From 7e8fcd7a8defad35b76763e0e32090d88f67c4dd Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:05:04 -0500 Subject: [PATCH 01/66] add help to AIMALL module --- modules/m3/applications/aimall/19.10.12.lua | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/modules/m3/applications/aimall/19.10.12.lua b/modules/m3/applications/aimall/19.10.12.lua index 0116f971..24c53a93 100644 --- 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. +]]) \ No newline at end of file From dde0e018b7d3d25380d3fb8ec465fa0311b4129c Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:07:25 -0500 Subject: [PATCH 02/66] add help to alphafold --- modules/m3/applications/alphafold/2.3.2.lua | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/m3/applications/alphafold/2.3.2.lua b/modules/m3/applications/alphafold/2.3.2.lua index ecc7a537..cd76bbaa 100644 --- 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. +]]) From 9fb291364a9f47e88ec8fca57f99dd3a4040b399 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:09:01 -0500 Subject: [PATCH 03/66] add help to amber modules --- modules/m3/applications/amber/22.lua | 7 +++++++ modules/m3/applications/amber/24.lua | 6 ++++++ 2 files changed, 13 insertions(+) diff --git a/modules/m3/applications/amber/22.lua b/modules/m3/applications/amber/22.lua index 7c75ef65..c12f3832 100644 --- 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. +]]) \ No newline at end of file diff --git a/modules/m3/applications/amber/24.lua b/modules/m3/applications/amber/24.lua index f00aeecf..66bde7f0 100644 --- 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 From 8a881595385ba4f8c8818477581ce19333837c02 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:11:09 -0500 Subject: [PATCH 04/66] add help to ampl --- modules/m3/applications/ampl/20231031.lua | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/modules/m3/applications/ampl/20231031.lua b/modules/m3/applications/ampl/20231031.lua index 1a3dc263..3fdb0319 100644 --- 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. +]]) \ No newline at end of file From d5714f5bed5776ba6198b7170e229a56cd8d5313 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:15:09 -0500 Subject: [PATCH 05/66] add help to ansys hfss --- modules/m3/applications/ansys/electronics/23.1.lua | 9 +++++++++ modules/m3/applications/ansys/electronics/23.2.lua | 9 +++++++++ modules/m3/applications/ansys/electronics/24.2.lua | 9 +++++++++ 3 files changed, 27 insertions(+) diff --git a/modules/m3/applications/ansys/electronics/23.1.lua b/modules/m3/applications/ansys/electronics/23.1.lua index 1b2f00cd..bca1d59c 100644 --- 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 index b4726978..0d16abfe 100644 --- 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 index 5a6d3eff..4a71a280 100644 --- 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) From 7de769d6df88767895cbb43f25e81ceb2c68da58 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:16:39 -0500 Subject: [PATCH 06/66] add help for ansys workbench / fluent / mech --- modules/m3/applications/ansys/fluidstructures/23.2.lua | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/modules/m3/applications/ansys/fluidstructures/23.2.lua b/modules/m3/applications/ansys/fluidstructures/23.2.lua index b849ff6d..668ccab5 100644 --- 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 From 6082eda974c9b4574162d6754172c1b48947987c Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:17:50 -0500 Subject: [PATCH 07/66] add help to apptainer --- modules/m3/applications/apptainer/1.1.6.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/m3/applications/apptainer/1.1.6.lua b/modules/m3/applications/apptainer/1.1.6.lua index cfb53360..047455df 100644 --- 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. +]]) \ No newline at end of file From 1c95bd770f38fccb8d8bbcc3b48be09f8b6f1212 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:19:07 -0500 Subject: [PATCH 08/66] add help to blender --- modules/m3/applications/blender/4.0.2.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/m3/applications/blender/4.0.2.lua b/modules/m3/applications/blender/4.0.2.lua index 162caa36..2667fbb8 100644 --- 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. +]]) \ No newline at end of file From 6fc2fcf206512ad36bc95bb7cb0b5b9471233094 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:21:06 -0500 Subject: [PATCH 09/66] add help to cfour moudles --- modules/m3/applications/cfour/2.1/mpi.lua | 6 ++++++ modules/m3/applications/cfour/2.1/nompi.lua | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/modules/m3/applications/cfour/2.1/mpi.lua b/modules/m3/applications/cfour/2.1/mpi.lua index 46796767..5cdd5b94 100644 --- 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. +]]) \ No newline at end of file diff --git a/modules/m3/applications/cfour/2.1/nompi.lua b/modules/m3/applications/cfour/2.1/nompi.lua index 5bad9df9..39fdcee4 100644 --- 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. +]]) \ No newline at end of file From 2d888d39d091705a275a49f1ce9983e3d4838678 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:22:46 -0500 Subject: [PATCH 10/66] add help to charmm --- modules/m3/applications/charmm/c47b2.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/m3/applications/charmm/c47b2.lua b/modules/m3/applications/charmm/c47b2.lua index d4e904f7..0bd86d82 100644 --- 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. +]]) \ No newline at end of file From 554c4d73d0066eb6fc3156ecbb331387f46412bb Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:24:07 -0500 Subject: [PATCH 11/66] add help for comsol --- modules/m3/applications/comsol/6.1.lua | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/modules/m3/applications/comsol/6.1.lua b/modules/m3/applications/comsol/6.1.lua index 47e8e836..0fe7a32e 100644 --- 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. +]]) \ No newline at end of file From db7e0d8c0aa9c898f370c114b84d8a0870a49743 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:26:31 -0500 Subject: [PATCH 12/66] add help for cplex --- modules/m3/applications/cplex/22.1.1.lua | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/modules/m3/applications/cplex/22.1.1.lua b/modules/m3/applications/cplex/22.1.1.lua index 4b85e271..7c1c6f74 100644 --- 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 +]]) \ No newline at end of file From 6a413fb41b279c3a2b6a942fcd19c1b7caaeaaf0 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:30:19 -0500 Subject: [PATCH 13/66] add help for crystal --- modules/m3/applications/crystal/23/1.0.1-1.lua | 8 ++++++++ modules/m3/applications/crystal/23/1.0.1.lua | 8 ++++++++ 2 files changed, 16 insertions(+) diff --git a/modules/m3/applications/crystal/23/1.0.1-1.lua b/modules/m3/applications/crystal/23/1.0.1-1.lua index 4e533d0a..3d509c9d 100644 --- 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 index abb95273..9fbce199 100644 --- 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. +]]) \ No newline at end of file From cce28ce7cf317599be3a7ec4f9dfc243e7f8f823 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:32:08 -0500 Subject: [PATCH 14/66] add help for deMon --- modules/m3/applications/demon/6.2.2.lua | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/m3/applications/demon/6.2.2.lua b/modules/m3/applications/demon/6.2.2.lua index e40f7f96..ae0027b3 100644 --- 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 +]]) From 50d9021dece6ff3a93d4382ae68311b3f2e0d391 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:38:31 -0500 Subject: [PATCH 15/66] add help to SAOImageDS9 --- modules/m3/applications/ds9/8.4.1.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/m3/applications/ds9/8.4.1.lua b/modules/m3/applications/ds9/8.4.1.lua index 7d3c20c6..3d6e1102 100644 --- 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 +]]) \ No newline at end of file From b4084b2c1743d3dd9094bdd36162e63a6ed06b9f Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:39:58 -0500 Subject: [PATCH 16/66] add help for dynare --- modules/m3/applications/dynare/5.4.lua | 7 +++++++ modules/m3/applications/dynare/5.5.lua | 7 +++++++ 2 files changed, 14 insertions(+) diff --git a/modules/m3/applications/dynare/5.4.lua b/modules/m3/applications/dynare/5.4.lua index 16dab286..c6cdd524 100644 --- 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. +]]) \ No newline at end of file diff --git a/modules/m3/applications/dynare/5.5.lua b/modules/m3/applications/dynare/5.5.lua index 88ecabcd..b7f14239 100644 --- 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. +]]) \ No newline at end of file From 498eb0c02827779a8aa61166ebbdc61211e85f22 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:41:53 -0500 Subject: [PATCH 17/66] add help for emacs --- modules/m3/applications/emacs/26.1.