Problem with libmeep.so

[DiegoGuisasola]

Hello everyone, I opened an issue in which I asked how to install Meep. Now that I've Build from source I'm facing a problem and is the one shown in the screenshot below:

How can I make it work?

Thanks in advance!

[ChristopherHogan]

The only advice I can offer is to rebuild everything, and make sure you follow the instructions here very carefully. Don't just blindly run the script; read it and understand it. It includes comments that require changes depending on the Ubuntu version.

Some things to check:

$ which meep
# By default, this should be /usr/local/bin/meep

# Try the built meep instead of the installed meep
$ cd ~/install/meep/scheme # This is the default build location
$ ./meep

[DiegoGuisasola]

I did read it and the script I used is the same one I used in other computers with the same ubuntu version and I didn't get any trouble with those computers. How can I uninstall meep completely in order to install it again?

Thanks in advance.

[ChristopherHogan]

How can I uninstall meep completely in order to install it again?

Go to where you built meep (~/install/meep if you didn't modify the script) and run make uninstall.

[DiegoGuisasola]

Ok, I run meep from $ cd ~/install/meep/scheme # This is the default build location $ ./meep

and it is working but when I run ir from a new terminal in a different working directory, i keep getting the same error. The script I used to install it is:

#!/bin/bash

set -e

RPATH_FLAGS="-Wl,-rpath,/usr/local/lib:/usr/lib/x86_64-linux-gnu/hdf5/openmpi"
MY_LDFLAGS="-L/usr/local/lib -L/usr/lib/x86_64-linux-gnu/hdf5/openmpi ${RPATH_FLAGS}"
MY_CPPFLAGS="-I/usr/local/include -I/usr/include/hdf5/openmpi"

sudo apt-get update

# If building on Ubuntu 18.04LTS, replace libpng16-dev with libpng-dev,
# and libpython3.5-dev with libpython3-dev.
sudo apt-get -y install     \
    libblas-dev             \
    liblapack-dev           \
    libgmp-dev              \
    swig                    \
    libgsl-dev              \
    autoconf                \
    pkg-config              \
    libpng-dev              \
    git                     \
    guile-2.0-dev           \
    libfftw3-dev            \
    libhdf5-openmpi-dev     \
    hdf5-tools              \

mkdir -p ~/install

cd ~/install
git clone https://github.com/NanoComp/harminv.git
cd harminv/
sh autogen.sh --enable-shared
make && sudo make install

cd ~/install
git clone https://github.com/NanoComp/libctl.git
cd libctl/
sh autogen.sh --enable-shared
make && sudo make install

cd ~/install
git clone https://github.com/NanoComp/h5utils.git
cd h5utils/
sh autogen.sh CC=mpicc LDFLAGS="${MY_LDFLAGS}" CPPFLAGS="${MY_CPPFLAGS}"
make && sudo make install

cd ~/install
git clone https://github.com/NanoComp/mpb.git
cd mpb/
sh autogen.sh --enable-shared CC=mpicc LDFLAGS="${MY_LDFLAGS}" CPPFLAGS="${MY_CPPFLAGS}" --with-hermitian-eps
make && sudo make install

cd ~/install
git clone https://github.com/HomerReid/libGDSII.git
cd libGDSII/
sh autogen.sh
make && sudo make install

sudo pip3 install --upgrade pip
# If pip3 doesn't work on ubuntu 18.04, just use pip
pip3 install --user --no-cache-dir mpi4py
export HDF5_MPI="ON"
pip3 install --user --no-binary=h5py h5py

cd ~/install
git clone https://github.com/NanoComp/meep.git
cd meep/
sh autogen.sh --enable-shared --with-mpi PYTHON=python3 \
    CC=mpicc CXX=mpic++ LDFLAGS="${MY_LDFLAGS}" CPPFLAGS="${MY_CPPFLAGS}"
make && sudo make install

And, as you can see, I did take into account the fact that I'm using Ubuntu 18.04. Any thoughts?

[ChristopherHogan]

What is the output of

$ which meep

[ChristopherHogan]

And the installation script output would help.

[DiegoGuisasola]

What is the output of

$ which meep

And the installation script output would help.

You mean, should I run the script again? Because I already closed the terminal that I used to run the script.

Note 1: I haven't uninstalled Meep yet because I'm running some bash scripts from: `$ cd ~/install/meep/scheme

[ChristopherHogan]

You mean, should I run the script again? Because I already closed the terminal that I used to run the script.

The configure settings should be saved, so you should be able to do

$ cd ~/install/meep
$ make clean
$ make > output.log 2>&1
$ sudo  make install >> output.log 2>&1

Then post the contents of output.log here.

[ChristopherHogan]

Also, please don't post updates in comments like Note 1 because Github does not email notifications for edits and I am unlikely to see them.

[DiegoGuisasola]

Also, please don't post updates in comments like Note 1 because Github does not email notifications for edits and I am unlikely to see them.

My bad, I'm new to this and I'm slowly learning. Thanks for your help, though!

You mean, should I run the script again? Because I already closed the terminal that I used to run the script.

The configure settings should be saved, so you should be able to do

$ cd ~/install/meep
$ make clean
$ make > output.log 2>&1
$ sudo  make install >> output.log 2>&1

Then post the contents of output.log here.

This part is taking a while but there is an output.log already created in that folder, it might not be a complete log tho, so I'll just wait for it to finish and after that I'll send you the log.

