Compile meep on CentOS7 failed? #1946

rolly-ng · 2022-02-11T10:49:38Z

rolly-ng
Feb 11, 2022

Dear MEEP developers,

I tried to compile meep on a CentOS 7 with GCC 7.5.0, but I failed when it reached the scheme folder.
https://github.com/NanoComp/meep/edit/master/contrib/build-meep.sh
Previous trials on Ubuntu 16.04/18.04 was successful. Please help and thank you!

cd /home/rollyng/meep/src
gitclone https://github.com/NanoComp/meep.git
repo=meep.git
name=meep
echo meep.git meep
meep.git meep
'[' -d meep ']'
cd meep
git pull
Already up-to-date.
cd meep/
autogensh --with-mpi --with-openmp PYTHON=python3
sh autogen.sh PKG_CONFIG_PATH=/pkgconfig RPATH_FLAGS=-Wl,-rpath,/home/rollyng/meep/lib:/usr/lib64/openmpi/lib 'LDFLAGS=-L/home/rollyng/meep/lib -L/usr/lib64/openmpi/lib -Wl,-rpath,/home/rollyng/meep/lib:/usr/lib64/openmpi/lib' 'CFLAGS=-I/home/rollyng/meep/include -I/usr/include/openmpi-x86_64/' 'CPPFLAGS=-I/home/rollyng/meep/include -I/usr/include/openmpi-x86_64/' --disable-static --enable-shared --prefix=/home/rollyng/meep --with-libctl=/home/rollyng/meep/share/libctl --with-mpi --with-openmp PYTHON=python3
autoreconf: Entering directory .' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force -I m4 autoreconf: configure.ac: tracing autoreconf: running: libtoolize --force libtoolize: putting auxiliary files in .'.
libtoolize: linking file ./ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIR, m4'.
libtoolize: linking file m4/libtool.m4' libtoolize: linking file m4/ltoptions.m4'
libtoolize: linking file m4/ltsugar.m4' libtoolize: linking file m4/ltversion.m4'
libtoolize: linking file m4/lt~obsolete.m4' autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --force-missing autoreconf: Leaving directory .'
autoreconf: Entering directory .' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force -I m4 autoreconf: configure.ac: tracing autoreconf: running: libtoolize --force libtoolize: putting auxiliary files in .'.
libtoolize: linking file ./ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIR, m4'.
libtoolize: linking file m4/libtool.m4' libtoolize: linking file m4/ltoptions.m4'
libtoolize: linking file m4/ltsugar.m4' libtoolize: linking file m4/ltversion.m4'
libtoolize: linking file m4/lt~obsolete.m4' autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --force-missing autoreconf: Leaving directory .'
autoreconf: Entering directory .' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force -I m4 autoreconf: configure.ac: tracing autoreconf: running: libtoolize --force libtoolize: putting auxiliary files in .'.
libtoolize: linking file ./ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIR, m4'.
libtoolize: linking file m4/libtool.m4' libtoolize: linking file m4/ltoptions.m4'
libtoolize: linking file m4/ltsugar.m4' libtoolize: linking file m4/ltversion.m4'
libtoolize: linking file m4/lt~obsolete.m4' autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --force-missing autoreconf: Leaving directory .'
checking for a BSD-compatible install... /usr/bin/install -c
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checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... yes
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checking whether the C compiler works... yes
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checking for suffix of executables...
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checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for mpic++... mpic++
checking for MPI_Init... yes
checking for mpi.h... yes
checking for extra flag needed to combine stdio.h and mpi.h... none
checking whether mpic++ supports C++11 features by default... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for C++ compiler vendor... gnu
checking whether C++ compiler accepts -fstrict-aliasing... yes
checking whether C++ compiler accepts -ffast-math... yes
checking for gcc architecture flag...
checking for x86 cpuid 0 output... 16:756e6547:6c65746e:49656e69
checking for x86 cpuid 1 output... 50655:26010800:fffa3223:f8bfbff
checking whether C++ compiler accepts -mtune=pentium2... no
checking whether C++ compiler accepts -mcpu=pentium2... no
checking whether C++ compiler accepts -mpentium2... no
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checking whether C++ compiler accepts -mpentiumpro... no
checking for gcc architecture flag... unknown
checking whether C++ compiler accepts -O3 -fstrict-aliasing... yes
checking for OpenMP flag of C++ compiler... -fopenmp
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
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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... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu 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... @
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checking command to parse /usr/bin/nm -B output from gcc object... ok
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checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
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checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
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... no
checking how to run the C++ preprocessor... mpic++ -E
