To build the preCICE adapter for CalculiX with PaStiX, it is first necessary to build PaStiX. A manual build is necessary for most steps, as specific compilation flags must be used for the dependencies: pre-built packages cannot be used. In particular, PaStiX (and CalculiX) must be compiled with flags to use 8-byte integers. On this page, we provide a step-by-step building guide of the adapter, tested on Ubuntu 20.04. This should work with some modifications on other systems. You may also need to tweak this depending on your needs, e.g. if you want to build some dependencies yourself instead of using a package manager.
Make sure you have a working installation of preCICE. Also run these installation commands, (after a call to
sudo apt update and
sudo apt upgrade) :
sudo apt install build-essential cmake git gfortran flex bison zlib1g-dev nvidia-cuda-toolkit-gcc libspooles-dev libyaml-cpp-dev
Downloading CalculiX source
This guide assumes Calculix’s source code is in the user’s home folder
/home/user_name, with the alias
~. If you don’t want to follow this convention, you may have to adapt slightly the instructions below. Download can be done on command line:
cd ~ && wget http://www.dhondt.de/ccx_2.17.src.tar.bz2 bunzip2 ccx_2.17.src.tar.bz2 tar -xvf ccx_2.17.src.tar
This contains the source code of CalculiX, but also scripts useful for building some libraries below with the correct flags.
Building PaStiX dependencies
It is assumed that all these libraries will be built on the user home folder,
~. Minor modifications will be required otherwise.
PaStiX requires OpenBLAS, hwloc, Scotch and PaRSEC. All of these will be built before PaStiX itself. We need to build them from source because specific flags are necessary to work with CalculiX’ version of PaStiX, mostly the use of 8 bytes integers.
Clone OpenBLAS source code and build it with 8-byte integers.
cd ~ git clone https://github.com/xianyi/OpenBLAS.git mv OpenBLAS ./OpenBLAS_i8 cd OpenBLAS_i8 make -j 4 INTERFACE64=1 sudo make install
You can also specify a custom installation path (to avoid calling
sudo) by using the
PREFIX=path/to/install option of the Makefile.
This library will be put in a subfolder of the PaStiX folder.
mkdir -p ~/PaStiX/ cd ~/PaStiX/ wget https://download.open-mpi.org/release/hwloc/v2.1/hwloc-2.1.0.tar.bz2 bunzip2 hwloc-2.1.0.tar.bz2 && tar -xf hwloc-2.1.0.tar cp ~/CalculiX/ccx_2.17/src/make_hwloc.sh ~/PaStiX/hwloc-2.1.0/make_hwloc.sh cd hwloc-2.1.0 ./configure --prefix=$HOME/PaStiX/hwloc_i8 CC=gcc CXX=g++ make -j8 make install
cd ~/PaStiX && git clone -b pastix-6.0.2 --single-branch https://bitbucket.org/mfaverge/parsec.git cd parsec cp ~/CalculiX/ccx_2.17/src/make_parsec.sh ~/PaStiX/parsec ./make_parsec.sh
cd ~/PaStiX wget https://gitlab.inria.fr/scotch/scotch/-/archive/master/scotch-master.tar.gz tar -xf scotch-master.tar.gz cp ~/CalculiX/ccx_2.17/src/make_scotch.sh ~/PaStiX/scotch-master cd scotch-master ./make_scotch.sh
cd ~/PaStiX git clone https://github.com/Dhondtguido/PaStiX4CalculiX mv PaStiX4CalculiX pastix_src cd pastix_src rm make_pastix.sh cp ~/CalculiX/ccx_2.17/src/make_pastix.sh . ./make_pastix.sh
make_pastix.shfile; be sure to use the one in the CalculiX folder and not the one from PaStiX!
- On some occasions, a Python script called by CMake (
cmake_modules/morse_cmake/modules/precision_generator/genDependencies.py) generates an incorrect Makefile because of errors in regular expressions. This should be fixed by calling
pip install regex(which requires installing the
python3-pipUbuntu package). You may also need to replace the
import reline in that script by
import regex as re, but the necessity seems to fluctuate among different machines.
- Some parts of the code require older versions of the GNU compilers. You may have to replace
gcc-7and similarly for
make_pastix.shscript. This requires installing the relevant Ubuntu packages.
Building ARPACK, a CalculiX dependency
Calculix relies on ARPACK, and when built with PaStiX, we cannot rely on standard distributions of that library, because it doesn’t feature 8-byte integers by default. We need to build the ARPACK code (update: original page seems to be down) ourselves:
cd ~ wget https://web.archive.org/web/20220526222500fw_/https://www.caam.rice.edu/software/ARPACK/SRC/arpack96.tar.gz wget https://web.archive.org/web/20220526222500fw_/https://www.caam.rice.edu/software/ARPACK/SRC/patch.tar.gz zcat arpack96.tar.gz | tar -xvf - zcat patch.tar.gz | tar -xvf -
Before building the library, the following modifications are required:
PLATby the appropriate suffix (the adapter’s makefile assumes INTEL)
ARmake.inc, change the Fortran compilation flags to add
-fdefault-integer-8. You may also need to remove the flag
- If you extracted the archive on another folder than your home repository, update
- In the file
UTIL/second.f, comment with a star the line containing
Once all of these are done, run
make lib in the
Building the adapter
To build the adapter, clone its repository and checkout the
2.17 branch :
git clone -b v2.17 https://github.com/precice/calculix-adapter cd calculix-adapter
Fixing the code
Due to some conflicts between CalculiX, PaStiX and the adapter (both CalculiX and PaStiX have a
pastix.h file, and neither of them is local from the point of view of the adapter), some changes are required in the CalculiX codebase. We provide a script,
pastix_pre_build.sh that does these changes. Run it.
To build the adapter, use the provided
Makefile_i8_PaStiX: the regular Makefile would build the adapter without PaStiX. Assuming you followed the previous steps, it should be useable without modifications other than giving Calculix’ path; otherwise, some other paths updates could be required. You also need to ensure then Makefile finds the required dependencies when calling
pkg-config. This can be done by changing the
PKG_PATH_CONFIG environment variable. Assuming you used suggested paths, this would look like this:
Then you can build the adapter with this command in the
calculix-adapter (and be sure to checkout the
2.17 branch) folder :
make -f Makefile_i8_PaStiX -j 4 CCX=~/CalculiX/ccx_2.17/src
Once the build is successful, the adapter should be in
Updating shared libraries
Running the adapter at this point should fail because of a missing shared library:
libparsec.so.2. You can fix this by adding its path to the environment variable
export LD_LIBRARY_PATH=:$LD_LIBRARY_PATH:~/PaStiX/parsec_i8/lib. You may have to do this everytime you load a new terminal, which is why we advise you to make this change permanent, for instance by adding this export commande at the end of your