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/m3/applications/emacs/26.1.lua b/modules/m3/applications/emacs/26.1.lua index e6d6a2c5..48efc994 100644 --- 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. +]]) \ No newline at end of file From 2e1c499055eaaa24979f4baec1413d8535faadbb Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:43:00 -0500 Subject: [PATCH 18/66] add eog help --- modules/m3/applications/eog/3.28.4.lua | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/m3/applications/eog/3.28.4.lua b/modules/m3/applications/eog/3.28.4.lua index 8e41a96a..748886f3 100644 --- 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 +]]) \ No newline at end of file From f4481e30fabb57a4f0de9ce3209c148411fdc72d Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:45:54 -0500 Subject: [PATCH 19/66] add help for es --- modules/m3/applications/es/0.98.1.lua | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/modules/m3/applications/es/0.98.1.lua b/modules/m3/applications/es/0.98.1.lua index 33a24b30..f15cce07 100644 --- 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 +]]) + + From 1e352c0d9591254c5e014a3464bebe14ff3a8d70 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:47:21 -0500 Subject: [PATCH 20/66] add help for evince --- modules/m3/applications/evince/42.3.lua | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/m3/applications/evince/42.3.lua b/modules/m3/applications/evince/42.3.lua index 7216075f..636ee7f4 100644 --- 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. +]]) From 9edd21fbdf087a07cd3ada6dff514f4d15f0cdf8 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:49:16 -0500 Subject: [PATCH 21/66] add help for gamess --- modules/m3/applications/gamess/2022.2.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/m3/applications/gamess/2022.2.lua b/modules/m3/applications/gamess/2022.2.lua index 83e50e5a..7c98990c 100644 --- a/modules/m3/applications/gamess/2022.2.lua +++ b/modules/m3/applications/gamess/2022.2.lua @@ -7,3 +7,10 @@ load("gcc/11.2.0", "openmpi/4.1.4-7al4h2x", "openblas/0.3.21-fh35exj") prepend_path("PATH", gmspath) setenv("GMSPATH", gmspath) +help([[Name: GAMESS ab initio Quantum Chemistry Package +Version: 2022.2 +Website: https://www.msg.chem.iastate.edu/gamess/ + +The General Atomic and Molecular Electronic Structure System (GAMESS) +is a general ab initio quantum chemistry package. +]]) \ No newline at end of file From 649c6b82cdebc06d85a5a28b623b499648b5088f Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:51:36 -0500 Subject: [PATCH 22/66] add help to gaussian modules --- modules/m3/applications/gaussian/g09d.lua | 7 +++++++ modules/m3/applications/gaussian/g16c/haswell.lua | 8 ++++++++ modules/m3/applications/gaussian/g16c/zen3.lua | 7 +++++++ 3 files changed, 22 insertions(+) diff --git a/modules/m3/applications/gaussian/g09d.lua b/modules/m3/applications/gaussian/g09d.lua index 88131406..da6ee68a 100644 --- a/modules/m3/applications/gaussian/g09d.lua +++ b/modules/m3/applications/gaussian/g09d.lua @@ -14,3 +14,10 @@ family("gaussian") load("apptainer") prepend_path("PATH", "/hpc/m3/apps/gaussian/g09d/g09") +help([[Name: Gaussian +Version: g09 +Website: https://gaussian.com/ +License Owners: Chemistry + + Gaussian series of electronic structure programs, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. +]]) \ No newline at end of file diff --git a/modules/m3/applications/gaussian/g16c/haswell.lua b/modules/m3/applications/gaussian/g16c/haswell.lua index 2b1e55fe..13912fc6 100644 --- a/modules/m3/applications/gaussian/g16c/haswell.lua +++ b/modules/m3/applications/gaussian/g16c/haswell.lua @@ -25,3 +25,11 @@ setenv("GAUSS_ARCHDIR","/hpc/m3/apps/gaussian/g16c02/g16/arch") append_path("LD_LIBRARY_PATH","/hpc/m3/apps/gaussian/g16c02/g16/bsd:/hpc/m3/apps/gaussian/g16c02/g16:/hpc/m3/apps/gaussian/g16c02/gv/lib") setenv("GAUSS_LEXEDIR","/hpc/m3/apps/gaussian/g16c02/g16/linda-exe") append_path("PATH","/hpc/m3/apps/gaussian/g16c02/gauopen:/hpc/m3/apps/gaussian/g16c02/g16/bsd:/hpc/m3/apps/gaussian/g16c02/g16") + +help([[Name: Gaussian +Version: g16c +Website: https://gaussian.com/ +License Owners: Chemistry + +Gaussian series of electronic structure programs, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. +]]) \ No newline at end of file diff --git a/modules/m3/applications/gaussian/g16c/zen3.lua b/modules/m3/applications/gaussian/g16c/zen3.lua index f7dbc052..455632ba 100644 --- a/modules/m3/applications/gaussian/g16c/zen3.lua +++ b/modules/m3/applications/gaussian/g16c/zen3.lua @@ -17,3 +17,10 @@ setenv("g16root", g16root) setenv("GAUSS_SCRDIR", os.getenv("SCRATCH")) source_sh('bash', pathJoin(g16root, "g16/bsd/g16.profile")) +help([[Name: Gaussian +Version: g16c +Website: https://gaussian.com/ +License Owners: Chemistry + +Gaussian series of electronic structure programs, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. +]]) From e2a510fd669c8360b398feaeff5bf9bc676cd0c4 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:52:32 -0500 Subject: [PATCH 23/66] add help for gaussview --- modules/m3/applications/gaussview/6.0.16.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/m3/applications/gaussview/6.0.16.lua b/modules/m3/applications/gaussview/6.0.16.lua index d31b4da8..1fedbc6c 100644 --- a/modules/m3/applications/gaussview/6.0.16.lua +++ b/modules/m3/applications/gaussview/6.0.16.lua @@ -13,3 +13,10 @@ family("gaussview") LmodWarning("GaussView can only be used from an HPC Portal remote desktop session.") prepend_path("PATH","/hpc/m3/apps/gaussian/gv") +help([[Name: GaussView +Version: 6 +Website: https://gaussian.com/ +License Owners: Chemistry + +Graphical interface used with Gaussian +]]) \ No newline at end of file From 24b10a205fe5ea0623cafd312725e0aa0f9fa149 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 11:58:11 -0500 Subject: [PATCH 24/66] add help to gedit --- modules/m3/applications/gedit/3.28.1.lua | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/m3/applications/gedit/3.28.1.lua b/modules/m3/applications/gedit/3.28.1.lua index 533914fd..4367a10a 100644 --- a/modules/m3/applications/gedit/3.28.1.lua +++ b/modules/m3/applications/gedit/3.28.1.lua @@ -16,3 +16,9 @@ local img_path = pathJoin(img_directory, img_name) build_command(img_path, 'gedit') +help([[Name: gedit +Version: 3.28.1 +Website: https://gedit-technology.github.io/apps/gedit/ + +gedit is an easy-to-use and general-purpose text editor. +]]) \ No newline at end of file From d5f89dfd51a6eff9e25ce40dd6b5226bc1e8d183 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:01:13 -0500 Subject: [PATCH 25/66] add help for gurobi module --- modules/m3/applications/gurobi/10.0.1.lua | 8 ++++++++ modules/m3/applications/gurobi/11.0.1.lua | 8 ++++++++ 2 files changed, 16 insertions(+) diff --git a/modules/m3/applications/gurobi/10.0.1.lua b/modules/m3/applications/gurobi/10.0.1.lua index a61d9595..0cbdc561 100644 --- a/modules/m3/applications/gurobi/10.0.1.lua +++ b/modules/m3/applications/gurobi/10.0.1.lua @@ -8,3 +8,11 @@ setenv("GRB_LICENSE_FILE", "/hpc/m3/apps/gurobi/10.0.1/linux64/client.lic") append_path("LD_LIBRARY_PATH","/hpc/m3/apps/gurobi/10.0.1/linux64/lib") append_path("CPATH", "/hpc/m3/apps/gurobi/10.0.1/linux64/include") append_path("LIBRARY_PATH","/hpc/m3/apps/gurobi/10.0.1/linux64/lib") + +help([[Name: Gurobi +Version: 10.0.1 +Website: https://www.gurobi.com/ +License Owners : free academic site license (Merlin) + +Gurobi optimization software +]]) \ No newline at end of file diff --git a/modules/m3/applications/gurobi/11.0.1.lua b/modules/m3/applications/gurobi/11.0.1.lua index 9d1ba175..a0c46813 100644 --- a/modules/m3/applications/gurobi/11.0.1.lua +++ b/modules/m3/applications/gurobi/11.0.1.lua @@ -8,3 +8,11 @@ setenv("GRB_LICENSE_FILE", "/hpc/m3/apps/gurobi/11.0.1/linux64/client.lic") append_path("LD_LIBRARY_PATH","/hpc/m3/apps/gurobi/11.0.1/linux64/lib") append_path("CPATH", "/hpc/m3/apps/gurobi/11.0.1/linux64/include") append_path("LIBRARY_PATH","/hpc/m3/apps/gurobi/11.0.1/linux64/lib") + +help([[Name: Gurobi +Version: 11.0.1 +Website: https://www.gurobi.com/ +License Owners : free academic site license (Merlin) + +Gurobi optimization software +]]) \ No newline at end of file From 39542aecb3eef9387fe0db0a8677744f5e1e969e Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:02:46 -0500 Subject: [PATCH 26/66] add help for idl --- modules/m3/applications/idl/8.0.lua | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/m3/applications/idl/8.0.lua b/modules/m3/applications/idl/8.0.lua index 33fdd8f8..929d50e2 100644 --- a/modules/m3/applications/idl/8.0.lua +++ b/modules/m3/applications/idl/8.0.lua @@ -2,3 +2,9 @@ whatis("IDL 8.0") always_load("apptainer") set_alias("idl", "apptainer run /hpc/m3/containers/idl/idl_8.0.simg") +help([[Name: IDL +Version: 8.0 +Website: https://www.nv5geospatialsoftware.com/Products/IDL + +IDL : The Interactive Data Language Visualization Solution +]]) \ No newline at end of file From d7e80259cde0a1763509786ac3af765493306ad5 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:03:52 -0500 Subject: [PATCH 27/66] add help for julia --- modules/m3/applications/julia/1.10.4.lua | 6 ++++++ modules/m3/applications/julia/1.8.5.lua | 6 ++++++ modules/m3/applications/julia/1.9.1.lua | 6 ++++++ 3 files changed, 18 insertions(+) diff --git a/modules/m3/applications/julia/1.10.4.lua b/modules/m3/applications/julia/1.10.4.lua index e9bb8153..81fb5df7 100644 --- a/modules/m3/applications/julia/1.10.4.lua +++ b/modules/m3/applications/julia/1.10.4.lua @@ -6,3 +6,9 @@ prepend_path("PATH", pathJoin(root, "bin")) prepend_path("MANPATH", pathJoin(root, "share/man")) prepend_path("LD_LIBRARY_PATH", pathJoin(root, "lib")) +help([[Name: Julia +Version: 1.10.4 +Website: https://julialang.org/ + +The Julia Programming Language +]]) \ No newline at end of file diff --git a/modules/m3/applications/julia/1.8.5.lua b/modules/m3/applications/julia/1.8.5.lua index 0b454a9a..b84ed1ae 100644 --- a/modules/m3/applications/julia/1.8.5.lua +++ b/modules/m3/applications/julia/1.8.5.lua @@ -6,3 +6,9 @@ prepend_path("PATH", pathJoin(root, "bin")) prepend_path("MANPATH", pathJoin(root, "share/man")) prepend_path("LD_LIBRARY_PATH", pathJoin(root, "lib")) +help([[Name: Julia +Version: 1.8.5 +Website: https://julialang.org/ + +The Julia Programming Language +]]) \ No newline at end of file diff --git a/modules/m3/applications/julia/1.9.1.lua b/modules/m3/applications/julia/1.9.1.lua index 2617d495..bf5a4086 100644 --- a/modules/m3/applications/julia/1.9.1.lua +++ b/modules/m3/applications/julia/1.9.1.lua @@ -6,3 +6,9 @@ prepend_path("PATH", pathJoin(root, "bin")) prepend_path("MANPATH", pathJoin(root, "share/man")) prepend_path("LD_LIBRARY_PATH", pathJoin(root, "lib")) +help([[Name: Julia +Version: 1.9.1 +Website: https://julialang.org/ + +The Julia Programming Language +]]) \ No newline at end of file From 6f40f8195447431389233cdb776c332e1f8062ea Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:05:34 -0500 Subject: [PATCH 28/66] add help to mathematica --- modules/m3/applications/mathematica/13.3.0.lua | 9 +++++++++ modules/m3/applications/mathematica/14.0.0.lua | 9 +++++++++ 2 files changed, 18 insertions(+) diff --git a/modules/m3/applications/mathematica/13.3.0.lua b/modules/m3/applications/mathematica/13.3.0.lua index 49fce5b1..8569d5de 100644 --- a/modules/m3/applications/mathematica/13.3.0.lua +++ b/modules/m3/applications/mathematica/13.3.0.lua @@ -40,3 +40,12 @@ else -- not work append_path("PATH","/hpc/m3/apps/mathematica/13.3.0/executables/") end + +help([[Name: Mathematica +Version: 13.3.0 +Website: https://www.wolfram.com/mathematica/ +License Owners: SMU site license + + +Wolfram Mathematica is a software system with built-in libraries for several areas of technical computing that allow machine learning, statistics, symbolic computation, data manipulation, network analysis, time series analysis, NLP, optimization, plotting functions and various types of data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other programming languages. +]]) \ No newline at end of file diff --git a/modules/m3/applications/mathematica/14.0.0.lua b/modules/m3/applications/mathematica/14.0.0.lua index 9b76b1be..2f7ecfdd 100644 --- a/modules/m3/applications/mathematica/14.0.0.lua +++ b/modules/m3/applications/mathematica/14.0.0.lua @@ -41,3 +41,12 @@ else -- not work append_path("PATH",mathematica_execs) end + +help([[Name: Mathematica +Version: 14.0.0 +Website: https://www.wolfram.com/mathematica/ +License Owners: SMU site license + + +Wolfram Mathematica is a software system with built-in libraries for several areas of technical computing that allow machine learning, statistics, symbolic computation, data manipulation, network analysis, time series analysis, NLP, optimization, plotting functions and various types of data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other programming languages. +]]) \ No newline at end of file From 7deb0b32dadce316082185a8c2f4893086901fff Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:06:41 -0500 Subject: [PATCH 29/66] add help for matlab --- modules/m3/applications/matlab/r2023a.lua | 10 ++++++++++ modules/m3/applications/matlab/r2024a.lua | 9 +++++++++ 2 files changed, 19 insertions(+) diff --git a/modules/m3/applications/matlab/r2023a.lua b/modules/m3/applications/matlab/r2023a.lua index 44f9ac78..1e88e88f 100644 --- a/modules/m3/applications/matlab/r2023a.lua +++ b/modules/m3/applications/matlab/r2023a.lua @@ -3,3 +3,13 @@ family("matlab") prepend_path("PATH","/hpc/m3/apps/matlab/r2023a/bin") prepend_path("LD_LIBRARY_PATH","/hpc/m3/apps/matlab/r2023a/bin/glnxa64/") setenv("MATLABROOT","/hpc/m3/apps/matlab/r2023a") + + +help([[Name: Matlab +Version: 2023a +Website: https://www.mathworks.com/ +License Owners: SMU site license + + +MATLAB is a programming and numeric computing platform used by millions of engineers and scientists to analyze data, develop algorithms, and create models. +]]) \ No newline at end of file diff --git a/modules/m3/applications/matlab/r2024a.lua b/modules/m3/applications/matlab/r2024a.lua index a7aaf733..c24a794b 100644 --- a/modules/m3/applications/matlab/r2024a.lua +++ b/modules/m3/applications/matlab/r2024a.lua @@ -3,3 +3,12 @@ family("matlab") prepend_path("PATH","/hpc/m3/apps/Matlab/r2024a/bin") prepend_path("LD_LIBRARY_PATH","/hpc/m3/apps/Matlab/r2024a/bin/glnxa64/") setenv("MATLABROOT","/hpc/m3/apps/Matlab/r2024a") + +help([[Name: Matlab +Version: 2024a +Website: https://www.mathworks.com/ +License Owners: SMU site license + + +MATLAB is a programming and numeric computing platform used by millions of engineers and scientists to analyze data, develop algorithms, and create models. +]]) From 1aaf609c7a4da34f968836cc803c536f7a8516c5 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:08:28 -0500 Subject: [PATCH 30/66] add help for mojo --- modules/m3/applications/mojo/0.6.1.lua | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/m3/applications/mojo/0.6.1.lua b/modules/m3/applications/mojo/0.6.1.lua index 12200474..4a6367ad 100644 --- a/modules/m3/applications/mojo/0.6.1.lua +++ b/modules/m3/applications/mojo/0.6.1.lua @@ -22,3 +22,9 @@ for _, executable in ipairs(executables) do build_command(executable) end +help([[Name: Mojo +Version: 0.6.1 +Website: https://www.modular.com/mojo + +Mojo is a new programming language that bridges the gap between research and production by combining Python syntax and ecosystem with systems programming and metaprogramming features. +]]) From 39e1a7cfd19c1e90afd43c35b3c4d7883447d8bd Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:09:43 -0500 Subject: [PATCH 31/66] add help for molden --- modules/m3/applications/molden/6.9.lua | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/m3/applications/molden/6.9.lua b/modules/m3/applications/molden/6.9.lua index 12402a8b..ac6de343 100644 --- a/modules/m3/applications/molden/6.9.lua +++ b/modules/m3/applications/molden/6.9.lua @@ -27,3 +27,9 @@ for _, executable in ipairs(executables) do build_command(executable) end +help([[Name: Molden +Version: 6.9 +Website: https://www.theochem.ru.nl/molden/ + +Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac +]]) \ No newline at end of file From 98fd84e9638b6029d5428d5d6eeedf5fd7319e7b Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:11:29 -0500 Subject: [PATCH 32/66] add molpro help --- modules/m3/applications/molpro/2022.3.lua | 6 ++++++ modules/m3/applications/molpro/2024.1.lua | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/modules/m3/applications/molpro/2022.3.lua b/modules/m3/applications/molpro/2022.3.lua index 20d0cbbd..2a98eb1c 100644 --- a/modules/m3/applications/molpro/2022.3.lua +++ b/modules/m3/applications/molpro/2022.3.lua @@ -3,3 +3,9 @@ family("molpro") conflict("molpro") prepend_path("PATH","/hpc/m3/apps/molpro/2022.3/bin") +help([[Name: Molpro +Version: 2022.3 +Website: https://www.molpro.net/ + +Molpro is a comprehensive system of ab initio programs for advanced molecular electronic structure calculations +]]) \ No newline at end of file diff --git a/modules/m3/applications/molpro/2024.1.lua b/modules/m3/applications/molpro/2024.1.lua index 76249033..a916df84 100644 --- a/modules/m3/applications/molpro/2024.1.lua +++ b/modules/m3/applications/molpro/2024.1.lua @@ -3,3 +3,9 @@ family("molpro") conflict("molpro") prepend_path("PATH","/hpc/m3/apps/molpro/2024.1/bin") +help([[Name: Molpro +Version: 2024.1 +Website: https://www.molpro.net/ + +Molpro is a comprehensive system of ab initio programs for advanced molecular electronic structure calculations +]]) \ No newline at end of file From 2c7c24141cc7f8417873834355ca3cfafbe97ea6 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:14:17 -0500 Subject: [PATCH 33/66] add help for nbo --- modules/m3/applications/nbo/7.0/i4.lua | 6 ++++++ modules/m3/applications/nbo/7.0/i8.lua | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/modules/m3/applications/nbo/7.0/i4.lua b/modules/m3/applications/nbo/7.0/i4.lua index 49f5f764..51f79164 100644 --- a/modules/m3/applications/nbo/7.0/i4.lua +++ b/modules/m3/applications/nbo/7.0/i4.lua @@ -11,3 +11,9 @@ prepend_path("PATH", root) setenv("GENEXE", pathJoin(bin, "gennbo." .. int .. ".exe")) setenv("NBOEXE", pathJoin(bin, "nbo6." .. int .. ".exe")) +help([[Name: TCI/NBO Software (i4) +Version: 7.0 +Website: https://charge.wisc.edu/chemistry/order_nbo7.aspx + +Natural Bond Orbitals from Theoretical Chemistry Institute -- University of Wisconsin +]]) \ No newline at end of file diff --git a/modules/m3/applications/nbo/7.0/i8.lua b/modules/m3/applications/nbo/7.0/i8.lua index 1ab40211..bb7ed14f 100644 --- a/modules/m3/applications/nbo/7.0/i8.lua +++ b/modules/m3/applications/nbo/7.0/i8.lua @@ -11,3 +11,9 @@ prepend_path("PATH", root) setenv("GENEXE", pathJoin(bin, "gennbo." .. int .. ".exe")) setenv("NBOEXE", pathJoin(bin, "nbo6." .. int .. ".exe")) +help([[Name: TCI/NBO Software (i8) +Version: 7.0 +Website: https://charge.wisc.edu/chemistry/order_nbo7.aspx + +Natural Bond Orbitals from Theoretical Chemistry Institute -- University of Wisconsin +]]) \ No newline at end of file From 41ecc4adef6a5bbe4f1528b57a11f9d8692aec0d Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:15:33 -0500 Subject: [PATCH 34/66] add orca help --- modules/m3/applications/orca/5.0.4.lua | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/m3/applications/orca/5.0.4.lua b/modules/m3/applications/orca/5.0.4.lua index 46289bc5..105275f3 100644 --- a/modules/m3/applications/orca/5.0.4.lua +++ b/modules/m3/applications/orca/5.0.4.lua @@ -6,3 +6,9 @@ load("gcc/11.2.0", "openmpi/4.1.6-a4ksrza") prepend_path("PATH", root) prepend_path("LD_LIBRARY_PATH", root) +help([[Name: ORCA Quantum Chemistry Package +Version: 5.0.4 +Website: https://www.faccts.de/orca/ + +RCA is a powerful and versatile quantum chemistry software package, primarily developed by the group of Prof. Frank Neese. +]]) \ No newline at end of file From 779f38de5812337c693163d2b1aba2df81d60635 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:16:36 -0500 Subject: [PATCH 35/66] add qchem help --- modules/m3/applications/q-chem/5.2.2.lua | 6 ++++++ modules/m3/applications/q-chem/6.0.2.lua | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/modules/m3/applications/q-chem/5.2.2.lua b/modules/m3/applications/q-chem/5.2.2.lua index 0ecbb604..0ee2708f 100644 --- a/modules/m3/applications/q-chem/5.2.2.lua +++ b/modules/m3/applications/q-chem/5.2.2.lua @@ -3,3 +3,9 @@ family("qchem") source_sh('bash', '/hpc/m3/apps/q-chem/5.2.2/qcenv.sh') +help([[Name: Q-Chem +Version: 5.2.2 +Website: https://www.q-chem.com/ + +Q-Chem is an ab initio quantum chemistry software package for fast and accurate simulations of molecular systems, including electronic and molecular structure, reactivities, properties, and spectra. +]]) \ No newline at end of file diff --git a/modules/m3/applications/q-chem/6.0.2.lua b/modules/m3/applications/q-chem/6.0.2.lua index 6ba11bec..27df10ba 100644 --- a/modules/m3/applications/q-chem/6.0.2.lua +++ b/modules/m3/applications/q-chem/6.0.2.lua @@ -3,3 +3,9 @@ family("qchem") source_sh('bash', '/hpc/m3/apps/q-chem/6.0.2/qcenv.sh') +help([[Name: Q-Chem +Version: 6.0.2 +Website: https://www.q-chem.com/ + +Q-Chem is an ab initio quantum chemistry software package for fast and accurate simulations of molecular systems, including electronic and molecular structure, reactivities, properties, and spectra. +]]) \ No newline at end of file From c2fd984812066946a2201b3d2d00bd7ee55f691d Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:18:01 -0500 Subject: [PATCH 36/66] add quantum atk help --- modules/m3/applications/quantum_atk/2022.03-SP1.lua | 7 +++++++ modules/m3/applications/quantum_atk/2022.12-SP1.lua | 7 +++++++ 2 files changed, 14 insertions(+) diff --git a/modules/m3/applications/quantum_atk/2022.03-SP1.lua b/modules/m3/applications/quantum_atk/2022.03-SP1.lua index 09d4b1a6..9daf9270 100644 --- a/modules/m3/applications/quantum_atk/2022.03-SP1.lua +++ b/modules/m3/applications/quantum_atk/2022.03-SP1.lua @@ -14,3 +14,10 @@ setenv("SNPSLMD_LICENSE_FILE", "27020@sengr7lic2.smu.edu") prepend_path("PATH", bin) append_path("LD_LIBRARY_PATH", lib) + +help([[Name: Synopsys Quantum ATK" +Version: 2022.03-SP1 +Website: https://www.synopsys.com/manufacturing/quantumatk.html + +QuantumATK - Atomistic Simulation Software +]]) \ No newline at end of file diff --git a/modules/m3/applications/quantum_atk/2022.12-SP1.lua b/modules/m3/applications/quantum_atk/2022.12-SP1.lua index e232c2fb..f936921d 100644 --- a/modules/m3/applications/quantum_atk/2022.12-SP1.lua +++ b/modules/m3/applications/quantum_atk/2022.12-SP1.lua @@ -15,3 +15,10 @@ setenv("SNPSLMD_LICENSE_FILE", "27020@sengr7lic2.smu.edu") prepend_path("PATH", bin) append_path("LD_LIBRARY_PATH", lib) + +help([[Name: Synopsys Quantum ATK" +Version: 2022.12-SP1 +Website: https://www.synopsys.com/manufacturing/quantumatk.html + +QuantumATK - Atomistic Simulation Software +]]) \ No newline at end of file From 14b45ec8ae4c4896482028a5d5686bb4e03eca71 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:21:57 -0500 Subject: [PATCH 37/66] add help for R --- modules/m3/applications/R/4.2.3.lua | 8 +++++++- modules/m3/applications/R/4.3.0.lua | 5 +++++ modules/m3/applications/R/4.3.2.lua | 6 ++++++ modules/m3/applications/R/4.4.0.lua | 6 ++++++ modules/m3/applications/quantum_atk/2022.03-SP1.lua | 2 +- 5 files changed, 25 insertions(+), 2 deletions(-) diff --git a/modules/m3/applications/R/4.2.3.lua b/modules/m3/applications/R/4.2.3.lua index 1a959450..518124bd 100644 --- 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') \ No newline at end of file diff --git a/modules/m3/applications/R/4.3.0.lua b/modules/m3/applications/R/4.3.0.lua index 0471e662..ec77d9cb 100644 --- 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 index 45c2cf89..5d837e17 100644 --- 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 index 89f84c07..fb58fd16 100644 --- 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/quantum_atk/2022.03-SP1.lua b/modules/m3/applications/quantum_atk/2022.03-SP1.lua index 9daf9270..e397e395 100644 --- a/modules/m3/applications/quantum_atk/2022.03-SP1.lua +++ b/modules/m3/applications/quantum_atk/2022.03-SP1.lua @@ -15,7 +15,7 @@ setenv("SNPSLMD_LICENSE_FILE", "27020@sengr7lic2.smu.edu") prepend_path("PATH", bin) append_path("LD_LIBRARY_PATH", lib) -help([[Name: Synopsys Quantum ATK" +help([[Name: Synopsys Quantum ATK Version: 2022.03-SP1 Website: https://www.synopsys.com/manufacturing/quantumatk.html From b70fd9714d488e3be9d5dd757446c55502ffdd2f Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:23:20 -0500 Subject: [PATCH 38/66] add help for sas --- modules/m3/applications/sas/9.4m7.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/m3/applications/sas/9.4m7.lua b/modules/m3/applications/sas/9.4m7.lua index 7d9f3e18..b482cd55 100644 --- a/modules/m3/applications/sas/9.4m7.lua +++ b/modules/m3/applications/sas/9.4m7.lua @@ -35,3 +35,10 @@ else prepend_path("PATH", "/hpc/m3/apps/sas/9.4_m7/SASFoundation/9.4") prepend_path("MANPATH", "/hpc/m3/apps/sas/9.4_m7/SASFoundation/9.4/utilities/man") end + +help([[Name: SAS +Version: 9.4_m7 +Website: https://www.sas.com/ + +SAS is a statistical software suite developed by SAS Institute for data management, advanced analytics, multivariate analysis, business intelligence, criminal investigation,[2] and predictive analytics. +]]) From 158fabae1f678f150987d32590e2c42a5d69228a Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:24:44 -0500 Subject: [PATCH 39/66] add help for snid --- modules/m3/applications/snid/5.0.lua | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/m3/applications/snid/5.0.lua b/modules/m3/applications/snid/5.0.lua index 6da204aa..d9363f2d 100644 --- a/modules/m3/applications/snid/5.0.lua +++ b/modules/m3/applications/snid/5.0.lua @@ -10,3 +10,9 @@ set_shell_function("snid", snid, snid) set_shell_function("logwave", logwave, logwave) set_shell_function("plotlnw", plotlnw, plotlnw) +help([[Name: Supernova Identification (SNID) +Version: 5.0 +Website: https://people.lam.fr/blondin.stephane/software/snid/index.html + +Supernova Identification (SNID) +]]) \ No newline at end of file From 7a652714e7373c497a7b5406e37526aae9854831 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:25:55 -0500 Subject: [PATCH 40/66] add help for stata --- modules/m3/applications/stata/mp-17.lua | 7 +++++++ modules/m3/applications/stata/mp-18.lua | 7 +++++++ 2 files changed, 14 insertions(+) diff --git a/modules/m3/applications/stata/mp-17.lua b/modules/m3/applications/stata/mp-17.lua index 863f3342..bdab6078 100644 --- a/modules/m3/applications/stata/mp-17.lua +++ b/modules/m3/applications/stata/mp-17.lua @@ -1,3 +1,10 @@ whatis("loads Stata MP - Parallel Edition, version 17 executables in current environment") prepend_path("PATH", "/hpc/m3/apps/stata/17") prepend_path("LD_LIBRARY_PATH", "/hpc/m3/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.2.0/ncurses-6.3-jpb7yevv22soniixg7h755bejzvyk6a7/lib/") + +help([[Name: Stata +Version: 17 +Website: https://www.stata.com/ + +Stata is a general-purpose statistical software package +]]) \ No newline at end of file diff --git a/modules/m3/applications/stata/mp-18.lua b/modules/m3/applications/stata/mp-18.lua index 6fad4f41..cb279d64 100644 --- a/modules/m3/applications/stata/mp-18.lua +++ b/modules/m3/applications/stata/mp-18.lua @@ -1,3 +1,10 @@ whatis("loads Stata MP - Parallel Edition, version 18 executables in current environment") prepend_path("PATH", "/hpc/m3/apps/stata/18") prepend_path("LD_LIBRARY_PATH", "/hpc/m3/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.2.0/ncurses-6.3-jpb7yevv22soniixg7h755bejzvyk6a7/lib/") + +help([[Name: Stata +Version: 18 +Website: https://www.stata.com/ + +Stata is a general-purpose statistical software package +]]) \ No newline at end of file From 77cb8d33b4b01a7bf291b41764e2ad89abb5e460 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:27:26 -0500 Subject: [PATCH 41/66] add Synopsys Photonic Solutions help --- .../applications/synopsys/photonicsolutions/2021.09-3.