[DiegoGuisasola]

Done:

make  all-recursive
make[1]: Entering directory '/home/andres/install/meep'
Making all in src
make[2]: Entering directory '/home/andres/install/meep/src'
make  all-am
make[3]: Entering directory '/home/andres/install/meep/src'
  CXX      array_slice.lo
  CXX      anisotropic_averaging.lo
  CXX      bands.lo
  CXX      boundaries.lo
  CXX      bicgstab.lo
  CXX      casimir.lo
  CXX      control_c.lo
  CXX      cw_fields.lo
  CXX      dft.lo
  CXX      dft_ldos.lo
  CXX      energy_and_flux.lo
  CXX      fields.lo
  CXX      loop_in_chunks.lo
  CXX      h5fields.lo
  CXX      h5file.lo
h5file.cpp: In member function ‘bool meep::h5file::dataset_exists(const char*)’:
h5file.cpp:97:41: warning: unused parameter ‘name’ [-Wunused-parameter]
 bool h5file::dataset_exists(const char *name) {
                                         ^~~~
h5file.cpp: In member function ‘void meep::h5file::read_size(const char*, int*, size_t*, int)’:
h5file.cpp:227:36: warning: unused parameter ‘dataname’ [-Wunused-parameter]
 void h5file::read_size(const char *dataname, int *rank, size_t *dims, int maxrank) {
                                    ^~~~~~~~
h5file.cpp:227:51: warning: unused parameter ‘rank’ [-Wunused-parameter]
 void h5file::read_size(const char *dataname, int *rank, size_t *dims, int maxrank) {
                                                   ^~~~
h5file.cpp:227:65: warning: unused parameter ‘dims’ [-Wunused-parameter]
 void h5file::read_size(const char *dataname, int *rank, size_t *dims, int maxrank) {
                                                                 ^~~~
h5file.cpp:227:75: warning: unused parameter ‘maxrank’ [-Wunused-parameter]
 void h5file::read_size(const char *dataname, int *rank, size_t *dims, int maxrank) {
                                                                           ^~~~~~~
h5file.cpp: In member function ‘meep::realnum* meep::h5file::read(const char*, int*, size_t*, int)’:
h5file.cpp:292:35: warning: unused parameter ‘dataname’ [-Wunused-parameter]
 realnum *h5file::read(const char *dataname, int *rank, size_t *dims, int maxrank) {
                                   ^~~~~~~~
h5file.cpp:292:50: warning: unused parameter ‘rank’ [-Wunused-parameter]
 realnum *h5file::read(const char *dataname, int *rank, size_t *dims, int maxrank) {
                                                  ^~~~
h5file.cpp:292:64: warning: unused parameter ‘dims’ [-Wunused-parameter]
 realnum *h5file::read(const char *dataname, int *rank, size_t *dims, int maxrank) {
                                                                ^~~~
h5file.cpp:292:74: warning: unused parameter ‘maxrank’ [-Wunused-parameter]
 realnum *h5file::read(const char *dataname, int *rank, size_t *dims, int maxrank) {
                                                                          ^~~~~~~
h5file.cpp: In member function ‘char* meep::h5file::read(const char*)’:
h5file.cpp:360:32: warning: unused parameter ‘dataname’ [-Wunused-parameter]
 char *h5file::read(const char *dataname) {
                                ^~~~~~~~
h5file.cpp: In member function ‘void meep::h5file::remove_data(const char*)’:
h5file.cpp:409:38: warning: unused parameter ‘dataname’ [-Wunused-parameter]
 void h5file::remove_data(const char *dataname) {
                                      ^~~~~~~~
h5file.cpp: In member function ‘void meep::h5file::create_data(const char*, int, const size_t*, bool, bool)’:
h5file.cpp:443:38: warning: unused parameter ‘dataname’ [-Wunused-parameter]
 void h5file::create_data(const char *dataname, int rank, const size_t *dims, bool append_data,
                                      ^~~~~~~~
h5file.cpp:443:52: warning: unused parameter ‘rank’ [-Wunused-parameter]
 void h5file::create_data(const char *dataname, int rank, const size_t *dims, bool append_data,
                                                    ^~~~
h5file.cpp:443:72: warning: unused parameter ‘dims’ [-Wunused-parameter]
 void h5file::create_data(const char *dataname, int rank, const size_t *dims, bool append_data,
                                                                        ^~~~
h5file.cpp:443:83: warning: unused parameter ‘append_data’ [-Wunused-parameter]
 void h5file::create_data(const char *dataname, int rank, const size_t *dims, bool append_data,
                                                                                   ^~~~~~~~~~~
h5file.cpp:444:31: warning: unused parameter ‘single_precision’ [-Wunused-parameter]
                          bool single_precision) {
                               ^~~~~~~~~~~~~~~~
h5file.cpp: In member function ‘void meep::h5file::extend_data(const char*, int, const size_t*)’:
h5file.cpp:534:38: warning: unused parameter ‘dataname’ [-Wunused-parameter]
 void h5file::extend_data(const char *dataname, int rank, const size_t *dims) {
                                      ^~~~~~~~
h5file.cpp:534:52: warning: unused parameter ‘rank’ [-Wunused-parameter]
 void h5file::extend_data(const char *dataname, int rank, const size_t *dims) {
                                                    ^~~~
h5file.cpp:534:72: warning: unused parameter ‘dims’ [-Wunused-parameter]
 void h5file::extend_data(const char *dataname, int rank, const size_t *dims) {
                                                                        ^~~~
h5file.cpp: In function ‘void meep::_write_chunk(hid_t, meep::h5file::extending_s*, int, const size_t*, const size_t*, hid_t, void*)’:
