From 8491d475411b03ce07ab5010ab6ea6e7c72cdb69 Mon Sep 17 00:00:00 2001 From: Chris Maffeo <cmaffeo2@illinois.edu> Date: Thu, 16 May 2024 18:50:24 -0500 Subject: [PATCH] Update README --- README | 112 ------------------------------------------------------ README.md | 53 ++++++++++++++++++++++++++ 2 files changed, 53 insertions(+), 112 deletions(-) delete mode 100644 README create mode 100644 README.md diff --git a/README b/README deleted file mode 100644 index aff911c..0000000 --- a/README +++ /dev/null @@ -1,112 +0,0 @@ -/==========================================================\ -| Atomic Resolution Brownian Dynamics (ARBD) - beta Oct 19 | -\==========================================================/ - -Brownian dynamics (BD) simulation is method for studying biomolecules, ions, and -nanomaterials that balances detail with computational efficiency. - -ARBD supports tabulated non-bonded and bonded interactions between BD -particles that can also be influenced by grid-specified -potentials. Uniquely, ARBD also allows grid-specified densities and -potentials to be associated with rigid body particles that rotate and -translate to represent larger molecules. Most importantly, the code is -designed to run quickly on modern NVIDIA GPUs. - -ARBD is a rewrite of the BrownianMover code, moving almost all computations to -the GPU and enabling grid-specified particle models. Please be aware that ARBD -is being actively developed and is offered without warranty. - - -/==========\ -| Building | -\==========/ - -To build, please run `make' in the src directory. - -If your CUDA toolkit is installed in a nonstandard location, you may specify -that location using the CUDA_PATH environment variable. For example: -make CUDA_PATH=/nonstandard/path/to/cuda - -Note that ARBD has been developed using CUDA-8.0 and targets NVIDIA GPUs featuring -6.0 compute capability. The code should work with devices with compute capability >=2.0, -but there are no guarantees. - -Older versions of CUDA are not compatible with SM 6.0, so you may need to change -the SMS variable in the makefile, or specify it as an argument to make. - - -/==============\ -| Installation | -\==============/ - -Please explore the examples in the 'tests' directory. - -For example, try the following commands: - -cd tests/argon-small -mkdir output -../../src/arbd BrownDyn.bd output/BrownDyn > output/BrownDyn.log - -You may use the '-g n' option to specify the n-th GPU on your machine, counting from 0. - -If you fail to compile and link the applications, we recommend running -`make clean` to remove object files. Sometimes we have encountered -CUDA related errors in binaries built in a "dirty" environment. - - -/========\ -| Citing | -\========/ - -If you publish results obtained using ARBD, please cite the following manuscripts: - -"DNA base-calling from a nanopore using a Viterbi algorithm" -Winston Timp, Jeffrey Comer, and Aleksei Aksimentiev -Biophys J 102(10) L37-9 (2012) - -"Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics" -Jeffrey Comer and Aleksei Aksimentiev. -J Phys Chem C Nanomater Interfaces 116:3376-3393 (2012). - -"Atoms-to-microns model for small solute transport through sticky nanochannels" -Rogan Carr, Jeffrey Comer, Mark D. Ginsberg, and Aleksei Aksimentiev -Lab Chip 11(22) 3766-73 (2011) - - -/=========\ -| Authors | -\=========/ - -ARBD is developed by the Aksimentiev group (http://bionano.physics.illinois.edu) -as a part of the NIH Center for Macromolecular Modeling and Bioinformatics -(http://www.ks.uiuc.edu/). - -Please direct questions or problems to Chris. - -Christopher Maffeo <cmaffeo2@illinois.edu> -Han-yi Chao -Jeffrey Comer -Max Belkin -Emmanual Guzman -Justin Dufresne -Terrance Howard - - -/====================\ -| Outstanding issues | -\====================/ - --- Not implemented -- - -* There are no checks to ensure that pairlists are recalculated before - particles further than the pairlist distance move to within the - cutoff - --- Bugs -- - -* A large amount of GPU memory for pairlists is allocated statically, - which may cause out-of-memory crashes in older hardware - -* If the number of pairs in the system exceeds the length of the array - allocated for pairlists, the non-bonded kernel will try to access - forbidden regions of memory, causing a crash diff --git a/README.md b/README.md new file mode 100644 index 0000000..46f4a65 --- /dev/null +++ b/README.md @@ -0,0 +1,53 @@ +# Atomic Resolution Brownian Dynamics (ARBD 2.0-alpha) + +Brownian dynamics (BD) simulation is method for studying biomolecules, +ions, and nanomaterials that balances detail with computational +efficiency. + +This development branch of ARBD has the aim of scaling ARBD up to +larger systems and accelerating to the hardware limits, while making +it easier to maintain diverse features. In particular we are seeking +speed and good scaling on multi-GPU clusters. + +## Building + +### Dependencies + +Linux workstation with CUDA-compatible GPU (minimum 3.5 compute capability) + - CMake >= 3.9 + - gcc >= 4.9 + - cuda >= 9.0 (> 11.5 recommended) + +### Build process + +From the root arbd directory (where this README is found), run: +``` +## Determine the compute capability of your CUDA-enabled graphics card +export CMAKE_CUDA_ARCHITECTURES="35;50;75;80" ;# especially important for CMake < 3.24.0 +## export CUDA_INCLUDE_DIRS="$CUDA_HOME/include" ;# optionally be explicit about cuda include paths; usually not needed +cmake -S src -B build && +( + cd build + make -j +) +``` + +If your CUDA toolkit is installed in a nonstandard location that CMake +is unable to find, you may provide use the environement variable +`CMAKE_CUDA_COMPILER` to specify the path to nvcc. You may also find +it neccesary to set the environment variable `CUDA_INCLUDE_DIRS` if +compilation fails due to the compiler being unable to find <cuda.h>. + +Note that ARBD has been developed using CUDA-9.0 and targets NVIDIA +GPUs featuring 6.0 compute capability. The code should work with +devices with compute capability >=2.0, but there are no guarantees. + +## Authors + +ARBD is developed by the Aksimentiev group +(http://bionano.physics.illinois.edu). + +Please direct questions or problems to Chris. + +- Christopher Maffeo <cmaffeo2@illinois.edu> +- Han-yi Chao -- GitLab