checking for ld used by mpic++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the mpic++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for mpic++ option to produce PIC... -fPIC -DPIC
checking if mpic++ PIC flag -fPIC -DPIC works... yes
checking if mpic++ static flag -static works... no
checking if mpic++ supports -c -o file.o... yes
checking if mpic++ supports -c -o file.o... (cached) yes
checking whether the mpic++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for sin in -lm... yes
checking for fftw_plan_dft_1d in -lfftw3... yes
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
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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... no
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC 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 -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
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/home/rollyng/meep/lib -L/usr/lib64/openmpi/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../.. -lfftw3 -lgfortran -lm -lquadmath
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 if sgemm_ is being linked in already... no
checking for sgemm_ in -lopenblas... yes
checking for cheev_... yes
checking for pkg-config... /usr/bin/pkg-config
checking for harminv >= 1.1... yes
checking HARMINV_CFLAGS... -I/usr/local/include
checking HARMINV_LIBS... -L/usr/local/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../.. -lharminv -lopenblas -lgfortran -lm -lquadmath
checking mpb.h usability... yes
checking mpb.h presence... yes
checking for mpb.h... yes
checking for maxwell_target_operator1 in -lmpb... yes
checking for cos in -lm... yes
checking for cblas_dgemm in -lgslcblas... yes
checking for gsl_sf_bessel_Jn in -lgsl... yes
checking for deflate in -lz... yes
checking for H5Pcreate in -lhdf5... yes
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checking hdf5.h usability... yes
checking hdf5.h presence... yes
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checking for H5Pset_mpi... no
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checking for mpirun... mpirun
checking for guile-config... guile-config
checking if linking to guile works... yes
checking libguile.h usability... yes
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checking for SCM_NEWSMOB... no
checking how to activate readline in Guile... ice-9 readline
checking for libctl dir... /home/rollyng/meep/share/libctl
checking for gen-ctl-io... gen-ctl-io
checking for ctl_get_vector3 in -lctl... yes
checking ctl.h usability... yes
checking ctl.h presence... yes
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checking whether libctl version is at least 4.2.0... ok
checking for libctl_quiet feature... yes
checking for vector3_dot in -lctlgeom... yes
checking libGDSII.h usability... yes
checking libGDSII.h presence... yes
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checking for C/C++ restrict keyword... __restrict
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checking for python version... 3.6
checking for python platform... linux
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checking for python extension module directory... ${exec_prefix}/lib/python3.6/site-packages
checking for Python include directory... /usr/local/include/python3.6m
checking Python.h usability... yes
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configure: WARNING: disabling Python wrappers
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating scheme/Makefile
config.status: creating scheme/meep.scm
config.status: creating libpympb/Makefile
config.status: creating python/Makefile
config.status: creating Makefile
config.status: creating meep-pkgconfig
config.status: creating src/Makefile
config.status: creating src/support/Makefile
config.status: creating tests/Makefile
config.status: creating src/meep/meep-config.h
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
make -j
make all-recursive
make[1]: Entering directory /home/rollyng/meep/src/meep' Making all in src make[2]: Entering directory /home/rollyng/meep/src/meep/src'
make all-recursive
make[3]: Entering directory /home/rollyng/meep/src/meep/src' Making all in support make[4]: Entering directory /home/rollyng/meep/src/meep/src/support'
make[4]: Nothing to be done for all'. make[4]: Leaving directory /home/rollyng/meep/src/meep/src/support'
make[4]: Entering directory `/home/rollyng/meep/src/meep/src'
CXX anisotropic_averaging.lo
CXX array_slice.lo
CXX bands.lo
CXX boundaries.lo
CXX cw_fields.lo
CXX bicgstab.lo
CXX casimir.lo
CXX dft.lo
CXX dft_ldos.lo
CXX energy_and_flux.lo
CXX fields.lo
CXX fields_dump.lo
CXX loop_in_chunks.lo
CXX h5fields.lo
CXX h5file.lo
CXX initialize.lo
CXX material_data.lo
CXX integrate.lo
CXX integrate2.lo
CXX monitor.lo
CXX mympi.lo
CXX multilevel-atom.lo
CXX output_directory.lo
CXX near2far.lo
CXX random.lo
CXX sources.lo
CXX step.lo
CXX stress.lo
CXX step_db.lo
CXX structure.lo
CXX structure_dump.lo
CXX susceptibility.lo
CXX time.lo
CXX update_eh.lo
CXX update_pols.lo
CXX vec.lo
CXX mpb.lo
CXX step_generic.lo
CXX meepgeom.lo
CXX step_generic_stride1.lo
CXX GDSIIgeom.lo
dft.cpp: In member function 'std::vector meep::fields::dft_monitor_size(meep::dft_fields, const meep::volume&, meep::component)':
