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Commit 2ffcae4d authored by Orgis, Dr. Thomas's avatar Orgis, Dr. Thomas
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libstationresponse, behind the scenes fix for pyBDSF (broken numpy install)

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DP3.log 0 → 100644
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View file @ 2ffcae4d
RRZ: re-using existing module setup (RRZ_SW_INIT present)
module: unloaded env/system-gcc
module: loaded env/2019Q4-cuda-gcc-openmpi
Module for pkgsrc-devel 2019Q4 loaded.
module: loaded pythonversion/3
TODO: Ensure conistent use of one openblas variant (the one cblas and numpy use)
CASAcore already installed.
Python-CASAcore already installed.
Dysco already installed.
AOFlagger already installed.
IDG already installed.
Installing DP3...
Using existing sources.
-- The C compiler identification is GNU 8.3.0
-- The CXX compiler identification is GNU 8.3.0
-- Check for working C compiler: /sw/compiler/gcc-8.3.0/bin/gcc
-- Check for working C compiler: /sw/compiler/gcc-8.3.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /sw/compiler/gcc-8.3.0/bin/g++
-- Check for working CXX compiler: /sw/compiler/gcc-8.3.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- HDF5: Using hdf5 compiler wrapper to determine CXX configuration
-- Found HDF5: /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libhdf5_cpp.so;/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libhdf5.so;/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.5") found components: C CXX
-- Found CFITSIO: /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libcfitsio.so
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: BLAS_LIBRARIES-PLACEHOLDER-FOR-EMPTY-LIBRARIES
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Found HDF5: /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libhdf5_cpp.so;/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libhdf5.so;/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.5")
-- Found the following Casacore components:
-- ms: /dev/shm/thor-lofar/casacore/lib/libcasa_ms.so
-- fits: /dev/shm/thor-lofar/casacore/lib/libcasa_fits.so
-- scimath: /dev/shm/thor-lofar/casacore/lib/libcasa_scimath.so
-- measures: /dev/shm/thor-lofar/casacore/lib/libcasa_measures.so
-- scimath_f: /dev/shm/thor-lofar/casacore/lib/libcasa_scimath_f.so
-- tables: /dev/shm/thor-lofar/casacore/lib/libcasa_tables.so
-- casa: /dev/shm/thor-lofar/casacore/lib/libcasa_casa.so
CMake Warning (dev) at /dev/shm/thor-lofar/idg/share/idgapi/cmake/idgapi-config.cmake:16 (set):
implicitly converting 'LOCATION' to 'STRING' type.
Call Stack (most recent call first):
CMakeLists.txt:33 (find_package)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Image domain gridder API libraries found.
-- Found Python3: /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/bin/python3.6 (found version "3.6.9") found components: Interpreter Development
-- Found Boost: /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include (found version "1.71.0") found components: date_time filesystem python36 program_options system unit_test_framework
-- LOFAR beam library found.
