T64 on Amos
Glen Hansen edited this page Nov 8, 2014
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1 revision
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AMOS does not, in general, support file transfer from arbitrary websites.
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On a different machine (not AMOS), download the TPLs
mkdir tpls cd tpls wget http://zlib.net/zlib-1.2.8.tar.gz wget http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.11/src/hdf5-1.8.11.tar.gz wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.2.tar.gz wget http://sourceforge.net/projects/boost/files/boost/1.55.0/boost_1_55_0.tar.gz wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz wget http://www.netlib.org/lapack/lapack-3.5.0.tgz wget http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz -
scp the TPL tarballs to AMOS
scp -r tpls cci:~/scratch/
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On AMOS q,
module load cmake/3.0.0 module load gnu-4.7.2
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Version 1.2.8
cd scratch/tpls tar -xzvf zlib-1.2.8.tar.gz cd zlib-1.2.8 CC=mpicc CFLAGS=-O3 ./configure --64 --static \ --prefix=/gpfs/u/home/PGES/PGESgnzw/scratch/tpls make make install
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Version 1.8.11
cd ~/scratch/tpls tar -xzvf hdf5-1.8.11.tar.gz cd hdf5-1.8.11 ./configure CC=mpicc FC=mpif90 CXX=mpicxx \ CXXFLAGS="-O3" CFLAGS="-O3" FCFLAGS="-O3" \ --enable-parallel --enable-shared=no \ --with-zlib=/gpfs/u/home/PGES/PGESgnzw/scratch/tpls \ --prefix=/gpfs/u/home/PGES/PGESgnzw/scratch/tpls make -j 8 make install
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Version 4.3.2
cd ~/scratch/tpls cd netcdf-4.3.2 -
Edit the file
include/netcdf.h. Make the following edits near line 228:#define NC_MAX_DIMS 65536 /* max dimensions per file */ #define NC_MAX_ATTRS 8192 #define NC_MAX_VARS 524288 /* max variables per file */ #define NC_MAX_NAME 256 #define NC_MAX_VAR_DIMS 8 /* max per variable dimensions */ -
Configure and build
mkdir build cd build export myprefix=/gpfs/u/home/PGES/PGESgnzw/scratch/tpls cmake \ -DCMAKE_C_COMPILER=mpicc \ -DCMAKE_C_FLAGS="-I${myprefix}/include -O2" \ -DCMAKE_EXE_LINKER_FLAGS="-L${myprefix}/lib -O2" \ -DCMAKE_INSTALL_PREFIX=${myprefix} \ -DENABLE_DAP=OFF -DBUILD_SHARED_LIBS=OFF -DENABLE_FSYNC=OFF -DENABLE_CDMREMOTE=OFF \ -DENABLE_DOXYGEN=OFF -DENABLE_NETCDF_4=ON -DCMAKE_BUILD_TYPE=RELEASE -DENABLE_EXAMPLES=OFF \ -DENABLE_TESTS=OFF -DCMAKE_SKIP_INSTALL_RPATH=ON \ -DZLIB_INCLUDE_DIRS=${myprefix}/include \ -DZLIB_LIBRARY=${myprefix}/lib/libz.a \ -DBUILD_UTILITIES=OFF \ .. make -j 8 make install
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Version 1.53.0
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Build boost with the commands