dft.cpp:1396:54: warning: narrowing conversion of 'reduced_dims[0]' from 'size_t {aka long unsigned int}' to 'int' inside { } [-Wnarrowing]
std::vector reduced_dims_vec = {reduced_dims[0], reduced_dims[1], reduced_dims[2]};
~~~~~~~~~~~~~~^
dft.cpp:1396:54: warning: narrowing conversion of 'reduced_dims[0]' from 'size_t {aka long unsigned int}' to 'int' inside { } [-Wnarrowing]
dft.cpp:1396:71: warning: narrowing conversion of 'reduced_dims[1]' from 'size_t {aka long unsigned int}' to 'int' inside { } [-Wnarrowing]
std::vector reduced_dims_vec = {reduced_dims[0], reduced_dims[1], reduced_dims[2]};
~~~~~~~~~~~~~~^
dft.cpp:1396:71: warning: narrowing conversion of 'reduced_dims[1]' from 'size_t {aka long unsigned int}' to 'int' inside { } [-Wnarrowing]
dft.cpp:1396:88: warning: narrowing conversion of 'reduced_dims[2]' from 'size_t {aka long unsigned int}' to 'int' inside { } [-Wnarrowing]
std::vector reduced_dims_vec = {reduced_dims[0], reduced_dims[1], reduced_dims[2]};
~~~~~~~~~~~~~~^
dft.cpp:1396:88: warning: narrowing conversion of 'reduced_dims[2]' from 'size_t {aka long unsigned int}' to 'int' inside { } [-Wnarrowing]
dft.cpp: In member function 'std::vectormeep::sourcedata meep::dft_fields::fourier_sourcedata(const meep::volume&, meep::component, meep::fields&, const std::complex)':
dft.cpp:1454:86: warning: narrowing conversion of 'idx' from 'ptrdiff_t {aka long int}' to 'size_t {aka long unsigned int}' inside { } [-Wnarrowing]
size_t site_ind[4] = {idx,idx + f->avg1,idx + f->avg2,idx + f->avg1 + f->avg2};
^
dft.cpp:1454:39: warning: narrowing conversion of '(idx + f->meep::dft_chunk::avg1)' from 'ptrdiff_t {aka long int}' to 'size_t {aka long unsigned int}' inside { } [-Wnarrowing]
size_t site_ind[4] = {idx,idx + f->avg1,idx + f->avg2,idx + f->avg1 + f->avg2};
~~~~^~~~~~~~~
dft.cpp:1454:53: warning: narrowing conversion of '(idx + f->meep::dft_chunk::avg2)' from 'ptrdiff_t {aka long int}' to 'size_t {aka long unsigned int}' inside { } [-Wnarrowing]
size_t site_ind[4] = {idx,idx + f->avg1,idx + f->avg2,idx + f->avg1 + f->avg2};
~~~~^~~~~~~~~
dft.cpp:1454:77: warning: narrowing conversion of '((idx + f->meep::dft_chunk::avg1) + f->meep::dft_chunk::avg2)' from 'ptrdiff_t {aka long int}' to 'size_t {aka long unsigned int}' inside { } [-Wnarrowing]
size_t site_ind[4] = {idx,idx + f->avg1,idx + f->avg2,idx + f->avg1 + f->avg2};
~~~~~~~~~~~~~~^~~~~~~~~
meepgeom.cpp: In copy constructor 'meep_geom::geom_epsilon::geom_epsilon(const meep_geom::geom_epsilon&)':
meepgeom.cpp:705:1: warning: base class 'class meep::material_function' should be explicitly initialized in the copy constructor [-Wextra]
geom_epsilon::geom_epsilon(const geom_epsilon &geps1) {
^~~~~~~~~~~~
meepgeom.cpp: In function 'std::complex meep_geom::cond_cmp(meep::component, const meep::vec&, double, meep_geom::geom_epsilon)':
meepgeom.cpp:2642:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
structure_dump.cpp: In member function 'void meep::structure::load(const char*, bool)':
structure_dump.cpp:558:6: warning: '%d' directive output may be truncated writing between 1 and 2 bytes into a region of size between 1 and 10 [-Wformat-truncation=]
void structure::load(const char filename, bool single_parallel_file) {
^~~~~~~~~
structure_dump.cpp:558:6: note: directive argument in the range [0, 20]
structure_dump.cpp:558:6: note: directive argument in the range [0, 5]
structure_dump.cpp:749:19: note: 'snprintf' output between 14 and 24 bytes into a destination of size 20
snprintf(dname, 20, "%c_%d_sigma_%d_%d", ft == 0 ? 'E' : 'H', i, c, d);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dft.cpp: In function '_ZN4meep9dft_chunk10update_dftEd._omp_fn.0':
dft.cpp:260:13: warning: 'f[0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
realnum f[2]; // real/imag field value at epsilon point
^
structure_dump.cpp: In member function 'void meep::structure::dump(const char, bool)':
structure_dump.cpp:90:6: warning: '' directive output may be truncated writing 1 byte into a region of size between 0 and 9 [-Wformat-truncation=]
void structure::dump(const char *filename, bool single_parallel_file) {
^~~~~~~~~
structure_dump.cpp:90:6: note: using the range [-2147483648, 2147483647] for directive argument
structure_dump.cpp:297:19: note: 'snprintf' output between 14 and 43 bytes into a destination of size 20
snprintf(dname, 20, "%c%d_sigma_%d_%d", ft == 0 ? 'E' : 'H', i, c, d);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meepgeom.cpp: In function 'void meep_geom::material_grids_addgradient_point(double*, vector3, double, meep_geom::geom_epsilon*, meep::component, meep::component, std::complex, std::complex, double, meep::grid_volume&, double)':
meepgeom.cpp:2849:28: warning: 'kind' may be used uninitialized in this function [-Wmaybe-uninitialized]
add_interpolate_weights(p.x, p.y, p.z, vcur, sz.x, sz.y, sz.z, 1,
```
                        scalegrad, ucur, kind, uval,
                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                        vector3_to_vec(p), geps, adjoint_c, forward_c,
                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                        fwd, adj, freq, gv, tol);
                        ~~~~~~~~~~~~~~~~~~~~~~~~
CXXLD    libmeep.la
```