-- Found LibXml2: /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libxml2.so (found version "2.9.10")
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.8")
-- Found PNG: /usr/lib/x86_64-linux-gnu/libpng.so (found version "1.6.37")
-- Found PkgConfig: /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/bin/pkg-config (found version "1.6.0")
-- Checking for module 'gtkmm-3.0>=3.0.0'
-- Found gtkmm-3.0, version 3.24.1
-- Checking for module 'sigc++-2.0'
-- Found sigc++-2.0, version 2.10.2
-- Found Armadillo: /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libarmadillo.so (found version "9.400.3")
-- Found PythonInterp: /sw/link/python3/bin/python (found version "3.6.9")
-- Build directory for Python extensions: /dev/shm/thor-lofar/DP3/build/lib/python3.6/site-packages
-- Installation directory for Python extensions: /dev/shm/thor-lofar/DP3/lib/python3.6/site-packages
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_Fortran_COMPILER
CMAKE_Fortran_FLAGS
-- Build files have been written to: /dev/shm/thor-lofar/DP3/build
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In file included from /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/boost/python/detail/is_xxx.hpp:8,
from /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/boost/python/detail/is_auto_ptr.hpp:9,
from /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/boost/python/detail/copy_ctor_mutates_rhs.hpp:8,
from /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/boost/python/detail/value_arg.hpp:7,
from /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/boost/python/object/forward.hpp:10,
from /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/boost/python/object/pointer_holder.hpp:16,
from /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/boost/python/to_python_indirect.hpp:10,
from /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/boost/python/converter/arg_to_python.hpp:10,
from /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/boost/python/call.hpp:15,
from /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/boost/python/object_core.hpp:14,
from /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/boost/python/args.hpp:22,
from /sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/boost/python.hpp:11,
from /dev/shm/thor-lofar/DP3/src/PythonDPPP/PythonStep.h:37,
from /dev/shm/thor-lofar/DP3/src/PythonDPPP/DPStepBase.h:25,
from /dev/shm/thor-lofar/DP3/src/PythonDPPP/PythonDPPP.cc:22:
/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/boost/python/detail/is_auto_ptr.hpp:17:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
BOOST_PYTHON_IS_XXX_DEF(auto_ptr, std::auto_ptr, 1)
^~~~~~~~
/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/boost/detail/is_xxx.hpp:20:4: note: in definition of macro ‘BOOST_DETAIL_IS_XXX_DEF’
qualified_name< BOOST_PP_ENUM_PARAMS_Z(1, nargs, T) > \
^~~~~~~~~~~~~~
/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/boost/python/detail/is_auto_ptr.hpp:17:1: note: in expansion of macro ‘BOOST_PYTHON_IS_XXX_DEF’
BOOST_PYTHON_IS_XXX_DEF(auto_ptr, std::auto_ptr, 1)
^~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/software/compiler/gcc-8.3.0/include/c++/8.3.0/memory:80,
from /dev/shm/thor-lofar/casacore/include/casacore/casa/Utilities/CountedPtr.h:32,
from /dev/shm/thor-lofar/casacore/include/casacore/casa/Arrays/ArrayBase.h:35,
from /dev/shm/thor-lofar/casacore/include/casacore/casa/Arrays/Array.h:35,
from /dev/shm/thor-lofar/casacore/include/casacore/casa/Arrays/Vector.h:33,
from /dev/shm/thor-lofar/DP3/src/PythonDPPP/../DPPP/DPBuffer.h:30,
from /dev/shm/thor-lofar/DP3/src/PythonDPPP/../DPPP/DPStep.h:30,
from /dev/shm/thor-lofar/DP3/src/PythonDPPP/../DPPP/DPInput.h:30,
from /dev/shm/thor-lofar/DP3/src/PythonDPPP/PythonStep.h:30,
from /dev/shm/thor-lofar/DP3/src/PythonDPPP/DPStepBase.h:25,
from /dev/shm/thor-lofar/DP3/src/PythonDPPP/PythonDPPP.cc:22:
/home/software/compiler/gcc-8.3.0/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
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[ 92%] Built target DPPP_OBJ
[ 94%] Built target dppp_testdyndppp
[ 96%] Built target IDGPredict
[ 98%] Built target DPPP
[100%] Built target _pythondppp
Install the project...
-- Install configuration: ""
-- Installing: /dev/shm/thor-lofar/DP3/bin/makesourcedb
-- Installing: /dev/shm/thor-lofar/DP3/bin/showsourcedb
-- Installing: /dev/shm/thor-lofar/DP3/bin/DPPP
-- Up-to-date: /dev/shm/thor-lofar/DP3/share/rfistrategies/LOFAR-LBA-default.rfis
-- Up-to-date: /dev/shm/thor-lofar/DP3/share/rfistrategies/LOFAR-HBA-default.rfis
-- Installing: /dev/shm/thor-lofar/DP3/lib/python3.6/site-packages/lofar/dppp/__init__.py
-- Installing: /dev/shm/thor-lofar/DP3/lib/python3.6/site-packages/lofar/pythondppp/_pythondppp.so
-- Installing: /dev/shm/thor-lofar/DP3/lib/python3.6/site-packages/lofar/pythondppp/__init__.py
Installed DP3.