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/m3/applications/synopsys/photonicsolutions/2021.09-3.lua b/modules/m3/applications/synopsys/photonicsolutions/2021.09-3.lua index 9cd239b7..dc4100c5 100644 --- a/modules/m3/applications/synopsys/photonicsolutions/2021.09-3.lua +++ b/modules/m3/applications/synopsys/photonicsolutions/2021.09-3.lua @@ -17,3 +17,10 @@ setenv("SNPSLMD_LICENSE_FILE", "27020@sengr7lic2.smu.edu") prepend_path("PATH", opto_link_base) prepend_path("PATH", rsoft_programpath) append_path("LD_LIBRARY_PATH", rsoft_programpath) + +help([[Name: Synopsys Photonic Solutions +Version: 2021.09-3 +Website: https://www.synopsys.com/photonic-solutions.html + +Synopsys Photonic Solutions +]]) \ No newline at end of file From 749b12a2d4e42ac0d36dc4edaedecb3a19b7d50a Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:28:20 -0500 Subject: [PATCH 42/66] add texlive help --- modules/m3/applications/texlive/2023.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/m3/applications/texlive/2023.lua b/modules/m3/applications/texlive/2023.lua index c30c1fc6..57c33eea 100644 --- a/modules/m3/applications/texlive/2023.lua +++ b/modules/m3/applications/texlive/2023.lua @@ -17,3 +17,10 @@ setenv('TEXMFSYSCONFIG', '/hpc/m3/apps/texlive/2023/texmf-config') setenv('TEXMFVAR', texmfvar) setenv('TEXMFCONFIG', texmfconfig) setenv('TEXMFHOME', texmfhome) + +help([[Name: TeX Live +Version: 2023 +Website: https://www.tug.org/texlive/ + +TeX Live is intended to be a straightforward way to get up and running with the TeX document production system +]]) \ No newline at end of file From d55c67955d1eed7009117d17b7cba44169b7a358 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:29:27 -0500 Subject: [PATCH 43/66] add vasp help --- modules/m3/applications/vasp/5.4.4.lua | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/modules/m3/applications/vasp/5.4.4.lua b/modules/m3/applications/vasp/5.4.4.lua index aa622a93..390dffad 100644 --- a/modules/m3/applications/vasp/5.4.4.lua +++ b/modules/m3/applications/vasp/5.4.4.lua @@ -17,4 +17,9 @@ load("gcc/11.2.0", "openmpi/4.1.4-7al4h2x", "openblas/0.3.21-s5husbk") prepend_path("PATH","/hpc/m3/apps/vasp/vasp.5.4.4/bin") +help([[Name: VASP +Version: 5.4.4 +Website: https://www.vasp.at/ +The Vienna Ab initio Simulation Package: atomic scale materials modelling from first principles. +]]) From ce45f12dfdadeef6b6aa44747654934db91d0517 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:31:32 -0500 Subject: [PATCH 44/66] add vmd help --- modules/m3/applications/vmd/1.9.3.lua | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/m3/applications/vmd/1.9.3.lua b/modules/m3/applications/vmd/1.9.3.lua index 537e6b07..4eb1556d 100644 --- a/modules/m3/applications/vmd/1.9.3.lua +++ b/modules/m3/applications/vmd/1.9.3.lua @@ -2,3 +2,9 @@ whatis("VMD") prepend_path("PATH","/hpc/m3/apps/vmd/1.9.3/bin") append_path("LD_LIBRARY_PATH","/hpc/m3/apps/vmd/1.9.3/lib") +help([[Name: VMD +Version: 1.9.3 +Website: https://www.ks.uiuc.edu/Research/vmd/ + +VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. +]]) \ No newline at end of file From 6210b3830a0eade2ec214d569b79aad8f254a0de Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:32:49 -0500 Subject: [PATCH 45/66] add help for x13as --- modules/m3/applications/x13as/1.1.b60.lua | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/modules/m3/applications/x13as/1.1.b60.lua b/modules/m3/applications/x13as/1.1.b60.lua index 8593b11f..d2d3b658 100644 --- a/modules/m3/applications/x13as/1.1.b60.lua +++ b/modules/m3/applications/x13as/1.1.b60.lua @@ -1,5 +1,11 @@ whatis("x13as 1.1.b60") family("x13as") - append_path("PATH", "/hpc/m3/apps/x13as/1.1.b60") + +help([[Name: x13as +Version: 1.1.b60 +Website: https://www.census.gov/data/software/x13as.html + +X-13ARIMA-SEATS Seasonal Adjustment Program +]]) \ No newline at end of file From c236784e166e89a0c1f8ad6e66316ac4e32a0fcd Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:33:49 -0500 Subject: [PATCH 46/66] add conda help --- modules/m3/applications/conda.lua | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/modules/m3/applications/conda.lua b/modules/m3/applications/conda.lua index 67d0f5ce..18ef3a2c 100644 --- 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. +]]) \ No newline at end of file From 2706e3f5bf86898c9f1446ff58dc97af99b6f5b8 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:34:31 -0500 Subject: [PATCH 47/66] add help for spack --- modules/m3/applications/spack.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/m3/applications/spack.lua b/modules/m3/applications/spack.lua index db88c5bc..e092ee53 100644 --- a/modules/m3/applications/spack.lua +++ b/modules/m3/applications/spack.lua @@ -1,3 +1,10 @@ whatis("Spack") family("spack") source_sh('bash', '/hpc/m3/spack/share/spack/setup-env.sh') + +help([[Name: Spack +Version: several +Website: https://spack.io/ + +pack is a package manager for supercomputers, Linux, and macOS. +]]) \ No newline at end of file From 4e33643eb927dc72563995bbff468c279f22f5dd Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:36:06 -0500 Subject: [PATCH 48/66] add help for gcc --- modules/m3/applications/spack.lua | 2 +- modules/m3/compilers/gcc/11.2.0.lua | 6 ++++++ modules/m3/compilers/gcc/6.3.0.lua | 6 ++++++ 3 files changed, 13 insertions(+), 1 deletion(-) diff --git a/modules/m3/applications/spack.lua b/modules/m3/applications/spack.lua index e092ee53..2a82e03d 100644 --- a/modules/m3/applications/spack.lua +++ b/modules/m3/applications/spack.lua @@ -6,5 +6,5 @@ help([[Name: Spack Version: several Website: https://spack.io/ -pack is a package manager for supercomputers, Linux, and macOS. +Spack is a package manager for supercomputers, Linux, and macOS. ]]) \ No newline at end of file diff --git a/modules/m3/compilers/gcc/11.2.0.lua b/modules/m3/compilers/gcc/11.2.0.lua index 005911e2..49aef50f 100644 --- a/modules/m3/compilers/gcc/11.2.0.lua +++ b/modules/m3/compilers/gcc/11.2.0.lua @@ -18,3 +18,9 @@ setenv("OMPI_MCA_btl_openib_if_include","mlx5_0:1") setenv("OMPI_MCA_hwloc_base_binding_policy","core") setenv("UCX_NET_DEVICES","mlx5_0:1") +help([[Name: GNU gcc +Version: 11.2.0 +Website: https://gcc.gnu.org/ + +The GNU Compiler Collection +]]) diff --git a/modules/m3/compilers/gcc/6.3.0.lua b/modules/m3/compilers/gcc/6.3.0.lua index 01ddfe6c..322fa6c6 100644 --- a/modules/m3/compilers/gcc/6.3.0.lua +++ b/modules/m3/compilers/gcc/6.3.0.lua @@ -28,3 +28,9 @@ setenv("OMPI_MCA_btl_openib_if_include","mlx5_0:1") setenv("OMPI_MCA_hwloc_base_binding_policy","core") setenv("UCX_NET_DEVICES","mlx5_0:1") +help([[Name: GNU gcc +Version: 6.3.0 +Website: https://gcc.gnu.org/ + +The GNU Compiler Collection +]]) \ No newline at end of file From e55158c2ba984cf411f7191117d8cbba9bbbe88f Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:37:35 -0500 Subject: [PATCH 49/66] add help for intel compilers --- modules/m3/compilers/intel/2023.1.lua | 6 ++++++ modules/m3/compilers/intel/oneapi/2023.2.lua | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/modules/m3/compilers/intel/2023.1.lua b/modules/m3/compilers/intel/2023.1.lua index d2a4d25c..96f78486 100644 --- a/modules/m3/compilers/intel/2023.1.lua +++ b/modules/m3/compilers/intel/2023.1.lua @@ -4,3 +4,9 @@ family("compiler") append_path("MODULEPATH", "/hpc/m3/apps/intel/oneapi/2023.1/modulefiles") load("compiler/latest") +help([[Name: Intel OneAPI Compiler Suite +Version: 2023.1 +Website: https://www.intel.com/content/www/us/en/developer/tools/oneapi/overview.html + +The Intel® oneAPI DPC++/C++ Compiler gives developers even more confidence that their code is portable and reliably performant across existing and future CPU, GPU, and AI accelerator architectures. +]]) \ No newline at end of file diff --git a/modules/m3/compilers/intel/oneapi/2023.2.lua b/modules/m3/compilers/intel/oneapi/2023.2.lua index a0d6c25a..d842a3bc 100644 --- a/modules/m3/compilers/intel/oneapi/2023.2.lua +++ b/modules/m3/compilers/intel/oneapi/2023.2.lua @@ -13,3 +13,9 @@ append_path("MODULEPATH", "/hpc/m3/modules/spack/linux-ubuntu22.04-x86_64_v3/cud -- generic packages / dependencies append_path("MODULEPATH", "/hpc/m3/modules/spack/linux-ubuntu22.04-x86_64_v3/oneapi-2023.2.0/") +help([[Name: Intel OneAPI Compiler Suite +Version: 2023.2 +Website: https://www.intel.com/content/www/us/en/developer/tools/oneapi/overview.html + +The Intel® oneAPI DPC++/C++ Compiler gives developers even more confidence that their code is portable and reliably performant across existing and future CPU, GPU, and AI accelerator architectures. +]]) \ No newline at end of file From af6d4332d100b441d900bcb76aa41616cf114ec7 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:38:33 -0500 Subject: [PATCH 50/66] add help for nvhpc --- modules/m3/compilers/nvidia/21.3.lua | 6 ++++++ modules/m3/compilers/nvidia/23.5.lua | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/modules/m3/compilers/nvidia/21.3.lua b/modules/m3/compilers/nvidia/21.3.lua index 48d13f65..eeece44e 100644 --- a/modules/m3/compilers/nvidia/21.3.lua +++ b/modules/m3/compilers/nvidia/21.3.lua @@ -4,3 +4,9 @@ family("compiler") append_path("MODULEPATH", "/hpc/m3/apps/nvidia/hpc-sdk/21.3/modulefiles") load("nvhpc/21.3") +help([[Name: NVIDIA HPC SDK +Version: 21.3 +Website: https://developer.nvidia.com/hpc-sdk + +The NVIDIA HPC Software Development Kit (SDK) includes the proven compilers, libraries and software tools essential to maximizing developer productivity and the performance and portability of HPC applications. +]]) \ No newline at end of file diff --git a/modules/m3/compilers/nvidia/23.5.lua b/modules/m3/compilers/nvidia/23.5.lua index 2107b553..555f665b 100644 --- a/modules/m3/compilers/nvidia/23.5.lua +++ b/modules/m3/compilers/nvidia/23.5.lua @@ -11,3 +11,9 @@ setenv("OMPI_MCA_btl_openib_if_include","mlx5_0:1") setenv("OMPI_MCA_hwloc_base_binding_policy","core") setenv("UCX_NET_DEVICES","mlx5_0:1") +help([[Name: NVIDIA HPC SDK +Version: 23.5 +Website: https://developer.nvidia.com/hpc-sdk + +The NVIDIA HPC Software Development Kit (SDK) includes the proven compilers, libraries and software tools essential to maximizing developer productivity and the performance and portability of HPC applications. +]]) \ No newline at end of file From 2fd7e2e8a38ea9919bfb7600463d834d66ba139b Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:39:27 -0500 Subject: [PATCH 51/66] add help for rust --- modules/m3/compilers/rust/1.71.0.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/m3/compilers/rust/1.71.0.lua b/modules/m3/compilers/rust/1.71.0.lua index c8c5d0d4..bb85116a 100644 --- a/modules/m3/compilers/rust/1.71.0.lua +++ b/modules/m3/compilers/rust/1.71.0.lua @@ -4,3 +4,10 @@ family("rust") prepend_path("PATH", "/hpc/m3/apps/rust/1.71.0/bin") prepend_path("LD_LIBRARY_PATH", "/hpc/m3/apps/rust/1.71.0/lib") prepend_path("MANPATH", "/hpc/m3/apps/rust/1.71.0/share/man/") + +help([[Name: Rust +Version: 1.71.0 +Website: https://www.rust-lang.org/ + +A language empowering everyone to build reliable and efficient software. +]]) \ No newline at end of file From d3111767e6ea0bc70edef4762231531a6c5aacd9 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:40:15 -0500 Subject: [PATCH 52/66] add help for hpc-x --- modules/m3/mpi/gcc-11.2.0/hpc-x/2.14.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/m3/mpi/gcc-11.2.0/hpc-x/2.14.lua b/modules/m3/mpi/gcc-11.2.0/hpc-x/2.14.lua index df88217f..85f758ea 100644 --- a/modules/m3/mpi/gcc-11.2.0/hpc-x/2.14.lua +++ b/modules/m3/mpi/gcc-11.2.0/hpc-x/2.14.lua @@ -50,3 +50,10 @@ setenv("SHMEM_HOME","/hpc/m3/apps/hpcx/hpcx-v2.14-gcc-inbox-ubuntu22.04-cuda11-g prepend_path("PATH","/hpc/m3/apps/hpcx/hpcx-v2.14-gcc-inbox-ubuntu22.04-cuda11-gdrcopy2-nccl2.16-x86_64/hpcx-ompi-gcc-11.2.0/bin") prepend_path("LD_LIBRARY_PATH","/hpc/m3/apps/hpcx/hpcx-v2.14-gcc-inbox-ubuntu22.04-cuda11-gdrcopy2-nccl2.16-x86_64/hpcx-ompi-gcc-11.2.0/lib") prepend_path("LIBRARY_PATH","/hpc/m3/apps/hpcx/hpcx-v2.14-gcc-inbox-ubuntu22.04-cuda11-gdrcopy2-nccl2.16-x86_64/hpcx-ompi-gcc-11.2.0/lib") + +help([[Name: HPC-X +Version: 2.14 +Website: https://developer.nvidia.com/networking/hpc-x + +NVIDIA® HPC-X® is a comprehensive software package that includes Message Passing Interface (MPI), Symmetrical Hierarchical Memory (SHMEM) and Partitioned Global Address Space (PGAS) communications libraries, and various acceleration packages. +]]) \ No newline at end of file From af244e1fbb4a0155f35f45ea6e14ad20301a7803 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:41:32 -0500 Subject: [PATCH 53/66] add hpcx help for mp --- modules/mp/mpi/aocc-4.1.0/hpc-x/2.14.lua | 7 +++++++ modules/mp/mpi/gcc-11.2.0/hpc-x/2.14.lua | 7 +++++++ modules/mp/mpi/gcc-11.2.0/hpc-x/2.17.1.lua | 7 +++++++ modules/mp/mpi/gcc-13.2.0/hpc-x/2.17.1.lua | 7 +++++++ modules/mp/mpi/oneapi-2023.2.0/hpc-x/2.14.lua | 7 +++++++ 5 files changed, 35 insertions(+) diff --git a/modules/mp/mpi/aocc-4.1.0/hpc-x/2.14.lua b/modules/mp/mpi/aocc-4.1.0/hpc-x/2.14.lua index c16a59c2..d4fe7871 100644 --- a/modules/mp/mpi/aocc-4.1.0/hpc-x/2.14.lua +++ b/modules/mp/mpi/aocc-4.1.0/hpc-x/2.14.lua @@ -58,3 +58,10 @@ setenv("SHMEM_HOME","/hpc/mp/apps/hpcx/hpcx-v2.14-gcc-inbox-ubuntu22.04-cuda11-g prepend_path("PATH","/hpc/mp/apps/hpcx/hpcx-v2.14-gcc-inbox-ubuntu22.04-cuda11-gdrcopy2-nccl2.16-x86_64/hpcx-ompi-aocc-4.1.0/bin") prepend_path("LD_LIBRARY_PATH","/hpc/mp/apps/hpcx/hpcx-v2.14-gcc-inbox-ubuntu22.04-cuda11-gdrcopy2-nccl2.16-x86_64/hpcx-ompi-aocc-4.1.0/lib") prepend_path("LIBRARY_PATH","/hpc/mp/apps/hpcx/hpcx-v2.14-gcc-inbox-ubuntu22.04-cuda11-gdrcopy2-nccl2.16-x86_64/hpcx-ompi-aocc-4.1.0/lib") + +help([[Name: HPC-X +Version: 2.14 +Website: https://developer.nvidia.com/networking/hpc-x + +NVIDIA® HPC-X® is a comprehensive software package that includes Message Passing Interface (MPI), Symmetrical Hierarchical Memory (SHMEM) and Partitioned Global Address Space (PGAS) communications libraries, and various acceleration packages. +]]) \ No newline at end of file diff --git a/modules/mp/mpi/gcc-11.2.0/hpc-x/2.14.lua b/modules/mp/mpi/gcc-11.2.0/hpc-x/2.14.lua index f36b27a5..81b29dd9 100644 --- a/modules/mp/mpi/gcc-11.2.0/hpc-x/2.14.lua +++ b/modules/mp/mpi/gcc-11.2.0/hpc-x/2.14.lua @@ -58,3 +58,10 @@ setenv("SHMEM_HOME","/hpc/mp/apps/hpcx/hpcx-v2.14-gcc-inbox-ubuntu22.04-cuda11-g prepend_path("PATH","/hpc/mp/apps/hpcx/hpcx-v2.14-gcc-inbox-ubuntu22.04-cuda11-gdrcopy2-nccl2.16-x86_64/hpcx-ompi-gcc-11.2.0/bin") prepend_path("LD_LIBRARY_PATH","/hpc/mp/apps/hpcx/hpcx-v2.14-gcc-inbox-ubuntu22.04-cuda11-gdrcopy2-nccl2.16-x86_64/hpcx-ompi-gcc-11.2.0/lib") prepend_path("LIBRARY_PATH","/hpc/mp/apps/hpcx/hpcx-v2.14-gcc-inbox-ubuntu22.04-cuda11-gdrcopy2-nccl2.16-x86_64/hpcx-ompi-gcc-11.2.0/lib") + +help([[Name: HPC-X +Version: 2.14 +Website: https://developer.nvidia.com/networking/hpc-x + +NVIDIA® HPC-X® is a comprehensive software package that includes Message Passing Interface (MPI), Symmetrical Hierarchical Memory (SHMEM) and Partitioned Global Address Space (PGAS) communications libraries, and various acceleration packages. +]]) \ No newline at end of file diff --git a/modules/mp/mpi/gcc-11.2.0/hpc-x/2.17.1.lua b/modules/mp/mpi/gcc-11.2.0/hpc-x/2.17.1.lua index e3517603..85be0ef5 100644 --- a/modules/mp/mpi/gcc-11.2.0/hpc-x/2.17.1.lua +++ b/modules/mp/mpi/gcc-11.2.0/hpc-x/2.17.1.lua @@ -60,3 +60,10 @@ setenv("SHMEM_HOME",pathJoin(HPCX_HOME,OMPI_DIR)) prepend_path("PATH",pathJoin(HPCX_HOME,OMPI_DIR,"/bin")) prepend_path("LD_LIBRARY_PATH",pathJoin(HPCX_HOME,OMPI_DIR,"/lib")) prepend_path("LIBRARY_PATH",pathJoin(HPCX_HOME,OMPI_DIR,"/lib")) + +help([[Name: HPC-X +Version: 2.17.1 +Website: https://developer.nvidia.com/networking/hpc-x + +NVIDIA® HPC-X® is a comprehensive software package that includes Message Passing Interface (MPI), Symmetrical Hierarchical Memory (SHMEM) and Partitioned Global Address Space (PGAS) communications libraries, and various acceleration packages. +]]) \ No newline at end of file diff --git a/modules/mp/mpi/gcc-13.2.0/hpc-x/2.17.1.lua b/modules/mp/mpi/gcc-13.2.0/hpc-x/2.17.1.lua index 9ed95dbb..0cf5313c 100644 --- a/modules/mp/mpi/gcc-13.2.0/hpc-x/2.17.1.lua +++ b/modules/mp/mpi/gcc-13.2.0/hpc-x/2.17.1.lua @@ -60,3 +60,10 @@ setenv("SHMEM_HOME",pathJoin(HPCX_HOME,OMPI_DIR)) prepend_path("PATH",pathJoin(HPCX_HOME,OMPI_DIR,"/bin")) prepend_path("LD_LIBRARY_PATH",pathJoin(HPCX_HOME,OMPI_DIR,"/lib")) prepend_path("LIBRARY_PATH",pathJoin(HPCX_HOME,OMPI_DIR,"/lib")) + +help([[Name: HPC-X +Version: 2.17.1 +Website: https://developer.nvidia.com/networking/hpc-x + +NVIDIA® HPC-X® is a comprehensive software package that includes Message Passing Interface (MPI), Symmetrical Hierarchical Memory (SHMEM) and Partitioned Global Address Space (PGAS) communications libraries, and various acceleration packages. +]]) \ No newline at end of file diff --git a/modules/mp/mpi/oneapi-2023.2.0/hpc-x/2.14.lua b/modules/mp/mpi/oneapi-2023.2.0/hpc-x/2.14.lua index ddc8b525..06d040ad 100644 --- a/modules/mp/mpi/oneapi-2023.2.0/hpc-x/2.14.lua +++ b/modules/mp/mpi/oneapi-2023.2.0/hpc-x/2.14.lua @@ -58,3 +58,10 @@ setenv("SHMEM_HOME","/hpc/mp/apps/hpcx/hpcx-v2.14-gcc-inbox-ubuntu22.04-cuda11-g prepend_path("PATH","/hpc/mp/apps/hpcx/hpcx-v2.14-gcc-inbox-ubuntu22.04-cuda11-gdrcopy2-nccl2.16-x86_64/hpcx-ompi-oneapi-2023.2.0/bin") prepend_path("LD_LIBRARY_PATH","/hpc/mp/apps/hpcx/hpcx-v2.14-gcc-inbox-ubuntu22.04-cuda11-gdrcopy2-nccl2.16-x86_64/hpcx-ompi-oneapi-2023.2.0/lib") prepend_path("LIBRARY_PATH","/hpc/mp/apps/hpcx/hpcx-v2.14-gcc-inbox-ubuntu22.04-cuda11-gdrcopy2-nccl2.16-x86_64/hpcx-ompi-oneapi-2023.2.0/lib") + +help([[Name: HPC-X +Version: 2.14 +Website: https://developer.nvidia.com/networking/hpc-x + +NVIDIA® HPC-X® is a comprehensive software package that includes Message Passing Interface (MPI), Symmetrical Hierarchical Memory (SHMEM) and Partitioned Global Address Space (PGAS) communications libraries, and various acceleration packages. +]]) \ No newline at end of file From 2d840c747ffd3aa710a6ff652bf7c3876953b575 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:43:24 -0500 Subject: [PATCH 54/66] add help to cuda compat libs --- .../cuda_compat_libs/cuda_12.4_compat.