h5file.cpp:599:32: warning: unused parameter ‘data_id’ [-Wunused-parameter]
 static void _write_chunk(hid_t data_id, h5file::extending_s *cur, int rank,
                                ^~~~~~~
h5file.cpp:599:62: warning: unused parameter ‘cur’ [-Wunused-parameter]
 static void _write_chunk(hid_t data_id, h5file::extending_s *cur, int rank,
                                                              ^~~
h5file.cpp:599:71: warning: unused parameter ‘rank’ [-Wunused-parameter]
 static void _write_chunk(hid_t data_id, h5file::extending_s *cur, int rank,
                                                                       ^~~~
h5file.cpp:600:40: warning: unused parameter ‘chunk_start’ [-Wunused-parameter]
                          const size_t *chunk_start, const size_t *chunk_dims, hid_t datatype,
                                        ^~~~~~~~~~~
h5file.cpp:600:67: warning: unused parameter ‘chunk_dims’ [-Wunused-parameter]
                          const size_t *chunk_start, const size_t *chunk_dims, hid_t datatype,
                                                                   ^~~~~~~~~~
h5file.cpp:600:85: warning: unused parameter ‘datatype’ [-Wunused-parameter]
                          const size_t *chunk_start, const size_t *chunk_dims, hid_t datatype,
                                                                                     ^~~~~~~~
h5file.cpp:601:32: warning: unused parameter ‘data’ [-Wunused-parameter]
                          void *data) {
                                ^~~~
h5file.cpp: In member function ‘void meep::h5file::write(const char*, const char*)’:
h5file.cpp:706:32: warning: unused parameter ‘dataname’ [-Wunused-parameter]
 void h5file::write(const char *dataname, const char *data) {
                                ^~~~~~~~
h5file.cpp:706:54: warning: unused parameter ‘data’ [-Wunused-parameter]
 void h5file::write(const char *dataname, const char *data) {
                                                      ^~~~
h5file.cpp: In function ‘void meep::_read_chunk(hid_t, int, const size_t*, const size_t*, hid_t, void*)’:
h5file.cpp:737:31: warning: unused parameter ‘data_id’ [-Wunused-parameter]
 static void _read_chunk(hid_t data_id, int rank, const size_t *chunk_start,
                               ^~~~~~~
h5file.cpp:737:44: warning: unused parameter ‘rank’ [-Wunused-parameter]
 static void _read_chunk(hid_t data_id, int rank, const size_t *chunk_start,
                                            ^~~~
h5file.cpp:737:64: warning: unused parameter ‘chunk_start’ [-Wunused-parameter]
 static void _read_chunk(hid_t data_id, int rank, const size_t *chunk_start,
                                                                ^~~~~~~~~~~
h5file.cpp:738:39: warning: unused parameter ‘chunk_dims’ [-Wunused-parameter]
                         const size_t *chunk_dims, hid_t datatype, void *data) {
                                       ^~~~~~~~~~
h5file.cpp:738:57: warning: unused parameter ‘datatype’ [-Wunused-parameter]
                         const size_t *chunk_dims, hid_t datatype, void *data) {
                                                         ^~~~~~~~
h5file.cpp:738:73: warning: unused parameter ‘data’ [-Wunused-parameter]
                         const size_t *chunk_dims, hid_t datatype, void *data) {
                                                                         ^~~~
h5file.cpp: At global scope:
h5file.cpp:73:12: warning: ‘h5io_critical_section_tag’ defined but not used [-Wunused-variable]
 static int h5io_critical_section_tag = 0;
            ^~~~~~~~~~~~~~~~~~~~~~~~~
  CXX      initialize.lo
  CXX      integrate.lo
  CXX      integrate2.lo
  CXX      monitor.lo
  CXX      mympi.lo
  CXX      multilevel-atom.lo
  CXX      near2far.lo
near2far.cpp: In member function ‘double* meep::dft_near2far::flux(meep::direction, const meep::volume&, double)’:
near2far.cpp:394:20: warning: enumeration value ‘R’ not handled in switch [-Wswitch]
             switch (df) {
                    ^
near2far.cpp:394:20: warning: enumeration value ‘P’ not handled in switch [-Wswitch]
  CXX      output_directory.lo
output_directory.cpp: In member function ‘void meep::structure::set_output_directory(const char*)’:
output_directory.cpp:43:10: warning: ignoring return value of ‘int symlink(const char*, const char*)’, declared with attribute warn_unused_result [-Wunused-result]
   symlink(name, symlink_name);
   ~~~~~~~^~~~~~~~~~~~~~~~~~~~
  CXX      random.lo
  CXX      sources.lo
  CXX      step.lo
  CXX      step_db.lo
  CXX      stress.lo
  CXX      structure.lo
  CXX      structure_dump.lo
structure_dump.cpp: In member function ‘void meep::structure::dump(const char*)’:
structure_dump.cpp:87:6: 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) {
      ^~~~~~~~~
structure_dump.cpp:87:6: note: using the range [-2147483648, 2147483647] for directive argument
In file included from /usr/include/stdio.h:862:0,
                 from structure_dump.cpp:21:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: note: ‘__builtin___snprintf_chk’ output between 14 and 43 bytes into a destination of size 20
        __bos (__s), __fmt, __va_arg_pack ());
                                            ^
structure_dump.cpp: In member function ‘void meep::structure::load(const char*)’:
structure_dump.cpp:453:6: 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) {
      ^~~~~~~~~
structure_dump.cpp:453:6: note: directive argument in the range [0, 20]
