Skip to content

Latest commit

 

History

History
108 lines (76 loc) · 3.93 KB

Boston.md

File metadata and controls

108 lines (76 loc) · 3.93 KB
Raw

System info

AlmaLinux release 8.8 (Sapphire Caracal)
Linux scc2 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Mon Jul 24 04:58:00 EDT 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 python3 gcc/12.2.0 openmpi/4.1.5 cmake/3.22.2 gmplib/6.2.1 mpfr/4.2.1 boost/1.69.0 openblas/0.3.23

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 /usr2/collab/vdommes/install/sdpb-<VERSION> folder, where <VERSION> denotes specific version.

You may list all available versions via

ls /usr2/collab/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

/usr2/collab/vdommes/install/sdpb-master/bin/sdpb --help

Batch script example

qsub /usr2/collab/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.: ./run_sdpb_example.sh.o8388881. 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"

Elemental

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

FLINT

NB: when compiling FLINT on a login node, SDPB fails at runtime with SIGILL #0 __funlockfile #1 n_is_probabprime #2 comb error.

You should compile it on a compute node, e.g. loading interactive session via qrsh.

git clone https://github.com/flintlib/flint.git
cd flint
./bootstrap.sh
./configure --prefix=$HOME/install --disable-static --disable-pthread --with-gmp=$SCC_GMPLIB_DIR --with-mpfr=$SCC_MPFR_DIR CC=mpicc CXX=mpicxx
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 && make install
cd ..

sdpb

git clone https://github.com/davidsd/sdpb.git
cd sdpb 
./waf configure --elemental-dir=$HOME/install --rapidjson-dir=$HOME/install --libarchive-dir=$HOME/install --gmpxx-dir=$SCC_GMPLIB_DIR --mpfr-dir=$SCC_MPFR_DIR --flint-dir=$HOME/install --cblas-dir=$SCC_OPENBLAS_DIR --prefix=$HOME/install/sdpb-master
./waf # -j 1
./test/run_all_tests.sh
./waf install
cd ..