Merge pull request #205 from SouthernMethodistUniversity/add_module_help

Add module help
SouthernMethodistUniversity · Aug 9, 2024 · 49c7bf1 · 49c7bf1
2 parents cf5ff3e + 07a4391
commit 49c7bf1
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diff --git a/modules/m3/applications/R/4.2.3.lua b/modules/m3/applications/R/4.2.3.lua
@@ -1,5 +1,11 @@
 
 help([[
+Name: R
+Version: 4.2.3
+Website: https://www.r-project.org/
+
+R is a language and environment for statistical computing and graphics.
+
 To use R:
 
 R -- launches an R terminal
@@ -39,4 +45,4 @@ setenv('R_LIBS_USER', user_libs)
 unsetenv('XDG_RUNTIME_DIR')
 
 build_command('R')
-build_command('Rscript')
+build_command('Rscript')
diff --git a/modules/m3/applications/R/4.3.0.lua b/modules/m3/applications/R/4.3.0.lua
@@ -1,5 +1,10 @@
 
 help([[
+Name: R
+Version: 4.3.0
+Website: https://www.r-project.org/
+
+R is a language and environment for statistical computing and graphics.
 To use R:
 
 R -- launches an R terminal

diff --git a/modules/m3/applications/R/4.3.2.lua b/modules/m3/applications/R/4.3.2.lua
@@ -1,5 +1,11 @@
 
 help([[
+Name: R
+Version: 4.3.2
+Website: https://www.r-project.org/
+
+R is a language and environment for statistical computing and graphics.
+
 To use R:
 
 R -- launches an R terminal

diff --git a/modules/m3/applications/R/4.4.0.lua b/modules/m3/applications/R/4.4.0.lua
@@ -1,5 +1,11 @@
 
 help([[
+Name: R
+Version: 4.4.0
+Website: https://www.r-project.org/
+
+R is a language and environment for statistical computing and graphics.
+
 To use R:
 
 R -- launches an R terminal

diff --git a/modules/m3/applications/aimall/19.10.12.lua b/modules/m3/applications/aimall/19.10.12.lua
@@ -1,3 +1,11 @@
 whatis("AIMAll")
 prepend_path("PATH","/hpc/m3/apps/aimall/19.10.12")
 
+help([[Name: AIMAll  
+Version: 19.10.12
+Website: https://aim.tkgristmill.com/
+
+Computational Chemistry Using the Quantum Theory of Atoms in Molecules (QTAIM)
+
+AIMAll is an easy to use, accurate, reliable and efficient quantum chemistry software package for performing comprehensive, quantitative and visual QTAIM analyses of molecular systems - starting from molecular wavefunction data.
+]])
diff --git a/modules/m3/applications/alphafold/2.3.2.lua b/modules/m3/applications/alphafold/2.3.2.lua
@@ -21,3 +21,9 @@ setenv('ALPHAFOLD_DATA', '/work/data/alphafold/2.3.2')
 
 build_command('run_alphafold.sh', '/app/run_alphafold.sh')
 
+help([[Name: AlphaFold 
+Version: 2.3.2
+Website: https://deepmind.google/technologies/alphafold/
+
+AlphaFold is an AI system developed by Google DeepMind that predicts a protein’s 3D structure from its amino acid sequence. It regularly achieves accuracy competitive with experiment.
+]])
diff --git a/modules/m3/applications/amber/22.lua b/modules/m3/applications/amber/22.lua
@@ -9,3 +9,10 @@ load("openblas/0.3.21-s5husbk",
      "bzip2/1.0.8-ujseine")
 source_sh('bash', "/hpc/m3/apps/amber/amber22/amber.sh")
 load("openmpi/4.1.6-a4ksrza")
+
+help([[Name: Amber
+Version: 22
+Website: https://ambermd.org/
+
+Amber is a suite of biomolecular simulation programs.
+]])
diff --git a/modules/m3/applications/amber/24.lua b/modules/m3/applications/amber/24.lua
@@ -21,6 +21,12 @@ prepend_path("PERL5LIB","/hpc/m3/apps/amber/amber24_mpi/lib/perl")
 prepend_path("PYTHONPATH","/hpc/m3/apps/amber/amber24_mpi/lib/python3.11/site-packages")
 setenv("QUICK_BASIS","/hpc/m3/apps/amber/amber24_mpi/AmberTools/src/quick/basis")
 