structure_dump.cpp:453:6: note: directive argument in the range [0, 5]
In file included from /usr/include/stdio.h:862:0,
                 from structure_dump.cpp:21:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: note: ‘__builtin___snprintf_chk’ output between 14 and 24 bytes into a destination of size 20
        __bos (__s), __fmt, __va_arg_pack ());
                                            ^
  CXX      susceptibility.lo
susceptibility.cpp:159:13: warning: ‘bool meep::lorentzian_unstable(double, double, double)’ defined but not used [-Wunused-function]
 static bool lorentzian_unstable(double omega_0, double gamma, double dt) {
             ^~~~~~~~~~~~~~~~~~~
  CXX      time.lo
  CXX      update_eh.lo
  CXX      mpb.lo
  CXX      update_pols.lo
  CXX      vec.lo
  CXX      step_generic.lo
  CXX      meepgeom.lo
  CXX      GDSIIgeom.lo
  CXX      step_generic_stride1.lo
  CXXLD    libmeep.la
ar: `u' modifier ignored since `D' is the default (see `U')
  CXX      sphere-quad.o
  CXXLD    sphere_quad
make[3]: Leaving directory '/home/andres/install/meep/src'
make[2]: Leaving directory '/home/andres/install/meep/src'
Making all in tests
make[2]: Entering directory '/home/andres/install/meep/tests'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/home/andres/install/meep/tests'
Making all in scheme
make[2]: Entering directory '/home/andres/install/meep/scheme'
gen-ctl-io --cxx --header -o ctl-io.h meep.scm /usr/local/share/libctl
cp -f /usr/local/share/libctl/base/main.c main.cpp
cp -f /usr/local/share/libctl/utils/geom.c geom.cpp
gen-ctl-io --cxx --code -o ctl-io.cpp meep.scm /usr/local/share/libctl
gen-ctl-io --cxx --swig -o ctl-io.i meep.scm /usr/local/share/libctl
(perl -pe 's/%rename\(([A-Za-z0-9_]*)\) *([A-Za-z0-9:_]*);$/(define \2 (\1))/' meep_enum_renames.i | perl -pe 's/[A-Za-z0-9:_]*:://g' | perl -pe 's/_/-/g' | perl -pe 's,//,;,'; echo "(define Centered Dielectric)") > meep-enums.scm
swig -I../src -c++ -guile -o meep_wrap.cxx ./meep.i
patch -p0 meep_wrap.cxx < ./meep_wrap.patch
patching file meep_wrap.cxx
Hunk #1 succeeded at 778 (offset 27 lines).
sed -i.bak '/(SCM_SMOB_PREDICATE(swig_tag, smob) || SCM_SMOB_PREDICATE(swig_collectable_tag, smob))/ s/swig_collectable_tag, smob)/swig_collectable_tag, smob) || SCM_SMOB_PREDICATE((swig_collectable_tag \& ~0xff00), (smob))/' meep_wrap.cxx;
make  all-am
make[3]: Entering directory '/home/andres/install/meep/scheme'
  CXX      meep-meep.o
  CXX      meep-structure.o
structure.cpp: In member function ‘virtual void geom_epsilon::eff_chi1inv_row(meep::component, double*, const meep::volume&, double, int)’:
structure.cpp:564:10: warning: ‘mat1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     mat2 = mat1;
     ~~~~~^~~~~~
  CXX      meep-meep_wrap.o
meep_wrap.cxx:1410:0: warning: "SCM_VECTORP" redefined
 #  define SCM_VECTORP(o) scm_vector_p(o)

In file included from /usr/include/guile/2.0/libguile.h:126:0,
                 from meep_wrap.cxx:749:
/usr/include/guile/2.0/libguile/deprecated.h:475:0: note: this is the location of the previous definition
 #define SCM_VECTORP(x)         scm_i_vectorp(x)

meep_wrap.cxx:1411:0: warning: "SCM_VECTOR_LENGTH" redefined
 #  define SCM_VECTOR_LENGTH(o) scm_c_vector_length(o)

In file included from /usr/include/guile/2.0/libguile.h:126:0,
                 from meep_wrap.cxx:749:
/usr/include/guile/2.0/libguile/deprecated.h:476:0: note: this is the location of the previous definition
 #define SCM_VECTOR_LENGTH(x)   scm_i_vector_length(x)

  CXX      meep-main.o
main.cpp: In function ‘char* make_name(const char*, const char*)’:
main.cpp:140:8: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
        if (ndir > 5 && !strcmp(".libs", dir+ndir-5))
        ^~
main.cpp:142:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
    strcpy(base0, for_base); base = basename(base0);
    ^~~~~~
  CXX      meep-geom.o
geom.cpp: In function ‘boolean intersect_ray_with_segment(vector3, vector3, vector3, vector3, double*)’:
geom.cpp:2203:12: warning: ‘ss’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (s) *s=ss;
          ~~^~~
  CXX      meep-ctl-io.o
  CXXLD    meep
make[3]: Leaving directory '/home/andres/install/meep/scheme'
make[2]: Leaving directory '/home/andres/install/meep/scheme'
Making all in libpympb
make[2]: Entering directory '/home/andres/install/meep/libpympb'
  CXX      libpympb_la-pympb.lo
pympb.cpp: In member function ‘double py_mpb::mode_solver::compute_energy_in_objects(geometric_object_list)’:
pympb.cpp:24:22: warning: unused variable ‘n2’ [-Wunused-variable]
     int n1 = md->nx, n2 = md->ny, n3 = md->nz, i1, i2_, i3;                                        \
                      ^
pympb.cpp:2303:3: note: in expansion of macro ‘LOOP_XYZ’
   LOOP_XYZ(mdata) {
   ^~~~~~~~
pympb.cpp: In member function ‘cnumber py_mpb::mode_solver::compute_field_integral(py_mpb::field_integral_func, py_mpb::field_integral_energy_func, void*)’:
pympb.cpp:24:22: warning: unused variable ‘n2’ [-Wunused-variable]
     int n1 = md->nx, n2 = md->ny, n3 = md->nz, i1, i2_, i3;                                        \
                      ^
pympb.cpp:2359:3: note: in expansion of macro ‘LOOP_XYZ’
   LOOP_XYZ(mdata) {
   ^~~~~~~~
pympb.cpp: In member function ‘int py_mpb::mode_solver::mean_epsilon(symmetric_matrix*, symmetric_matrix*, mpb_real*, mpb_real, mpb_real, mpb_real, mpb_real, const mpb_real*)’:
pympb.cpp:347:75: warning: ‘mat2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                !(id2 < id1 && (id2 == id || meep_geom::material_type_equal(mat2, mat)))) {
