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Installation with quadruple precision

Quadruple precision is useful for numerically demanding cases, but it is not the default installation path. To build SPIDER with quadruple precision, you need to install SUNDIALS and PETSc manually with quadruple-precision support first, and then build SPIDER against that installation.

What is different from the standard install?

For quadruple precision:

  • you need a real GCC compiler, not Apple Clang on macOS;
  • you need a separate quadruple-precision SUNDIALS build;
  • you then configure PETSc with --with-precision=__float128 and point it to that SUNDIALS installation;
  • finally, you build SPIDER with PETSC_DIR and PETSC_ARCH set to that PETSc build.

1. Check that your compiler supports quadruple precision

The SPIDER docs note that quadruple precision requires a GCC compiler. On macOS, gcc often points to Apple Clang, which does not provide GNU quadruple-precision support.

Check your compiler:

gcc --version

If the output mentions Apple LLVM, install GCC separately and use that compiler binary instead.

A simple test is:

echo '#include<stdio.h>' > t.c && \
echo '#include<quadmath.h>' >> t.c && \
echo 'int main(){printf("It seems to work!\n");}' >> t.c && \
gcc t.c && ./a.out && rm -f t.c a.out

If that fails, your current compiler is not suitable for the quadruple-precision build.

2. Install SUNDIALS with quadruple precision

For quadruple precision, SPIDER uses a modified SUNDIALS build rather than PETSc’s default downloaded copy. The documented workflow is: clone the modified SUNDIALS repository, configure it with CMake, and set SUNDIALS_PRECISION=quadruple.

Check that CMake is available

Make sure that CMake is available: 

cmake --version
If it is not installed, follow the instructions here, or run:

sudo port install cmake

brew install cmake

sudo apt-get install cmake

cd /somewhere/to/install
mkdir -p sundials-quad
cd sundials-quad

git clone https://bitbucket.org/psanan/sundials-quad src
mkdir install build
cd build
cmake ../src
ccmake .

In ccmake, set values similar to:

Using the ccmake interface

When using the ccmake interface, make sure you type "c" to configure once you have entered these values, then "g" to generate and exit.

CMAKE_C_COMPILER: gcc
CMAKE_INSTALL_PREFIX: ../install
EXAMPLES_INSTALL_PATH: ../install/examples
SUNDIALS_PRECISION: quadruple

Then build and install:

make && make install

C compiler

Use the same C compiler here that you will use for PETSc.

3. Install PETSc with quadruple precision

Install the pinned snapshot if interested in reproducing previous results. Otherwise, install PETSc 3.19.

cd /somewhere/to/install
git clone https://gitlab.com/petsc/petsc -b main petsc-quad
cd petsc-quad
git checkout 63b725033a15f75ded7183cf5f88ec748e60783b

cd /somewhere/to/install
git clone https://gitlab.com/petsc/petsc petsc-3.19
cd petsc-3.19
git checkout v3.19.6

Configure it against the SUNDIALS installation you just built:

./configure \
  --with-debugging=0 \
  --with-fc=0 \
  --with-cxx=0 \
  --with-cc=gcc \
  --with-precision=__float128 \
  --with-sundials=1 \
  --with-sundials-dir=/somewhere/to/install/sundials-quad/install \
  --download-mpich \
  --download-f2cblaslapack \
  --COPTFLAGS="-g -O3" \
  --CXXOPTFLAGS="-g -O3"

Then follow PETSc’s terminal instructions to complete the build, and export the environment it reports:

export PETSC_DIR=/somewhere/to/install/petsc-quad
export PETSC_ARCH=arch-xxx-yyy

4. Build SPIDER against the quadruple-precision PETSc

Once PETSC_DIR and PETSC_ARCH point to your quadruple-precision PETSc build, build SPIDER normally:

cd /somewhere/to/install
git clone https://github.com/FormingWorlds/SPIDER.git
cd SPIDER

make clean
make -j

Then test your installation by following the steps in the testing guide.