WSClean already installed.
Installing pyBDSF.
Using existing sources.
look at /home/rznv039/lofar-work/pyBDSF-env.sh
build.log 0 → 100644
+ 92
− 0
View file @ 2ffcae4d
RRZ: re-using existing module setup (RRZ_SW_INIT present)
module: unloaded env/2019Q4-cuda-gcc-openmpi
Module for pkgsrc-devel 2019Q4 unloaded.
module: loaded env/2019Q4-cuda-gcc-openmpi
Module for pkgsrc-devel 2019Q4 loaded.
module: loaded pythonversion/3
TODO: Ensure conistent use of one openblas variant (the one cblas and numpy use)
CASAcore already installed.
Python-CASAcore already installed.
Dysco already installed.
AOFlagger already installed.
IDG already installed.
DP3 already installed.
WSClean already installed.
Installing pyBDSF.
Using existing sources.
running install
running bdist_egg
running egg_info
running build_src
build_src
building extension "bdsf._pytesselate" sources
f2py options: ['']
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/bdsf/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/bdsf' to include_dirs.
building extension "bdsf._cbdsm" sources
building extension "bdsf.nat.natgridmodule" sources
build_src: building npy-pkg config files
writing bdsf.egg-info/PKG-INFO
writing dependency_links to bdsf.egg-info/dependency_links.txt
writing requirements to bdsf.egg-info/requires.txt
writing top-level names to bdsf.egg-info/top_level.txt
writing manifest file 'bdsf.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
running mbuild
Building libminpack
Building libport3
dg7qts.f:331:22:
dg7qts.f:329:72:
DO 110 I = 2, P
2
dg7qts.f:331:22:
T = W(J) - W(I)
1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
dg7qts.f:368:22:
dg7qts.f:366:72:
DO 160 I = 2, P
2
dg7qts.f:368:22:
T = W(J) + W(I)
1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
customize UnixCCompiler
customize UnixCCompiler using BuildExt
customize UnixCCompiler
customize UnixCCompiler using BuildExt
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Found executable /home/software/compiler/gcc-8.3.0/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using BuildExt
building 'bdsf._pytesselate' extension
compiling C sources
C compiler: /sw/compiler/gcc-8.3.0/bin/gcc -DNDEBUG -march=ivybridge -O2 -fno-math-errno -ftree-vectorize -march=ivybridge -O2 -fno-math-errno -ftree-vectorize -I/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/include -I/sw/compiler/gcc-8.3.0/include -I/sw/compiler/cuda-10.2.89/include -I/usr/include -I/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include -I/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/ncurses -I/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/db4 -march=native -O3 -fno-math-errno -ftree-vectorize -fPIC
compile options: '-Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/bdsf -I/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/python3.6/site-packages/numpy/core/include -I/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/python3.6 -c'
compiling Fortran sources
Fortran f77 compiler: /home/software/compiler/gcc-8.3.0/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3
Fortran f90 compiler: /home/software/compiler/gcc-8.3.0/bin/gfortran -Wall -fno-second-underscore -fPIC -O3
Fortran fix compiler: /home/software/compiler/gcc-8.3.0/bin/gfortran -Wall -ffixed-form -fno-second-underscore -Wall -fno-second-underscore -fPIC -O3
compile options: '-Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/bdsf -I/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/python3.6/site-packages/numpy/core/include -I/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include/python3.6 -c'
gfortran:f77: src/fortran/pytess_simple.f
gfortran:f77: src/fortran/pytess_roundness.f
src/fortran/pytess_roundness.f:30:24:
roundfacold(i)=roundfac(i)
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
/home/software/compiler/gcc-8.3.0/bin/gfortran -Wall -shared -Wall -shared -shared -L/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib -Wl,-R/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib -L/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/lib/openmpi -Wl,-R/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/lib/openmpi -L/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/lib -Wl,-R/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/lib -L/sw/compiler/gcc-8.3.0/lib64 -Wl,-R/sw/compiler/gcc-8.3.0/lib64 -L/sw/compiler/gcc-8.3.0/lib -Wl,-R/sw/compiler/gcc-8.3.0/lib -L/sw/compiler/cuda-10.2.89/lib64 -Wl,-R/sw/compiler/cuda-10.2.89/lib64 -lgsl -lcblas -lopenblas_openmp -Wl,--as-needed build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/bdsf/_pytesselatemodule.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/bdsf/fortranobject.o build/temp.linux-x86_64-3.6/src/fortran/pytess_simple.o build/temp.linux-x86_64-3.6/src/fortran/pytess_roundness.o -L/sw/compiler/gcc-8.3.0/lib64/../lib64 -L/sw/compiler/gcc-8.3.0/lib64/../lib64 -L/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib -lpython3.6 -lgfortran -o build/lib.linux-x86_64-3.6/bdsf/_pytesselate.so
gfortran: error: : No such file or directory
gfortran: error: : No such file or directory
error: Command "/home/software/compiler/gcc-8.3.0/bin/gfortran -Wall -shared -Wall -shared -shared -L/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib -Wl,-R/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib -L/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/lib/openmpi -Wl,-R/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/lib/openmpi -L/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/lib -Wl,-R/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/lib -L/sw/compiler/gcc-8.3.0/lib64 -Wl,-R/sw/compiler/gcc-8.3.0/lib64 -L/sw/compiler/gcc-8.3.0/lib -Wl,-R/sw/compiler/gcc-8.3.0/lib -L/sw/compiler/cuda-10.2.89/lib64 -Wl,-R/sw/compiler/cuda-10.2.89/lib64 -lgsl -lcblas -lopenblas_openmp -Wl,--as-needed build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/bdsf/_pytesselatemodule.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/bdsf/fortranobject.o build/temp.linux-x86_64-3.6/src/fortran/pytess_simple.o build/temp.linux-x86_64-3.6/src/fortran/pytess_roundness.o -L/sw/compiler/gcc-8.3.0/lib64/../lib64 -L/sw/compiler/gcc-8.3.0/lib64/../lib64 -L/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib -lpython3.6 -lgfortran -o build/lib.linux-x86_64-3.6/bdsf/_pytesselate.so" failed with exit status 1
build_lofar_cepH.sh
+ 3
− 4
View file @ 2ffcae4d
......@@ -21,8 +21,6 @@ INSTALLDIR=${1:-$HOME/opt/lofar_200318}
# This takes whatever python is linked to python3.
PYTHON_VERSION=$(python3 --version | cut -f 2 -d ' ' | cut -f 1,2 -d .)
PYTHON_VERSION_NODOT=$(echo $PYTHON_VERSION|tr -d .)
cmake=`which cmake`
make=`which make`
export CC=`which gcc`
export CXX=`which g++`
# ThOr: Fortran is at least checked for by some builds.
......@@ -408,6 +406,7 @@ if [ ! -e $prefix/.done ]; then
-DIDGAPI_INCLUDE_DIRS:PATH=$INSTALLDIR/idg/include \
-DIDGAPI_LIBRARIES:PATH=$INSTALLDIR/idg/lib/libidg-api.so \
-DLOFAR_STATION_RESPONSE_DIR:PATH=$INSTALLDIR/LOFARBeam/include \
-DLOFAR_STATION_RESPONSE_LIB=$INSTALLDIR/LOFARBeam/lib/libstationresponse.so \
-DAOFLAGGER_INCLUDE_DIR=$INSTALLDIR/aoflagger/include \
-DAOFLAGGER_LIB=$INSTALLDIR/aoflagger/lib/libaoflagger.so \
../src &&
......@@ -489,9 +488,9 @@ if [ ! -e $prefix/.done ]; then
touch $prefix/.done
else
echo pyBDSF already installed.
fi
fi || exit 1
exit
exit # Did not get to lsmtool yet.
if [ ! -d $INSTALLDIR/lsmtool ]; then
echo Installing LSMTool.