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
pympb.cpp:341:75: warning: ‘mat1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                              (id1 == id2 || meep_geom::material_type_equal(mat1, mat2)))) {
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
  CXXLD    libpympb.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/home/andres/install/meep/libpympb'
Making all in python
make[2]: Entering directory '/home/andres/install/meep/python'
swig -Wextra -I../src -I../libpympb -I..  -outdir . -c++ -python -o meep-python.cxx ./meep.i
swig -Wextra -I../src -I../libpympb -I..  -I../libpympb -outdir . -c++ -python -o mpb-python.cxx ./mpb.i
cp meep.py __init__.py
echo "__version__ = '1.8.0-3-ge0eff85'" >> __init__.py
if [[ "3.0.12" = 3.0.12 ]]; then \
    sed -i.bak '/^if _swig_python_version_info >= (2, 7, 0):/,/^else:/d' __init__.py; \
    sed -i.bak 's/    import _meep/from . import _meep/' __init__.py; \
fi
if [[ "3.0.12" == 3.0.12 ]]; then \
    sed -i.bak '/^if _swig_python_version_info >= (2, 7, 0):/,/^else:/d' mpb.py; \
    sed -i.bak 's/    import _mpb/from . import _mpb/' mpb.py; \
fi
make  all-am
make[3]: Entering directory '/home/andres/install/meep/python'
  CXX      _meep_la-meep-python.lo
meep-python.cxx: In function ‘PyObject* _wrap_abort__varargs__(PyObject*, PyObject*, PyObject*)’:
meep-python.cxx:20331:103: warning: unused parameter ‘varargs’ [-Wunused-parameter]
 SWIGINTERN PyObject *_wrap_abort__varargs__(PyObject *SWIGUNUSEDPARM(self), PyObject *args, PyObject *varargs) {
                                                                                                       ^~~~~~~
meep-python.cxx: In function ‘PyObject* _wrap_master_printf__varargs__(PyObject*, PyObject*, PyObject*)’:
meep-python.cxx:86976:111: warning: unused parameter ‘varargs’ [-Wunused-parameter]
 SWIGINTERN PyObject *_wrap_master_printf__varargs__(PyObject *SWIGUNUSEDPARM(self), PyObject *args, PyObject *varargs) {
                                                                                                               ^~~~~~~
meep-python.cxx: In function ‘PyObject* _wrap_debug_printf__varargs__(PyObject*, PyObject*, PyObject*)’:
meep-python.cxx:87015:110: warning: unused parameter ‘varargs’ [-Wunused-parameter]
 SWIGINTERN PyObject *_wrap_debug_printf__varargs__(PyObject *SWIGUNUSEDPARM(self), PyObject *args, PyObject *varargs) {
                                                                                                              ^~~~~~~
meep-python.cxx: In function ‘PyObject* _wrap_master_fprintf__varargs__(PyObject*, PyObject*, PyObject*)’:
meep-python.cxx:87054:112: warning: unused parameter ‘varargs’ [-Wunused-parameter]
 SWIGINTERN PyObject *_wrap_master_fprintf__varargs__(PyObject *SWIGUNUSEDPARM(self), PyObject *args, PyObject *varargs) {
                                                                                                                ^~~~~~~
  CXXLD    _meep.la
ar: `u' modifier ignored since `D' is the default (see `U')
  CXX      _mpb_la-mpb-python.lo
In file included from mpb-python.cxx:3164:0:
typemap_utils.cpp:835:18: warning: ‘PyObject* gobj_list_to_py_list(geometric_object_list*)’ defined but not used [-Wunused-function]
 static PyObject *gobj_list_to_py_list(geometric_object_list *objs) {
                  ^~~~~~~~~~~~~~~~~~~~
  CXXLD    _mpb.la
ar: `u' modifier ignored since `D' is the default (see `U')
cp meep.py __init__.py
echo "__version__ = '1.8.0-3-ge0eff85'" >> __init__.py
if [[ "3.0.12" = 3.0.12 ]]; then \
    sed -i.bak '/^if _swig_python_version_info >= (2, 7, 0):/,/^else:/d' __init__.py; \
    sed -i.bak 's/    import _meep/from . import _meep/' __init__.py; \
fi
if [[ "3.0.12" == 3.0.12 ]]; then \
    sed -i.bak '/^if _swig_python_version_info >= (2, 7, 0):/,/^else:/d' mpb.py; \
    sed -i.bak 's/    import _mpb/from . import _mpb/' mpb.py; \
fi
mkdir -p meep
cp __init__.py ./geom.py ./simulation.py ./source.py ./materials.py .libs/_meep.so meep
mkdir -p meep/mpb
cp .libs/_mpb.so meep/mpb
cp ./mpb.py meep/mpb/__init__.py
cp ./solver.py ./mpb_data.py meep/mpb
make[3]: Leaving directory '/home/andres/install/meep/python'
make[2]: Leaving directory '/home/andres/install/meep/python'
make[2]: Entering directory '/home/andres/install/meep'
make[2]: Leaving directory '/home/andres/install/meep'
make[1]: Leaving directory '/home/andres/install/meep'
Making install in src
make[1]: Entering directory '/home/andres/install/meep/src'
make  install-am
make[2]: Entering directory '/home/andres/install/meep/src'
make[3]: Entering directory '/home/andres/install/meep/src'
 /bin/mkdir -p '/usr/local/lib'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   libmeep.la '/usr/local/lib'
libtool: install: /usr/bin/install -c .libs/libmeep.so.13.0.0 /usr/local/lib/libmeep.so.13.0.0
libtool: install: (cd /usr/local/lib && { ln -s -f libmeep.so.13.0.0 libmeep.so.13 || { rm -f libmeep.so.13 && ln -s libmeep.so.13.0.0 libmeep.so.13; }; })
libtool: install: (cd /usr/local/lib && { ln -s -f libmeep.so.13.0.0 libmeep.so || { rm -f libmeep.so && ln -s libmeep.so.13.0.0 libmeep.so; }; })
libtool: install: /usr/bin/install -c .libs/libmeep.lai /usr/local/lib/libmeep.la
libtool: install: /usr/bin/install -c .libs/libmeep.a /usr/local/lib/libmeep.a
libtool: install: chmod 644 /usr/local/lib/libmeep.a
libtool: install: ranlib /usr/local/lib/libmeep.a
