Application

by

Compiling cmake-3.21.3 on Rocky Linux 8.5

If you are compiling the cmake-3.21.3 on Rocky Linux 8.5, and encounter the issues

-- Could NOT find OpenSSL, try to set the path to OpenSSL root folder in the system variable OPENSSL_ROOT_DIR (missing: OPENSSL_CRYPTO_LIBRARY OPENSSL_INCLUDE_DIR)

The problem is easy to resolve, you just need to install the openssl and openssl-devel libraries

# dnf install openssl openssl-devel

You should be able to bootrap easily.

Alternatively, instead of using ./boostrap, you can use the traditional configure command

#./configure --prefix=/usr/local/cmake-3.21.3
# make
# make install
by

Compiling ORCA-4.2.1 with OpenMPI-3.1.4

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

Prerequisites that I use.

Unpacking ORCA-4.2.1

% tar -xvf orca_4_2_1_linux_x86-64_openmpi314.tar.xz
.....
.....
orca_4_2_1_linux_x86-64_openmpi314/autoci_rhf_poly1_sigma
orca_4_2_1_linux_x86-64_openmpi314/orca_eprnmr_mpi
orca_4_2_1_linux_x86-64_openmpi314/autoci_uhf_poly1_sigma
orca_4_2_1_linux_x86-64_openmpi314/orca_casscf
orca_4_2_1_linux_x86-64_openmpi314/autoci_iprocisd_sigma_alpha_doublet_mpi
orca_4_2_1_linux_x86-64_openmpi314/autoci_rohf_cisd_product
orca_4_2_1_linux_x86-64_openmpi314/orca_gstep
orca_4_2_1_linux_x86-64_openmpi314/contrib/
orca_4_2_1_linux_x86-64_openmpi314/contrib/G2_MP2.cmp
orca_4_2_1_linux_x86-64_openmpi314/contrib/W2_2.cmp
orca_4_2_1_linux_x86-64_openmpi314/contrib/G2_MP2_SV.cmp
orca_4_2_1_linux_x86-64_openmpi314/contrib/G2_MP2_SVP.cmp
orca_4_2_1_linux_x86-64_openmpi314/orca4.2-eula.pdf
orca_4_2_1_linux_x86-64_openmpi314/Third_Party_Licenses_ORCA_4.2.pdf

Running ORCA. If your environment has Module Environment

% module load openmpi/3.1.4/gcc-6.5.0

If not, you have to pacify PATH and LD_LIBRARY_PATH, MANPATH

export PATH=$PATH:$OPENMPI_HOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$OPENMPI_HOME/lib:$OPENMPI_HOME/lib64
export MANPATH=$MANPATH:$OPENMPI_HOME/share

Typical Input file

Calling ORCA requires full pathing

/usr/local/orca_4_2_1_linux_x86-64_openmpi314/orca $INPUT > $OUTPUT "--bind-to core --verbose"

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
.....
.....
by

Compiling pybind11 with GNU-6.5

The Project Website can be found at https://github.com/pybind/pybind11

pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. Its goals and syntax are similar to the excellent Boost.Python library by David Abrahams: to minimize boilerplate code in traditional extension modules by inferring type information using compile-time introspection.

The Compiling Steps can be found at https://pybind11.readthedocs.io/en/stable/basics.html

mkdir build
cd build
cmake .. -DDOWNLOAD_EIGEN=ON -DDOWNLOAD_CATCH=ON
make check -j 4
by

Licensing Errors for ANSYS IcePak Solver

If you are encountering issues like the one below. 

"If you have this error "Failed to enable features using current license settings. Note that Pro, Premium, Enterprise licenses are available on your server. To use these licenses check the corresponding option. For more information, search "PPE" in the help documentation. Failover feature "ANSYS IcePak Solver" is not available. Request name aice_solv does not exist in the....."

by

Compiling OpenFOAM-9 with Third-Party-9 with Intel MPI on CentOS 7

Step 1a: Get the Software

If you do have root access to the machine, the recommended installation directory is $HOME/OpenFOAM . If you have root permissions and the installation is for more than one user, one of the ‘standard’ locations can be used, e.g. /usr/local/OpenFOAM. 