+help([[Name: Amber
+Version: 24
+Website: https://ambermd.org/
+
+Amber is a suite of biomolecular simulation programs.
+]])
 
 --[[
 module load gcc/11.2.0

diff --git a/modules/m3/applications/ampl/20231031.lua b/modules/m3/applications/ampl/20231031.lua
@@ -3,3 +3,11 @@ family("ampl")
 conflict("ampl")
 
 append_path("PATH", "/hpc/m3/apps/ampl/ampl_20231031")
+
+help([[Name: AMPL
+Version: 20231031
+Website: https://ampl.com/
+License Owners : Merlin / Teaching Eval Version
+
+AMPL is an algebraic modeling language to describe and solve high-complexity problems for large-scale mathematical computing.
+]])
diff --git a/modules/m3/applications/ansys/electronics/23.1.lua b/modules/m3/applications/ansys/electronics/23.1.lua
@@ -1,6 +1,15 @@
 whatis("ANSYS Electronics Package R23.1")
 family("ansys")
 
+help([[Name: Ansys Electronics Desktop (HFSS)
+Version: 23R1
+Website: https://www.ansys.com/
+License Owners : SMU?
+
+Ansys Electronics
+Electromagnetic, Signal Integrity, Thermal and Electro-Mechanical Simulation Solutions
+]])
+
 local container_name=os.getenv("APPTAINER_CONTAINER") or  ""
 
 -- Ansys 23.1 doesn't support Ubuntu 22.04 directly, so this install

diff --git a/modules/m3/applications/ansys/electronics/23.2.lua b/modules/m3/applications/ansys/electronics/23.2.lua
@@ -1,6 +1,15 @@
 whatis("ANSYS Electronics Package R23.2")
 family("ansys")
 
+help([[Name: Ansys Electronics Desktop (HFSS)
+Version: 23R2
+Website: https://www.ansys.com/
+License Owners : SMU?
+
+Ansys Electronics
+Electromagnetic, Signal Integrity, Thermal and Electro-Mechanical Simulation Solutions
+]])
+
 local container_name=os.getenv("APPTAINER_CONTAINER") or  ""
 
 -- Ansys 23.2 needs GUI stuff not installed on compute nodes, so this install

diff --git a/modules/m3/applications/ansys/electronics/24.2.lua b/modules/m3/applications/ansys/electronics/24.2.lua
@@ -1,6 +1,15 @@
 whatis("ANSYS Electronics Package R24.2")
 family("ansys")
 
+help([[Name: Ansys Electronics Desktop (HFSS)
+Version: 24R2
+Website: https://www.ansys.com/
+License Owners : SMU?
+
+Ansys Electronics
+Electromagnetic, Signal Integrity, Thermal and Electro-Mechanical Simulation Solutions
+]])
+
 local ansys_home="/hpc/m3/apps/ansys/24R2/AnsysEM/v242/Linux64/"
 
 append_path("PATH",ansys_home)

diff --git a/modules/m3/applications/ansys/fluidstructures/23.2.lua b/modules/m3/applications/ansys/fluidstructures/23.2.lua
@@ -1,6 +1,14 @@
 whatis("ANSYS Fluid and Structures Package R23.2")
 family("ansys")
 
+help([[Name: Ansys 
+Version: 23R2
+Website: https://www.ansys.com/
+License Owners : SMU?
+
+Ansys Fluent, Mechanical, Workbench
+]])
+
 local container_name=os.getenv("APPTAINER_CONTAINER") or  ""
 
