Appendix1. Configuration of Installed Software
Note
This section only includes a part of the configurations of the installed software.
Open MPI
Open MPI 2.1.3 (for GCC)
w/o CUDA
INSTALL_DIR=/apps/openmpi/2.1.3/gcc4.8.5 [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v2.1/openmpi-2.1.3.tar.bz2 [username@g0001 ~]$ tar zxf openmpi-2.1.3.tar.bz2 [username@g0001 ~]$ cd openmpi-2.1.3 [username@g0001 openmpi-2.1.3]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-mpi-thread-multiple \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log 2>&1 [username@g0001 openmpi-2.1.3]$ make -j8 > make.log 2>&1 [username@g0001 openmpi-2.1.3]$ su [root@g0001 openmpi-2.1.3]# make install 2>&1 | tee make_install.log [root@g0001 openmpi-2.1.3]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 8.0.61.2
INSTALL_DIR=/apps/openmpi/2.1.3/gcc4.8.5_cuda8.0.61.2 [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v2.1/openmpi-2.1.3.tar.bz2 [username@g0001 ~]$ tar zxf openmpi-2.1.3.tar.bz2 [username@g0001 ~]$ cd openmpi-2.1.3 [username@g0001 ~]$ module load cuda/8.0/8.0.61.2 [username@g0001 openmpi-2.1.3]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-mpi-thread-multiple \ --with-cuda=$CUDA_HOME \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log 2>&1 [username@g0001 openmpi-2.1.3]$ make -j8 > make.log 2>&1 [username@g0001 openmpi-2.1.3]$ su [root@g0001 openmpi-2.1.3]# make install 2>&1 | tee make_install.log [root@g0001 openmpi-2.1.3]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 9.0.176.2
INSTALL_DIR=/apps/openmpi/2.1.3/gcc4.8.5_cuda9.0.176.2 [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v2.1/openmpi-2.1.3.tar.bz2 [username@g0001 ~]$ tar zxf openmpi-2.1.3.tar.bz2 [username@g0001 ~]$ cd openmpi-2.1.3 [username@g0001 ~]$ module load cuda/9.0/9.0.176.2 [username@g0001 openmpi-2.1.3]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-mpi-thread-multiple \ --with-cuda=$CUDA_HOME \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log 2>&1 [username@g0001 openmpi-2.1.3]$ make -j8 > make.log 2>&1 [username@g0001 openmpi-2.1.3]$ su [root@g0001 openmpi-2.1.3]# make install 2>&1 | tee make_install.log [root@g0001 openmpi-2.1.3]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 9.1.85.3
INSTALL_DIR=/apps/openmpi/2.1.3/gcc4.8.5_cuda9.1.85.3 [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v2.1/openmpi-2.1.3.tar.bz2 [username@g0001 ~]$ tar zxf openmpi-2.1.3.tar.bz2 [username@g0001 ~]$ cd openmpi-2.1.3 [username@g0001 ~]$ module load cuda/9.1/9.1.85.3 [username@g0001 openmpi-2.1.3]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-mpi-thread-multiple \ --with-cuda=$CUDA_HOME \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log 2>&1 [username@g0001 openmpi-2.1.3]$ make -j8 > make.log 2>&1 [username@g0001 openmpi-2.1.3]$ su [root@g0001 openmpi-2.1.3]# make install 2>&1 | tee make_install.log [root@g0001 openmpi-2.1.3]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 9.2.88.1