cd ~/scratch/tpls tar -xzvf boost_1_55_0.tar.gz cd boost_1_55_0 echo "using gcc : 4.7.2 : /bgsys/drivers/ppcfloor/gnu-linux-4.7.2/bin/powerpc64-bgq-linux-g++ ;" \ >> ./tools/build/v2/user-config.jam echo "using mpi : /bgsys/drivers/ppcfloor/comm/gcc/bin/mpicxx ;" \ >> ./tools/build/v2/user-config.jam ./bootstrap.sh \ --with-libraries=signals,regex,filesystem,system,mpi,serialization,thread,program_options,exception \ --prefix=/gpfs/u/home/PGES/PGESgnzw/scratch/tpls ./b2 -j 8 ./b2 -j 8 install
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Version 4.0.3
cd ~/scratch/tpls tar -xzvf parmetis-4.0.3.tar.gz cd parmetis-4.0.3/ -
Edit 'metis.h' to use 'IDXTYPEWIDTH' of 64
vi metis/include/metis.h #define IDXTYPEWIDTH 64 -
Build using CMake
cd build export metis=/gpfs/u/home/PGES/PGESgnzw/scratch/tpls/parmetis-4.0.3/metis cmake \ -DCMAKE_INSTALL_PREFIX=/gpfs/u/home/PGES/PGESgnzw/scratch/tpls \ -DMETIS_PATH=$metis \ -DGKLIB_PATH=$metis/GKlib \ -DCMAKE_C_COMPILER=mpicc \ -DCMAKE_CXX_COMPILER=mpicxx \ .. make -j 8 make install cp libmetis/libmetis.a /gpfs/u/home/PGES/PGESgnzw/scratch/tpls/lib cp $metis/include/metis.h /gpfs/u/home/PGES/PGESgnzw/scratch/tpls/include
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Version 3.5.0
cd ~/scratch/tpls tar -xzvf lapack-3.5.0.tgz cd lapack-3.5.0 mkdir build cd build ccmake .. edit CMAKE_INSTALL_PREFIX=/gpfs/u/home/PGES/PGESgnzw/scratch/tpls c g make -j 4 make install
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Version 4.3
cd ~/scratch/tpls tar -xzvf superlu_4.3.tar.gz cd SuperLU_4.3/ mkdir /gpfs/u/home/PGES/PGESgnzw/scratch/tpls/superlu mkdir /gpfs/u/home/PGES/PGESgnzw/scratch/tpls/superlu/include mkdir /gpfs/u/home/PGES/PGESgnzw/scratch/tpls/superlu/lib -
Edit make.inc for your machine and environment
PLAT = _linux SuperLUroot = /gpfs/u/home/PGES/PGESgnzw/scratch/tpls/superlu SUPERLULIB = $(SuperLUroot)/lib/libsuperlu_4.3.a TMGLIB = libtmglib.a BLASDEF = -DUSE_VENDOR_BLAS BLASLIB = -L/gpfs/u/home/PGES/PGESgnzw/scratch/tpls/lib/libblas.a LIBS = $(SUPERLULIB) $(BLASLIB) ARCH = ar ARCHFLAGS = cr RANLIB = ranlib CC = mpicc CFLAGS = -DPRNTlevel=0 -O3 NOOPTS = FORTRAN = mpif90 FFLAGS = -O3 LOADER = $(CC) LOADOPTS = CDEFS = -DNoChange MATLAB = -
Build SuperLU
make cd SRC cp *.h /gpfs/u/home/PGES/PGESgnzw/scratch/tpls/superlu/include rm /gpfs/u/home/PGES/PGESgnzw/scratch/tpls/superlu/lib/libsuperlu_4.3.a dlamch.o slamch.o
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do-configure script
#!/bin/sh export TRILINOS_HOME=/gpfs/u/home/PGES/PGESgnzw/scratch/trilinos/src BUILD_DIR=`pwd` INSTALL_DIR=/gpfs/u/home/PGES/PGESgnzw/scratch/trilinos/install MPI_BASE_DIR=/bgsys/drivers/ppcfloor/comm/gcc TPL_DIR=/gpfs/u/home/PGES/PGESgnzw/scratch/tpls BOOST_DIR=$TPL_DIR ZLIB_DIR=$TPL_DIR SUPERLU_DIR=$TPL_DIR/superlu NETCDF=$TPL_DIR HDFDIR=$TPL_DIR PARMETISDIR=$TPL_DIR export BOOST_ROOT=$BOOST_DIR EXTRA_ARGS=$@ cmake \ -D Trilinos_EXTRA_REPOSITORIES:STRING=SCOREC \ -D Trilinos_CONFIGURE_OPTIONS_FILE:FILEPATH=$TRILINOS_HOME/sampleScripts/AlbanySettings.cmake \ -D CMAKE_BUILD_TYPE:STRING=NONE \ \ -D CMAKE_C_FLAGS:STRING="-O2" \ -D