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/mp/cuda_compatibility/cuda_compat_libs/cuda_12.4_compat.lua b/modules/mp/cuda_compatibility/cuda_compat_libs/cuda_12.4_compat.lua index ac505db6..f3e0508e 100644 --- a/modules/mp/cuda_compatibility/cuda_compat_libs/cuda_12.4_compat.lua +++ b/modules/mp/cuda_compatibility/cuda_compat_libs/cuda_12.4_compat.lua @@ -2,3 +2,10 @@ append_path("LD_PRELOAD", "/hpc/mp/apps/nvidia/compatibility_drivers/12.4/libcud append_path("LD_PRELOAD", "/hpc/mp/apps/nvidia/compatibility_drivers/12.4/libcudadebugger.so.550.54.15") append_path("LD_PRELOAD", "/hpc/mp/apps/nvidia/compatibility_drivers/12.4/libnvidia-nvvm.so.550.54.15") append_path("LD_PRELOAD", "/hpc/mp/apps/nvidia/compatibility_drivers/12.4/libnvidia-ptxjitcompiler.so.550.54.15") + +help([[Name: Cuda Compatibility Libraries +Version: 12.4 +Website: https://docs.nvidia.com/deploy/cuda-compatibility/ + +Compatibility libraries to allow newer new versions of Cuda to run +]]) \ No newline at end of file From 7f16388d2e39181406bc932518c7fb1eb02f857e Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:44:58 -0500 Subject: [PATCH 55/66] add help for aocc --- modules/mp/compilers/amd/aocc/4.1.0.lua | 7 +++++-- modules/mp/cuda_compatibility/cuda_compat_libs/12.2.lua | 6 ++++++ 2 files changed, 11 insertions(+), 2 deletions(-) diff --git a/modules/mp/compilers/amd/aocc/4.1.0.lua b/modules/mp/compilers/amd/aocc/4.1.0.lua index 73c101bc..d8fd7ac3 100644 --- a/modules/mp/compilers/amd/aocc/4.1.0.lua +++ b/modules/mp/compilers/amd/aocc/4.1.0.lua @@ -21,9 +21,12 @@ prepend_path("LD_LIBRARY_PATH","/hpc/mp/apps/amd/aocc-compiler-4.1.0/lib") prepend_path("LD_LIBRARY_PATH","/hpc/mp/apps/amd/aocc-compiler-4.1.0/lib32") prepend_path("C_INCLUDE_PATH","/hpc/mp/apps/amd/aocc-compiler-4.1.0/include") prepend_path("CPLUS_INCLUDE_PATH","/hpc/mp/apps/amd/aocc-compiler-4.1.0/include") -help([[ AOCC - loads AOCC compiler setup +help([[Name: AMD Optimizing C/C++ and Fortran Compilers (AOCC) +Version: 4.1.0 +Website: https://www.amd.com/en/developer/aocc.html + +AOCC is a high-performance x86 CPU compiler for C, C++, and Fortran programming languages. ]]) diff --git a/modules/mp/cuda_compatibility/cuda_compat_libs/12.2.lua b/modules/mp/cuda_compatibility/cuda_compat_libs/12.2.lua index 1b3de71a..e11a4dd9 100644 --- a/modules/mp/cuda_compatibility/cuda_compat_libs/12.2.lua +++ b/modules/mp/cuda_compatibility/cuda_compat_libs/12.2.lua @@ -7,3 +7,9 @@ prepend_path("LD_PRELOAD","/hpc/mp/apps/nvidia/compatibility_drivers/12.2/libcud prepend_path("LD_PRELOAD","/hpc/mp/apps/nvidia/compatibility_drivers/12.2/libnvidia-nvvm.so.535.104.05") prepend_path("LD_PRELOAD","/hpc/mp/apps/nvidia/compatibility_drivers/12.2/libnvidia-ptxjitcompiler.so.535.104.05") +help([[Name: Cuda Compatibility Libraries +Version: 12.2 +Website: https://docs.nvidia.com/deploy/cuda-compatibility/ + +Compatibility libraries to allow newer new versions of Cuda to run +]]) \ No newline at end of file From f296acd8fe4a88960add974ec781ec170d951449 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:45:48 -0500 Subject: [PATCH 56/66] add help for gcc --- modules/m3/compilers/gcc/11.2.0.lua | 2 +- modules/m3/compilers/gcc/6.3.0.lua | 2 +- modules/mp/compilers/gcc/11.2.0.lua | 7 +++++++ modules/mp/compilers/gcc/13.2.0.lua | 8 +++++--- 4 files changed, 14 insertions(+), 5 deletions(-) diff --git a/modules/m3/compilers/gcc/11.2.0.lua b/modules/m3/compilers/gcc/11.2.0.lua index 49aef50f..94164f94 100644 --- a/modules/m3/compilers/gcc/11.2.0.lua +++ b/modules/m3/compilers/gcc/11.2.0.lua @@ -18,7 +18,7 @@ setenv("OMPI_MCA_btl_openib_if_include","mlx5_0:1") setenv("OMPI_MCA_hwloc_base_binding_policy","core") setenv("UCX_NET_DEVICES","mlx5_0:1") -help([[Name: GNU gcc +help([[Name: GNU GCC Version: 11.2.0 Website: https://gcc.gnu.org/ diff --git a/modules/m3/compilers/gcc/6.3.0.lua b/modules/m3/compilers/gcc/6.3.0.lua index 322fa6c6..6843c0a6 100644 --- a/modules/m3/compilers/gcc/6.3.0.lua +++ b/modules/m3/compilers/gcc/6.3.0.lua @@ -28,7 +28,7 @@ setenv("OMPI_MCA_btl_openib_if_include","mlx5_0:1") setenv("OMPI_MCA_hwloc_base_binding_policy","core") setenv("UCX_NET_DEVICES","mlx5_0:1") -help([[Name: GNU gcc +help([[Name: GNU GCC Version: 6.3.0 Website: https://gcc.gnu.org/ diff --git a/modules/mp/compilers/gcc/11.2.0.lua b/modules/mp/compilers/gcc/11.2.0.lua index f3f82b26..26b131c2 100644 --- a/modules/mp/compilers/gcc/11.2.0.lua +++ b/modules/mp/compilers/gcc/11.2.0.lua @@ -10,3 +10,10 @@ append_path("MODULEPATH", "/hpc/mp/spack_modules/linux-ubuntu22.04-zen2/cuda/gcc -- generic packages / dependencies append_path("MODULEPATH", "/hpc/mp/spack_modules/linux-ubuntu22.04-zen2/gcc-11.2.0/") + +help([[Name: GNU GCC +Version: 11.2.0 +Website: https://gcc.gnu.org/ + +The GNU Compiler Collection +]]) \ No newline at end of file diff --git a/modules/mp/compilers/gcc/13.2.0.lua b/modules/mp/compilers/gcc/13.2.0.lua index b931b66b..998316ea 100644 --- a/modules/mp/compilers/gcc/13.2.0.lua +++ b/modules/mp/compilers/gcc/13.2.0.lua @@ -27,7 +27,9 @@ setenv("CXX","/hpc/mp/repos/spack/opt/spack/linux-ubuntu22.04-zen2/gcc-11.2.0/gc setenv("FC","/hpc/mp/repos/spack/opt/spack/linux-ubuntu22.04-zen2/gcc-11.2.0/gcc-13.2.0-6sn65ps6yami7ktiqicswzuv5rpbbkec/bin/gfortran") setenv("F77","/hpc/mp/repos/spack/opt/spack/linux-ubuntu22.04-zen2/gcc-11.2.0/gcc-13.2.0-6sn65ps6yami7ktiqicswzuv5rpbbkec/bin/gfortran") -help([[Name : gcc +help([[Name: GNU GCC Version: 13.2.0 -Target : zen2 -]]) +Website: https://gcc.gnu.org/ + +The GNU Compiler Collection +]]) \ No newline at end of file From fbba2febedba6c2abd6e680964cdcf38e8d0da20 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:46:09 -0500 Subject: [PATCH 57/66] add help for intel compiler --- modules/mp/compilers/intel/oneapi/2023.2.lua | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/mp/compilers/intel/oneapi/2023.2.lua b/modules/mp/compilers/intel/oneapi/2023.2.lua index 50417b7c..2a7eadc0 100644 --- a/modules/mp/compilers/intel/oneapi/2023.2.lua +++ b/modules/mp/compilers/intel/oneapi/2023.2.lua @@ -13,3 +13,9 @@ append_path("MODULEPATH", "/hpc/mp/spack_modules/linux-ubuntu22.04-zen2/cuda/one -- generic packages / dependencies append_path("MODULEPATH", "/hpc/mp/spack_modules/linux-ubuntu22.04-zen2/oneapi-2023.2.0/") +help([[Name: Intel OneAPI Compiler Suite +Version: 2023.2 +Website: https://www.intel.com/content/www/us/en/developer/tools/oneapi/overview.html + +The Intel® oneAPI DPC++/C++ Compiler gives developers even more confidence that their code is portable and reliably performant across existing and future CPU, GPU, and AI accelerator architectures. +]]) \ No newline at end of file From dca55cf49f68eba985c0616f2a1e47f2270927eb Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:46:36 -0500 Subject: [PATCH 58/66] add help for nvhpc --- modules/mp/compilers/nvidia/nvhpc/23.7.lua | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/mp/compilers/nvidia/nvhpc/23.7.lua b/modules/mp/compilers/nvidia/nvhpc/23.7.lua index 22bee9d0..bd7491dd 100644 --- a/modules/mp/compilers/nvidia/nvhpc/23.7.lua +++ b/modules/mp/compilers/nvidia/nvhpc/23.7.lua @@ -13,3 +13,9 @@ setenv("UCX_NET_DEVICES","mlx5_0:1,mlx5_1:1,mlx5_2:1,mlx5_3:1,mlx5_6:1,mlx5_7:1, -- setenv("OMPI_MCA_hwloc_base_binding_policy","core") -- setenv("UCX_NET_DEVICES","mlx5_0:1") +help([[Name: NVIDIA HPC SDK +Version: 23.7 +Website: https://developer.nvidia.com/hpc-sdk + +The NVIDIA HPC Software Development Kit (SDK) includes the proven compilers, libraries and software tools essential to maximizing developer productivity and the performance and portability of HPC applications. +]]) \ No newline at end of file From 18da93c77c6d846595a91c11cadc9e6e41dd17f0 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:46:57 -0500 Subject: [PATCH 59/66] add help for spack --- modules/mp/apps/spack.