[SIESTA-L] Free Energy Calculation by Siesta

[Narendranath Ghosh]

Dear All,
Thank you very much for introducing me to a wonderful forum.
Please let me know how I calculate free energy change of a reaction, I am
interested in calculating free energy profile for CO2 reduction steps.
Thanks in advance.

Regards,
Dr. N N Ghsoh
University of Gour Banga
India-73211
‪Dr. NARENDRA NATH GHOSH‬ - ‪Google Scholar‬


-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

Re: [SIESTA-L] Installing Siesta GPU acclerated version

[Narendranath Ghosh]

Dear All,
Thank you very much for introducing me to a wonderful forum.
I am new in Siesta.
Please let me know how I calculate free energy change of a reaction, I am
interested in calculating free energy profile for CO2 reduction steps.
Thanks in advance.

Regards,
Dr. N N Ghsoh
University of Gour Banga
India-73211
‪Dr. NARENDRA NATH GHOSH‬ - ‪Google Scholar‬




On Fri, Jul 1, 2022 at 1:31 AM Mohammed Ghadiyali <
mohammed.ghadiy...@kaust.edu.sa> wrote:

> Hello,
>
> Thanks for the information, I’ll try to install it as per the instructions
> provided.
>
> Regards,
> Ghadiyali Mohammed Kader
> Post Doctoral Fellow
> King Abdullah University of Science and Technology
> On 29 Jun 2022, 11:06 PM +0300, Alberto Garcia , wrote:
>
> Hello,
>
> We are writing a section on GPUs in the documentation, but until it is
> ready you can use the ideas below:
>
>
> There are two ways to take advantage of GPUs (enabled only for the solver
> stage, which typically takes up the most time):
>
> -- Using the ELPA library and its native interface in Siesta (this method
> is available for Siesta versions 4.1.5 and up)
>
> -- Using the ELSI library (for Siesta "MaX" versions
> (see the Guide to Siesta Versions in
> https://urldefense.com/v3/__https://gitlab.com/siesta-project/siesta/-/wikis/Guide-to-Siesta-versions__;!!Nmw4Hv0!zoGYljExKqs1b-VkrSmFhJ6futBuvXnhXa2RrwwV6TwhqqPzKFcb7n5hg1lr7CF5rT0insiOyeJscp-ZjrM4f0RLn3Di2A$
> )
>
> In both cases the special installation instructions involve only enabling
> GPU support in either ELPA or ELSI, and using the proper options in Siesta.
>
> For the first method the fdf options to enable GPUs are (example):
>
> diag-algorithm elpa-2
> diag-elpa-usegpu T
> diag-blocksize 16
> # Optional
> number-of-eigenstates 17320
> use-tree-timer T
>
>
> For the second (ELSI) method:
>
> solution-method elsi
> elsi-solver elpa
> elsi-elpa-gpu 1
> elsi-elpa-flavor 2
>
> # Optional
> number-of-eigenstates 17320
> use-tree-timer T
> elsi-output-level 3
>
> The installation of ELPA and ELSI with GPU support is system-specific, but
> you can get inspiration from the following examples:
>
> * ELPA (on Marconi-100 at CINECA, with IBM P9 chips and nVidia A100 GPUs,
> using the gcc compiler):
>
> Script to configure:
>
> #!/bin/sh
>
> # (Need to define properly the symbols used below)
> # Note that the P9 does not use the typical Intel kernels
>
> FC=mpifort CC=mpicc CXX=mpic++ \
> CFLAGS="-O3 -mcpu=native -std=c++11" \
> FCFLAGS="-O3 -mcpu=native -ffree-line-length-none"
> LDFLAGS="${SCALAPACK_LIBS} ${LAPACK_LIBS}" \
> ../configure \
> --with-cuda-path=${CUDA_HOME} \
> --with-cuda-sdk-path=${CUDA_HOME} \
> --enable-nvidia-gpu --with-NVIDIA-GPU-compute-capability=sm_70 \
> --enable-NVIDIA-gpu-memory-debug --enable-nvtx \
> --disable-sse-assembly --disable-sse --disable-avx --disable-avx2
> --disable-avx512 \
> --enable-c-tests=no --prefix=$PRJ/bin/gcc/elpa/2021.05.002.jul22
>
>
> (Adapt the options to your system)
>
> * ELSI
>
> SET(CMAKE_INSTALL_PREFIX "$ENV{BASE_DIR}/elsi/2.6.2" CACHE STRING
> "Installation dir")
>
> SET(CMAKE_Fortran_COMPILER "mpif90" CACHE STRING "MPI Fortran compiler")
> SET(CMAKE_C_COMPILER "mpicc" CACHE STRING "MPI C compiler")
> SET(CMAKE_CXX_COMPILER "mpicxx" CACHE STRING "MPI C++ compiler")
>
> SET(CMAKE_Fortran_FLAGS "-O2 -g -fbacktrace -fdump-core" CACHE STRING
> "Fortran flags")
> SET(CMAKE_C_FLAGS "-O2 -g -std=c99" CACHE STRING "C flags")
> SET(CMAKE_CXX_FLAGS "-O2 -g -std=c++11" CACHE STRING "C++ flags")
> SET(CMAKE_CUDA_FLAGS "-O3 -arch=sm_70 -std=c++11" CACHE STRING "CUDA
> flags")
> # Workaround: specify -std=c++11 in CMAKE_CUDA_FLAGS to avoid __ieee128
> gcc/cuda bug
>
> SET(USE_GPU_CUDA ON CACHE BOOL "Use CUDA-based GPU acceleration in ELPA")
> SET(ENABLE_PEXSI ON CACHE BOOL "Enable PEXSI")
> SET(ENABLE_TESTS ON CACHE BOOL "Enable tests")
> #SET(ADD_UNDERSCORE OFF CACHE BOOL "Do not suffix C functions with an
> underscore")
>
> SET(LIB_PATHS
> "/cineca/prod/opt/libraries/lapack/3.9.0/gnu--8.4.0/lib;/cineca/prod/opt/libraries/scalapack/2.1.0/spectrum_mpi--10.3.1--binary/lib;/cineca/prod/opt/compilers/cuda/11.0/none/lib64;/cineca/prod/opt/libraries/essl/6.2.1/binary/lib64"
> CACHE STRING "External library paths")
>
> SET(LIBS "scalapack;lapack;essl;cublas;cudart" CACHE STRING "External
> libraries")
> You should modify appropriately the location and version numbers of your
> libraries.
>
> Finally, a note about the importance of the proper execution incantation,
> for "pinning" the MPI ranks to the appropriate GPU:
>
> (There are probably better and more streamlined ways to do this)
>
> For this example I use the 32 cores (2x16) in Marconi for MPI tasks, no
> OpenMP, and do not take advantage of the 4x hyperthreading.
>
> The slurm script I typically use is: (gcc_env et al are my own Lmod
> modules)
>
> =
> #!/bin/bash
> #SBATCH --job-name=test