Hi, c7420, after a minor improvement, it seems the blue-boxed installation script works box (with openmpi) also on Debian Jenny. The updated version is temporarily here: https://gist.github.com/FilipDominec/6e6e62ccf8b22c1c4e40
I verified that both the meep example (ring.ctl) and my python-meep examples https://github.com/FilipDominec/python-meep-utils) produced expected results. There are two problems: 1) I did not modify the installation to work with mpich instead of opempi. Perhaps it can be done easily, I did not check. 2) Interestingly enough, harminv that was installed by the script at Debian Jenny does not work; it did not find any oscillators from sample data, whereas the exactly same setup worked reliably on my working computer. I will try to find out why. Filip 2015-03-23 16:12 GMT+01:00, c7...@gmx.net <c7...@gmx.net>: > I just tried the blue boxed script out of the box (with mpi) and with > changing "libhdf5-openmpi-dev" to "libhdf5-serial-dev" in line number > #17 and excluding the "--with-mpi" command in meep's "configure" > routine. They both cannot find the hdf5 libraries. > > Here is the output of "find /usr/lib -name '*hdf5*'", which should show > all my installed hdf5 libraries. > > /usr/lib/python2.7/dist-packages/scipy/io/matlab/tests/data/testhdf5_7.4_GLNX86.mat > /usr/lib/python2.7/dist-packages/tables/tests/test_hdf5compat.py > /usr/lib/python2.7/dist-packages/tables/tests/test_hdf5compat.pyc > /usr/lib/python2.7/dist-packages/tables/hdf5Extension.py > /usr/lib/python2.7/dist-packages/tables/hdf5Extension.pyc > /usr/lib/python2.7/dist-packages/tables/hdf5extension.x86_64-linux-gnu.so > /usr/lib/x86_64-linux-gnu/libhdf5_serial_fortran.so.8.0.2 > /usr/lib/x86_64-linux-gnu/libhdf5_serial_hl.so.8.0.2 > /usr/lib/x86_64-linux-gnu/libhdf5_openmpihl_fortran.so.8.0.2 > /usr/lib/x86_64-linux-gnu/libhdf5_openmpi_fortran.so.8 > /usr/lib/x86_64-linux-gnu/libhdf5_serial_hl.so.8 > /usr/lib/x86_64-linux-gnu/libhdf5_serial_fortran.so > /usr/lib/x86_64-linux-gnu/libhdf5_openmpi_fortran.so.8.0.2 > /usr/lib/x86_64-linux-gnu/libhdf5_serial_fortran.so.8 > /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.8.0.2 > /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so > /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so > /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.8.0.2 > /usr/lib/x86_64-linux-gnu/hdf5 > /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5hl_fortran.a > /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so > /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.so > /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.a > /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.settings > /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl.so > /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5hl_fortran.so > /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so > /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl.a > /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_fortran.a > /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_fortran.so > /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.a > /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.a > /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5hl_fortran.a > /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.settings > /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5_hl.so > /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5hl_fortran.so > /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so > /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5_hl.a > /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5_fortran.a > /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5_fortran.so > /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.a > /usr/lib/x86_64-linux-gnu/libhdf5_serialhl_fortran.a > /usr/lib/x86_64-linux-gnu/libhdf5_serialhl_fortran.so > /usr/lib/x86_64-linux-gnu/libhdf5_hl_cpp.so > /usr/lib/x86_64-linux-gnu/libhdf5_serial.settings > /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.8.0.2 > /usr/lib/x86_64-linux-gnu/libhdf5_serial_hl.a > /usr/lib/x86_64-linux-gnu/libhdf5_hl_cpp.a > /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.8 > /usr/lib/x86_64-linux-gnu/libhdf5_serial_hl.so > /usr/lib/x86_64-linux-gnu/libhdf5_hl_cpp.so.8.0.2 > /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc > /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc > /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-openmpi.pc > /usr/lib/x86_64-linux-gnu/libhdf5_openmpi_fortran.a > /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.a > /usr/lib/x86_64-linux-gnu/libhdf5_openmpi_hl.a > /usr/lib/x86_64-linux-gnu/libhdf5_serialhl_fortran.so.8.0.2 > /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.settings > /usr/lib/x86_64-linux-gnu/libhdf5_openmpi_hl.so.8.0.2 > /usr/lib/x86_64-linux-gnu/libhdf5_openmpi_hl.so.8 > /usr/lib/x86_64-linux-gnu/libhdf5_openmpihl_fortran.a > /usr/lib/x86_64-linux-gnu/libhdf5_serial.a > /usr/lib/x86_64-linux-gnu/libhdf5_serialhl_fortran.so.8 > /usr/lib/x86_64-linux-gnu/libhdf5_openmpi_hl.so > /usr/lib/x86_64-linux-gnu/libhdf5_hl_cpp.so.8 > /usr/lib/x86_64-linux-gnu/libhdf5_serial.so > /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.8 > /usr/lib/x86_64-linux-gnu/libhdf5_openmpi_fortran.so > /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.8 > /usr/lib/x86_64-linux-gnu/libhdf5_openmpihl_fortran.so > /usr/lib/x86_64-linux-gnu/libhdf5_cpp.a > /usr/lib/x86_64-linux-gnu/libhdf5_openmpihl_fortran.so.8 > /usr/lib/x86_64-linux-gnu/libhdf5_serial_fortran.a > /usr/lib/jni/libjhdf5.so > > I also tried to add the libraries separately with: > export > LD_RUN_PATH="/usr/local/lib/:/usr/lib/x86_64-linux-gnu/hdf5/openmpi/" > > but no luck. > > > On Mon, 2015-03-23 at 09:10 +0100, Filip Dominec wrote: >> Hi, >> from what you wrote, I feel motivated to help you. Not only are there >> many users of python-meep, but even more I am wondering what may be >> wrong with that blue box script. I would be thankful if you help me >> find this out. >> >> Python-meep should really be a frontend for MEEP; all interfacing with >> HDF5 files is done through the libmeep.so's built-in functions. If >> libmeep.so behaves differently, you perhaps use two different versions >> of the library. Note that the blue script installs into /usr/local/lib >> instead of the default /usr/lib. This is to allow coexistence with the >> libraries from the repository. Python-meep then loads the libmeep >> library from /usr/local/lib, but by default, meeps loads the latter. I >> guess that's it. >> >> To find the actual problem: About a month ago, I made a change in the >> procedure, changing line #17 to replace 'libhdf5-serial-dev' with >> 'libhdf5-openmpi-dev'. Although both versions worked on my system >> (ubuntu 13.10), the second one should be faster. Can you remember >> which version you used? Can you please recompile meep and python-meep >> again, testing these two (serial / openmpi) versions? >> >> Best, >> Filip >> >> >> >> >> 2015-03-23 2:25 GMT+01:00, c7...@gmx.net <c7...@gmx.net>: >> > That script is actually what I based my build on, and from what I can >> > tell it is working fine for the most part. However, what is not working >> > are the HDF5 output functions in MPI mode and using python-meep. If you >> > use OpenMPI, the program will continue to run forever because it can't >> > write to the files. The processes are blocking each other. OpenMPI >> > doesn't tell you that, MPICH however does. >> > >> > This does not seem to be problem with Meep, but with python-meep. I >> > wrote a small *.ctl script to test the output functions and they work. >> > Somehow python-meep is using the wrong hdf5 libraries (the ones that >> > don't have mpi enabled), if that is even possible. I thought it was >> > "just" a frontend for meep. >> > >> > Installing Meep from the repositories on Debian Jessie was the first >> > thing I did, then I compiled python-meep against those and got the it >> > running. Non-MPI worked flawless. MPI-Mode worked, but without the hdf5 >> > functions. >> > >> > Then I tried to compile everything myself, because I could not find any >> > answers on the matter, and that is when I encountered my original >> > problem with "./configure" not finding HDF5 libraries either. >> > >> > >> > >> > On Sun, 2015-03-22 at 22:17 +0100, Filip Dominec wrote: >> >> Hi, I would traditionally refer you to the blue-boxed compilation >> >> procedure at http://f.dominec.eu/meep/index.html#install >> >> >> >> I tested it on different Ubuntu/Debian machines. Does it work on your >> >> system? >> >> >> >> Filip >> >> >> >> 2015-03-22 3:07 GMT+01:00, c7...@gmx.net <c7...@gmx.net>: >> >> > Unfortunately that didn't work, but it definitely has something to do >> >> > with >> >> > the MPI. I just compiled all packages without it and MEEP finds the >> >> > libraries. >> >> > Something is preventing meep from finding the HDF5 packages when it >> >> > is >> >> > compiled with mpi-support. >> >> > >> >> > Greetings >> >> > c7420 >> >> > >> >> > Gesendet: Sonntag, 22. März 2015 um 00:34 Uhr >> >> > Von: "Pavel Ivanov" <pavel.ivanov.2...@googlemail.com> >> >> > An: c7...