 -- Ansys 23.2 needs GUI stuff not installed on compute nodes, so this install

diff --git a/modules/m3/applications/apptainer/1.1.6.lua b/modules/m3/applications/apptainer/1.1.6.lua
@@ -4,3 +4,10 @@ prepend_path("PATH","/hpc/sys/apps/apptainer/current/bin")
 source_sh('bash', '/hpc/sys/apps/apptainer/current/share/bash-completion/completions/apptainer')
 source_sh('bash', '/hpc/sys/apps/apptainer/current/share/bash-completion/completions/singularity')
 setenv("APPTAINER_BIND","/tmp,/hpc,/lustre/work/client,/lustre/scratch/client,/work,/cm/local/apps/slurm,/var/lib/sss,/etc/passwd")
+
+help([[Name: Apptainer
+Version: 1.1.6
+Website: https://apptainer.org/
+
+pptainer is an open source container platform designed to be simple, fast, and secure. Many container platforms are available, but Apptainer is designed for ease-of-use on shared systems and in high performance computing (HPC) environments.
+]])
diff --git a/modules/m3/applications/blender/4.0.2.lua b/modules/m3/applications/blender/4.0.2.lua
@@ -3,3 +3,10 @@ family("blender")
 conflict("blender")
 
 append_path("PATH", "/hpc/m3/apps/blender/4.0.2")
+
+help([[Name: Blender
+Version: 4.0.2
+Website: https://www.blender.org/
+
+Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.
+]])
diff --git a/modules/m3/applications/cfour/2.1/mpi.lua b/modules/m3/applications/cfour/2.1/mpi.lua
@@ -8,3 +8,9 @@ local bin  = pathJoin(root, "bin")
 load("gcc/11.2.0", "openmpi/4.1.4-7al4h2x", "openblas/0.3.21-iofurbe")
 prepend_path("PATH", bin)
 
+help([[Name: CFOUR
+Version: 2.1 (mpi)
+Website: https://cfour.uni-mainz.de/cfour/
+
+CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. 
+]])
diff --git a/modules/m3/applications/cfour/2.1/nompi.lua b/modules/m3/applications/cfour/2.1/nompi.lua
@@ -8,3 +8,9 @@ local bin  = pathJoin(root, "bin")
 load("gcc/11.2.0", "openblas/0.3.21-iofurbe")
 prepend_path("PATH", bin)
 
+help([[Name: CFOUR
+Version: 2.1 (mpi)
+Website: https://cfour.uni-mainz.de/cfour/
+
+CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. 
+]])
diff --git a/modules/m3/applications/charmm/c47b2.lua b/modules/m3/applications/charmm/c47b2.lua
@@ -3,3 +3,10 @@ whatis("CHARMM")
 load("gcc/11.2.0", "openmpi/4.1.4-7al4h2x", "fftw/3.3.10-gz7qiki")
 prepend_path("PATH", "/hpc/m3/apps/charmm/c47b2/bin")
 
