Encountering shm_open permission denied issues with hpcx

If you are using Nvidia hpc-x and encountering issues like the one below during your MPI Run

shm_open(file_name=/ucx_shm_posix_77de2cf3 flags=0xc2) failed: Permission denied

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:

% chmod 777 /dev/shm 
% ls -ld /dev/shm
drwxrwxrwx 2 root root 40 Jul  6 15:18 /dev/sh

Installing CP2K with Nvidia HPCX on Rocky Linux 8.5

What is HPCX?

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/

Getting the CP2K

git clone --recursive https://github.com/cp2k/cp2k.git cp2k

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

% /usr/bin/ld: cannot find /usr/lib64/liblsan.so.0.0.0
% dnf install liblsan -y

If you encounter error like the ones below for fftw libraries,

/usr/bin/ld: cannot find -lfftw3_mpi
collect2: error: ld returned 1 exit status

You have to go to the supporting package libraries and do some editing.

% cd /usr/local/software/cp2k/tools/toolchain/install/fftw-3.3.10/lib
% ln -s libfftw3.a libfftw3_mpi.a
% ln -s libfftw3.la libfftw3_mpi.la

Try again

% cd /usr/local/software/cp2k
% make -j 32 ARCH=local VERSION="ssmp sdbg psmp pdbg"

If successful, you should see binaries at /usr/local/software/cp2k/exe/local

GCCGO Error During GCC-10.4.0 Compilation on CentOS 7

If you encounter “gccgo: error: ../x86_64-pc-linux-gnu/libgo/libgotool.a: No such file or directory”

.....
.....
/home/user1/gcc-10.4.0/host-x86_64-pc-linux-gnu/gcc/gccgo -B/home/user1/gcc-10.4.0/host-x86_64-pc-linux-gnu/gcc/ -B/usr/x86_64-pc-linux-gnu/bin/ -B/usr/x86_64-pc-linux-gnu/lib/ -isystem /usr/x86_64-pc-linux-gnu/include -isystem /usr/x86_64-pc-linux-gnu/sys-include   -g -O2 -I ../x86_64-pc-linux-gnu/libgo -static-libstdc++ -static-libgcc  -L ../x86_64-pc-linux-gnu/libgo -L ../x86_64-pc-linux-gnu/libgo/.libs -o go ../.././gotools/../libgo/go/cmd/go/alldocs.go ../.././gotools/../libgo/go/cmd/go/go11.go ../.././gotools/../libgo/go/cmd/go/main.go ../x86_64-pc-linux-gnu/libgo/libgotool.a  
gccgo: error: ../x86_64-pc-linux-gnu/libgo/libgotool.a: No such file or directory
make[2]: *** [Makefile:821: go] Error 1
make[2]: Leaving directory '/home/user1/gcc-10.4.0/host-x86_64-pc-linux-gnu/gotools'
make[1]: *** [Makefile:14649: all-gotools] Error 2
make[1]: Leaving directory '/home/user1/gcc-10.4.0'
make: *** [Makefile:997: all] Error 2

The issue can be easily resolved by not building gcc in the same directory as the source code. At GCC Home

% ./contrib/download_prerequisites
% mkdir build
% ../configure --prefix=/usr/local/gcc-10.4.0 --disable-multilib --enable-languages=all
% make -j 8
% make install

Compiling GCC-10.4.0 on CentOS-7

Step 1: Download the TarBall version of GCC version. If you want to take look at all the available versions, you can take a look at http://ftp.mirrorservice.org/sites/sourceware.org/pub/gcc/releases/

For this blog entry, we will install GCC-10.4.0. First thing first, let’s get the Tarball

% wget http://ftp.mirrorservice.org/sites/sourceware.org/pub/gcc/releases/gcc-10.4.0/gcc-10.4.0.tar.gz

Step 2: Make sure the bzip2 is available in the System

% yum install bzip2 bzip2-devel

Step 3: Untar the TarBall

% tar -zxvf gcc-10.4.0.tar.gz
% cd gcc-10.4.0 

Step 4: Download the prerequisites and start configuring the GCC

% ./contrib/download_prerequisites
% ./configure --prefix=/usr/local/gcc-10.4.0 --disable-multilib --enable-languages=all
% make -j 8
% make install

Step 5: Verify the Installation

% gcc --version