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Compilation of Quantum espresso v6.7 - PW

• Intel Parallel Studio XE 2019 was used.
• OpenMPI 4.1.0 compiled with this Intel compiler was used.

Compilation of OpenMPI

export PATH=/opt/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64:$PATH
export LD_LIBRARY_PATH=/opt/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin:/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64

I am using SGE, so

% ./configure --enable-static --prefix=some_openmpi_directory --enable-mpi-compatibility --with-sge

After make && make install, setting PATH

export PATH=some_openmpi_directory/bin:$PATH

Compilation of QE-PW

% ./configure FFT_LIBS="/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/interfaces/fftw3xf/libfftw3xf_intel.a" LIBDIRS="/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64"

Modify make.inc as follows:

SCALAPACK_LIBS = -L/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64

IFLAGS         = -I$(TOPDIR)/include -I$(TOPDIR)/FoX/finclude -I/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/include -I/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/include/fftw

DFLAGS         =  -D__MPI -D__SCALAPACK -D__FFTW

Then

% make -j8 pw

For my purpose, I don't run make install. A symbolic link of pw.x is found in ./bin/ dir.

Run test:

% cd PW/examples/example01
% ./run_example

Usage:

% mpirun pw.x -i some_input.in > some_output.out

Compilation of QE-PHonon

After the compilation of QE-PW,

% make -j8 ph

Run test:

% cd PHonon/examples/example01
% ./run_example

Usage:

% mpirun ph.x -in some_input.in > some_output.out

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VirtualBox upgrade on macOS

Upgrading VirtualBox on macOS disabled to run VM. This was because of security setting of macOS. The following steps perhaps worked:

1. Reboot macOS
2. System Preferences -> Security & Privacy
3. Unlock and pushing some button around "Allow apps downloaded from:" and macOS is automatically rebooted.

Then it started to work.

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Change timezone on linxu

sudo timedatectl set-timezone Asia/Tokyo

How to Set or Change the Time Zone in Linux | Linuxize

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Use conda-forge as default

% cat .condarc
channel_priority: strict
channels:
  - conda-forge
  - defaults

https://conda-forge.org/docs/user/tipsandtricks.html

Header files of mkl

% conda install -c conda-forge mkl-include

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Use conda-forge as default

% cat .condarc
channel_priority: strict
channels:
  - conda-forge
  - defaults

https://conda-forge.org/docs/user/tipsandtricks.html

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Resize windows in emacs

Currently I'm using emacs in terminal. Resizing windows by mouse pointers is impossible. I need to learn the keybindings. What is most important is to resize windows evenly, which is C-x + as found below:

How to change size of split screen emacs windows? - Stack Overflow

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Convert matplotlib imshow, contourf, and pcolormesh images to an image format

Saving a plot by matplotlib imshow, contourf, or pcolormesh to a pdf file via savefig. It can be opened by Illustrator to handle it as a vector illustration. To use the illustration in a manuscript made by latex, it is exported in an image format. To do this, I needed some trials-and-errors. Finally I got the following setting in a satisfactory quality:

• Jpeg
• Resolution: High (300 ppi)
• Anti-aliasing: Art Optimized (Supersampling)
• Quality: 10 (highest)