INSTALL_DIR=/apps/openmpi/2.1.3/gcc4.8.5_cuda9.2.88.1 [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v2.1/openmpi-2.1.3.tar.bz2 [username@g0001 ~]$ tar zxf openmpi-2.1.3.tar.bz2 [username@g0001 ~]$ cd openmpi-2.1.3 [username@g0001 ~]$ module load cuda/9.2.88.1 [username@g0001 openmpi-2.1.3]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-mpi-thread-multiple \ --with-cuda=$CUDA_HOME \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log 2>&1 [username@g0001 openmpi-2.1.3]$ make -j8 > make.log 2>&1 [username@g0001 openmpi-2.1.3]$ su [root@g0001 openmpi-2.1.3]# make install 2>&1 | tee make_install.log [root@g0001 openmpi-2.1.3]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
Open MPI 3.1.0 (for GCC)
w/o CUDA
INSTALL_DIR=/apps/openmpi/3.1.0/gcc4.8.5 [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.0.tar.bz2 [username@g0001 ~]$ tar zxf openmpi-3.1.0.tar.bz2 [username@g0001 ~]$ cd openmpi-3.1.0 [username@g0001 openmpi-3.1.0]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log 2>&1 [username@g0001 openmpi-3.1.0]$ make -j8 > make.log 2>&1 [username@g0001 openmpi-3.1.0]$ su [root@g0001 openmpi-3.1.0]# make install 2>&1 | tee make_install.log [root@g0001 openmpi-3.1.0]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 8.0.61.2
INSTALL_DIR=/apps/openmpi/3.1.0/gcc4.8.5_cuda8.0.61.2 [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.0.tar.bz2 [username@g0001 ~]$ tar zxf openmpi-3.1.0.tar.bz2 [username@g0001 ~]$ cd openmpi-3.1.0 [username@g0001 ~]$ module load cuda/8.0/8.0.61.2 [username@g0001 ~]$ INSTALL_DIR=/apps/openmpi/3.1.0/gcc4.8.5_cuda8.0.61.2 [username@g0001 openmpi-3.1.0]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-orterun-prefix-by-default \ --with-cuda=$CUDA_HOME \ --with-sge \ 2>&1 | tee configure.log 2>&1 [username@g0001 openmpi-3.1.0]$ make -j8 > make.log 2>&1 [username@g0001 openmpi-3.1.0]$ su [root@g0001 openmpi-3.1.0]# make install 2>&1 | tee make_install.log [root@g0001 openmpi-3.1.0]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 9.0.176.2
INSTALL_DIR=/apps/openmpi/3.1.0/gcc4.8.5_cuda9.0.176.2 [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.0.tar.bz2 [username@g0001 ~]$ tar zxf openmpi-3.1.0.tar.bz2 [username@g0001 ~]$ cd openmpi-3.1.0 [username@g0001 ~]$ module load cuda/9.0/9.0.176.2 [username@g0001 openmpi-3.1.0]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-orterun-prefix-by-default \ --with-cuda=$CUDA_HOME \ --with-sge \ 2>&1 | tee configure.log 2>&1 [username@g0001 openmpi-3.1.0]$ make -j8 > make.log 2>&1 [username@g0001 openmpi-3.1.0]$ su [root@g0001 openmpi-3.1.0]# make install 2>&1 | tee make_install.log [root@g0001 openmpi-3.1.0]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 9.1.85.3
INSTALL_DIR=/apps/openmpi/3.1.0/gcc4.8.5_cuda9.1.85.3 [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.0.tar.bz2 [username@g0001 ~]$ tar zxf openmpi-3.1.0.tar.bz2 [username@g0001 ~]$ cd openmpi-3.1.0 [username@g0001 ~]$ module load cuda/9.1/9.1.85.3 [username@g0001 openmpi-3.1.0]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-orterun-prefix-by-default \ --with-cuda=$CUDA_HOME \ --with-sge \ 2>&1 | tee configure.log 2>&1 [username@g0001 openmpi-3.1.0]$ make -j8 > make.log 2>&1 [username@g0001 openmpi-3.1.0]$ su [root@g0001 openmpi-3.1.0]# make install 2>&1 | tee make_install.log [root@g0001 openmpi-3.1.0]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 9.2.88.1