CMAKE_CXX_FLAGS:STRING="-O2" \ \ -D TPL_ENABLE_MPI:BOOL=ON \ -D MPI_BASE_DIR:PATH=$MPI_BASE_DIR \ -D Trilinos_EXTRA_LINK_FLAGS:STRING="-ldl" \ \ -D TPL_ENABLE_Matio:BOOL=OFF \ -D SEACAS_ENABLE_SEACASSVDI:BOOL=OFF \ -D Trilinos_ENABLE_SEACASFastq:BOOL=OFF \ -D Trilinos_ENABLE_SEACASBlot:BOOL=OFF \ -D Trilinos_ENABLE_SEACASPLT:BOOL=OFF \ -D TPL_ENABLE_X11:BOOL=OFF \ \ -D CMAKE_VERBOSE_MAKEFILE:BOOL=OFF \ -D Trilinos_VERBOSE_CONFIGURE:BOOL=OFF \ \ -D Boost_INCLUDE_DIRS:PATH=$BOOST_DIR/include \ -D BoostAlbLib_INCLUDE_DIRS:PATH=$BOOST_DIR/include \ -D Boost_LIBRARY_DIRS:PATH=$BOOST_DIR/lib \ -D BoostAlbLib_LIBRARY_DIRS:PATH=$BOOST_DIR/lib \ \ -D TPL_ENABLE_Netcdf:STRING=ON \ -D Netcdf_INCLUDE_DIRS:PATH="${NETCDF}/include" \ -D Netcdf_LIBRARY_DIRS:PATH="${NETCDF}/lib64" \ -D TPL_Netcdf_LIBRARIES:STRING="$NETCDF/lib64/libnetcdf.a;$HDFDIR/lib/libhdf5_hl.a;$HDFDIR/lib/libhdf5.a;$ \ -D TPL_ENABLE_HDF5:STRING=ON \ -D HDF5_INCLUDE_DIRS:PATH="${HDFDIR}/include" \ -D HDF5_LIBRARY_DIRS:PATH="${HDFDIR}/lib" \ -D TPL_HDF5_LIBRARIES:STRING="$HDFDIR/lib/libhdf5.a;$ZLIB_DIR/lib/libz.a" \ \ -D TPL_ENABLE_Zlib:STRING=ON \ -D Zlib_INCLUDE_DIRS:PATH="${ZLIB_DIR}/include" \ -D Zlib_LIBRARY_DIRS:PATH="${ZLIB_DIR}/lib" \ \ -D TPL_ENABLE_ParMETIS:STRING=ON \ -D ParMETIS_INCLUDE_DIRS:PATH="${PARMETISDIR}/include" \ -D ParMETIS_LIBRARY_DIRS:PATH="${PARMETISDIR}/lib" \ \ -D Trilinos_ENABLE_SCOREC:BOOL=ON \ -D SCOREC_DISABLE_STRONG_WARNINGS:BOOL=ON \ \ -D Trilinos_ENABLE_ThyraTpetraAdapters:BOOL=ON \ -D Trilinos_ENABLE_Ifpack2:BOOL=ON \ -D Trilinos_ENABLE_Amesos2:BOOL=ON \ -D Trilinos_ENABLE_MueLu:BOOL=ON \ \ -D Zoltan_ENABLE_ULONG_IDS:BOOL=ON \ \ -D Teuchos_ENABLE_COMPLEX:BOOL=OFF \ \ -D TPL_ENABLE_SuperLU:STRING=ON \ -D SuperLU_INCLUDE_DIRS:PATH="${SUPERLU_DIR}/include" \ -D SuperLU_LIBRARY_DIRS:PATH="${SUPERLU_DIR}/lib" \ \ -D Trilinos_ASSERT_MISSING_PACKAGES:BOOL=OFF \ -D CMAKE_INSTALL_PREFIX:PATH=${INSTALL_DIR} \ \ -D TPL_ENABLE_BLAS:STRING=ON \ -D TPL_BLAS_LIBRARIES:FILEPATH="${TPL_DIR}/lib/libblas.a" \ \ -D TPL_ENABLE_LAPACK:STRING=ON \ -D TPL_LAPACK_LIBRARIES:FILEPATH="${TPL_DIR}/lib/liblapack.a" \ \ $EXTRA_ARGS \ ${TRILINOS_HOME} -
Build Trilinos
make -j 4 make install
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CMake configure script:
#!/bin/sh export TRILINOS_INSTALL_DIR=/gpfs/u/home/PGES/PGESgnzw/scratch/trilinos/install cmake \ -D ALBANY_TRILINOS_DIR:FILEPATH="$TRILINOS_INSTALL_DIR" \ -D ENABLE_LCM:BOOL=ON \ -D ENABLE_QCAD:BOOL=OFF \ -D ENABLE_LCM_SPECULATIVE:BOOL=OFF \ -D ENABLE_LAME:BOOL=OFF \ -D CMAKE_VERBOSE_MAKEFILE:BOOL=OFF \ -D ENABLE_DEBUGGING:BOOL=OFF \ -D ENABLE_CHECK_FPE:BOOL=OFF \ -D ENABLE_HYDRIDE:BOOL=OFF \ -D ENABLE_SCOREC:BOOL=ON \ -D ENABLE_SEE:BOOL=OFF \ -D ENABLE_FELIX:BOOL=OFF \ -D ENABLE_MOR:BOOL=OFF \ -D ENABLE_ALBANY_CI:BOOL=OFF \ -D ENABLE_ASCR:BOOL=OFF \ -D ENABLE_SG_MP:BOOL=OFF \ -D ENABLE_64BIT_INT:BOOL=ON \ -D ENABLE_ALBANY_EPETRA_EXE:BOOL=OFF \ ../ -
Build Albany
make -j 4 make install