A comprehensive and full-featured computational physics suite for boundary-element analysis of electromagnetic scattering, fluctuation-induced phenomena (Casimir forces and radiative heat transfer), nanophotonics, RF device engineering, electrostatics, and more. Includes a core library with C++ and python APIs as well as many command-line applications.
I've been trying to install scuff-em for MacOS Catalina following the instructions in the documentation, linked here. However, I've been having no luck with this and have tried various things, which I'll outline below. As far as I understand from #154, these instructions work for High Sierra.
I'll outline my process and perhaps there is some update to these steps that will allow things to work on Catalina. It's possible I'm doing something wrong here, so please let me know if that's the case. I'm a bit new to this.
I start with a freshly cloned repo after doing all of the setup / external package installation steps outlined in the docs. I'm running this in a conda environment. At the bottom of this post, I've pasted the output of running sh autogen.sh --prefix=${HOME}/scuff-em-installation after setting the environment variables and specifying --without-hdf5 in the config file. As far as I can tell, there are no errors.
Running make install -j 4 also seems to work without any issue.
I then run into errors in the examples. For DiffractionPatterns, documented here I get the following errors when trying to use scuff-analyze in the RenameMesh function:
dyld: Symbol not found: __ZN5scuff11RWGGeometry12CheckGTCListENSt3__16vectorIPNS_9GTComplexENS1_9allocatorIS4_EEEE
Similar Symbol not found errors occur when trying scuff-scatter on other examples.
I've also tried compiling gcc-8 and g++-8 with no luck. Running autogen.sh without setting any environment variables also does not work.
I'd be extremely grateful for any help or pointing in the right direction. Thank you!
Output from autogen.sh:
autoreconf: Entering directory `.'
autoreconf: configure.ac: not using Gettext
autoreconf: running: aclocal --force -I m4
autoreconf: configure.ac: tracing
autoreconf: running: glibtoolize --force
glibtoolize: putting auxiliary files in '.'.
glibtoolize: linking file './ltmain.sh'
glibtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
glibtoolize: linking file 'm4/libtool.m4'
glibtoolize: linking file 'm4/ltoptions.m4'
glibtoolize: linking file 'm4/ltsugar.m4'
glibtoolize: linking file 'm4/ltversion.m4'
glibtoolize: linking file 'm4/lt~obsolete.m4'
autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoconf --force
autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoheader --force
autoreconf: running: automake --add-missing --force-missing
configure.ac:10: installing './compile'
configure.ac:10: installing './config.guess'
configure.ac:10: installing './config.sub'
configure.ac:9: installing './install-sh'
configure.ac:9: installing './missing'
Makefile.am: installing './INSTALL'
applications/scuff-analyze/Makefile.am: installing './depcomp'
libs/python/Makefile.am:11: installing './py-compile'
parallel-tests: installing './test-driver'
autoreconf: Leaving directory `.'
autoreconf: Entering directory `.'
autoreconf: configure.ac: not using Gettext
autoreconf: running: aclocal --force -I m4
autoreconf: configure.ac: tracing
autoreconf: running: glibtoolize --force
glibtoolize: putting auxiliary files in '.'.
glibtoolize: linking file './ltmain.sh'
glibtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
glibtoolize: linking file 'm4/libtool.m4'
glibtoolize: linking file 'm4/ltoptions.m4'
glibtoolize: linking file 'm4/ltsugar.m4'
glibtoolize: linking file 'm4/ltversion.m4'
glibtoolize: linking file 'm4/lt~obsolete.m4'
autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoconf --force
autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoheader --force
autoreconf: running: automake --add-missing --force-missing
configure.ac:10: installing './compile'
configure.ac:9: installing './missing'
applications/scuff-analyze/Makefile.am: installing './depcomp'
autoreconf: Leaving directory `.'
autoreconf: Entering directory `.'
autoreconf: configure.ac: not using Gettext
autoreconf: running: aclocal --force -I m4
autoreconf: configure.ac: tracing
autoreconf: running: glibtoolize --force
glibtoolize: putting auxiliary files in '.'.
glibtoolize: linking file './ltmain.sh'
glibtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
glibtoolize: linking file 'm4/libtool.m4'
glibtoolize: linking file 'm4/ltoptions.m4'
glibtoolize: linking file 'm4/ltsugar.m4'
glibtoolize: linking file 'm4/ltversion.m4'
glibtoolize: linking file 'm4/lt~obsolete.m4'
autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoconf --force
autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoheader --force
autoreconf: running: automake --add-missing --force-missing
configure.ac:10: installing './compile'
configure.ac:9: installing './missing'
applications/scuff-analyze/Makefile.am: installing './depcomp'
autoreconf: Leaving directory `.'