libtool: finish: PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/sbin" ldconfig -n /usr/local/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /usr/local/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the 'LD_RUN_PATH' environment variable
     during linking
   - use the '-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to '/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /bin/mkdir -p '/usr/local/include'
 /usr/bin/install -c -m 644 meep.hpp '/usr/local/include'
 /bin/mkdir -p '/usr/local/include/meep'
 /usr/bin/install -c -m 644 meep/mympi.hpp meep/vec.hpp meepgeom.hpp material_data.hpp '/usr/local/include/meep'
make[3]: Leaving directory '/home/andres/install/meep/src'
make[2]: Leaving directory '/home/andres/install/meep/src'
make[1]: Leaving directory '/home/andres/install/meep/src'
Making install in tests
make[1]: Entering directory '/home/andres/install/meep/tests'
make[2]: Entering directory '/home/andres/install/meep/tests'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/andres/install/meep/tests'
make[1]: Leaving directory '/home/andres/install/meep/tests'
Making install in scheme
make[1]: Entering directory '/home/andres/install/meep/scheme'
make  install-am
make[2]: Entering directory '/home/andres/install/meep/scheme'
make[3]: Entering directory '/home/andres/install/meep/scheme'
 /bin/mkdir -p '/usr/local/bin'
  /bin/bash ../libtool   --mode=install /usr/bin/install -c meep '/usr/local/bin'
libtool: install: /usr/bin/install -c .libs/meep /usr/local/bin/meep
 /bin/mkdir -p '/usr/local/share/meep'
 /usr/bin/install -c -m 644 meep.scm meep-enums.scm casimir.scm materials.scm '/usr/local/share/meep'
make[3]: Leaving directory '/home/andres/install/meep/scheme'
make[2]: Leaving directory '/home/andres/install/meep/scheme'
make[1]: Leaving directory '/home/andres/install/meep/scheme'
Making install in libpympb
make[1]: Entering directory '/home/andres/install/meep/libpympb'
make[2]: Entering directory '/home/andres/install/meep/libpympb'
 /bin/mkdir -p '/usr/local/lib'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   libpympb.la '/usr/local/lib'
libtool: warning: relinking 'libpympb.la'
libtool: install: (cd /home/andres/install/meep/libpympb; /bin/bash "/home/andres/install/meep/libtool"  --silent --tag CXX --mode=relink mpic++ -O3 -fstrict-aliasing -mtune=native -Wall -W -version-info 13:0:0 -o libpympb.la -rpath /usr/local/lib libpympb_la-pympb.lo ../src/libmeep.la -lGDSII -lz -lgsl -lgslcblas -lm -lmpb -L/usr/local/lib -lharminv -llapack -lblas -lm -lf2c -lm -llapack -lblas -lfftw3 -lm -lfftw3 -lm -lf2c )
libtool: install: /usr/bin/install -c .libs/libpympb.so.13.0.0T /usr/local/lib/libpympb.so.13.0.0
libtool: install: (cd /usr/local/lib && { ln -s -f libpympb.so.13.0.0 libpympb.so.13 || { rm -f libpympb.so.13 && ln -s libpympb.so.13.0.0 libpympb.so.13; }; })
libtool: install: (cd /usr/local/lib && { ln -s -f libpympb.so.13.0.0 libpympb.so || { rm -f libpympb.so && ln -s libpympb.so.13.0.0 libpympb.so; }; })
libtool: install: /usr/bin/install -c .libs/libpympb.lai /usr/local/lib/libpympb.la
libtool: install: /usr/bin/install -c .libs/libpympb.a /usr/local/lib/libpympb.a
libtool: install: chmod 644 /usr/local/lib/libpympb.a
libtool: install: ranlib /usr/local/lib/libpympb.a
libtool: finish: PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/sbin" ldconfig -n /usr/local/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /usr/local/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the 'LD_RUN_PATH' environment variable
     during linking
   - use the '-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to '/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /bin/mkdir -p '/usr/local/include/meep'
 /usr/bin/install -c -m 644 pympb.hpp '/usr/local/include/meep'
make[2]: Leaving directory '/home/andres/install/meep/libpympb'
make[1]: Leaving directory '/home/andres/install/meep/libpympb'
Making install in python
make[1]: Entering directory '/home/andres/install/meep/python'
cp meep.py __init__.py
echo "__version__ = '1.8.0-3-ge0eff85'" >> __init__.py
if [[ "3.0.12" = 3.0.12 ]]; then \
    sed -i.bak '/^if _swig_python_version_info >= (2, 7, 0):/,/^else:/d' __init__.py; \
    sed -i.bak 's/    import _meep/from . import _meep/' __init__.py; \
fi
if [[ "3.0.12" == 3.0.12 ]]; then \
    sed -i.bak '/^if _swig_python_version_info >= (2, 7, 0):/,/^else:/d' mpb.py; \
    sed -i.bak 's/    import _mpb/from . import _mpb/' mpb.py; \
fi
make  install-am
make[2]: Entering directory '/home/andres/install/meep/python'
cp meep.py __init__.py
echo "__version__ = '1.8.0-3-ge0eff85'" >> __init__.py
if [[ "3.0.12" = 3.0.12 ]]; then \
    sed -i.bak '/^if _swig_python_version_info >= (2, 7, 0):/,/^else:/d' __init__.py; \
    sed -i.bak 's/    import _meep/from . import _meep/' __init__.py; \
fi
if [[ "3.0.12" == 3.0.12 ]]; then \
    sed -i.bak '/^if _swig_python_version_info >= (2, 7, 0):/,/^else:/d' mpb.py; \
    sed -i.bak 's/    import _mpb/from . import _mpb/' mpb.py; \
fi
mkdir -p meep
cp __init__.py ./geom.py ./simulation.py ./source.py ./materials.py .libs/_meep.so meep
mkdir -p meep/mpb
cp .libs/_mpb.so meep/mpb
cp ./mpb.py meep/mpb/__init__.py
cp ./solver.py ./mpb_data.py meep/mpb
make[3]: Entering directory '/home/andres/install/meep/python'
 /bin/mkdir -p '/usr/local/lib/python3.6/site-packages/meep'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   _meep.la '/usr/local/lib/python3.6/site-packages/meep'
libtool: warning: relinking '_meep.la'