+help([[Name: CHARMM
+Version: c47b2
+Website: https://www.academiccharmm.org/
+
+Chemistry at HARvard Macromolecular Mechanics
+A molecular simulation program with broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques including QM/MM, MM/CG, and a range of implicit solvent models. 
+]])
diff --git a/modules/m3/applications/comsol/6.1.lua b/modules/m3/applications/comsol/6.1.lua
@@ -2,3 +2,11 @@ whatis("COMSOL 6.1")
 family("comsol")
 conflict("comsol")
 prepend_path("PATH","/hpc/m3/apps/comsol/comsol61/multiphysics/bin")
+
+help([[Name: Comsol  
+Version: 6.1
+Website: https://www.comsol.com/
+License Owners : SMU?
+
+COMSOL Multiphysics is a finite element analyzer, solver, and simulation software package for various physics and engineering applications, especially coupled phenomena and multiphysics.
+]])
diff --git a/modules/m3/applications/conda.lua b/modules/m3/applications/conda.lua
@@ -2,3 +2,11 @@ whatis("Anaconda Python Distribution")
 family("conda")
 source_sh('bash', '/hpc/m3/apps/conda/etc/profile.d/conda.sh')
 source_sh('bash', '/hpc/m3/apps/conda/etc/profile.d/mamba.sh')
+
+
+help([[Name: Conda
+Version: several
+Website: https://docs.conda.io/projects/conda/en/stable/
+
+Conda provides package, dependency, and environment management for any language.
+]])
diff --git a/modules/m3/applications/cplex/22.1.1.lua b/modules/m3/applications/cplex/22.1.1.lua
@@ -25,3 +25,11 @@ append_path("LIBRARY_PATH","/hpc/m3/apps/cplex/CPLEX_Studio2211/opl/bin/x86-64_l
 append_path("CPATH", "/hpc/m3/apps/cplex/CPLEX_Studio2211/cplex/include")
 append_path("CPATH", "/hpc/m3/apps/cplex/CPLEX_Studio2211/cpoptimizer/include")
 append_path("CPATH", "/hpc/m3/apps/cplex/CPLEX_Studio2211/opl/include")
+
+help([[Name: IBM ILOG CPLEX Optimizer 
+Version: 22.1.1
+Website: https://www.ibm.com/products/ilog-cplex-optimization-studio/cplex-optimizer
+License Owners: academic license
+
+High-performance optimization solver for linear, mixed-integer and quadratic programming
+]])
diff --git a/modules/m3/applications/crystal/23/1.0.1-1.lua b/modules/m3/applications/crystal/23/1.0.1-1.lua
@@ -15,4 +15,12 @@ conflict("crystal")
 load("gcc/11.2.0", "openmpi/4.1.6")
 prepend_path("PATH","/hpc/m3/apps/crystal/23_1")
 
+help([[Name: Crystal 
+Version: 23 v1.0.1-1
+Website: https://www.crystal.unito.it/
+License Owners : CATCO group
+
+CRYSTAL is a quantum chemistry ab initio program, designed primarily for calculations on crystals (3 dimensions), slabs (2 dimensions) and polymers (1 dimension) using translational symmetry, but it can also be used for single molecules.
+]])
+
 
diff --git a/modules/m3/applications/crystal/23/1.0.1.lua b/modules/m3/applications/crystal/23/1.0.1.lua
@@ -15,3 +15,11 @@ conflict("crystal")
 load("gcc", "openmpi")
 append_path("LD_LIBRARY_PATH", "/hpc/m3/apps/intel/oneapi/2023.1/compiler/2023.1.0/linux/compiler/lib/intel64_lin")
 prepend_path("PATH","/hpc/m3/apps/crystal/23/v1.0.1")
+
+help([[Name: Crystal 
+Version: 23 v1.0.1
+Website: https://www.crystal.unito.it/
+License Owners : CATCO group
+
+CRYSTAL is a quantum chemistry ab initio program, designed primarily for calculations on crystals (3 dimensions), slabs (2 dimensions) and polymers (1 dimension) using translational symmetry, but it can also be used for single molecules.
+]])
diff --git a/modules/m3/applications/demon/6.2.2.lua b/modules/m3/applications/demon/6.2.2.lua
@@ -12,3 +12,9 @@ setenv("CREX_ROOT", root)
 prepend_path("MANPATH", pathJoin(base, "man"))
 append_path("PATH", pathJoin(base, "bin"))
 
+help([[Name: deMon
+Version: 6.2.2
+Website: http://www.demon-software.com/
+
+A software package for density functional theory (DFT) calculations
+]])
diff --git a/modules/m3/applications/ds9/8.4.1.lua b/modules/m3/applications/ds9/8.4.1.lua
@@ -1,3 +1,10 @@
 whatis("SAOImage DS9 Version 8.4.1")
 prepend_path("PATH","/hpc/m3/apps/ds9/8.4.1")
 
