Compiling zlib-1.2.11 with GNU 6

A Massively Spiffy Yet Delicately Unobtrusive Compression Library

Prerequisites

GNU 6.5

Compiling

wget http://www.zlib.net/zlib-1.2.11.tar.gz
tar -xvzf zlib-1.2.11.tar.gz
cd zlib-1.2.11
./configure --prefix=/usr/local/zlib-1.2.11-gcc6
make check

Test Failed… does not support .pth files

If you are doing a setup.py with specific directories

python setup.py install --prefix=/home/user1

If you are getting a PythonPath Error something like this.

TEST FAILED: /home/user1/lib/python3.7/site-packages/ does NOT support .pth files error: bad install directory or PYTHONPATH

You are attempting to install a package to a directory that is not on PYTHONPATH and which Python does not read ".pth" files from. 
The installation directory you specified (via --install-dir, --prefix, or the distutils default setting) was: /home/user1/lib/python3.7/site-packages/

and your PYTHONPATH environment variable currently contains:

You can solve like by putting in your .bashrc.

export PYTHONPATH="${PYTHONPATH}:/home/user1/lib/python3.7/site-packages/"
source ~/.bashrc

Installing SCons-3.1.2 with Intel Python Distribution

What is SCons?

SCons is an Open Source software construction tool—that is, a next-generation build tool. Think of SCons as an improved, cross-platform substitute for the classic Make utility with integrated functionality similar to autoconf/automake and compiler caches such as ccache. In short, SCons is an easier, more reliable and faster way to build software.

For more information, see https://scons.org/

Prerequisites

Python 3 Distribution. For this I used the Intel Python Distribution

Get the Source Code

git clone https://github.com/SCons/scons.git

Setup scons directory and run the setup script

cd $HOME/scons
/usr/local/intel/2020/intelpython3/bin/python setup.py install

Do note that the scons will write a site package at /usr/local/intel/2020/intelpython3/lib/python3.7/site-packages/SCons-3.9.9a993-py3.7.egg . You need to allow the necessary permission

Testing the package

cd /usr/local/scons
python runtest.py SCons/BuilderTests.py
1/1 (100.00%) /usr/local/intel/2020/intelpython3//bin/python SCons/BuilderTests.py
......................................
----------------------------------------------------------------------
Ran 38 tests in 0.096s
OK

References:

  1. SCons: A software construction tool
  2. SCons GitHub Site

 

Compiling Gromacs-2019.3 with Intel MKL and CUDA

Prerequisites

GCC-6.5 Compilers and associates libraries
m4-1.4.18
mpfr-3.1.4
cmake-3.15.1
gmp-6.1.0
mpc-1.0.3

Intel Compilers and Prerequisites

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

Create a setup file

touch gromacs_cpu.sh

Put the following into the gromacs_cpu.sh

CC=mpicc CXX=mpicxx cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=on -DGMX_FFT_LIBRARY=mkl
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2019.3_intel18_mkl -DREGRESSIONTEST_DOWNLOAD=ON
-DCMAKE_C_FLAGS:STRING="-cc=icc -O3 -xHost -ip"
-DCMAKE_CXX_FLAGS:STRING="-cxx=icpc -O3 -xHost -ip" 
-DGMX_GPU=off -DCMAKE_BUILD_TYPE=Release
./gromacs_cpu.sh
make
make install

Testing and Verification

$ source /your/installation/prefix/here/bin/GMXRC
./gmxtest.pl all -np 2

Compiling Gromacs-2019.3 with Intel 2018 and MKL

Prerequisites

GCC-6.5 Compilers and associates libraries
m4-1.4.18
mpfr-3.1.4
cmake-3.15.1
gmp-6.1.0
mpc-1.0.3

Intel Compilers and Prerequisites

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

Create a setup file

touch gromacs_cpu.sh

Put the following into the gromacs_cpu.sh

CC=mpicc CXX=mpicxx cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx
-DGMX_MPI=on -DGMX_FFT_LIBRARY=mkl -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2019.3_intel18_mkl 
-DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_FLAGS:STRING="-cc=icc -O3 -xHost -ip" 
-DCMAKE_CXX_FLAGS:STRING="-cxx=icpc -O3 -xHost -ip" -DGMX_GPU=off -DCMAKE_BUILD_TYPE=Release
./gromacs_cpu.sh
make
make install

Testing and Verification

$ source /your/installation/prefix/here/bin/GMXRC
./gmxtest.pl all -np 2

G16NBO is currently configured with only 100000000 words Errors

If you encounter errors when you use NBO7 with Gaussian G16a

This calculation is attempting to allocate 299857248 words of scratch memory,
but G16NBO is currently configured with only 100000000 words. If you have the
NBO6 source distribution, you can reconfigure G16NBO by editing maxmem.fh in
nbo6/src/g16nbo/include and rebuilding the executables.

Dynamic memory allocation in the GenNBO, G09NBO, and G16NBO interfaces to NBO7 has been implemented. The issue has been fixed with the latest download from NBO7 site.

Remember to update  gennbo.sh at your NBO directory

# Examples:

# setenv NBOMEM 50mw
# setenv NBOMEM 512mb
# setenv NBOMEM 1gb

setenv NBOMEM 1gb

References:

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Solving environment: failed with initial frozen solve. Retrying with flexible solve

When I was loading my anaconda-2020, I’ve received this error.

conda install -c conda-forge opencv

And I got this error

Solving environment: failed with initial frozen solve. Retrying with flexible solve....

There was this thread from github which was useful and it help a lot! https://github.com/conda/conda/issues/9367

Step 1: To resolve, Create an environment called opencv using

conda create -n opencv

Step 2: Activate it

conda activate opencv

Step 3: Install it again

conda install -c anaconda opencv

(which install opencv 3, but not the most recent 4. In order to create a second environment called opencv4. Use above code to create and activate and do a standard download:

conda install -c conda-forge opencv

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