Application

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/usr/bin/ld: cannot find -liberty on Rocky Linux 8

I was trying to install CP2K on Rocky Linux 8 using the Installing CP2K with Nvidia HPCX on Rocky Linux 8.5 and I encountered an issue 

libtool: warning: library '/usr/local/hpcx-v2.17.1-gcc-mlnx_ofed-redhat8-cuda12-x86_64/ucc/lib/libucc.la' was moved.
/usr/bin/ld: cannot find -liberty
collect2: error: ld returned 1 exit status

The Resolution can be done by installing binutils-devel

# dnf install binutils-devel
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Updating ANSYS 2023R2 License Server Information for Linux Client using the command line

If you are updating ANSYS License Server Information for ANSYS Client using only the command line, do the following

# vim usr/local/ansys_inc/shared_files/licensing/ansyslmd.ini
SERVER=1055@IP_Address_Of_ANSYS_LIC_SVR
ANSYSLI_SERVERS=2325@IP_Address_Of_ANSYS_LIC_SVR

Make sure the 1055, 1056, 2325 Ports of the License Server are opened.

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Could not load the Qt platform plugin “xcb” in “” even though it was found in Rocky Linux 8

I was installing ANSYS 2023 R2 on Rocky Linux 8 and I encoutnered the error

qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: xcb.

Solution

# dnf install python3-qt5
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Installing VASP-6.4.2 with Intel-2023.1

For full Requirements for installing VASP-6.4.2, do take a look at Installing VASP.6.X.X

Requirements Needs

Step 1: Prepare the makefile.include

Select the appropriate makefile.include from arch folder that you resemble your environment. In my case

$ cp arch/makefile.include  ./makefile.include

Step 2: Source Intel Environment

$ source /usr/local/intel/2023.1/setvars.sh
:: initializing oneAPI environment ...
   -bash: BASH_VERSION = 4.4.20(1)-release
   args: Using "$@" for setvars.sh arguments:
:: advisor -- latest
:: ccl -- latest
:: clck -- latest
:: compiler -- latest
:: dal -- latest
:: debugger -- latest
:: dev-utilities -- latest
:: dnnl -- latest
:: dpcpp-ct -- latest
:: dpl -- latest
:: inspector -- latest
:: intelpython -- latest
:: ipp -- latest
:: ippcp -- latest
:: ipp -- latest
:: itac -- latest
:: mkl -- latest
:: mpi -- latest
:: tbb -- latest
:: vtune -- latest
:: oneAPI environment initialized ::

Step 3: Prepare the Intel Optimised BLAS95, LAPACK95 and FFTW.

Step 4: Build VASP

I like to use “-j1” as I want the compilation to stop on first error

$ make DEPS=1 -j1 all

Step 5: Test

$ make test
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No rule to make target `pyamff_fortran/*.f90′, needed by `pyamff_fortran/*.o’.

If you are having this error during your compilation with VASP-6.4.2 and VTST, if you are encountering the error

error message;
No rule to make target `pyamff_fortran/*.f90', needed by `pyamff_fortran/*.o'. Stop.

Solution

Make sure you have updated the LIB in makefile inside src/

# vim /usr/local/vasp-6.4.2-vtst/vasp.6.4.2/src/makefile
LIB=lib parser pyamff_fortran

For more information, do take a look at Configuring VTST with VASP-6.4.2 with Intel 2023.1

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Configuring VTST with VASP-6.4.2 with Intel 2023.1

Taken from VTST.Tools Installation Guide

The VTST•Tools has a Fortran component which can be linked into the VASP code as well as a collection of scripts.

Step 1: Download the VTST Code

Download the VTST Code (vtstcode.tgz) at http://theory.cm.utexas.edu/vtsttools/download.html 

Step 2: Building VTST code into VASP

To install, download the files in vtsttools/vtstcode, choose a version, and copy the files in the directory into your vasp source directory. The file chain.F is replaced, so back up the old version. There are other files in the package: neb.F, dynmat.F, dimer.F, lanczos.F, sd.F, cg.F, qm.F, lbfgs.F, bfgs.F, fire.F, and opt.F in and vtstcode6.4/ directories. The vtstcode6.4/ directory contains another file called ml_pyamff.F and directory named pyamff_fortran/, which interface to a machine learning package PyAMFF.

In my situation, I put it in /usr/local/vasp-6.4.2-vtst/vasp.6.4.2/src

$ cd /usr/local/vasp-6.4.2-vtst/vasp.6.4.2/src
$ tar -zxvf vtstcode-198.tgz
$ cd vtstcode-198/vtstcode6.4
$ cp -Rv * /usr/local/vasp-6.4.2-vtst/vasp.6.4.2/src

Step 3: Find the variable SOURCE in the .objects file (a hidden file in src/)

Find the variable SOURCE in the .objects file (a hidden file in src/), which defines which objects will be built, and add the following objects before chain.o:

$ cd /usr/local/vasp-6.4.2-vtst/vasp.6.4.2/src
$ ls -al .objects
$ vim .objects

Around line 126, before chain.o, insert the following

bfgs.o dynmat.o instanton.o lbfgs.o sd.o cg.o dimer.o bbm.o \
fire.o lanczos.o neb.o qm.o \
pyamff_fortran/*.o ml_pyamff.o \
opt.o

Step 4: Update the LIB in makefile inside src/

# vim /usr/local/vasp-6.4.2-vtst/vasp.6.4.2/src/makefile
LIB=lib parser pyamff_fortran

To be continued with VASP Installation later.

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Compiling Quantum ESPRESSO-7.2 with Intel-2023.1 on Rocky Linux 8

Step 1: Download the package from Quantum ESPRESSO. You have to register and login before you can download.

# tar -zxvf qe-7.2.tar.gz

Step 2: Source Intel Environment

$ source /usr/local/intel/2023.1/setvars.sh
:: initializing oneAPI environment ...
   -bash: BASH_VERSION = 4.4.20(1)-release
   args: Using "$@" for setvars.sh arguments:
:: advisor -- latest
:: ccl -- latest
:: clck -- latest
:: compiler -- latest
:: dal -- latest
:: debugger -- latest
:: dev-utilities -- latest
:: dnnl -- latest
:: dpcpp-ct -- latest
:: dpl -- latest
:: inspector -- latest
:: intelpython -- latest
:: ipp -- latest
:: ippcp -- latest
:: ipp -- latest
:: itac -- latest
:: mkl -- latest
:: mpi -- latest
:: tbb -- latest
:: vtune -- latest
:: oneAPI environment initialized ::

Step 3: Remember to Prepare the Intel Optimised BLAS95, LAPACK95 and FFTW. Do take a look at

Step 4: Compile the QE

Once you have loaded the Intel Configuration costly, QE will detect and configure. Compilation is very simple. 

# ./configure --prefix=/usr/local/qe-2.7 ----with-scalapack=intel --enable-shared --enable-openmp | tee Configure.out
# make all
# make install

Step 5: Optional (If you wish to reconfigure again, do a clean up)

Do a clean up by using the command 

# make veryclean
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Compiling VASP.6.3.0 using Nvidia hpcx, gcc-12.3 and MKL on Rocky Linux 8.7

For information, do take a look at VASP – Install VASP.6.X.X

VASP support several compilers. But we will be focusing on Nvidia hpcx only for this blog. To compile Nvidia hpcx, do take a look at Installing and using Mellanox HPC-X Software Toolkit

You may want to use Nvida hpcx. You may want to module use

export HPCX_HOME=/usr/local/hpcx-v2.15-gcc-MLNX_OFED_LINUX-5-redhat8-cuda12-gdrcopy2-nccl2.17-x86_64
module use $HPCX_HOME/modulefiles

----------------- /usr/local/hpcx-v2.15 --------------------------------------------
hpcx  hpcx-debug  hpcx-debug-ompi  hpcx-mt  hpcx-mt-ompi  hpcx-ompi  hpcx-prof  hpcx-prof-ompi  hpcx-stack

You can untar the VASP.6.3.3. and potpaw_PBE.54

% tar -xvf vasp.6.3.0.tar
% tar -xvf potpaw_PBE.54.tar

At the installation base of vasp.6.3.0 base

% cp arch/makefile.include.gnu_ompi_mkl_omp ./makefile.include

You will need the latest GNU GCC-10 or the latest for a successful compile. I compiled with GCC-12.3. You may want to take a look at Compiling GCC 12.1.0 on Rocky Linux 8.5

If you are using OneAPI Intel MKL, you can use module use after compilation. It will not be covered in this write-up. But you can:

% module use /usr/local/intel/2023.1/modulefiles

Finally,

% module load mkl/latest
% module load gnu/gcc-12.3
% module load hpcx
% make veryclean
% make DEPS=1 -j
.....
.....
make[2]: Leaving directory '/usr/local/vasp/vasp.6.3.0/build/std'
make[1]: Leaving directory '/usr/local/vasp/vasp.6.3.0/build/std'

In the bin directory, you should see vasp_gam vasp_ncl vasp_std

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Gromacs Error – log: Protocol “https” not supported or disabled in libcurl

Downloading: https://ftp.gromacs.org/regressiontests/regressiontests-2020.6.tar.gz
CMake Error at tests/CMakeLists.txt:58 (message):
  error: downloading
  'https://ftp.gromacs.org/regressiontests/regressiontests-2020.6.tar.gz'
  failed

  status_code: 1

  status_string: "Unsupported protocol"

  log: Protocol "https" not supported or disabled in libcurl

  Closing connection -1

If you compiling Gromacs-2020.6 with Plumed2-2.7.2, do follow the Regression Test Errors during Gromacs Compilation. The Key issues are 

DREGRESSIONTEST_DOWNLOAD=OFF -DREGRESSIONTEST_PATH=../regressiontests-2020.2

If you can download the regressiontests-2020.6.tar.gz and get the regressiontest PATH correct, it should work without issues.

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Unable to Install hdf5, hdf5-devel and hdf5-static on Rocky Linux 8.7

If you are doing a dnf install on hdf5 packages, you will notice errors like the one below

nothing provides libsz.so.2()(64bit) needed by hdf5-1.10.5-4.el8.x86_64
(try to add '--skip-broken' to skip uninstallable packages or '--nobest' to use not only best candidate packages)

To resolve the issue, you will need to install and enable PowerTools

Step 1: Install DNF plugins package

dnf install dnf-plugins-core

Step 2: Install EPEL

The reason is that some software from its source code requires some dependencies that are available in EPEL

dnf install epel-release

Step 3: Enable PowerTools repository on Rocky Linux 8

dnf config-manager --set-enabled powertools

Step 4: Now try installing HDF5

dnf install hdf5 hdf5-devel hdf5-static