# wget -O - http://dl.openfoam.org/source/9 | tar xvz
# wget -O - http://dl.openfoam.org/third-party/9 | tar xvz

Step 1b: The files unpack to produce directories OpenFOAM-9-version-9 and ThirdParty-9-version-9, which need to be renamed as follows:

# mv OpenFOAM-9-version-9 OpenFOAM-9
# mv ThirdParty-9-version-9 ThirdParty-9

Step 2a: Load Intel Compilers. I loaded the Intel Parallel Cluster Suite 2018

# source /usr/local/intel/2018u3/bin/compilervars.sh intel64
# source /usr/local/intel/2018u3/mkl/bin/mklvars.sh intel64
# source /usr/local/intel/2018u3/impi/2018.3.222/bin64/mpivars.sh intel64
# source /usr/local/intel/2018u3/parallel_studio_xe_2018/bin/psxevars.sh intel64
# export MPI_ROOT=/usr/local/intel/2018u3/impi/2018.3.222/intel64

Step 2b: Create softlink for include64 and lib64 for Intel MPI (if requried only). You can check first. If it is there, it should be something like this. 

# ls -l /usr/local/intel/2018u3/impi/2018.3.222/intel64/include64
# lrwxrwxrwx 1 root hpccentrifyusers 7 Aug  9  2019 /usr/local/intel/2018u3/impi/2018.3.222/intel64/include64 -> include

If not there, you may want to do this. 

# cd /usr/local/intel/2018u3/impi/2018.3.222/intel64
# ln -s include include64
# ln -s lib lib64

Step 3: Edit the OpenFOAM bashrc

# vim /usr/local/OpenFOAM/OpenFOAM-9/etc/bashrc
.....
export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \
export FOAM_INST_DIR=/usr/local/$WM_PROJECT
.....
#- Compiler location:
#    WM_COMPILER_TYPE= system | ThirdParty (OpenFOAM)
export WM_COMPILER_TYPE=system

#- Compiler:
#    WM_COMPILER = Gcc | Gcc48 ... Gcc62 | Clang | Icc
export WM_COMPILER=Icc
unset WM_COMPILER_ARCH WM_COMPILER_LIB_ARCH

#- Memory addressing:
#    On a 64bit OS this can be 32bit or 64bit
#    On a 32bit OS addressing is 32bit and this option is not used
#    WM_ARCH_OPTION = 32 | 64
export WM_ARCH_OPTION=64

#- Precision:
#    WM_PRECISION_OPTION = SP | DP | LP
export WM_PRECISION_OPTION=DP

#- Label size:
#    WM_LABEL_SIZE = 32 | 64
export WM_LABEL_SIZE=32

#- Optimised, debug, profiling:
#    WM_COMPILE_OPTION = Opt | Debug | Prof
export WM_COMPILE_OPTION=Opt

#- MPI implementation:
#    WM_MPLIB = SYSTEMOPENMPI | OPENMPI | SYSTEMMPI | MPICH | MPICH-GM | HPMPI
#               | MPI | FJMPI | QSMPI | SGIMPI | INTELMPI
export WM_MPLIB=INTELMPI

#- Operating System:
#    WM_OSTYPE = POSIX | ???
export WM_OSTYPE=POSIX
.....

Step 4a: Edit the ThirdParty-9 scotch_6.0.9 Packages

$ cd /usr/local/OpenFOAM/ThirdParty-9/scotch_6.0.9/src

Step 4b: Copy the right Architecture and place it with the directory that holds the Makefile. For example we wanted “Makefile.inc.x86-64_pc_linux2.icc.impi”

# cp /usr/local/OpenFOAM/ThirdParty-9/scotch_6.0.9/src/Make.inc/Makefile.inc.x86-64_pc_linux2.icc.impi /usr/local/OpenFOAM/ThirdParty-9/scotch_6.0.9/src

Step 5: Go back to OpenFOAM source directory

# source /usr/local/OpenFOAM/OpenFOAM-9/etc/bashrc
# cd /usr/local/OpenFOAM/OpenFOAM-9
# ./Allwmake -j 16 | tee Allwmake.log

by

Compiling Clustal Omega 1.24 on CentOS 7

Overview

Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks.