......
download 0 → 100644
+ 0
− 0
View file @ 2ffcae4d
File added
pyBDSF-env.sh 0 → 100644
+ 93
− 0
View file @ 2ffcae4d
cd /dev/shm/thor-lofar/pyBDSF/src
declare -x AOFLAGGER_VERSION="v2.14.0"
declare -x BOOST_DOT_VERSION="1.67.0"
declare -x BOOST_VERSION="1_67_0"
declare -x CASACORE_VERSION="latest"
declare -x CC="/sw/compiler/gcc-8.3.0/bin/gcc"
declare -x CFITSIO_VERSION="3.47"
declare -x CFLAGS="-march=native -O3 -fno-math-errno -ftree-vectorize"
declare -x CPATH="/dev/shm/thor-lofar//DP3/include:/dev/shm/thor-lofar//aoflagger/include:/dev/shm/thor-lofar//LOFARBeam/include:/dev/shm/thor-lofar//idg/include:/dev/shm/thor-lofar//casacore/include:/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include:/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/include:/sw/compiler/gcc-8.3.0/include:/sw/compiler/cuda-10.2.89/include"
declare -x CPATH_modshare="/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include:1:/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/include:1:/sw/compiler/gcc-8.3.0/include:1:/sw/compiler/cuda-10.2.89/include:1"
declare -x CUDA_DIR="/sw/compiler/cuda-10.2.89"
declare -x CUDA_HOME="/sw/compiler/cuda-10.2.89"
declare -x CUDA_PATH="/sw/compiler/cuda-10.2.89"
declare -x CXX="/sw/compiler/gcc-8.3.0/bin/g++"
declare -x CXXFLAGS="-D_GLIB_USE_CXX_ABI=1 -DBOOST_NO_CXX11_SCOPED_ENUMS -march=native -O3 -fno-math-errno -ftree-vectorize"
declare -x C_INCLUDE_PATH_modshare="/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include:1:/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/include:1:/sw/compiler/gcc-8.3.0/include:1:/sw/compiler/cuda-10.2.89/include:1"
declare -x DYSCO_VERSION="v1.2.0"
declare -x FC="/sw/compiler/gcc-8.3.0/bin/gfortran"
declare -x FCFLAGS="-march=native -O3 -fno-math-errno -ftree-vectorize"
declare -x FFTW_VERSION="3.3.8"
declare -x HDF5_VERSION="1.8.21"
declare -x HOME="/home/rznv039"
declare -x INCLUDE_modshare="/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/include:1"
declare -x INFOPATH="/sw/compiler/gcc-8.3.0/share/info:/usr/share/info"
declare -x INFOPATH_modshare="/sw/compiler/gcc-8.3.0/share/info:1:/usr/share/info:1"
declare -x J="64"
declare -x LANG="en_US.UTF-8"
declare -x LANGUAGE="en_US:en"
declare -x LC_ADDRESS="de_DE.UTF-8"
declare -x LC_IDENTIFICATION="de_DE.UTF-8"
declare -x LC_MEASUREMENT="de_DE.UTF-8"
declare -x LC_MONETARY="de_DE.UTF-8"
declare -x LC_NAME="de_DE.UTF-8"
declare -x LC_NUMERIC="de_DE.UTF-8"
declare -x LC_PAPER="de_DE.UTF-8"
declare -x LC_TELEPHONE="de_DE.UTF-8"
declare -x LC_TIME="de_DE.UTF-8"
declare -x LDFLAGS="-lgsl -lcblas -lopenblas_openmp -Wl,--as-needed"
declare -x LD_RUN_PATH="/dev/shm/thor-lofar//DP3/lib:/dev/shm/thor-lofar//aoflagger/lib:/dev/shm/thor-lofar//LOFARBeam/lib:/dev/shm/thor-lofar//idg/lib:/dev/shm/thor-lofar//casacore/lib:/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib:/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/lib/openmpi:/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/lib:/sw/compiler/gcc-8.3.0/lib64:/sw/compiler/gcc-8.3.0/lib:/sw/compiler/cuda-10.2.89/lib64"
