Configuration problems with Abinit 8.10.2

JimEvans · Post by **JimEvans** » Sun Feb 03, 2019 3:14 am

Hello everyone,

I'm having problems with the configuration step that I cannot work out. Here is my .ac file:

prefix="/usr/local"
with_trio_flavor="netcdf"
with_netcdf_incs="-I/usr/lib/netcdf/include"
with_netcdf_libs="-L/usr/lib/netcdf/lib -lnetcdff -lnetcdf"
with_fft_flavor="fftw3"
with_fft_incs="-I/usr/include"
with_fft_libs="-L/usr/lib/x86-64-linux-gnu -lfftw3 -lfftw3f"
with_linalg_flavor="atlas"
with_linalg_inc="-I/usr/include"
with_linalg_libs="-L/usr/lib/x86_64-linux-gnu -llapack -lf77blas -lcblas -latlas"
with_dft_flavor="atompaw+bigdft+libxc+wannier90"
with_atompaw_bins="/usr/local/bin"
with_atompaw_incs="-I/usr/local/include"
with_atompaw_libs="-L/usr/local/lib"
with_bigdft_incs="-I/usr/local/include"
with_bigdft_libs="-L/usr/local/lib -lbigdft -lPSolver-1 -labinit"
with_libxc_incs="-I/usr/lib/libxc/include"
with_libxc_libs="-L/usr/lib/libxc/lib -lxc"
with_wannier90_bins="-L/usr/local/bin"
with_wannier90_libs="-L/usr/local/lib -lwannier"

I am a newbie to compiling and installing large packages in Linux. I've checked and all the libraries, binaries, and includes seem to be in the right place. However, when I run configure, it stops at

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checking whether NetCDF Fortran wrappers work... no

with the error

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configure: error: external netcdf support does not work

If I set with_trio_flavor="none", the configuration then will proceed until it hits the libxc step, then stops at

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checking whether LibXC has Fortran support... no

with the error message

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configure: WARNING: package: libxc - preq= - working=no - incs=-I/usr/lib/libxc/include libs=-L/usr/lib/libxc/lib -lxc
configure: error: external libxc support does not work

I suspect that somehow the process is not finding the libraries properly, and I don't know why.
I am using Lubuntu 18.10 on an x86 64-bit laptop.

Thanks!

JIM

Post by **jbeuken** » Mon Feb 04, 2019 4:13 pm

Hi,

we need more infos

- what is the fortran compiler ? GNU 8.2 ?
- MPI or serial ? if MPI, missing "with_mpi_prefix" if location is not standard
- something missing in : with_atompaw_libs="-L/usr/local/lib" -latompaw
- what are the outputs of these commands :

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dpkg -l | grep netcdf
dpkg -l | grep atlas
dpkg -l | grep -i libxc
ls -al /usr/lib/libxc/libx*

A+

jmb

JimEvans · Post by **JimEvans** » Tue Feb 05, 2019 8:53 pm

Hi,

I have gfortran 8.2, and I am trying to install in serial.
The output of "dpkg -l | grep netcdf" is:

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ii  libnetcdf-dev                                 1:4.6.1-3                                  amd64        creation, access, and sharing of scientific data
ii  libnetcdf13:amd64                             1:4.6.1-3                                  amd64        Interface for scientific data access to large binary data

The output of "dpkg -l | grep atlas" is:

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ii  libatlas-base-dev:amd64                       3.10.3-7build1                             amd64        Automatically Tuned Linear Algebra Software, generic static
ii  libatlas3-base:amd64                          3.10.3-7build1                             amd64        Automatically Tuned Linear Algebra Software, generic shared

The output of "dpkg -l | grep -i libxc" is:

