Hi,
I recently compiled MEEP on my Ubuntu 64 machine. However, after
monkeying around a bit with the libraries (all installed from packages)
MPB (also installed from the deb package) has stopped working properly
with HDF5 (I tried several .ctl files that worked before, including the
example ones). Here's what I get:
HDF5-DIAG: Error detected in HDF5 library version: 1.6.4 thread
46912545313568. Back trace follows.
#000: ../../../src/H5F.c line 3146 in H5Fclose(): decrementing file
ID failed
major(07): Atom layer
minor(18): Unable to close file
#001: ../../../src/H5F.c line 3092 in H5F_close(): unable to flush cache
major(08): Meta data cache layer
minor(38): Unable to flush data from cache
#002: ../../../src/H5F.c line 2849 in H5F_flush(): low level flush failed
major(05): Low-level I/O layer
minor(25): Write failed
#003: ../../../src/H5FD.c line 3578 in H5FD_flush(): driver flush
request failed
major(22): Virtual File Layer
minor(29): Unable to initialize object
#004: ../../../src/H5FDsec2.c line 876 in H5FD_sec2_flush(): unable
to extend file properly
major(05): Low-level I/O layer
minor(23): Seek failed
CHECK failure on line 400 of ../../../../src/matrixio/matrixio.c: error
closing HDF file
MEEP, however, works just fine with HDF5 now. Using ldd on both the MPB
and the MEEP binaries shows that they both use the same hdf5 library:
~$ ldd /usr/bin/mpb
libctl.so.2 => /usr/lib/libctl.so.2 (0x00002aaaaabc2000)
libguile.so.12 => /usr/lib/libguile.so.12 (0x00002aaaaaccc000)
libguile-ltdl.so.1 => /usr/lib/libguile-ltdl.so.1
(0x00002aaaaae81000)
libcrypt.so.1 => /lib/libcrypt.so.1 (0x00002aaaaaf86000)
libm.so.6 => /lib/libm.so.6 (0x00002aaaab0ba000)
libhdf5-1.6.4.so.0 => /usr/lib/libhdf5-1.6.4.so.0
(0x00002aaaab23f000)
libz.so.1 => /usr/lib/libz.so.1 (0x00002aaaab457000)
liblapack.so.3 => /usr/lib/atlas/liblapack.so.3
(0x00002aaaab56e000)
libcblas.so.3 => /usr/lib/libcblas.so.3 (0x00002aaaabdd3000)
libf77blas.so.3 => /usr/lib/libf77blas.so.3 (0x00002aaaabef5000)
libatlas.so.3 => /usr/lib/libatlas.so.3 (0x00002aaaac019000)
libfftw.so.2 => /usr/lib/libfftw.so.2 (0x00002aaaac8b9000)
libg2c.so.0 => /usr/lib/libg2c.so.0 (0x00002aaaaca26000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00002aaaacb56000)
libc.so.6 => /lib/libc.so.6 (0x00002aaaacc63000)
libdl.so.2 => /lib/libdl.so.2 (0x00002aaaace9c000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00002aaaacf9f000)
libblas.so.3 => /usr/lib/atlas/libblas.so.3 (0x00002aaaad0b4000)
/lib64/ld-linux-x86-64.so.2 (0x00002aaaaaaab000)
~$ ldd /usr/local/bin/meep
libctl.so.3 => /usr/lib/libctl.so.3 (0x00002aaaaabc2000)
libguile.so.12 => /usr/lib/libguile.so.12 (0x00002aaaaacd4000)
libguile-ltdl.so.1 => /usr/lib/libguile-ltdl.so.1
(0x00002aaaaae89000)
libdl.so.2 => /lib/libdl.so.2 (0x00002aaaaaf8e000)
libcrypt.so.1 => /lib/libcrypt.so.1 (0x00002aaaab091000)
libhdf5-1.6.4.so.0 => /usr/lib/libhdf5-1.6.4.so.0
(0x00002aaaab1c4000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00002aaaab3dc000)
libz.so.1 => /usr/lib/libz.so.1 (0x00002aaaab4f2000)
libgsl.so.0 => /usr/lib/libgsl.so.0 (0x00002aaaab608000)
libgslcblas.so.0 => /usr/lib/libgslcblas.so.0 (0x00002aaaab8ab000)
libfftw3.so.3 => /usr/lib/libfftw3.so.3 (0x00002aaaab9d9000)
libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00002aaaabb90000)
libm.so.6 => /lib/libm.so.6 (0x00002aaaabd8d000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00002aaaabf13000)
libc.so.6 => /lib/libc.so.6 (0x00002aaaac020000)
/lib64/ld-linux-x86-64.so.2 (0x00002aaaaaaab000)
Any ideas on what I did to screw up my MPB and how to un-screw it would
be greatly appreciated.
Regards,
Roel Arts
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