declare -x LD_RUN_PATH_modshare="/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/lib:1:/sw/compiler/cuda-10.2.89/lib64:1:/sw/compiler/gcc-8.3.0/lib:1:/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib:1:/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/lib/openmpi:1:/sw/compiler/gcc-8.3.0/lib64:1"
declare -x LESSCLOSE="/usr/bin/lesspipe %s %s"
declare -x LESSOPEN="| /usr/bin/lesspipe %s"
declare -x LIBRARY_PATH="/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib:/sw/compiler/gcc-8.3.0/lib64:/sw/compiler/gcc-8.3.0/lib:/sw/compiler/cuda-10.2.89/lib64"
declare -x LIBRARY_PATH_modshare="/sw/compiler/cuda-10.2.89/lib64:1:/sw/compiler/gcc-8.3.0/lib:1:/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib:1:/sw/compiler/gcc-8.3.0/lib64:1"
declare -x LOADEDMODULES="site/lgc:/sw/CORE/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4:env/2019Q4-cuda-gcc-openmpi:pythonversion/3"
declare -x LOADEDMODULES_modshare="/sw/CORE/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4:1:pythonversion/3:1:env/2019Q4-cuda-gcc-openmpi:1:site/lgc:1"
declare -x LOGNAME="rznv039"
declare -x LS_COLORS="rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:"
declare -x MAIL="/var/mail/rznv039"
declare -x MANPATH="/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/man:/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/gnu/man:/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/share/man:/sw/compiler/gcc-8.3.0/share/man:/sw/compiler/cuda-10.2.89/doc/man:/sw/rrz/share/man:/sw/modules/man:/usr/share/man"
declare -x MANPATH_modshare="/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/man:1:/sw/compiler/gcc-8.3.0/share/man:1:/sw/compiler/cuda-10.2.89/doc/man:1:/sw/modules/man:1:/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/gnu/man:1:/usr/share/man:1:/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/share/man:1:/sw/rrz/share/man:1"
declare -x MODULEPATH="/sw/LIB/2019Q4-cuda-gcc-openmpi:/home/software/modulefiles/DEVELOPMENT:/home/software/modulefiles/TOOLS:/sw/BASE:/sw/TOOL:/sw/APP"
declare -x MODULEPATH_modshare="/sw/LIB/2019Q4-cuda-gcc-openmpi:1:/home/software/modulefiles/DEVELOPMENT:1:/sw/APP:1:/home/software/modulefiles/TOOLS:1:/sw/TOOL:1:/sw/BASE:1"
declare -x MODULESHOME="/sw/modules/tcl"
declare -x OLDPWD="/dev/shm/thor-lofar/pyBDSF"
declare -x PATH="/dev/shm/thor-lofar//DP3/bin:/dev/shm/thor-lofar//aoflagger/bin:/dev/shm/thor-lofar//LOFARBeam/bin:/dev/shm/thor-lofar//idg/bin:/dev/shm/thor-lofar//casacore/bin:/sw/link/python3/bin:/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/bin:/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/gnu/bin:/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/bin:/sw/compiler/gcc-8.3.0/bin:/sw/compiler/cuda-10.2.89/bin:/home/rznv039/bin:/sw/rrz/bin:/sw/tools/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games"