make[4]: Leaving directory /home/rollyng/meep/src/meep/src' make[3]: Leaving directory /home/rollyng/meep/src/meep/src'
make[2]: Leaving directory /home/rollyng/meep/src/meep/src' Making all in tests make[2]: Entering directory /home/rollyng/meep/src/meep/tests'
make[2]: Nothing to be done for all'. make[2]: Leaving directory /home/rollyng/meep/src/meep/tests'
Making all in scheme
make[2]: Entering directory /home/rollyng/meep/src/meep/scheme' gen-ctl-io --cxx --header -o ctl-io.h meep.scm /home/rollyng/meep/share/libctl gen-ctl-io --cxx --swig -o ctl-io.i meep.scm /home/rollyng/meep/share/libctl swig -I../src -c++ -guile -o meep_wrap.cxx ./meep.i ../src/meep/vec.hpp:28: Error: Syntax error in input(1). make[2]: *** [meep_wrap.cxx] Error 1 make[2]: *** Waiting for unfinished jobs.... make[2]: Leaving directory /home/rollyng/meep/src/meep/scheme'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/rollyng/meep/src/meep'
make: *** [all] Error 2

Answered by oskooi

Feb 12, 2022

If you want just the Python API, you can add --without-scheme as a configure option which will compile without the Scheme interface (which has been deprecated). Also, have you tried the specific build instructions for CentOS 7 from the user manual?

View full answer

oskooi · 2022-02-12T16:21:47Z

oskooi
Feb 12, 2022
Collaborator

If you want just the Python API, you can add --without-scheme as a configure option which will compile without the Scheme interface (which has been deprecated). Also, have you tried the specific build instructions for CentOS 7 from the user manual?