libtool: install: (cd /home/andres/install/meep/python; /bin/bash "/home/andres/install/meep/libtool"  --silent --tag CXX --mode=relink mpic++ -O3 -fstrict-aliasing -mtune=native -Wall -W -module -version-info 13:0:0 -o _meep.la -rpath /usr/local/lib/python3.6/site-packages/meep _meep_la-meep-python.lo ../src/libmeep.la -lctlgeom -lGDSII -lz -lgsl -lgslcblas -lm -lmpb -L/usr/local/lib -lharminv -llapack -lblas -lm -lf2c -lm -llapack -lblas -lfftw3 -lm -lfftw3 -lm -lf2c )
libtool: install: /usr/bin/install -c .libs/_meep.so.13.0.0T /usr/local/lib/python3.6/site-packages/meep/_meep.so.13.0.0
libtool: install: (cd /usr/local/lib/python3.6/site-packages/meep && { ln -s -f _meep.so.13.0.0 _meep.so.13 || { rm -f _meep.so.13 && ln -s _meep.so.13.0.0 _meep.so.13; }; })
libtool: install: (cd /usr/local/lib/python3.6/site-packages/meep && { ln -s -f _meep.so.13.0.0 _meep.so || { rm -f _meep.so && ln -s _meep.so.13.0.0 _meep.so; }; })
libtool: install: /usr/bin/install -c .libs/_meep.lai /usr/local/lib/python3.6/site-packages/meep/_meep.la
libtool: install: /usr/bin/install -c .libs/_meep.a /usr/local/lib/python3.6/site-packages/meep/_meep.a
libtool: install: chmod 644 /usr/local/lib/python3.6/site-packages/meep/_meep.a
libtool: install: ranlib /usr/local/lib/python3.6/site-packages/meep/_meep.a
libtool: finish: PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/sbin" ldconfig -n /usr/local/lib/python3.6/site-packages/meep
----------------------------------------------------------------------
Libraries have been installed in:
   /usr/local/lib/python3.6/site-packages/meep

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the 'LD_RUN_PATH' environment variable
     during linking
   - use the '-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to '/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
cp meep.py __init__.py
echo "__version__ = '1.8.0-3-ge0eff85'" >> __init__.py
if [[ "3.0.12" = 3.0.12 ]]; then \
    sed -i.bak '/^if _swig_python_version_info >= (2, 7, 0):/,/^else:/d' __init__.py; \
    sed -i.bak 's/    import _meep/from . import _meep/' __init__.py; \
fi
if [[ "3.0.12" == 3.0.12 ]]; then \
    sed -i.bak '/^if _swig_python_version_info >= (2, 7, 0):/,/^else:/d' mpb.py; \
    sed -i.bak 's/    import _mpb/from . import _mpb/' mpb.py; \
fi
 /bin/mkdir -p '/usr/local/lib/python3.6/site-packages/meep'
 /usr/bin/install -c -m 644 geom.py __init__.py source.py simulation.py materials.py '/usr/local/lib/python3.6/site-packages/meep'
Byte-compiling python modules...
geom.py__init__.pysource.pysimulation.pymaterials.py
Byte-compiling python modules (optimized versions) ...
geom.py__init__.pysource.pysimulation.pymaterials.py
 /bin/mkdir -p '/usr/local/lib/python3.6/site-packages/meep/mpb'
 /usr/bin/install -c -m 644 mpb.py solver.py mpb_data.py '/usr/local/lib/python3.6/site-packages/meep/mpb'
 /bin/mkdir -p '/usr/local/lib/python3.6/site-packages/meep/mpb'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   _mpb.la '/usr/local/lib/python3.6/site-packages/meep/mpb'
libtool: warning: relinking '_mpb.la'
libtool: install: (cd /home/andres/install/meep/python; /bin/bash "/home/andres/install/meep/libtool"  --silent --tag CXX --mode=relink mpic++ -O3 -fstrict-aliasing -mtune=native -Wall -W -module -version-info 13:0:0 -o _mpb.la -rpath /usr/local/lib/python3.6/site-packages/meep/mpb _mpb_la-mpb-python.lo ../libpympb/libpympb.la -lctlgeom -lGDSII -lz -lgsl -lgslcblas -lm -lmpb -L/usr/local/lib -lharminv -llapack -lblas -lm -lf2c -lm -llapack -lblas -lfftw3 -lm -lfftw3 -lm -lf2c )
libtool: install: /usr/bin/install -c .libs/_mpb.so.13.0.0T /usr/local/lib/python3.6/site-packages/meep/mpb/_mpb.so.13.0.0
libtool: install: (cd /usr/local/lib/python3.6/site-packages/meep/mpb && { ln -s -f _mpb.so.13.0.0 _mpb.so.13 || { rm -f _mpb.so.13 && ln -s _mpb.so.13.0.0 _mpb.so.13; }; })
libtool: install: (cd /usr/local/lib/python3.6/site-packages/meep/mpb && { ln -s -f _mpb.so.13.0.0 _mpb.so || { rm -f _mpb.so && ln -s _mpb.so.13.0.0 _mpb.so; }; })
libtool: install: /usr/bin/install -c .libs/_mpb.lai /usr/local/lib/python3.6/site-packages/meep/mpb/_mpb.la
libtool: install: /usr/bin/install -c .libs/_mpb.a /usr/local/lib/python3.6/site-packages/meep/mpb/_mpb.a
libtool: install: chmod 644 /usr/local/lib/python3.6/site-packages/meep/mpb/_mpb.a
libtool: install: ranlib /usr/local/lib/python3.6/site-packages/meep/mpb/_mpb.a
libtool: finish: PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/sbin" ldconfig -n /usr/local/lib/python3.6/site-packages/meep/mpb
----------------------------------------------------------------------
Libraries have been installed in:
   /usr/local/lib/python3.6/site-packages/meep/mpb

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the 'LD_RUN_PATH' environment variable
     during linking
   - use the '-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to '/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make  install-data-hook
make[4]: Entering directory '/home/andres/install/meep/python'
mv /usr/local/lib/python3.6/site-packages/meep/mpb/mpb.py /usr/local/lib/python3.6/site-packages/meep/mpb/__init__.py
make[4]: Leaving directory '/home/andres/install/meep/python'
make[3]: Leaving directory '/home/andres/install/meep/python'
make[2]: Leaving directory '/home/andres/install/meep/python'
make[1]: Leaving directory '/home/andres/install/meep/python'
make[1]: Entering directory '/home/andres/install/meep'
make[2]: Entering directory '/home/andres/install/meep'
make[2]: Nothing to be done for 'install-exec-am'.