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/mp/apps/spack.lua b/modules/mp/apps/spack.lua index 3d197b0b..289ff2f2 100644 --- a/modules/mp/apps/spack.lua +++ b/modules/mp/apps/spack.lua @@ -1 +1,8 @@ source_sh('bash', '/hpc/mp/repos/spack/share/spack/setup-env.sh') + +help([[Name: Spack +Version: several +Website: https://spack.io/ + +Spack is a package manager for supercomputers, Linux, and macOS. +]]) \ No newline at end of file From 448dc1972c8f134446abc96c03e94298a9751df1 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:47:19 -0500 Subject: [PATCH 60/66] add help for conda --- modules/mp/apps/conda.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/mp/apps/conda.lua b/modules/mp/apps/conda.lua index 0e5755ac..9e30e02d 100644 --- a/modules/mp/apps/conda.lua +++ b/modules/mp/apps/conda.lua @@ -1,2 +1,9 @@ source_sh('bash', '/hpc/mp/apps/conda/etc/profile.d/conda.sh') source_sh('bash', '/hpc/mp/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. +]]) \ No newline at end of file From 313a440c234b28b0d1b88782c9e789ffbb6bd7f8 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:48:56 -0500 Subject: [PATCH 61/66] add lammps help --- modules/mp/apps/lammps/may22.lua | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/mp/apps/lammps/may22.lua b/modules/mp/apps/lammps/may22.lua index 768885f2..fac3df72 100644 --- a/modules/mp/apps/lammps/may22.lua +++ b/modules/mp/apps/lammps/may22.lua @@ -11,3 +11,9 @@ end build_command('lmp') +help([[Name: LAMMPS +Version: 04May2022 +Website: https://www.lammps.org/ + +LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It's an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. +]]) \ No newline at end of file From ee686b57cbafa51e22393e8d0b5d3c2b22068d22 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:49:27 -0500 Subject: [PATCH 62/66] add Julia help --- modules/mp/apps/julia/1.10.4.lua | 6 ++++++ modules/mp/apps/julia/1.9.2.lua | 7 +++++++ 2 files changed, 13 insertions(+) diff --git a/modules/mp/apps/julia/1.10.4.lua b/modules/mp/apps/julia/1.10.4.lua index 1f2e0a29..f575619a 100644 --- a/modules/mp/apps/julia/1.10.4.lua +++ b/modules/mp/apps/julia/1.10.4.lua @@ -6,3 +6,9 @@ prepend_path("PATH", pathJoin(root, "bin")) prepend_path("MANPATH", pathJoin(root, "share/man")) prepend_path("LD_LIBRARY_PATH", pathJoin(root, "lib")) +help([[Name: Julia +Version: 1.10.4 +Website: https://julialang.org/ + +The Julia Programming Language +]]) \ No newline at end of file diff --git a/modules/mp/apps/julia/1.9.2.lua b/modules/mp/apps/julia/1.9.2.lua index 87cf0eb8..16185f29 100644 --- a/modules/mp/apps/julia/1.9.2.lua +++ b/modules/mp/apps/julia/1.9.2.lua @@ -5,3 +5,10 @@ local root = "/hpc/mp/apps/julia/1.9.2" prepend_path("PATH", pathJoin(root, "bin")) prepend_path("MANPATH", pathJoin(root, "share/man")) prepend_path("LD_LIBRARY_PATH", pathJoin(root, "lib")) + +help([[Name: Julia +Version: 1.9.2 +Website: https://julialang.org/ + +The Julia Programming Language +]]) \ No newline at end of file From 8724dbbd8dc2e606b42d60cbcbafbd752c77dcb6 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:50:02 -0500 Subject: [PATCH 63/66] add gaussian help --- modules/mp/apps/gaussian/g16c02.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/mp/apps/gaussian/g16c02.lua b/modules/mp/apps/gaussian/g16c02.lua index 7bff925b..fe1768a2 100644 --- a/modules/mp/apps/gaussian/g16c02.lua +++ b/modules/mp/apps/gaussian/g16c02.lua @@ -16,3 +16,10 @@ setenv("g16root", "/hpc/mp/apps/gaussian/g16c02") setenv("GAUSS_SCRDIR", os.getenv("SCRATCH")) source_sh('bash', '/hpc/mp/apps/gaussian/g16c02/g16/bsd/g16.profile') +help([[Name: Gaussian +Version: g16c02 +Website: https://gaussian.com/ +License Owners: Chemistry + +Gaussian series of electronic structure programs, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. +]]) \ No newline at end of file From 9e63ad3448dc06f8f3699c1b2163de968c3828f4 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:50:38 -0500 Subject: [PATCH 64/66] add apptainer help --- modules/mp/apps/apptainer/1.1.9.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/mp/apps/apptainer/1.1.9.lua b/modules/mp/apps/apptainer/1.1.9.lua index 59eec7a5..28f9d15b 100644 --- a/modules/mp/apps/apptainer/1.1.9.lua +++ b/modules/mp/apps/apptainer/1.1.9.lua @@ -4,3 +4,10 @@ prepend_path("PATH","/hpc/mp/apps/apptainer/1.1.9/bin") source_sh('bash', '/hpc/mp/apps/apptainer/1.1.9/share/bash-completion/completions/singularity') source_sh('bash', '/hpc/mp/apps/apptainer/1.1.9/share/bash-completion/completions/apptainer') setenv("APPTAINER_BIND","/hpc,/work,/scratch") + +help([[Name: Apptainer +Version: 1.1.9 +Website: https://apptainer.org/ + +Apptainer 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. +]]) \ No newline at end of file From 498a40622266aa2d5bd188d23d35ab7e182db189 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 12:51:06 -0500 Subject: [PATCH 65/66] add amber help --- modules/mp/apps/amber/22.lua | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/mp/apps/amber/22.lua b/modules/mp/apps/amber/22.lua index bb4f6e27..ad8c3939 100644 --- a/modules/mp/apps/amber/22.lua +++ b/modules/mp/apps/amber/22.lua @@ -18,3 +18,10 @@ prepend_path("LD_LIBRARY_PATH", "/hpc/mp/apps/amber/AmberTools23/lib") prepend_path("PERL5LIB", "/hpc/mp/apps/amber/AmberTools23/lib/perl") prepend_path("PYTHONPATH", "/hpc/mp/apps/amber/AmberTools23/lib/python3.10/site-packages") setenv("QUICK_BASIS","/hpc/mp/apps/amber/AmberTools23/AmberTools/src/quick/basis") + +help([[Name: Amber +Version: 22 +Website: https://ambermd.org/ + +Amber is a suite of biomolecular simulation programs. +]]) \ No newline at end of file From 07a43914f39039852c7fecdfbb016e35d44f5110 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 9 Aug 2024 13:50:35 -0500 Subject: [PATCH 66/66] add scripts to help parse installed software --- utils/module_tools/parse_module_info.py | 24 +++++++++++ utils/module_tools/parse_spack_installs.py | 49 ++++++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 utils/module_tools/parse_module_info.py create mode 100644 utils/module_tools/parse_spack_installs.py diff --git a/utils/module_tools/parse_module_info.py b/utils/module_tools/parse_module_info.py new file mode 100644 index 00000000..0ccba712 --- /dev/null +++ b/utils/module_tools/parse_module_info.py @@ -0,0 +1,24 @@ +import pathlib + +module_files = list(pathlib.Path('../../modules').rglob('*.lua')) + +print(module_files) + +with open('installed_software.txt', 'w') as f: + for mod_file in module_files: + software_name = "" + software_version = "" + software_source = "staff installed" + software_website = "" + with open(mod_file) as cur_module: + Lines = cur_module.readlines() + for line in Lines: + if "[[Name:" in line: + software_name = line.split(":", 1)[1].strip() + elif "Version:" in line: + software_version = line.split(":", 1)[1].strip() + elif "Website:" in line: + software_website = line.split(":", 1)[1].strip() + + if software_name != "": + f.write(software_name + ',' + software_version + ',' + software_source + ',' + software_website + '\n') \ No newline at end of file diff --git a/utils/module_tools/parse_spack_installs.py b/utils/module_tools/parse_spack_installs.py new file mode 100644 index 00000000..187fc7e8 --- /dev/null +++ b/utils/module_tools/parse_spack_installs.py @@ -0,0 +1,49 @@ +import argparse # for command line input options +import json # for json files +import pathlib # for file path features +import io # for buffers +import subprocess # for running commands + +# Set up command line options +parser = argparse.ArgumentParser( + description='Generate a software config file from spack.') +parser.add_argument('-o', '--outfile', + help="File to save output to (defaults to software.json)", + type=pathlib.Path) +# parse the input +args = parser.parse_args() + +if args.outfile is None: + outfile = pathlib.Path('spack_software.csv') +else: + outfile = args.outfile + +# get the full software list from spack +command = "spack list --format version_json" +proc = subprocess.Popen(command.split(), shell=False, text=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) +data, err = proc.communicate() +raw_spack = json.loads(data) +#print(raw_spack) + +# get the installed software from spack +command = "spack find --json" +proc = subprocess.Popen(command.split(), shell=False, text=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) +data, err = proc.communicate() +installed_spack = json.loads(data) + +# now loop over all installed packages and add homepages +with open('installed_software.txt', 'w') as f: + for app in installed_spack: + software_name = app["name"] + software_version = app["version"] + software_source = "spack" + software_website = "" + + # find homepage from full list + for test_app in raw_spack: + if test_app["name"] == app["name"]: + software_website = test_app["homepage"] + break + + if software_name != "": + f.write(software_name + ',' + software_version + ',' + software_source + ',' + software_website + '\n')