@gmx.net >> >> > Betreff: Re: [Meep-discuss] Meep can't find HDF5 libraries during >> >> > ./configure >> >> > Dear C7420, >> >> > >> >> > Try configuring and building all packages (not just HDF5 library) by >> >> > forcing >> >> > building scripts into using MPI versions of compilers. Here is an >> >> > example >> >> > from my notes: >> >> > CC=mpicc CXX=mpicxx F77=mpif77 ./configure --prefix=/home/el1pi/opt >> >> > --enable-parallel >> >> > make >> >> > make install >> >> > >> >> > Sometimes, it helps. Hopefully, it will help this time. >> >> > >> >> > best wishes >> >> > pavlo >> >> > >> >> > >> >> > >> >> > On 21/03/15 20:35, c7...@gmx.net wrote: >> >> >> >> >> >> Dear Meep-Users, >> >> >> I am failing to compile meep with MPICH and HDF5. I successfully >> >> >> build >> >> >> mpich-3.1.4 and hdf5-1.8.9.tar from source on a Debian Jessie >> >> >> machine. >> >> >> (Yes, I tried the precompiled packages too. They throw out errors >> >> >> when >> >> >> trying to write to the hdf5 files in mpi-mode.) >> >> >> The following problem may not have anything to do with the >> >> >> repository >> >> >> packages not working properly, but I tried to compile the programs >> >> >> myself >> >> >> anyway and all of the dependencies compile without errors. Only Meep >> >> >> can't >> >> >> find the HDF5 libraries in the custom location. >> >> >> >> >> >> This is the bash function I used to compile HDF5: >> >> >> function HDF5 { >> >> >> tar -xf hdf5-1.8.14.tar >> >> >> cd ./hdf5-1.8.14 >> >> >> export CC="$BUILD_DIR/bin/mpicc" >> >> >> export F77="$BUILD_DIR/bin/mpif77" >> >> >> export CXX="$BUILD_DIR/bin/mpic++" >> >> >> ./configure --prefix=$BUILD_DIR --enable-parallel 2>&1 | tee >> >> >> ../Output/HDF5_configure.out >> >> >> make 2>&1 | tee ../Output/HDF5_make.out >> >> >> make check 2>&1 | tee ../Output/HDF5_make_check.out >> >> >> make install 2>&1 | tee ../Output/HDF5_make_install.out >> >> >> cd .. >> >> >> rm -r -f ./hdf5-1.8.14 >> >> >> export CC="gcc" >> >> >> export F77="f77" >> >> >> export CXX="g++" >> >> >> } >> >> >> >> >> >> >> >> >> After Installing libctl, MPICH and HarmInv+OpenBLAS I tried: >> >> >> >> >> >> export CFLAGS=" -fPIC"; export CXXFLAGS=" -fPIC"; export FFLAGS=" >> >> >> -fPIC" >> >> >> export CC="gcc"; export F77="f77"; export CXX="g++" >> >> >> export CPPFLAGS="-I$BUILD_DIR/include" >> >> >> export LDFLAGS="-L$BUILD_DIR/lib" >> >> >> export LD_RUN_PATH="-L$BUILD_DIR/lib" >> >> >> export PATH="$BUILD_DIR/bin:$PATH" >> >> >> >> >> >> function MEEP { >> >> >> tar -xf meep-1.2.1.tar.gz >> >> >> cd ./meep-1.2.1 >> >> >> export MPICXX="$BUILD_DIR/bin/mpic++" >> >> >> ./configure --with-mpi --prefix=$BUILD_DIR >> >> >> --with-libctl="$BUILD_DIR/share/libctl" 2>&1 | tee >> >> >> ../Output/MEEP_configure.out >> >> >> #make 2>&1 | tee ../Output/MEEP_make.out >> >> >> #make install 2>&1 | tee ../Output/MEEP_make_install.out >> >> >> cd .. >> >> >> rm -rf ./meep-1.2.1 >> >> >> } >> >> >> >> >> >> >> >> >> BELOW is the Output of the ./configure command from the function >> >> >> above. >> >> >> >> >> >> 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 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 for mpic++... /home/neutronst4r/Install/build/bin/mpic++ >> >> >> checking for mpi.h... yes >> >> >> checking for extra flag needed to combine stdio.h and mpi.h... none >> >> >> checking build system type... x86_64-unknown-linux-gnu >> >> >> checking host system type... x86_64-unknown-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 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 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... @ >> >> >> 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 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 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... no >> >> >> checking whether to build static libraries... yes >> >> >> checking how to run the C++ preprocessor... >> >> >> /home/neutronst4r/Install/build/bin/mpic++ -E >> >> >> checking for ld used by >> >> >> /home/neutronst4r/Install/build/bin/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 /home/neutronst4r/Install/build/bin/mpic++ >> >> >> linker >> >> >> (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes >> >> >> checking for /home/neutronst4r/Install/build/bin/mpic++ option to >> >> >> produce >> >> >> PIC... -fPIC -DPIC >> >> >> checking if /home/neutronst4r/Install/build/bin/mpic++ PIC flag >> >> >> -fPIC >> >> >> -DPIC works... yes >> >> >> checking if /home/neutronst4r/Install/build/bin/mpic++ static flag >> >> >> -static >> >> >> works... yes >> >> >> checking if /home/neutronst4r/Install/build/bin/mpic++ supports -c >> >> >> -o >> >> >> file.o... yes >> >> >> checking if /home/neutronst4r/Install/build/bin/mpic++ supports -c >> >> >> -o >> >> >> file.o... (cached) yes >> >> >> checking whether the /home/neutronst4r/Install/build/bin/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 