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System info

Rocky Linux release 8.7 (Green Obsidian)
Linux holylogin02.rc.fas.harvard.edu 4.18.0-425.10.1.el8_7.x86_64 #1 SMP Thu Jan 12 16:32:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

Useful links

Load modules

For compiling and/or running SDPB, you have to load modules first:

module load python gcc/12.2.0-fasrc01 cmake/3.25.2-fasrc01 openmpi/4.1.5-fasrc01 gmp/6.2.1-fasrc01 mpfr/4.2.0-fasrc01

You may run module -t list to view loaded modules, and module purge to unload all modules.

You may also add this command to your ~/.bashrc file, so that modules will load automatically.

Use existing SDPB installation

Choose SDPB version

SDPB is installed in /n/home02/vdommes/install/sdpb-<VERSION> folder, where <VERSION> denotes specific version.

You may list all available versions via

ls /n/home02/vdommes/install | grep sdpb

Fo example, sdpb-master is built from the latest master branch ( run sdpb --version to see commit hash, e.g. SDPB 2.5.1-130-g88b1c9ae), and sdpb-3.0.0 is a stable 3.0.0 release.

Examples below are for sdpb-master. You may replace it with another version, e.g. sdpb-3.0.0. In that case, please refer to 3.0.0 documentation.

Run SDPB

/n/home02/vdommes/install/sdpb-master/bin/sdpb --help

Batch script example

sbatch /n/home02/vdommes/install/sdpb-master/share/sdpb_example.sh

This command submits sdpb_example.sh to the queueing system.

sdpb_example.sh loads modules and runs pmp2sdp+sdpb for a simple problem. See script code and comments for more details.

Script output is written to the log file in the current directory, e.g.: ./sdpb_example.sh.26306151.out. SDPB output files are written to the ./out/ folder in the current directory.

Build SDPB from sources

Use RPATH instead of RUNPATH in mpicxx linker, to fix shared library loading in SDPB:

export OMPI_LDFLAGS="$(mpicxx --showme:link) -Wl,--disable-new-dtags"

Boost

wget https://boostorg.jfrog.io/artifactory/main/release/1.83.0/source/boost_1_83_0.tar.bz2
tar -jxf boost_1_83_0.tar.bz2
cd boost_1_83_0
./bootstrap.sh --prefix=$HOME/install --without-libraries=python
./b2 -j 16 --prefix=$HOME/install
./b2 --prefix=$HOME/install install
cd ..

Elemental

git clone https://gitlab.com/bootstrapcollaboration/elemental.git
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/install -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc
make && make install

FLINT

git clone https://github.com/flintlib/flint.git
cd flint
./bootstrap.sh
./configure --prefix=$HOME/install --disable-static
make #-j1
make check
make install 
cd ..

RapidJSON

git clone https://github.com/Tencent/rapidjson.git
cp -r rapidjson/include $HOME/install

libarchive

wget http://www.libarchive.org/downloads/libarchive-3.7.1.tar.xz
tar -xf libarchive-3.7.1.tar.xz
cd libarchive-3.7.1
./configure --prefix=$HOME/install
make -j 16 && make install
cd ..

sdpb

git clone https://github.com/davidsd/sdpb.git
cd sdpb
./waf configure --boost-dir=$HOME/install --elemental-dir=$HOME/install --rapidjson-dir=$HOME/install --libarchive-dir=$HOME/install --flint-dir=$HOME/install --cblas-incdir=/usr/include/openblas --prefix=$HOME/install/sdpb-master
./waf # -j 1
./test/run_all_tests.sh
./waf install