of dependencies. For instance, loading the R programming language would be done by loading the "r" module - any dependencies would be handled behind the scenes by the module system without any user intervention.

Common commands

What you want to do Lmod command (Frontenac cluster) "Use" command (SW cluster)
See all available software module avail use -l
See a short description of what each package does module spider <no equivalent>
Load the software package "packageName" module load packageName use packageName
Use a specific version of a software package module load packageName/version use packageName-version
View currently loaded packages module list <no equivalent>
Unload a package module unload packageName <no equivalent>
Unload all packages module purge use none

Please note that all commands are case-sensitive. For an extremely comprehensive set of documenation on using the module system (such as how to write your own modules), you can refer to the official Lmod documentation here: http://lmod.readthedocs.io/en/latest/

Local vs. Compute Canada software

Software on the Frontenac cluster can come from two locations: locally or from Compute Canada's centralized software stack. The Compute Canada software stack is standardized, and contains a set of software that is identically compiled and setup across every cluster it is installed on. This is a fantastic tool for reproducibility and scaling your work across multiple clusters: the same software will work the same way, regardless of where you are using it. There is also a large amount of locally installed software as well. This is how most software requiring licensing or other special local considerations is installed. Using both sets of software is identical- just run module load softwareName.

Please note that if you are the first user to use a Compute Canada software package on a node (or it has not been used in some time), the software may initially appear to "hang" and do nothing for several seconds on launch. This is normal - the software is being re-downloaded and cached on the local system. To tell if a piece of software being used is coming from this centralized stack, you can run which <some_command>. If the output begins with /cvmfs, it is part of the Compute Canada software stack.

List of all installed software

This is a comprehensive list of software installed on the Frontenac cluster. Note that some software is loaded by default.

Software Name Package Name / version Usage Notes
ABINIT abinit/8.2.2
ABySS abyss/1.9.0
AGOUTI agouti/v0.3.3
ALLPATHS-LG allpaths-lg/52488
Anaconda Python distribution anaconda/2.7.13
anaconda/3.5.3
ARPACK arpack-ng/3.4.0
BamTools bamtools/2.4.1
BCFtools bcftools/1.4
beagle-lib beagle-lib/2.1.2
BEAST beast/2.4.0
BEDTools bedtools/2.26.0
Bioperl bioperl/1.7.1
BLAST blast+/2.6.0
BLAT blat/3.5
Boost boost/1.60.0
Boost MPI libraries boost-mpi/1.60.0
Bowtie bowtie/1.1.2
Bowtie2 bowtie2/2.3.0
BWA bwa/0.7.15
CLHEP clhep/2.3.1.1
Cufflinks cufflinks/2.1.1
Eclipse eclipse/4.6.0
Eigen eigen/3.3.2
FastQC fastqc/0.11.5
FFTW fftw/3.3.5
Gaussian gaussian/g09e1_sse4
gaussian/g16a3_sse4
GCC gcc/4.8.5
gcc/5.4.0
GDAL gdal/2.1.3
Geant4 geant4/10.02.p03
GEOS geos/3.6.1
GLPK glpk/4.61
GMAP + GSNAP gmap-gsnap/2017-04-13
GROMACS gromacs/4.6.7
gromacs/5.0.7
gromacs/5.1.4
gromacs/2016.3
GSL gsl/2.2.1
HDF5 hdf5/1.8.18
HDF5 MPI libraries hdf5-mpi/1.8.18
HPL hpl/2.2
htslib htslib/1.4
igraph igraph/0.7.1
IMPUTE2 impute2/2.3.2
Intel Math Kernel Library (MKL) imkl/11.3.4.258
imkl/2017.1.132
Intel Compiler Suite (local version) ics/2017u1
Intel Compiler Suite (CC version) intel/2016.4
intel/2017.1
InterProScan interproscan/5.23-62.0
JAGS jags/4.2.0
JasPer jasper/1.900.1
Java 8 java/1.8.0_121
Jellyfish jellyfish/2.2.6
Julia julia/0.5.1
Libxc libxc/3.0.0
MACH mach/1.0.18
MATLAB matlab/R2017a
MATLAB Compiler Runtime mcr/R2013a
mcr/R2014a
mcr/R2014b
mcr/R2015a
mcr/R2015b
mcr/R2016a
mcr/R2016b
METIS metis/4.0.3
metis/5.1.0
Minimac2 minimac2/2014.9.15
Minimac3 minimac3/2.0.1
Mothur mothur/1.39.4
MrBayes mrbayes/3.2.6
NetCDF netcdf/4.4.1.1
NetCDF MPI libraries netcdf-mpi/4.4.1.1
NetCDF C++ netcdf-c++/4.2
NetCDF C++ MPI libraries netcdf-c++-mpi/4.2
NetCDF C++4 MPI libraries netcdf-c++4-mpi/4.3.0
NetCDF Fortran MPI libraries netcdf-fortran-mpi/4.4.4
Octave octave/4.2.1
OpenMPI openmpi/2.0.2
ParaView paraview/5.3.0
ParaView Offscreen support paraview-offscreen/5.3.0
Perl 5 perl/5.22.2
PETSc petsc/3.7.5
petsc-64bits
PGI compilers pgi/17.3
Picard Tools picard/2.1.1
Python python/2.7.13
python/3.5.2
Python 2 Scipy Stack python27-scipy-stack/2017a
Qhull qhull/2015.2
qrupdate qrupdate/1.1.2
Qt GUI toolkit qt/4.8.7
qt/5.6.1
Quantum ESPRESSO quantumespresso/6.0
R r/3.3.3
Ray ray/2.3.1
Redundans redundans/a6621dc
Repast for High Performance Computing repasthpc/2.2.0
SAMTools samtools/0.1.20
samtools/1.3.1
SIESTA siesta/4.0
Apache Spark spark/2.1.0
Stacks stacks/1.45
SuiteSparse suitesparse/4.5.4
SuperLU superlu/5.1.1
Intel Threading Building Blocks (TBB) tbb/2017.2.132
TopHat 2 tophat/2.1.1
TransDecoder transdecoder/3.0.1
Trimmomatic trimmomatic/0.36
Trinity trinity/2.4.0
WPS wps/3.8.0
wps/3.8.1
WRF wrf/3.8.0
wrf/3.8.1
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