INSTALL_DIR=/apps/openmpi/3.1.0/gcc4.8.5_cuda9.2.88.1 [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.0.tar.bz2 [username@g0001 ~]$ tar zxf openmpi-3.1.0.tar.bz2 [username@g0001 ~]$ cd openmpi-3.1.0 [username@g0001 ~]$ module load cuda/9.2/9.2.88.1 [username@g0001 openmpi-3.1.0]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-orterun-prefix-by-default \ --with-cuda=$CUDA_HOME \ --with-sge \ 2>&1 | tee configure.log 2>&1 [username@g0001 openmpi-3.1.0]$ make -j8 > make.log 2>&1 [username@g0001 openmpi-3.1.0]$ su [root@g0001 openmpi-3.1.0]# make install 2>&1 | tee make_install.log [root@g0001 openmpi-3.1.0]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
Open MPI 2.1.6 (for PGI18.5)
w/o CUDA
INSTALL_DIR='/apps/openmpi/2.1.6/pgi18.5' [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v2.1/openmpi-2.1.6.tar.gz [username@g0001 ~]$ tar zxf openmpi-2.1.6.tar.gz [username@g0001 ~]$ module load pgi/18.5 [username@g0001 ~]$ export CPP=cpp [username@g0001 ~]$ cd openmpi-2.1.6 [username@g0001 openmpi-2.1.6]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-mpi-thread-multiple \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log [username@g0001 openmpi-2.1.6]$ make -j 8 2>&1 | tee make.log [username@g0001 openmpi-2.1.6]$ su [root@g0001 openmpi-2.1.6]# make install [root@g0001 openmpi-2.1.6]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 8.0.61.2
INSTALL_DIR='/apps/openmpi/2.1.6/pgi18.5_cuda8.0.61.2' [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v2.1/openmpi-2.1.6.tar.gz [username@g0001 ~]$ tar zxf openmpi-2.1.6.tar.gz [username@g0001 ~]$ module load pgi/18.5 [username@g0001 ~]$ export CPP=cpp [username@g0001 ~]$ module load cuda/8.0/8.0.61.2 [username@g0001 ~]$ cd openmpi-2.1.6 [username@g0001 openmpi-2.1.6]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-mpi-thread-multiple \ --with-cuda=$CUDA_HOME \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log [username@g0001 openmpi-2.1.6]$ make -j 8 2>&1 | tee make.log [username@g0001 openmpi-2.1.6]$ su [root@g0001 openmpi-2.1.6]# make install [root@g0001 openmpi-2.1.6]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 9.0.176.2
INSTALL_DIR='/apps/openmpi/2.1.6/pgi18.5_cuda9.0.176.2' [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v2.1/openmpi-2.1.6.tar.gz [username@g0001 ~]$ tar zxf openmpi-2.1.6.tar.gz [username@g0001 ~]$ module load pgi/18.5 [username@g0001 ~]$ export CPP=cpp [username@g0001 ~]$ module load cuda/9.0/9.0.176.2 [username@g0001 ~]$ cd openmpi-2.1.6 [username@g0001 openmpi-2.1.6]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-mpi-thread-multiple \ --with-cuda=$CUDA_HOME \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log [username@g0001 openmpi-2.1.6]$ make -j 8 2>&1 | tee make.log [username@g0001 openmpi-2.1.6]$ su [root@g0001 openmpi-2.1.6]# make install [root@g0001 openmpi-2.1.6]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 9.1.85.3