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... x86_64-apple-darwin19.0.0
checking host system type... x86_64-apple-darwin19.0.0
checking how to print strings... printf
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc-7 -fopenmp
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-7 -fopenmp accepts -g... yes
checking for gcc-7 -fopenmp option to accept ISO C89... none needed
checking whether gcc-7 -fopenmp understands -c and -o together... yes
checking dependency style of gcc-7 -fopenmp... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc-7 -fopenmp... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking how to convert x86_64-apple-darwin19.0.0 file names to x86_64-apple-darwin19.0.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin19.0.0 file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc-7 -fopenmp object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking how to run the C preprocessor... gcc-7 -fopenmp -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc-7 -fopenmp supports -fno-rtti -fno-exceptions... no
checking for gcc-7 -fopenmp option to produce PIC... -fno-common -DPIC
checking if gcc-7 -fopenmp PIC flag -fno-common -DPIC works... yes
checking if gcc-7 -fopenmp static flag -static works... no
checking if gcc-7 -fopenmp supports -c -o file.o... yes
checking if gcc-7 -fopenmp supports -c -o file.o... (cached) yes
checking whether the gcc-7 -fopenmp linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin19.0.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking whether to enable maintainer-specific portions of Makefiles... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++-7 -fopenmp accepts -g... yes
checking dependency style of g++-7 -fopenmp... gcc3
checking how to run the C++ preprocessor... g++-7 -fopenmp -E
checking for ld used by g++-7 -fopenmp... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking whether the g++-7 -fopenmp linker (/usr/bin/ld) supports shared libraries... yes
checking for g++-7 -fopenmp option to produce PIC... -fno-common -DPIC
checking if g++-7 -fopenmp PIC flag -fno-common -DPIC works... yes
checking if g++-7 -fopenmp static flag -static works... no
checking if g++-7 -fopenmp supports -c -o file.o... yes
checking if g++-7 -fopenmp supports -c -o file.o... (cached) yes
checking whether the g++-7 -fopenmp linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin19.0.0 dyld
checking how to hardcode library paths into programs... immediate
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gfortran option to produce PIC... -fno-common
checking if gfortran PIC flag -fno-common works... yes
checking if gfortran static flag -static works... no
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin19.0.0 dyld
checking how to hardcode library paths into programs... immediate
checking how to get verbose linking output from gfortran... -v
checking for Fortran 77 libraries of gfortran... -L/usr/local/opt/openblas/lib -L/usr/local/Cellar/gcc/9.2.0_2/lib/gcc/9/gcc/x86_64-apple-darwin19/9.2.0 -L/usr/local/Cellar/gcc/9.2.0_2/lib/gcc/9/gcc/x86_64-apple-darwin19/9.2.0/../../.. -lgfortran -lquadmath -lm
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking for OpenMP flag of C++ compiler... -fopenmp
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... -D_THREAD_SAFE
checking for PTHREAD_PRIO_INHERIT... yes
configure: WARNING: building without HDF5 support
checking for sgemm_ in -lopenblas... yes
checking for cheev_... yes
checking for readline in -lreadline... yes
checking for DCUTRI in -lDCUTRI... no
checking execinfo.h usability... yes
checking execinfo.h presence... yes
checking for execinfo.h... yes
checking for backtrace... yes
checking for cos in -lm... yes
checking for cblas_dgemm in -lgslcblas... no
checking for gsl_sf_legendre_array_n in -lgsl... no
checking libGDSII.h usability... no
checking libGDSII.h presence... no
checking for libGDSII.h... no
checking for isnan... yes
checking for isinf... yes
checking for erf... yes
checking for erfc... yes
checking for copysign... yes
checking for python... /Users/twhughes/anaconda3/envs/scuff/bin/python
checking for python version... 3.8
checking for python platform... darwin
checking for python script directory... ${prefix}/lib/python3.8/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python3.8/site-packages
checking for Python include directory... /Users/twhughes/anaconda3/envs/scuff/include/python3.8
checking Python.h usability... yes
checking Python.h presence... yes
checking for Python.h... yes
checking for Numpy include directory... /Users/twhughes/anaconda3/envs/scuff/lib/python3.8/site-packages/numpy/core/include
checking for numpy/arrayobject.h... yes
checking tr1/unordered_map usability... yes
checking tr1/unordered_map presence... yes
checking for tr1/unordered_map... yes
checking whether g++-7 -fopenmp supports C++11 features with -std=gnu++11... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating m4/Makefile
config.status: creating scuff-em-pkgconfig
