Install¶

This page summarizes the build and setup information from the repository README.

System Requirements¶

Linux, with Ubuntu 16.04 or newer recommended
macOS 10.10 or newer
CMake 3.5 or newer
GNU gcc and gfortran 14.2 or newer
BLAS and LAPACK
ARPACK or ARPACK-NG
FFTW 3.3 or newer, with double, single, and threaded builds
libcurl 7 or newer
libTIFF 4 or newer
jbigkit 2 or newer, optional
Python 3.10 or newer

If BLAS, LAPACK, or ARPACK are not available, they will be downloaded and compiled.

Obtain The Source¶

Download and unpack the stable release:

gunzip SIMPLE-3.0.0.tar.gz
tar -xvf SIMPLE-3.0.0.tar
cd SIMPLE-3.0.0

Or clone the repository to install the version under active development:

git clone https://github.com/hael/SIMPLE.git
cd SIMPLE

Standard Build¶

mkdir build
cd build
cmake ..
make -j install

Environment Setup¶

Bash Shell¶

BASH users should append the contents of add2.bashrc to the bash configuration file ~/.bashrc with the following command:

cat add2.bashrc >> ~/.bashrc

C shell¶

TCSH/CSH users can use the following command instead:

cat add2.tcshrc >> ~/.tcshrc

Manual Configuration¶

Alternatively, the following changes can also be made manually in the default configuration file for the shell such as ~/.bashrc, ~/.tcshrc or ~/.zshrc to setup the relevant environment variables.

Add these paths to the PATH environemnt variable:

<simple_path>/build/bin
<simple_path>/build/scripts

Set the SIMPLE_PATH environment vairable:

SIMPLE_PATH=<simple_path>

Custom Installation¶

To change the installation directory, use the following Cmake option before running make install:

cmake -DCMAKE_INSTALL_PREFIX=<install_dir> ..
make -j install

In case of non-standard location for gcc/gfortran compilers or FFTW, provide the paths to Cmake as follows:

FC=<gfortran_path> CC=<gcc_path> FFTW_DIR=<fftw_path> cmake ..
make -j install

For instance, on MacOS such locations could be:

Macports: FC=/opt/local/bin/gfortran FFTW_DIR=/opt/local
Fink users: FC=/sw/bin/gfortran FFTW_DIR=/sw/
Homebrew: FC=/usr/local/bin/gfortran FFTW_DIR=/usr/local/

For more advanced FFTW installations, see Installation of FFTW below.

Developer Installation and Updates¶

Get the developemnt version of SIMPLE by cloning the git repository:

git clone https://github.com/hael/SIMPLE.git
cd SIMPLE

Run the following commands to install the debug build type:

mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=debug ..
make -j install

Or use one of the helper build script such as compile_clean.sh provided in the SIMPLE directory for various installation cases. Install SIMPLE with the compile_debug.sh shell script

bash compile_debug.sh

GUI Build With NICE (New Interface for CryoEM)¶

Use the compile_gui.sh script to install SIMPLE with the NICE GUI support:

bash compile_gui.sh

Or use run the following commands:

mkdir build
cd build
cmake .. -D NICE=on
make -j install
nice_local

Testing the Build¶

To check a build, compile it with the tests (the default: ./compile_clean.sh also runs the fast test gate at the end of the build; --exclude-tests skips both) and run the unit tests. Execute the following in a separate terminal to ensure the environment variables have been correctly set:

simple_test_exec test=units

It runs every fast unit-test suite in one process and creates its own folder SIMPLE_TEST_units_date, which holds the report (simple_test_units_report.txt) and any temporary files. It ends with a summary of the checks; if any check fails, the summary lists it and the program exits with a non-zero status. The folder can be safely removed. If you detect an error, please carefully check the SIMPLE and FFTW installations and the gfortran version. If you still have issues, please file a help ticket on the webpage.

FFTW Installation¶

SIMPLE requires three versions of the FFTW library. A double-precision, a single-precision and a threaded-single precision build.

Copy the source from the FFTW homepage () and unpack it:

wget ftp://ftp.fftw.org/pub/fftw/fftw-3.3.8.tar.gz
tar zxvf fftw-3.3.8.tar.gz
cd fftw-3.3.8

By default, the bootstrap script configures and builds the double precision and threaded libraries:

./bootstrap.sh --prefix=/usr/local
make -j
sudo make install
make distclean

Now build the single-precision libraries:

./bootstrap.sh --prefix=/usr/local --enable-single
make -j
sudo make install
make distclean

New Mac Installation¶

Install homebrew

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Add brew to your path

Install the dependencies git, gcc, OpenBLAS, LAPACK, ARPACK, libtiff, jbigkit and cmake – make sure you have a python version higher than 3.10

brew install git
brew install cmake
brew install gcc
brew install openblas
brew install lapack
brew install arpack
brew install libtiff
brew install jbigkit
brew install python@3.10

Install fftw and libraries as described above

Install SIMPLE

git clone https://github.com/hael/SIMPLE.git
cd SIMPLE
mkdir build
cd build
cmake -D NICE=on ..
make -j install
cat add2.bashrc >> ~/.zshrc