INSTALL_DIR='/apps/openmpi/2.1.6/pgi18.5_cuda9.1.85.3' [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v2.1/openmpi-2.1.6.tar.gz [username@g0001 ~]$ tar zxf openmpi-2.1.6.tar.gz [username@g0001 ~]$ module load pgi/18.5 [username@g0001 ~]$ export CPP=cpp [username@g0001 ~]$ module load cuda/9.1/9.1.85.3 [username@g0001 ~]$ cd openmpi-2.1.6 [username@g0001 openmpi-2.1.6]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-mpi-thread-multiple \ --with-cuda=$CUDA_HOME \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log [username@g0001 openmpi-2.1.6]$ make -j 8 2>&1 | tee make.log [username@g0001 openmpi-2.1.6]$ su [root@g0001 openmpi-2.1.6]# make install [root@g0001 openmpi-2.1.6]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 9.2.88.1
INSTALL_DIR='/apps/openmpi/2.1.6/pgi18.5_cuda9.2.88.1' [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v2.1/openmpi-2.1.6.tar.gz [username@g0001 ~]$ tar zxf openmpi-2.1.6.tar.gz [username@g0001 ~]$ module load pgi/18.5 [username@g0001 ~]$ export CPP=cpp [username@g0001 ~]$ module load cuda/9.2/9.2.88.1 [username@g0001 ~]$ cd openmpi-2.1.6 [username@g0001 openmpi-2.1.6]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-mpi-thread-multiple \ --with-cuda=$CUDA_HOME \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log [username@g0001 openmpi-2.1.6]$ make -j 8 2>&1 | tee make.log [username@g0001 openmpi-2.1.6]$ su [root@g0001 openmpi-2.1.6]# make install [root@g0001 openmpi-2.1.6]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 9.2.148.1
INSTALL_DIR='/apps/openmpi/2.1.6/pgi18.5_cuda9.2.148.1' [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v2.1/openmpi-2.1.6.tar.gz [username@g0001 ~]$ tar zxf openmpi-2.1.6.tar.gz [username@g0001 ~]$ module load pgi/18.5 [username@g0001 ~]$ export CPP=cpp [username@g0001 ~]$ module load cuda/9.2/9.2.148.1 [username@g0001 ~]$ cd openmpi-2.1.6 [username@g0001 openmpi-2.1.6]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-mpi-thread-multiple \ --with-cuda=$CUDA_HOME \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log [username@g0001 openmpi-2.1.6]$ make -j 8 2>&1 | tee make.log [username@g0001 openmpi-2.1.6]$ su [root@g0001 openmpi-2.1.6]# make install [root@g0001 openmpi-2.1.6]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
Open MPI 3.1.3 (for PGI18.5)
w/o CUDA
INSTALL_DIR='/apps/openmpi/3.1.3/pgi18.5' [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.3.tar.gz [username@g0001 ~]$ tar zxf openmpi-3.1.3.tar.gz [username@g0001 ~]$ module load pgi/18.5 [username@g0001 ~]$ export CPP=cpp [username@g0001 ~]$ cd openmpi-3.1.3 [username@g0001 openmpi-3.1.3]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log [username@g0001 openmpi-3.1.3]$ make -j 8 2>&1 | tee make.log [username@g0001 openmpi-3.1.3]$ su [root@g0001 openmpi-3.1.3]# make install [root@g0001 openmpi-3.1.3]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 8.0.61.2
INSTALL_DIR='/apps/openmpi/3.1.3/pgi18.5_cuda8.0.61.2' [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.3.tar.gz [username@g0001 ~]$ tar zxf openmpi-3.1.3.tar.gz [username@g0001 ~]$ module load pgi/18.5 [username@g0001 ~]$ export CPP=cpp [username@g0001 ~]$ module load cuda/8.0/8.0.61.2 [username@g0001 ~]$ cd openmpi-3.1.3 [username@g0001 openmpi-3.1.3]$ ./configure \ --prefix=$INSTALL_DIR \ --with-cuda=$CUDA_HOME \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log [username@g0001 openmpi-3.1.3]$ make -j 8 2>&1 | tee make.log [username@g0001 openmpi-3.1.3]$ su [root@g0001 openmpi-3.1.3]# make install [root@g0001 openmpi-3.1.3]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 9.0.176.2