+help([[Name: SAOImageDS9
+Version: 8.4.1
+Website: https://sites.google.com/cfa.harvard.edu/saoimageds9
+
+SAOImageDS9
+An image display and visualization tool for astronomical data
+]])
diff --git a/modules/m3/applications/dynare/5.4.lua b/modules/m3/applications/dynare/5.4.lua
@@ -17,3 +17,10 @@ prepend_path("LD_PRELOAD", "/usr/lib/x86_64-linux-gnu/libstdc++.so.6")
 append_path("PATH", "/hpc/m3/apps/dynare/5.4/bin")
 append_path("LIBRARY_PATH","/hpc/m3/apps/dynare/5.4/lib")
 append_path("MATLABPATH","/hpc/m3/apps/dynare/5.4/lib/dynare/matlab/")
+
+help([[Name: Dynare
+Version: 5.4
+Website: https://www.dynare.org/
+
+Dynare is a software platform for handling a wide class of economic models, in particular dynamic stochastic general equilibrium (DSGE) and overlapping generations (OLG) models.
+]])
diff --git a/modules/m3/applications/dynare/5.5.lua b/modules/m3/applications/dynare/5.5.lua
@@ -17,3 +17,10 @@ prepend_path("LD_PRELOAD", "/usr/lib/x86_64-linux-gnu/libstdc++.so.6")
 append_path("PATH", "/hpc/m3/apps/dynare/5.5/bin")
 append_path("LIBRARY_PATH","/hpc/m3/apps/dynare/5.5/lib")
 append_path("MATLABPATH","/hpc/m3/apps/dynare/5.5/lib/dynare/matlab/")
+
+help([[Name: Dynare
+Version: 5.5
+Website: https://www.dynare.org/
+
+Dynare is a software platform for handling a wide class of economic models, in particular dynamic stochastic general equilibrium (DSGE) and overlapping generations (OLG) models.
+]])
diff --git a/modules/m3/applications/emacs/26.1.lua b/modules/m3/applications/emacs/26.1.lua
@@ -16,3 +16,10 @@ local img_path      = pathJoin(img_directory, img_name)
 
 build_command(img_path, 'emacs')
 
+
+help([[Name: GNU Emacs
+Version: 26.1
+Website: https://www.gnu.org/software/emacs/
+
+An extensible, customizable, free/libre text editor — and more.
+]])
diff --git a/modules/m3/applications/eog/3.28.4.lua b/modules/m3/applications/eog/3.28.4.lua
@@ -16,3 +16,9 @@ local img_path      = pathJoin(img_directory, img_name)
 
 build_command(img_path, 'eog')
 
+help([[Name: Eye of Gnome
+Version: 3.28.4
+Website: https://help.gnome.org/users/eog/
+
+Eye of Gnome image viewer
+]])
diff --git a/modules/m3/applications/es/0.98.1.lua b/modules/m3/applications/es/0.98.1.lua
@@ -23,3 +23,11 @@ for _, executable in ipairs(executables) do
   build_command(img_path, executable)
 end
 
+help([[Name: ES: Elementary Supernova Spectrum Synthesis
+Version: 0.98.1
+Website: https://c3.lbl.gov/es/
+
+ES: Elementary Supernova Spectrum Synthesis
+]])
+
+
diff --git a/modules/m3/applications/evince/42.3.lua b/modules/m3/applications/evince/42.3.lua
@@ -16,3 +16,9 @@ local img_path      = pathJoin(img_directory, img_name)
 
 build_command(img_path, 'evince')
 
+help([[Name: Evince
+Version: 42.3
+Website: https://wiki.gnome.org/Apps/Evince
+
+Evince is a document viewer for multiple document formats. 
+]])