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 >> >> >> checking whether we are using the GNU Fortran 77 compiler... yes >> >> >> checking whether f77 accepts -g... yes >> >> >> checking whether we are using the GNU Fortran 77 compiler... >> >> >> (cached) >> >> >> yes >> >> >> checking whether f77 accepts -g... (cached) yes >> >> >> checking if libtool supports shared libraries... yes >> >> >> checking whether to build shared libraries... no >> >> >> checking whether to build static libraries... yes >> >> >> checking for f77 option to produce PIC... -fPIC >> >> >> checking if f77 PIC flag -fPIC works... yes >> >> >> checking if f77 static flag -static works... yes >> >> >> 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... >> >> >> -L/home/neutronst4r/Install/build/lib >> >> >> -L/usr/lib/gcc/x86_64-linux-gnu/4.9 >> >> >> -L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../x86_64-linux-gnu >> >> >> -L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../../lib >> >> >> -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu >> >> >> -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../.. >> >> >> -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 for sgemm_... no >> >> >> checking for ATL_xerbla in -latlas... yes >> >> >> checking for sgemm_ in -lf77blas... yes >> >> >> checking for cblas_dgemm in -lcblas... yes >> >> >> checking for cheev_... no >> >> >> checking for cheev_ in -llapack... yes >> >> >> checking for pkg-config... /usr/bin/pkg-config >> >> >> checking for harminv >= 1.1... yes >> >> >> checking HARMINV_CFLAGS... >> >> >> checking HARMINV_LIBS... -lharminv >> >> >> checking mpb.h usability... no >> >> >> checking mpb.h presence... no >> >> >> checking for mpb.h... no >> >> >> checking for cblas_cgemm... 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 H5Pset_mpi... no >> >> >> checking for H5Pset_fapl_mpio... no >> >> >> checking for mpirun... mpirun >> >> >> checking for guile-config... guile-config >> >> >> checking if linking to guile works... yes >> >> >> checking libguile.h usability... yes >> >> >> checking libguile.h presence... yes >> >> >> checking for libguile.h... yes >> >> >> checking guile/gh.h usability... no >> >> >> checking guile/gh.h presence... no >> >> >> checking for guile/gh.h... no >> >> >> checking for scm_make_smob_type... yes >> >> >> checking for SCM_SMOB_PREDICATE... no >> >> >> checking for SCM_SMOB_DATA... no >> >> >> checking for SCM_NEWSMOB... no >> >> >> checking how to activate readline in Guile... ice-9 readline >> >> >> checking for libctl dir... >> >> >> /home/neutronst4r/Install/build/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 >> >> >> checking for ctl.h... yes >> >> >> checking whether libctl version is at least 3.2.0... ok >> >> >> checking for libctl_quiet feature... yes >> >> >> checking for basename in -lgen... no >> >> >> checking for feenableexcept... yes >> >> >> checking whether feenableexcept declaration is usable... yes >> >> >> checking whether to catch and ignore SIGFPE signals... no >> >> >> checking whether time.h and sys/time.h may both be included... yes >> >> >> checking sys/time.h usability... yes >> >> >> checking sys/time.h presence... yes >> >> >> checking for sys/time.h... yes >> >> >> checking for BSDgettimeofday... no >> >> >> checking for gettimeofday... yes >> >> >> checking for cblas_ddot... yes >> >> >> checking for cblas_daxpy... yes >> >> >> checking for jn... yes >> >> >> checking for C/C++ restrict keyword... __restrict >> >> >> 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 examples/Makefile >> >> >> config.status: creating libctl/Makefile >> >> >> config.status: creating libctl/meep.scm >> >> >> config.status: creating config.h >> >> >> config.status: executing depfiles commands >> >> >> config.status: executing libtool commands >> >> >> >> >> >> >> >> >> >> >> >> If anyone could help me out on this one, I would be very grateful. >> >> >> >> >> >> Greetings >> >> >> c7420 >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> >> meep-discuss mailing list >> >> >> meep-discuss@ab-initio.mit.edu >> >> >> http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss >> > >> > >> > >> > _______________________________________________ >> > meep-discuss mailing list >> > meep-discuss@ab-initio.mit.edu >> > http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss > > > > _______________________________________________ > meep-discuss mailing list > meep-discuss@ab-initio.mit.edu > http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss _______________________________________________ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