INSTALL_DIR='/apps/openmpi/3.1.3/pgi18.5_cuda9.0.176.2' [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.3.tar.gz [username@g0001 ~]$ tar zxf openmpi-3.1.3.tar.gz [username@g0001 ~]$ module load pgi/18.5 [username@g0001 ~]$ export CPP=cpp [username@g0001 ~]$ module load cuda/9.0/9.0.176.2 [username@g0001 ~]$ cd openmpi-3.1.3 [username@g0001 openmpi-3.1.3]$ ./configure \ --prefix=$INSTALL_DIR \ --with-cuda=$CUDA_HOME \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log [username@g0001 openmpi-3.1.3]$ make -j 8 2>&1 | tee make.log [username@g0001 openmpi-3.1.3]$ su [root@g0001 openmpi-3.1.3]# make install [root@g0001 openmpi-3.1.3]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 9.1.85.3
INSTALL_DIR='/apps/openmpi/3.1.3/pgi18.5_cuda9.1.85.3' [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.3.tar.gz [username@g0001 ~]$ tar zxf openmpi-3.1.3.tar.gz [username@g0001 ~]$ module load pgi/18.5 [username@g0001 ~]$ export CPP=cpp [username@g0001 ~]$ module load cuda/9.1/9.1.85.3 [username@g0001 ~]$ cd openmpi-3.1.3 [username@g0001 openmpi-3.1.3]$ ./configure \ --prefix=$INSTALL_DIR \ --with-cuda=$CUDA_HOME \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log [username@g0001 openmpi-3.1.3]$ make -j 8 2>&1 | tee make.log [username@g0001 openmpi-3.1.3]$ su [root@g0001 openmpi-3.1.3]# make install [root@g0001 openmpi-3.1.3]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 9.2.88.1
INSTALL_DIR='/apps/openmpi/3.1.3/pgi18.5_cuda9.2.88.1' [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.3.tar.gz [username@g0001 ~]$ tar zxf openmpi-3.1.3.tar.gz [username@g0001 ~]$ module load pgi/18.5 [username@g0001 ~]$ export CPP=cpp [username@g0001 ~]$ module load cuda/9.2/9.2.88.1 [username@g0001 ~]$ cd openmpi-3.1.3 [username@g0001 openmpi-3.1.3]$ ./configure \ --prefix=$INSTALL_DIR \ --with-cuda=$CUDA_HOME \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log [username@g0001 openmpi-3.1.3]$ make -j 8 2>&1 | tee make.log [username@g0001 openmpi-3.1.3]$ su [root@g0001 openmpi-3.1.3]# make install [root@g0001 openmpi-3.1.3]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
CUDA 9.2.148.1
INSTALL_DIR='/apps/openmpi/3.1.3/pgi18.5_cuda9.2.148.1' [username@g0001 ~]$ wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.3.tar.gz [username@g0001 ~]$ tar zxf openmpi-3.1.3.tar.gz [username@g0001 ~]$ module load pgi/18.5 [username@g0001 ~]$ export CPP=cpp [username@g0001 ~]$ module load cuda/9.2/9.2.148.1 [username@g0001 ~]$ cd openmpi-3.1.3 [username@g0001 openmpi-3.1.3]$ ./configure \ --prefix=$INSTALL_DIR \ --with-cuda=$CUDA_HOME \ --enable-orterun-prefix-by-default \ --with-sge \ 2>&1 | tee configure.log [username@g0001 openmpi-3.1.3]$ make -j 8 2>&1 | tee make.log [username@g0001 openmpi-3.1.3]$ su [root@g0001 openmpi-3.1.3]# make install [root@g0001 openmpi-3.1.3]# echo "btl_openib_warn_default_gid_prefix = 0" >> $INSTALL_DIR/etc/openmpi-mca-params.conf
MVAPICH2 (for GCC)
w/o CUDA