declare -x PATH_modshare="/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/bin:1:/usr/bin:1:/sw/link/python3/bin:1:/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/gnu/bin:1:/sw/compiler/gcc-8.3.0/bin:1:/usr/local/bin:1:/home/rznv039/bin:999999999:/bin:1:/sw/tools/bin:1:/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/bin:1:/sbin:1:/sw/compiler/cuda-10.2.89/bin:1:/usr/sbin:1:/usr/games:1:/sw/rrz/bin:1:/usr/local/sbin:1:/usr/local/cuda/bin:1:/usr/local/games:1"
declare -x PERL5LIB="/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/perl/site_perl"
declare -x PERL5LIB_modshare="/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/perl/site_perl:1"
declare -x PKG_CONFIG_PATH="/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/share/pkgconfig:/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/pkgconfig:/lib/x86_64-linux-gnu/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/lib/pkgconfig:/usr/share/pkgconfig"
declare -x PKG_CONFIG_PATH_modshare="/usr/lib/x86_64-linux-gnu/pkgconfig:1:/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/share/pkgconfig:1:/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/pkgconfig:1:/usr/share/pkgconfig:1:/usr/lib/pkgconfig:1:/lib/x86_64-linux-gnu/pkgconfig:1"
declare -x PWD="/dev/shm/thor-lofar/pyBDSF/src"
declare -x PYBDSF_VERSION="v1.8.12"
declare -x PYTHONPATH="/dev/shm/thor-lofar//pyBDSF/lib/python3.6/site-packages:/dev/shm/thor-lofar//python-casacore/lib/python3.6/site-packages:"
declare -x PYTHON_CASACORE_VERSION="3.1.1"
declare -x QT_QPA_PLATFORMTHEME="appmenu-qt5"
declare -x RRZ_LOCAL_TMPDIR="/tmp/rznv039"
declare -x RRZ_PKG_PREFIX="/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4"
declare -x RRZ_SW_BINPREFIX="/sw"
declare -x RRZ_SW_INIT="1"
declare -x RRZ_SW_PREFIX="/sw"
declare -x RRZ_TMPDIR="/tmp"
declare -x SHELL="/bin/bash"
declare -x SHLVL="2"
declare -x SSH_CLIENT="192.168.79.62 50140 22"
declare -x SSH_CONNECTION="192.168.79.62 50140 192.168.79.35 22"
declare -x SSH_TTY="/dev/pts/3"
declare -x TERM="screen.xterm-256color"
declare -x TMPDIR="/tmp"
declare -x USER="rznv039"
declare -x WCSLIB_VERSION="latest"
declare -x WSCLEAN_VERSION="latest"
declare -x XDG_CONFIG_DIRS="/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/etc/xdg"
declare -x XDG_CONFIG_DIRS_modshare="/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/etc/xdg:1"
declare -x XDG_DATA_DIRS="/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/share"
declare -x XDG_DATA_DIRS_modshare="/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/share:1"
declare -x XDG_RUNTIME_DIR="/run/user/6783"
declare -x XDG_SESSION_ID="28620"
declare -x _LMFILES_="/sw/BASE/site/lgc:/sw/CORE/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4:/sw/BASE/env/2019Q4-cuda-gcc-openmpi:/sw/TOOL/pythonversion/3"
declare -x _LMFILES__modshare="/sw/BASE/env/2019Q4-cuda-gcc-openmpi:1:/sw/BASE/site/lgc:1:/sw/CORE/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4:1:/sw/TOOL/pythonversion/3:1"