config.status: WARNING: 'scuff-em-pkgconfig.in' seems to ignore the --datarootdir setting
config.status: creating libs/Makefile
config.status: creating libs/libIncField/Makefile
config.status: creating libs/libSpherical/Makefile
config.status: creating libs/libMDInterp/Makefile
config.status: creating libs/libMatProp/Makefile
config.status: creating libs/libMatProp/cmatheval/Makefile
config.status: creating libs/libSGJC/Makefile
config.status: creating libs/libSubstrate/Makefile
config.status: creating libs/libSubstrate/tests/Makefile
config.status: creating libs/libTriInt/Makefile
config.status: creating libs/libhmat/Makefile
config.status: creating libs/libhrutil/Makefile
config.status: creating libs/libscuff/Makefile
config.status: creating libs/libStaticSolver/Makefile
config.status: creating libs/libscuffSolver/Makefile
config.status: creating libs/libscuffSolver/tests/Makefile
config.status: creating libs/python/Makefile
config.status: creating applications/Makefile
config.status: creating applications/scuff-analyze/Makefile
config.status: creating applications/scuff-caspol/Makefile
config.status: creating applications/scuff-cas3D/Makefile
config.status: creating applications/scuff-ldos/Makefile
config.status: creating applications/scuff-neq/Makefile
config.status: creating applications/scuff-plotEpsMu/Makefile
config.status: creating applications/scuff-rf/Makefile
config.status: creating applications/scuff-scatter/Makefile
config.status: creating applications/scuff-spectrum/Makefile
config.status: creating applications/scuff-static/Makefile
config.status: creating applications/scuff-tmatrix/Makefile
config.status: creating applications/scuff-transmission/Makefile
config.status: creating examples/Makefile
config.status: creating examples/DiffractionPatterns/Makefile
config.status: creating examples/CorrugatedDisc/Makefile
config.status: creating examples/CubeTorus/Makefile
config.status: creating examples/GetTMatrix/Makefile
config.status: creating examples/HalfSpaceLDOS/Makefile
config.status: creating examples/HalfSpaceLDOS/mshFiles/Makefile
config.status: creating examples/HalfSpaceLDOS/scuffgeoFiles/Makefile
config.status: creating examples/ImplicitSubstrate/Makefile
config.status: creating examples/MicrostripDevices/Makefile
config.status: creating examples/NanorodResonantModes/Makefile
config.status: creating examples/PaulTrap/Makefile
config.status: creating examples/PlateWithHole/Makefile
config.status: creating examples/PerforatedThinFilm/Makefile
config.status: creating examples/PlatonicSolids/Makefile
config.status: creating examples/pythonCapacitance/Makefile
config.status: creating examples/SolidSphere/Makefile
config.status: creating examples/SphericalShell/Makefile
config.status: creating examples/SiliconBeams/Makefile
config.status: creating examples/SiO2Spheres/Makefile
config.status: creating examples/StriplineCapacitor/Makefile
config.status: creating examples/TwoBodyCapacitors/Makefile
config.status: creating examples/TwoDimensionalCylinders/Makefile
config.status: creating examples/ThinFilm/Makefile
config.status: creating examples/WireAntenna/Makefile
config.status: creating examples/YagiUdaAntennas/Makefile
config.status: creating tests/Makefile
config.status: creating tests/Mie/Makefile
config.status: creating tests/Fresnel/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
configure: **
configure: ** The configure process was successful.
configure: ** Now type 'make' to compile and sudo 'make install'.
configure: **
I've been trying to install scuff-em for MacOS Catalina following the instructions in the documentation, linked here. However, I've been having no luck with this and have tried various things, which I'll outline below. As far as I understand from #154, these instructions work for High Sierra.
I'll outline my process and perhaps there is some update to these steps that will allow things to work on Catalina. It's possible I'm doing something wrong here, so please let me know if that's the case. I'm a bit new to this.
I start with a freshly cloned repo after doing all of the setup / external package installation steps outlined in the docs. I'm running this in a conda environment. At the bottom of this post, I've pasted the output of running
sh autogen.sh --prefix=${HOME}/scuff-em-installationafter setting the environment variables and specifying--without-hdf5in theconfigfile. As far as I can tell, there are no errors.Running
make install -j 4also seems to work without any issue.I then run into errors in the examples. For
DiffractionPatterns, documented here I get the following errors when trying to usescuff-analyzein theRenameMeshfunction:Similar
Symbol not founderrors occur when tryingscuff-scatteron other examples.I've also tried compiling
gcc-8andg++-8with no luck. Runningautogen.shwithout setting any environment variables also does not work.I'd be extremely grateful for any help or pointing in the right direction. Thank you!
Output from
autogen.sh: