Error in detecting liblzma.so.5.0.7 [SOLVED]

[sheng]

Hi,
I am using the newest abinit 7.8.2, and I notice that it is dependent on liblzma library to work.
The problem is that while I have the library version 5.0.7 installed and paths correctly configured, Abinit won't accept any version other than liblzma.so.0.
I have circumvent this by creating a symbolic link to liblzma.so.5.0.7 by the name of liblzma.so.0.
Is this the correct way to do this?

Thank you

Goh

[jbeuken]

Hi,

some precisions are required to help you...

- OS
- your configure command ( or your .ac and/or the config.log file(s)... )
- result of the command : ldd src/98_main/abinit

jmb

[sheng]

Sorry for late reply.

OS : Rocks 5.3 (Rolled Tacos)

config.ac:

Code: Select all

prefix="/share/apps/estools/abinit/7.8.2/"
enable_64bit_flags="yes"
enable_mpi="yes"
enable_mpi_io="yes"
enable_openmp="yes"
with_mpi_prefix="/share/apps/openmpi/1.8.1/gcc4.9.0"
with_trio_flavor="netcdf+etsf_io"
with_netcdf_incs="-I/share/apps/estools/netcdf/4.3.2/include"
with_netcdf_libs="-L/share/apps/estools/netcdf/4.3.2/lib -lnetcdf -lnetcdff"
with_etsf_io_incs="-I/share/apps/estools/etsf_io/1.0.4/include/gcc"
with_etsf_io_libs="-L/share/apps/estools/etsf_io/1.0.4/lib -letsf_io_low_level -letsf_io_utils -letsf_io"
with_fft_flavor="fftw3"
with_fft_incs="-I/share/apps/fftw/3.3.4/include"
with_fft_libs="-L/share/apps/fftw/3.3.4/lib -lfftw3 -lfftw3f"
with_linalg_flavor="atlas+scalapack"
with_linalg_incs="-I/share/apps/estools/ScaLAPACK/include -I/share/apps/ATLAS/3.10.1/include"
with_linalg_libs="-L/share/apps/estools/ScaLAPACK/lib -lscalapack -L/share/apps/ATLAS/3.10.1/lib -llapack -lf77blas -lcblas -latlas"
with_math_flavor="gsl"
with_math_incs="-I/share/apps/estools/gsl/1.16/include"
with_math_libs="-L/share/apps/estools/gsl/1.16/lib -lgsl -lgslcblas"
with_dft_flavor="atompaw+bigdft+libxc+wannier90"
with_atompaw_bins="/share/apps/estools/atompaw/4.0.0.10/bin"
with_atompaw_incs="-I/share/apps/estools/atompaw/4.0.0.10/include"
with_atompaw_libs="-L/share/apps/estools/atompaw/4.0.0.10/lib -latompaw"
with_bigdft_incs="-I/share/apps/estools/bigdft/1.7.1/include"
with_bigdft_libs="-L/share/apps/estools/libarchive/3.1.2/lib -larchive -L/share/apps/estools/bigdft/1.7.1/lib -lyaml -lbigdft-1 -labinit -L/share/apps/estools/etsf_io/1.0.4/lib -letsf_io_low_level -letsf_io_utils -letsf_io -L/share/apps/estools/netcdf/4.3.2/lib -lnetcdf -lnetcdff"
with_libxc_incs="-I/share/apps/estools/libxc/2.0.3/include"
with_libxc_libs="-L/share/apps/estools/libxc/2.0.3/lib -lxc"
with_wannier90_bins="/share/apps/estools/wannier90/2.0.0/bin"
with_wannier90_incs="-I/share/apps/estools/wannier90/2.0.0/include"
with_wannier90_libs="-L/share/apps/estools/wannier90/2.0.0/lib -lwannier"
enable_gw_dpc="yes"

result of ldd src/98_main/abinit:

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libarchive.so.13 => /share/apps/estools/libarchive/3.1.2/lib/libarchive.so.13 (0x00002b8ac16dc000)
   libyaml-0.so.2 => /share/apps/estools/bigdft/1.7.1/lib/libyaml-0.so.2 (0x00002b8ac1984000)
   libnetcdf.so.7 => /share/apps/estools/netcdf/4.3.2/lib/libnetcdf.so.7 (0x00002b8ac1ba3000)
   libnetcdff.so.6 => /share/apps/estools/netcdf/4.3.2/lib/libnetcdff.so.6 (0x00002b8ac1ebc000)
   libxc.so.1 => /share/apps/estools/libxc/2.0.3/lib/libxc.so.1 (0x00002b8ac2135000)
   libfftw3.so.3 => /share/apps/fftw/3.3.4/lib/libfftw3.so.3 (0x00002b8ac23d2000)
   libfftw3f.so.3 => /share/apps/fftw/3.3.4/lib/libfftw3f.so.3 (0x00002b8ac26ea000)
   libgsl.so.0 => /share/apps/estools/gsl/1.16/lib/libgsl.so.0 (0x00002b8ac29fa000)
   libgslcblas.so.0 => /share/apps/estools/gsl/1.16/lib/libgslcblas.so.0 (0x00002b8ac2e41000)
   librt.so.1 => /lib64/librt.so.1 (0x000000360dc00000)
   libmpi_usempi.so.1 => /share/apps/openmpi/1.8.1/gcc4.9.0/lib/libmpi_usempi.so.1 (0x00002b8ac30a6000)
   libmpi_mpifh.so.2 => /share/apps/openmpi/1.8.1/gcc4.9.0/lib/libmpi_mpifh.so.2 (0x00002b8ac33ad000)
   libmpi.so.1 => /share/apps/openmpi/1.8.1/gcc4.9.0/lib/libmpi.so.1 (0x00002b8ac3601000)
   libgfortran.so.3 => /share/apps/gcc/4.9.0/lib64/libgfortran.so.3 (0x00002b8ac38e9000)
   libm.so.6 => /lib64/libm.so.6 (0x000000360cc00000)
   libquadmath.so.0 => /share/apps/gcc/4.9.0/lib64/libquadmath.so.0 (0x00002b8ac3c13000)
   libpthread.so.0 => /lib64/libpthread.so.0 (0x000000360d400000)
   libgomp.so.1 => /share/apps/gcc/4.9.0/lib64/libgomp.so.1 (0x00002b8ac3e52000)
   libgcc_s.so.1 => /share/apps/gcc/4.9.0/lib64/libgcc_s.so.1 (0x00002b8ac4068000)
   libc.so.6 => /lib64/libc.so.6 (0x000000360c800000)
   libcrypto.so.6 => /lib64/libcrypto.so.6 (0x0000003884200000)
   liblzma.so.0 => /share/apps/estools/xz/5.0.7/lib/liblzma.so.0 (0x00002b8ac4280000)
   libbz2.so.1 => /usr/lib64/libbz2.so.1 (0x0000003620e00000)
   libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x0000003884a00000)
   libz.so.1 => /lib64/libz.so.1 (0x0000003883e00000)
   libhdf5_hl.so.8 => /share/apps/estools/hdf5/1.8.13/lib/libhdf5_hl.so.8 (0x00002b8ac44a6000)
   libhdf5.so.8 => /share/apps/estools/hdf5/1.8.13/lib/libhdf5.so.8 (0x00002b8ac46d4000)
   libdl.so.2 => /lib64/libdl.so.2 (0x000000360d000000)
   /lib64/ld-linux-x86-64.so.2 (0x000000360c400000)
   libopen-rte.so.7 => /share/apps/openmpi/1.8.1/gcc4.9.0/lib/libopen-rte.so.7 (0x00002b8ac4b8a000)
   libopen-pal.so.6 => /share/apps/openmpi/1.8.1/gcc4.9.0/lib/libopen-pal.so.6 (0x00002b8ac4e0b000)
   libnsl.so.1 => /lib64/libnsl.so.1 (0x000000360f800000)
   libutil.so.1 => /lib64/libutil.so.1 (0x0000003618000000)

[Jordan]

According to your cluster website you are running on CentOS 5.3.

Your ldd command return a found liblzma.so.0 which I guess is the symbolic link you created ?
This library is an API for compression which is not used directly by abinit but might be used by one of the packages you added or a library your linked with.

Usually for such generic libraries, there are several symbolic links to the same libxxxxx.so that are created during the installation process. Adding a new one should not be a problem.

If you run the test suite and don't have error/or very few/or with very small error tolerances, then I would say that everything works fine.

To do so, from where you are after typing make :

Code: Select all

cd tests
../../tests/runtests.py -j XX

when XX is the number of simultaneous tests (very often the number of cores your CPU has). This -j option is optional.

Cheers

Jordan

[sheng]

Hi, liblzma.so.0 is indeed the symbolic link I created to the new liblzma.so.7.
From what I notice there seems to be no problem running abinit so far.
It seems that abinit only accepts version 0 of the library, or is that intended specifically?

[Jordan]

Si I would said that everything works well.
Maybe the linker did something strange linking against .so.0 instead of the one you have.
As I said, usually there are all symbolic links to only one .so