export LDFLAGS='-L/dev/shm/thor-lofar//DP3/lib -Wl,-R/dev/shm/thor-lofar//DP3/lib -L/dev/shm/thor-lofar//aoflagger/lib -Wl,-R/dev/shm/thor-lofar//aoflagger/lib -L/dev/shm/thor-lofar//LOFARBeam/lib -Wl,-R/dev/shm/thor-lofar//LOFARBeam/lib -L/dev/shm/thor-lofar//idg/lib -Wl,-R/dev/shm/thor-lofar//idg/lib -L/dev/shm/thor-lofar//casacore/lib -Wl,-R/dev/shm/thor-lofar//casacore/lib -L/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib -Wl,-R/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib -L/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/lib/openmpi -Wl,-R/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/lib/openmpi -L/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/lib -Wl,-R/sw/env/cuda-10.2.89_gcc-8.3.0/openmpi/4.0.2/lib -L/sw/compiler/gcc-8.3.0/lib64 -Wl,-R/sw/compiler/gcc-8.3.0/lib64 -L/sw/compiler/gcc-8.3.0/lib -Wl,-R/sw/compiler/gcc-8.3.0/lib -L/sw/compiler/cuda-10.2.89/lib64 -Wl,-R/sw/compiler/cuda-10.2.89/lib64 -lgsl -lcblas -lopenblas_openmp -Wl,--as-needed'
export NPY_DISTUTILS_APPEND_FLAGS=1
echo run: python setup.py install --prefix=/dev/shm/thor-lofar//pyBDSF
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int main(){ return 0; }
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program hello
write(*,*) 'hello'
end program
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. /sw/profile/init.sh
module switch env env/2019Q4-cuda-gcc-openmpi
export INSTALL_PREFIX=/dev/shm/thor-lofar1
export CMAKE="$(which cmake)"
export CC="$(which gcc)"
export CXX="$(which g++)"
export FC="$(which gfortran)"
export CFLAGS="-march=native -O3 -fno-math-errno -ftree-vectorize"
export FCFLAGS="$CFLAGS"
export CXXFLAGS="-D_GLIB_USE_CXX_ABI=1 -DBOOST_NO_CXX11_SCOPED_ENUMS -march=native -O3 -fno-math-errno -ftree-vectorize"
# ThOr: Those should not be global, should they? Let's add -Wl,--as-needed,
# so that unnecessary libraries are dropped from the build.
export LDFLAGS="-lgsl -lcblas -Wl,--as-needed"
#export CMAKE_RPATH="-DCMAKE_BUILD_RPATH=$LD_RUN_PATH -DCMAKE_INSTALL_RPATH=$LD_RUN_PATH"
#export CMAKE_RPATH="-DCMAKE_LIBRARY_PATH=$LD_RUN_PATH"
LD_RUN_PATH=$INSTALL_PREFIX/casacore/lib:$LD_RUN_PATH
CMAKE_RPATH="-DCMAKE_SKIP_RPATH=ON"
run_cmake()
{
$CMAKE \
-DCMAKE_C_COMPILER="$CC" \
-DCMAKE_CXX_COMPILER="$CXX" \
-DCMAKE_Fortran_COMPILER="$FC" \
-DCMAKE_C_FLAGS="$CFLAGS" \
-DCMAKE_CXX_FLAGS="$CXXFLAGS" \
-DCMAKE_Fortran_FLAGS="$FCFLAGS" \
$CMAKE_RPATH \
"$@"
}
set -e
cd $INSTALL_PREFIX/casacore
rm -rf build
mkdir build
cd build
run_cmake \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_INSTALL_PREFIX=$INSTALL_PREFIX/casacore \
-DDATA_DIR:PATH=$INSTALL_PREFIX/casacore/data \
-DUSE_OPENMP=True \
-DUSE_FFTW3=True \
-DUSE_HDF5=True \
-DBUILD_PYTHON:BOOL=False \
-DBUILD_PYTHON3:BOOL=True \
../src
make -j32
make install
exit
-DBoost_LIBRARY_DIR_RELEASE:PATH=/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib
-DBoost_PYTHON_LIBRARY_RELEASE:FILEPATH=/sw/env/cuda-10.2.89_gcc-8.3.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libboost_python36.so
-DBOOST_PYTHON3_LIBRARY_NAME:STRING=python
-DENABLE_TABLELOCKING=OFF
../src/
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