INSTALL_DIR=/app/mvapich2/2.3rc2/gcc4.8.5 [username@g0001 ~]$ wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.3rc2.tar.gz [username@g0001 ~]$ tar zxf mvapich2-2.3rc2.tar.gz [username@g0001 ~]$ cd mvapich2-2.3rc2 [username@g0001 mvapich2-2.3rc2]$ ./configure --prefix=$INSTALL_DIR 2>&1 | tee configure.log [username@g0001 mvapich2-2.3rc2]$ make -j8 > make.log 2>&1 [username@g0001 mvapich2-2.3rc2]$ make check -j8 > make_check.log 2>&1 [username@g0001 mvapich2-2.3rc2]$ su [root@g0001 mvapich2-2.3rc2]# make install 2>&1 | tee make_install.log
CUDA 8.0.61.2
INSTALL_DIR=/apps/mvapich2/2.3rc2/gcc4.8.5_cuda8.0.61.2 [username@g0001 ~]$ wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.3rc2.tar.gz [username@g0001 ~]$ tar zxf mvapich2-2.3rc2.tar.gz [username@g0001 ~]$ cd mvapich2-2.3rc2 [username@g0001 mvapich2-2.3rc2]$ module load cuda/8.0/8.0.61.2 [username@g0001 mvapich2-2.3rc2]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-cuda \ --with-cuda=$CUDA_HOME \ 2>&1 | tee configure.log 2>&1 [username@g0001 mvapich2-2.3rc2]$ make -j8 > make.log 2>&1 [username@g0001 mvapich2-2.3rc2]$ make check -j8 > make_check.log 2>&1 [username@g0001 mvapich2-2.3rc2]$ su [root@g0001 mvapich2-2.3rc2]# make install 2>&1 | tee make_install.log
CUDA 9.0.176.2
INSTALL_DIR=/apps/mvapich2/2.3rc2/gcc4.8.5_cuda9.0.176.2 [username@g0001 ~]$ wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.3rc2.tar.gz [username@g0001 ~]$ tar zxf mvapich2-2.3rc2.tar.gz [username@g0001 ~]$ cd mvapich2-2.3rc2 [username@g0001 mvapich2-2.3rc2]$ module load cuda/9.0/9.0.176.2 [username@g0001 mvapich2-2.3rc2]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-cuda \ --with-cuda=$CUDA_HOME \ 2>&1 | tee configure.log 2>&1 [username@g0001 mvapich2-2.3rc2]$ make -j8 > make.log 2>&1 [username@g0001 mvapich2-2.3rc2]$ make check -j8 > make_check.log 2>&1 [username@g0001 mvapich2-2.3rc2]$ su [root@g0001 mvapich2-2.3rc2]# make install 2>&1 | tee make_install.log
CUDA 9.1.85.3
INSTALL_DIR=/apps/mvapich2/2.3rc2/gcc4.8.5_cuda9.1.85.3 [username@g0001 ~]$ wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.3rc2.tar.gz [username@g0001 ~]$ tar zxf mvapich2-2.3rc2.tar.gz [username@g0001 ~]$ cd mvapich2-2.3rc2 [username@g0001 mvapich2-2.3rc2]$ module load cuda/9.1/9.1.85.3 [username@g0001 mvapich2-2.3rc2]$ ./configure \ --prefix=$INSTALL_DIR \ --enable-cuda \ --with-cuda=$CUDA_HOME \ 2>&1 | tee configure.log 2>&1 [username@g0001 mvapich2-2.3rc2]$ make -j8 > make.log 2>&1 [username@g0001 mvapich2-2.3rc2]$ make check -j8 > make_check.log 2>&1 [username@g0001 mvapich2-2.3rc2]$ su [root@g0001 mvapich2-2.3rc2]# make install 2>&1 | tee make_install.log
CUDA 9.2.88.1
INSTALL_DIR=/apps/mvapich2/2.3rc2/gcc4.8.5_cuda9.2.88.1 [username@g0001 ~]$ wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.3rc2.tar.gz [username@g0001 ~]$ tar zxf mvapich2-2.3rc2.tar.gz [username@g0001 ~]$ cd mvapich2-2.3rc2 [username@g0001 mvapich2-2.3rc2]$ module load cuda/9.2/9.2.88.1 [username@g0001 mvapich2-2.3rc2]$ ./configure \ --prefix=INSTALL_DIR \ --enable-cuda \ --with-cuda=$CUDA_HOME \ 2>&1 | tee configure.log 2>&1 [username@g0001 mvapich2-2.3rc2]$ make -j8 > make.log 2>&1 [username@g0001 mvapich2-2.3rc2]$ make check -j8 > make_check.log 2>&1 [username@g0001 mvapich2-2.3rc2]$ su [root@g0001 mvapich2-2.3rc2]# make install 2>&1 | tee make_install.log