 /bin/mkdir -p '/usr/local/lib/pkgconfig'
 /usr/bin/install -c -m 644 meep.pc '/usr/local/lib/pkgconfig'
make[2]: Leaving directory '/home/andres/install/meep'
make[1]: Leaving directory '/home/andres/install/meep'

[ChristopherHogan]

What is the output of

$ ldd /usr/local/bin/meep

[DiegoGuisasola]

This one:

[ChristopherHogan]

Hmm. I'm not sure what's going on. Although I see that meep isn't linking with any hdf5 or BLAS. I'd probably need to see the output of configure next.

$ cd ~/install/meep
$ ./configure > configure.out 2 >&1

[DiegoGuisasola]

[ChristopherHogan]

Sorry, remove the space between 2 and >. Should be 2>&1.

[DiegoGuisasola]

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for g++... g++
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 g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
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... d:756e6547:6c65746e:49656e69
checking for x86 cpuid 1 output... 306c3:1100800:7ffafbbf:bfebfbff
checking whether C++ compiler accepts -mtune=native... yes
checking for gcc architecture flag... -mtune=native
checking whether C++ compiler accepts -O3 -fstrict-aliasing -mtune=native... yes
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
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 how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-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... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc 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... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -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 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... yes
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... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /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 g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
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checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ 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 latex2html... no
configure: WARNING: Cannot find latex2html in your path!
checking for sin in -lm... yes
checking for fftw_plan_dft_1d in -lfftw3... yes
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checking for f77... f77
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether f77 accepts -g... yes
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checking for f77 option to produce PIC... -fPIC
checking if f77 PIC flag -fPIC works... yes
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checking if f77 supports -c -o file.o... yes
checking if f77 supports -c -o file.o... (cached) yes
checking whether the f77 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 f77... -v
checking for Fortran 77 libraries of f77...  -lfftw3 -lm -lf2c
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, extra underscore
checking for sgemm_... no
checking for ATL_xerbla in -latlas... no
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checking for cheev_ in -llapack... 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 -lharminv -llapack -lblas -lm -lf2c -lm
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... no
configure: WARNING: Couldn't find the HDF5 library!!  Switching to --without-hdf5.
checking for guile-config... guile-config
checking if linking to guile works... yes
checking libguile.h usability... yes
checking libguile.h presence... yes
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checking sys/time.h usability... yes
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checking for gettimeofday... yes
checking for cblas_ddot... yes
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checking for jn... yes
checking for C/C++ restrict keyword... __restrict
checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.7/dist-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages
checking for Python include directory... /usr/include/python2.7
checking Python.h usability... no
checking Python.h presence... no
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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 Makefile
config.status: creating meep-pkgconfig
config.status: creating src/Makefile
config.status: creating tests/Makefile
config.status: creating scheme/Makefile
config.status: creating scheme/meep.scm
config.status: creating libpympb/Makefile
config.status: creating python/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands

[ChristopherHogan]

I'm stumped. For now, I would say use the built version at ~/install/meep/scheme/meep. I'll try to reproduce this next week.

[DiegoGuisasola]

Thank you very much and I apologize for asking too many questions. You are a great person!

[ChristopherHogan]

I updated the build script in #725. I ran that script as is (with the adjustments for 18.04) on a clean installation of Ubuntu 18.04 and everything worked as expected. Please try the script with those changes.

[ChristopherHogan]

The script you pasted above that you ran was modified from the original (you removed the Python libraries). I know I told you to do that since you were only interested in Scheme, but that would also mean changing several other things, and to avoid confusion, it's probably best to just run the full script as is.

[stevengj]

Sounds like this can be closed.

[DiegoGuisasola]

Yep, sorry for not closing it before. Thanks a lot for everything!

[closest-git]

您好，您的问题是否解决？我也遇到同样的问题