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
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.
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-2.6.0
is a stable 2.6.0 release.
Examples below are for sdpb-master
.
You may replace it with another version, e.g. sdpb-2.6.0
.
In that case, please refer
to 2.6.0 documentation.
/n/home02/vdommes/install/sdpb-master/bin/sdpb --help
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 sdp2input
+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.
Use RPATH
instead of RUNPATH
in mpicxx
linker, to fix shared library loading in SDPB:
export OMPI_LDFLAGS="$(mpicxx --showme:link) -Wl,--disable-new-dtags"
wget https://boostorg.jfrog.io/artifactory/main/release/1.83.0/source/boost_1_83_0.tar.bz2
tar -jxf boost_1_83_0.tar.bz2
cd boost_1_83_0
./bootstrap.sh --prefix=$HOME/install --without-libraries=python
./b2 -j 16 --prefix=$HOME/install
./b2 --prefix=$HOME/install install
cd ..
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
git clone https://github.com/Tencent/rapidjson.git
cp -r rapidjson/include $HOME/install
wget http://www.libarchive.org/downloads/libarchive-3.7.1.tar.xz
tar -xf libarchive-3.7.1.tar.xz
cd libarchive-3.7.1
./configure --prefix=$HOME/install
make -j 16 && make install
cd ..
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 --prefix=$HOME/install/sdpb-master
./waf # -j 1
./test/run_all_tests.sh
./waf install