1 reply

rolly-ng Feb 13, 2022
Author

Hello oskooi,
Thank you and I am trying to compile the latest meep 1.22.0 on a university cluster with the Intel compiler tools. The link above seems using the GNU compilers. What kind of modification should I need?
Here is what my .bashrc looks to load the intel compilers
source /home/rolly/Gromacs/gromacs-2020.2/install/bin/GMXRC source /opt/intel/bin/compilervars.sh intel64 source /opt/intel/impi/2018.4.274/bin64/mpivars.sh intel64 source /opt/intel/mkl/bin/mklvars.sh intel64 export CC=icc export CXX=icpc export F77=ifort export F90=ifort export FC=ifort export MPICC=mpiicc export MPICXX=mpiicpc export CFLAGS="-O3 -xHost -fno-alias -align" export FFLAGS="-O3 -xHost -fno-alias -align" export CXXFLAGS="-O3 -xHost -fno-alias -align" export FFLAGS="-I/opt/intel/impi/2018.4.274/include64/ -L/opt/intel/impi/2018.4.274/lib64/"
I noticed that meep needs a number of prerequisite packages,
(1) harminv
(2) libctl
(3) h5utils
(4) mpb
before meep package itself can be compile.

There are also a number of extra packages needed,
(i) hdf5
(ii) zlib
(iii) libmatheval
(iv) fftw3
(v) guile

I have compiled all above packages myself using the intel compiler, and I have installed these packages in separate build directories
--prefix=$HOME/Extra/build/
--prefix=$HOME/meep/build/

As I configure the meep package,
./configure --enable-maintainer-mode --prefix=/home/rolly/meep/build/meep CC=mpiicc --with-mpi --disable-static --enable-shared --with-libctl="/home/rolly/meep/build/libctl" --with-hdf5="/home/rolly/Extra/build/hdf5" --with-guile="/home/rolly/Extra/build/guile" LDFLAGS="-L/home/rolly/meep/build/libctl/lib -L/home/rolly/Extra/build/hdf5/lib -L/home/rolly/Extra/build/guile/lib" CPPFLAGS="-I/home/rolly/meep/build/libctl/include -I/home/rolly/Extra/build/hdf5/include -I/home/rolly/Extra/build/guile/include"

It produces error and stops,
checking mpb.h usability... yes
checking mpb.h presence... yes
checking for mpb.h... yes
checking for maxwell_target_operator1 in -lmpb... no
checking for maxwell_target_operator1 in -lmpb... (cached) no
configure: WARNING: MPB support is disabled
checking for cos in -lm... no
checking for cblas_dgemm in -lgslcblas... no
checking for gsl_sf_bessel_Jn in -lgsl... no
configure: WARNING: Missing GNU GSL library...Bessel-function field initialization will not be supported.
checking for mpirun... mpirun
checking for guile-config... guile-config
checking if linking to guile works... no

Can you please look into my problem. Thank you!

rolly-ng · 2022-02-13T17:28:15Z

rolly-ng
Feb 13, 2022
Author

Hello oskooi,
I have switch back to the GCC compiler to give a quick test of compiling meep on the CentOS7 machine. To my surprise, it does finish the make process only if I added the --without-scheme option, but it produce no binary file after all?
Can you please have a look at the screenshot? Thanks a lot

!

3 replies

oskooi Feb 14, 2022
Collaborator

If running make was successful then you should find the Python module meep.py in /home/rolly/NanoComp/src/meep/python. At this point, you should just need to add this directory to the shell environment variable PYTHONPATH. When building from source, you should also verify that the unit test suite passes (i.e., make check).

Note that if you are using icc to compile Meep, you typically also need to compile all the dependencies using icc as described in https://meep.readthedocs.io/en/latest/Build_From_Source/#picking-a-compiler.

rolly-ng Feb 14, 2022
Author

Hi, I have added the line in my .bashrc but python3 fails to import meep?
export PYTHONPATH=/home/rolly/NanoComp/src/meep/python:/home/rolly/Python3.6.5/lib/python3.6/site-packages

But, as I login again, and run python3 to import meep, it shows error.

