The error message indicates that the shared memory has no permission to be used, The permission of /dev/shm is found to be 755, not 777, causing the error. The issue can be resolved after the permission is changed to 777. To change and verify the changes:
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. For more information, do take a look at https://developer.nvidia.com/networking/hpc-x
What is CP2K?
CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi-empirical methods (AM1, PM3, PM6, RM1, MNDO, …), and classical force fields (AMBER, CHARMM, …). CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimisation, and transition state optimization using NEB or dimer method. (Detailed overview of features.). For more information, do take a look at https://www.cp2k.org/
Unpack hpcx and Optimised OpenMPI Libraries. For more information on installation, do take a look at Installing and Loading HPC-X
Extract hpcx.tbz into your current working directory.
% tar -xvf hpcx.tbz
% cd hpcx
% export HPCX_HOME=$PWD
% module use $HPCX_HOME/modulefiles
% module load hpcx
Use the CP2K Toolchain to Compile for the easiest
% cd cp2k
% cd /usr/local/software/cp2k/tools/toolchain
% ./install_cp2k_toolchain.sh --no-check-certificate --with-openmpi
Compiling the CP2K
.....
.....
==================== generating arch files ====================
arch files can be found in the /usr/local/software/cp2k/tools/toolchain/install/arch subdirectory
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local.ssmp
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local_static.ssmp
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local.sdbg
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local_coverage.sdbg
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local.psmp
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local.pdbg
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local_static.psmp
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local_warn.psmp
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local_coverage.pdbg
========================== usage =========================
Done!
Now copy:
cp /usr/local/software/cp2k/tools/toolchain/install/arch/* to the cp2k/arch/ directory
To use the installed tools and libraries and cp2k version
compiled with it you will first need to execute at the prompt:
source /usr/local/software/cp2k/tools/toolchain/install/setup
To build CP2K you should change directory:
cd cp2k/
make -j 80 ARCH=local VERSION="ssmp sdbg psmp pdbg"
Do exactly on the ending instruction
% cp /usr/local/software/cp2k/tools/toolchain/install/arch/* /usr/local/cp2k/arch
% source /usr/local/software/cp2k/tools/toolchain/install/setup
% cd /usr/local/software/cp2k
% make -j 32 ARCH=local VERSION="ssmp sdbg psmp pdbg"
If you encounter an error during making like the one below, just do an install for liblsan
This article is taken from Intel “Efficient Heterogeneous Parallel Programming Using OpenMP”. In this article, we will show you how to do CPU+GPU asynchronous calculations using OpenMP.
In some cases, offloading computations to an accelerator like a GPU means that the host CPU sits idle until the offloaded computations are finished. However, using the CPU and GPU resources simultaneously can improve the performance of an application. In OpenMP® programs that take advantage of heterogenous parallelism, the master clause can be used to exploit simultaneous CPU and GPU execution. In this article, we will show you how to do CPU+GPU asynchronous calculation using OpenMP. ….. ….. …..
The Intel® oneAPI DPC++/C++ Compiler was used with following command-line options: ‑O3 ‑Ofast ‑xCORE‑AVX512 ‑mprefer‑vector‑width=512 ‑ffast‑math ‑qopt‑multiple‑gather‑scatter‑by‑shuffles ‑fimf‑precision=low ‑fiopenmp ‑fopenmp‑targets=spir64=”‑fp‑model=precise”
….. ….. ….. OpenMP provides true asynchronous, heterogeneous execution on CPU+GPU systems. It’s clear from our timing results and VTune profiles that keeping the CPU and GPU busy in the OpenMP parallel region gives the best performance. We encourage you to try this approach.
ORCA is a general-purpose quantum chemistry package that is free of charge for academic users. The Project and Download Website can be found at ORCA Forum
You have to register yourself before you can participate in the forum or download ORCA-4.2.1. The current latest version for ORCA is 5.0.3. The package you might want to consider is ORCA 4.2.1, Linux, x86-64, .tar.xz Archive
For Input File usage, you may want to take a look at the ORCA 4.2.1 Manual found when you unpack or you can look at it online at orca_manual_4_2_1.pdf (enea.it) .
For example…….
! B3LYP def2-SVP SP
%tddft
tda false
nroots 50
triplets true
end
%pal
nprocs 32
end
* xyz 0 1 fac_irppy3.xyz
Ir 0.00000 0.00000 0.03016
N -1.05797 1.55546 -1.09121
N 1.87606 0.13850 -1.09121
.....
.....
% cd lammps-15Jun20/lib/kim
% tar Jxvf kim-api-2.1.3.txz
% cd kim-api-2.1.3
% mkdir build
% cd build
% cmake .. -DCMAKE_INSTALL_PREFIX=${PWD}/../../installed-kim-api-2.1.3
% make -j2
% make install
% cd /lammps-15Jun20/lib/kim/installed-kim-api-2.1.3/
% source ${PWD}/kim-api-X2.1.3/bin/kim-api-activate
% kim-api-collections-management install system EAM_ErcolessiAdams_1994_Al__MO_324507536345_002
Step 8: Compile USER-COLVARS
% cd lammps-15Jun/lib/colvars
% make -f Makefile.g++
–enable-orterun-prefix-by-default (Configure OMPI –enable-orterun-prefix-by-default and so that you do not need to add the prefix option) –enable-openib-rdmacm-ibaddr (To enable routing over IB) –enable-mpi-cxx (C++ bindings are no more built by default) –enable-mca-no-build=btl-uct (ecent OpenMPI versions contain a BTL component called ‘uct’, which can cause data corruption when enabled, due to conflict on malloc hooks between OPAL and UCM.)
The Linux Cluster 