Compilers and Libraries used

Compiling argtable-2.13

Compiling argtable-2.13 is very straightforward

% tar -zxvf argtable2-13.tar.gz
% cd argtable2-13
% ./configure --prefi=/usr/local/argtable2-13
% make
% make install

Compiling Clustal Omega 1.24. You can download the source code from http://www.clustal.org/omega/

% tar -zxvf clustal-omega-1.2.4.tar.gz
% cd clustal-omega-1.2.4
% ./configure --prefix=/usr/local/clustal-omega-1.2.4 CFLAGS='-I/usr/local/argtable2-13/include' LDFLAGS='-L/usr/local/argtable2-13/lib'
% make
% make install

References:

  1. http://www.clustal.org/omega/INSTALL
  2. http://argtable.sourceforge.net/
by

Resolving r.Java is not found (attached, “rJavaError”) on R-4.1.0

If you are installing rJava in R and you encountered this issue during install

% R
> install.packages("rJava")
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver    : ''
compiler    : ''
header prep.: ''
cpp flags   : ''
java libs   : ''
configure: error: Java Development Kit (JDK) is missing or not registered in R
Make sure R is configured with full Java support (including JDK). Run
R CMD javareconf
as root to add Java support to R.

If you don't have root privileges, run
R CMD javareconf -e
to set all Java-related variables and then install rJava.

ERROR: configuration failed for package ‘rJava’
* removing ‘/usr/local/R-4.1.0/lib64/R/library/rJava’

The downloaded source packages are in
        ‘/tmp/RtmpnllvN9/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("rJava") :
  installation of package ‘rJava’ had non-zero exit status
> install.packages("javareconf")
Warning message:
package ‘javareconf’ is not available for this version of R

The Issue is to fix the missing Java Support to R. You can download the Java version you required https://www.oracle.com/java/technologies/downloads/archive/ I chose version 11. I used the “Linux x64 Compressed Archive”. Installation was a breeze as it is just unpacking and java can be used immediately. But it is important to make sure the environment is fixed. For example, 

export JAVA_HOME=/usr/local/jdk-11.0.12
export PATH=$PATH:/usr/local/jdk-11.0.12/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/jdk-11.0.12/lib
export MANPATH=$MANPATH:/usr/local/jdk-11.0.12/share

Now you can run R. At the command prompt, type install.packages(“rJava”)

% R
> install.packages("rJava")
> library("rJava")

References:

  1. Installing the rJava package
by

curl: (28) Resolving timed out after 5515 milliseconds

If you encounter an error like curl: (28) Resolving timed out after 5515 milliseconds

[user1@hpc-node1 ~]# curl -fsS https://dlang.org/install.sh | bash -s dmd
curl: (28) Resolving timed out after 5515 milliseconds
curl: (28) Resolving timed out after 5512 milliseconds
curl: (28) Resolving timed out after 5514 milliseconds
curl: (28) Resolving timed out after 5513 milliseconds
curl: (28) Resolving timed out after 5514 milliseconds
curl: (28) Resolving timed out after 5514 milliseconds
curl: (28) Resolving timed out after 5515 milliseconds
curl: (28) Resolving timed out after 5514 milliseconds
curl: (28) Resolving timed out after 5515 milliseconds
curl: (28) Resolving timed out after 5515 milliseconds

It is likely a DNS Lookup Resolution Issue. You might want to take a look at /etc/resolv.conf . you may want to change the DNS to another nameserver that resolves faster like one from Google Public DNS IP Addresses

# Generated by NetworkManager
nameserver 192.168.0.1

To another nameserver, maybe like Google Public DNS IP Addresses. You can find more information at https://developers.google.com/speed/public-dns/docs/using

# Generated by NetworkManager
nameserver 8.8.8.8
nameserver 8.8.4.4
by

Software Rendering Mode for Fluent Launcher

When running Fluent from inside ANSYS Workbench on Linux. Hardware graphics rendering can fail and the Fluent application failed to start. This error can sometimes be prevented by switching to the software rendering mode. There are 2 approaches

Before Running Workbench, you may want to put this in your BASH Shell

% export HOOPS_PICTURE=x11/lin

In C Shell

% setenv HOOPS_PICTURE x11/lin

If you are using Fluent Launcher

Steps:

Open a Fluent set of cells
Right Click the Fluent setup cell and choose, edit
In the resulting Fluent launcher, choose +, Show More Options
Select the Environment tab
Add the following entry
HOOPS_PICTURE=x11/lin