[rolly@head ~]$ python3
Python 3.6.5 (default, Feb 13 2022, 17:13:31)
[GCC 5.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

import meep
Traceback (most recent call last):
File "/home/rolly/NanoComp/src/meep/python/meep.py", line 18, in swig_import_helper
fp, pathname, description = imp.find_module('_meep', [dirname(file)])
File "/home/rolly/Python3.6.5/lib/python3.6/imp.py", line 297, in find_module
raise ImportError(_ERR_MSG.format(name), name=name)
ImportError: No module named '_meep'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "", line 1, in
File "/home/rolly/NanoComp/src/meep/python/meep.py", line 28, in
_meep = swig_import_helper()
File "/home/rolly/NanoComp/src/meep/python/meep.py", line 20, in swig_import_helper
import _meep
ModuleNotFoundError: No module named '_meep'

rolly-ng Feb 14, 2022
Author

Hi, I have recompiled with intel icc and with scheme, I can see the binary meep file compiled. But it does not work yet.

[rolly@head ~]$ python3
Python 3.6.5 (default, Feb 13 2022, 17:13:31)
[GCC 5.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

import meep
Traceback (most recent call last):
File "/home/rolly/NanoComp/src/meep/python/meep.py", line 18, in swig_import_helper
fp, pathname, description = imp.find_module('_meep', [dirname(file)])
File "/home/rolly/Python3.6.5/lib/python3.6/imp.py", line 297, in find_module
raise ImportError(_ERR_MSG.format(name), name=name)
ImportError: No module named '_meep'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "", line 1, in
File "/home/rolly/NanoComp/src/meep/python/meep.py", line 28, in
_meep = swig_import_helper()
File "/home/rolly/NanoComp/src/meep/python/meep.py", line 20, in swig_import_helper
import _meep
ModuleNotFoundError: No module named '_meep'

quit
Use quit() or Ctrl-D (i.e. EOF) to exit
quit()
[rolly@head ~]$ which meep
~/NanoComp/build/bin/meep
[rolly@head ~]$ meep
Segmentation fault (core dumped)
[rolly@head ~]$ meep --version
Segmentation fault (core dumped)
[rolly@head ~]$ meep --help
Segmentation fault (core dumped)
[rolly@head ~]$

rolly-ng · 2022-02-14T07:05:28Z

rolly-ng
Feb 14, 2022
Author

Hi, I would like to clarify the dependence requirement to use icc compiler. I suppose parallel meep requires the following packages
(1) harminv (to be compile mpi version of icc, i.e. mpiicc)
(2) libctl (to be compile with mpi version of icc, i.e. mpiicc)
(3) h5utils (to be compile mpi version of icc, i.e. mpiicc)
(4) mpb (to be compile with mpi version of icc, i.e. mpiicc)
(5) libGDSII (to be compile with mpi version of icc, i.e. mpiicc)
(6) python3.6.5 (to be compile with icc)

In turns, these packages further requires extra packages
(1) fftw-3.3.10 (to be compile with mpi version of icc, i.e. mpiicc)
(2) hdf5 (to be compile with mpi version of icc, i.e. mpiicc)
(3) openmpi-2.1.1 (to be compile with mpi version of icc, i.e. mpiicc)
(4) libmatheval-1.1.11 (to be compile with mpi version of icc, i.e. mpiicc)
(5) guile-2.0.11 (not working with mpiicc, to be compile with gcc only)
(6) swig-rel-3.0.12 (not working with mpiicc, to be compile with gcc only)

Please correct my understanding of the above, thank you!

1 reply

rolly-ng Feb 14, 2022
Author

I wonder if the latest meep 1.22 does not work with the intel compilers ver. 2018.4.274? I have gcc 5.4.0 on the centos machine, do I need to update the gcc 7, 8 or 9 to compile for the latest meep? Thanks!

rolly-ng · 2022-02-14T17:25:03Z

rolly-ng
Feb 14, 2022
Author

Hi, after many trial and error, I have successfully compile meep with GCC 7.3.0. I have the scheme/guile binary which seems to work. But the python3 interface still fails.