Python
Python 2.7.15
INSTALL_DIR=/apps/python/2.7.15 [username@g0001 ~]$ wget https://www.python.org/ftp/python/2.7.15/Python-2.7.15.tar.xz [username@g0001 ~]$ tar Jxf Python-2.7.15.tar.xz [username@g0001 ~]$ cd Python-2.7.15 [username@g0001 Python-2.7.15]$ CXX=g++ ./configure \ --prefix=$INSTALL_DIR \ --enable-optimizations \ --enable-shared \ --with-ensurepip \ --enable-unicode=ucs4 \ --with-dbmliborder=gdbm:ndbm:bdb \ --with-system-expat \ --with-system-ffi \ > configure.log 2>&1 [username@g0001 Python-2.7.15]$ make -j8 > make.log 2>&1 [username@g0001 Python-2.7.15]$ make test > make_test.log 2>&1 [username@g0001 Python-2.7.15]$ su [root@g0001 Python-2.7.15]# make install 2>&1 | tee make_install.log [root@g0001 Python-2.7.15]# export PATH=$INSTALL_DIR/bin:$PATH [root@g0001 Python-2.7.15]# pip install virtualenv
R
R 3.5.0
INSTALL_DIR=/apps/R/3.5.0 [username@g0001 ~]$ wget https://cran.ism.ac.jp/src/base/R-3/R-3.5.0.tar.gz [username@g0001 ~]$ tar zxf R-3.5.0.tar.gz [username@g0001 ~]$ cd R-3.5.0 [username@g0001 R-3.5.0]$ ./configure --prefix=$INSTALL_DIR 2>&1 | tee configure.log [username@g0001 R-3.5.0]$ make 2>&1 | tee make.log [username@g0001 R-3.5.0]$ make check 2>&1 | tee make_check.log [username@g0001 R-3.5.0]$ su [username@g0001 R-3.5.0]# make install 2>&1 | tee make_install.log
NVIDIA Collective Communications Library (NCCL)
NCCL 1.3.5
CUDA 8.0.61.2
INSTALL_DIR=/apps/nccl/1.3.5/cuda8.0 [username@es1 ~]$ git clone https://github.com/NVIDIA/nccl.git [username@es1 ~]$ cd nccl [username@es1 nccl]$ module load cuda/8.0/8.0.61.2 [username@es1 nccl]$ make CUDA_HOME=$CUDA_HOME test [username@es1 nccl]$ su [root@es1 nccl]# mkdir -p $INSTALL_DIR [root@es1 nccl]# make PREFIX=$INSTALL_DIR install
CUDA 9.0.176.2
INSTALL_DIR=/apps/nccl/1.3.5/cuda9.0 [username@es1 ~]$ git clone https://github.com/NVIDIA/nccl.git [username@es1 ~]$ cd nccl [username@es1 nccl]$ module load cuda/9.0/9.0.176.2 [username@es1 nccl]$ make CUDA_HOME=$CUDA_HOME test [username@es1 nccl]$ su [root@es1 nccl]# mkdir -p $INSTALL_DIR [root@es1 nccl]# make PREFIX=$INSTALL_DIR install
CUDA 9.1.85.3
INSTALL_DIR=/apps/nccl/1.3.5/cuda9.1 [username@es1 ~]$ git clone https://github.com/NVIDIA/nccl.git [username@es1 ~]$ cd nccl [username@es1 nccl]$ module load cuda/9.1/9.1.85.3 [username@es1 nccl]$ make CUDA_HOME=$CUDA_HOME test [username@es1 nccl]$ su [root@es1 nccl]# mkdir -p $INSTALL_DIR [root@es1 nccl]# make PREFIX=$INSTALL_DIR install
CUDA 9.2.88.1
INSTALL_DIR=/apps/nccl/1.3.5/cuda9.2 [username@es1 ~]$ git clone https://github.com/NVIDIA/nccl.git [username@es1 ~]$ cd nccl [username@es1 nccl]$ module load cuda/9.2/9.2.88.1 [username@es1 nccl]$ make CUDA_HOME=$CUDA_HOME test [username@es1 nccl]$ su [root@es1 nccl]# mkdir -p $INSTALL_DIR [root@es1 nccl]# make PREFIX=$INSTALL_DIR install
Deep Learning Framework
Deep Learning Framework needs to be installed by user's privilege.
Big Data
Hadoop
INSTALL_DIR=/apps/hadoop/2.9.1 wget https://archive.apache.org/dist/hadoop/common/hadoop-2.9.1/hadoop-2.9.1.tar.gz sudo mkdir -p $INSTALL_DIR sudo tar xzf hadoop-2.9.1.tar.gz -C $INSTALL_DIR --strip=1 sudo chown -R root:root $INSTALL_DIR