This is my command, ./autogen.sh --enable-shared MPICC=mpicc MPICXX=mpic++ --prefix="$HOME/NanoComp/build" --with-mpi --with-openmp PYTHON=python3 --with-libctl="$HOME/NanoComp/build/share/libctl" LDFLAGS="-L$HOME/NanoComp/build/lib -L$HOME/Extra/build/lib/opemnpi" CPPFLAGS="-I$HOME/NanoComp/build/include -I$HOME/Extra/build/include/openmpi"

[rolly@head ~]$ which meep
~/NanoComp/build/bin/meep
[rolly@head ~]$ meep
Using MPI version 3.1, 1 processes
GNU Guile 2.0.11
Copyright (C) 1995-2014 Free Software Foundation, Inc.

Guile comes with ABSOLUTELY NO WARRANTY; for details type ,show w'. This program is free software, and you are welcome to redistribute it under certain conditions; type ,show c' for details.

Enter `,help' for help.
meep> ,q

But while I tried python3, it shows the same error.
[rolly@head ~]$ python3
Python 3.6.5 (default, Feb 14 2022, 23:53:30)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

import meep
Traceback (most recent call last):
File "/home/rolly/NanoComp/src/meep/python/meep.py", line 18, in swig_import_helper
fp, pathname, description = imp.find_module('_meep', [dirname(file)])
File "/home/rolly/Python3.6.5/lib/python3.6/imp.py", line 297, in find_module
raise ImportError(_ERR_MSG.format(name), name=name)
ImportError: No module named '_meep'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "", line 1, in
File "/home/rolly/NanoComp/src/meep/python/meep.py", line 28, in
_meep = swig_import_helper()
File "/home/rolly/NanoComp/src/meep/python/meep.py", line 20, in swig_import_helper
import _meep
ModuleNotFoundError: No module named '_meep'

I am sure there is somethng wrong with the python interface if compile on Centos7. Please check and thanks!
On Ubuntu 16.04 with working meep, I can see the directory ~/meep/lib/python3.5/site-packages/meep, which I export to the PYTHONPATH and get meep working.
But on Centos7, I cannot see the site-package directory, and the contents in the ~/NanoComp/src/meep/python is very different. How can I correct the problem? Thanks!

0 replies

stevengj · 2022-02-14T22:07:13Z

stevengj
Feb 14, 2022
Maintainer

It looks like you didn't run make install and are trying to run Meep directly from the source directory?

I would generally recommend trying to install it somewhere, and then set your PYTHONPATH to tell Python where to find it.

2 replies

rolly-ng Feb 15, 2022
Author

Dear Prof. Johnson,
Thanks very much for your attention. I have found the cause of my problem, as I have to install numpy to my Python3 then the site-package can be built. However, now I have another issue with mpi4py.

[rolly@head ~]$ python3
Python 3.8.12 (default, Feb 15 2022, 12:07:42)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

import meep
*** The MPI_Comm_rank() function was called before MPI_INIT was invoked.
*** This is disallowed by the MPI standard.
*** Your MPI job will now abort.
[head:39370] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!

If I uninstall mpi4py, then
[rolly@head ~]$ python3
Python 3.8.12 (default, Feb 15 2022, 12:07:42)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

import meep

**
** failed to load python MPI module (mpi4py)
** No module named 'mpi4py'
**

I don't have these problems on Ubuntu 16.04 anyway.
Thanks for your kind attention!

Best,
rolly

rolly-ng Feb 16, 2022
Author

Hi, I have found the cause of error to the mpi4py, I believe it is irrelevant to meep but to the way mpi4py is build. Since there are both Intel MPI and OpenMPI on the system, I have to specify which MPI to build for the mpi4py to get it working.
cd $HOME/NanoComp/src/mpi4py-3.1.3/
python3 setup.py build --mpi=$HOME/Extra/build
python3 setup.py install

rolly-ng · 2022-02-26T06:07:44Z

rolly-ng
Feb 26, 2022
Author

Hi, I would like to report that I have finally successful to install meep 1.22.0 on the centos7 cluster. I have realized that it works with gcc tools and I need to have to openmpi-3.1.6 compiled at first, then the hdf5 tools compiled to enable mpi support. Since the cluster runs slrum, I also need to compile openmpi-3.1.6 with the pmi option, so I can have srun support. After sorting out all the details, I am having a working meep binary to start computation. Thanks to all! By the way, there are 2 packages that I installed with yum, i.e. guile and swig, to save some efforts. Please close the issue, thank you once again!

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Compile meep on CentOS7 failed? #1946

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