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ii  libxcb-composite0:amd64                       1.13.1-1                                   amd64        X C Binding, composite extension
ii  libxcb-damage0:amd64                          1.13.1-1                                   amd64        X C Binding, damage extension
ii  libxcb-dri2-0:amd64                           1.13.1-1                                   amd64        X C Binding, dri2 extension
ii  libxcb-dri2-0-dev:amd64                       1.13.1-1                                   amd64        X C Binding, dri2 extension, development files
ii  libxcb-dri3-0:amd64                           1.13.1-1                                   amd64        X C Binding, dri3 extension
ii  libxcb-dri3-dev:amd64                         1.13.1-1                                   amd64        X C Binding, dri3 extension, development files
ii  libxcb-glx0:amd64                             1.13.1-1                                   amd64        X C Binding, glx extension
ii  libxcb-glx0-dev:amd64                         1.13.1-1                                   amd64        X C Binding, glx extension, development files
ii  libxcb-icccm4:amd64                           0.4.1-1ubuntu1                             amd64        utility libraries for X C Binding -- icccm
ii  libxcb-image0:amd64                           0.4.0-1build1                              amd64        utility libraries for X C Binding -- image
ii  libxcb-keysyms1:amd64                         0.4.0-1                                    amd64        utility libraries for X C Binding -- keysyms
ii  libxcb-present-dev:amd64                      1.13.1-1                                   amd64        X C Binding, present extension, development files
ii  libxcb-present0:amd64                         1.13.1-1                                   amd64        X C Binding, present extension
ii  libxcb-randr0:amd64                           1.13.1-1                                   amd64        X C Binding, randr extension
ii  libxcb-randr0-dev:amd64                       1.13.1-1                                   amd64        X C Binding, randr extension, development files
ii  libxcb-render-util0:amd64                     0.3.9-1                                    amd64        utility libraries for X C Binding -- render-util
ii  libxcb-render0:amd64                          1.13.1-1                                   amd64        X C Binding, render extension
ii  libxcb-render0-dev:amd64                      1.13.1-1                                   amd64        X C Binding, render extension, development files
ii  libxcb-shape0:amd64                           1.13.1-1                                   amd64        X C Binding, shape extension
ii  libxcb-shape0-dev:amd64                       1.13.1-1                                   amd64        X C Binding, shape extension, development files
ii  libxcb-shm0:amd64                             1.13.1-1                                   amd64        X C Binding, shm extension
ii  libxcb-sync-dev:amd64                         1.13.1-1                                   amd64        X C Binding, sync extension, development files
ii  libxcb-sync1:amd64                            1.13.1-1                                   amd64        X C Binding, sync extension
ii  libxcb-util1:amd64                            0.4.0-0ubuntu3                             amd64        utility libraries for X C Binding -- atom, aux and event
ii  libxcb-xfixes0:amd64                          1.13.1-1                                   amd64        X C Binding, xfixes extension
ii  libxcb-xfixes0-dev:amd64                      1.13.1-1                                   amd64        X C Binding, xfixes extension, development files
ii  libxcb-xinerama0:amd64                        1.13.1-1                                   amd64        X C Binding, xinerama extension
ii  libxcb-xkb1:amd64                             1.13.1-1                                   amd64        X C Binding, XKEYBOARD extension
ii  libxcb-xv0:amd64                              1.13.1-1                                   amd64        X C Binding, xv extension
ii  libxcb1:amd64                                 1.13.1-1                                   amd64        X C Binding
ii  libxcb1-dev:amd64                             1.13.1-1                                   amd64        X C Binding, development files
ii  libxcomposite1:amd64                          1:0.4.4-2                                  amd64        X11 Composite extension library
ii  libxcursor1:amd64                             1:1.1.15-1                                 amd64        X cursor management library

The /usr/lib/libxc directory contains no files, just bin, include, and lib directories. The lib directory contains

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libxc.a  libxcf03.a  libxcf03.la  libxcf90.a  libxcf90.la  libxc.la  pkgconfig

Thanks!

Jim

Post by **jbeuken** » Tue Feb 05, 2019 11:36 pm

well, very strange installation... Lubuntu seems very different that ubuntu

some packages seems installed in /usr/lib/PAKAGE like libxc, netcdf
others installed in /usr/lib/x86_64-linux-gnu

have you controled yours paths ?

for ex, outputs of

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ls -al /usr/lib/netcdf
ls -al /usr/lib/libxc

JimEvans · Post by **JimEvans** » Wed Feb 06, 2019 1:39 am

Hi,

Here is /usr/lib/netcdf:

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drwxr-xr-x   6 root root 4096 Jan 31 17:23 .
drwxr-xr-x 110 root root 4096 Jan 31 17:13 ..
drwxr-xr-x   2 root root 4096 Jan 31 17:39 bin
drwxr-xr-x   2 root root 4096 Jan 31 17:39 include
drwxr-xr-x   3 root root 4096 Jan 31 17:39 lib
drwxr-xr-x   5 root root 4096 Jan 31 17:23 share

and here is /usr/lib/libxc:

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drwxr-xr-x   5 root root 4096 Jan 30 18:37 .
drwxr-xr-x 110 root root 4096 Jan 31 17:13 ..
drwxr-xr-x   2 root root 4096 Jan 31 13:20 bin
drwxr-xr-x   2 root root 4096 Jan 31 13:20 include
drwxr-xr-x   3 root root 4096 Jan 31 13:20 lib

I'm not sure what you mean about controlling my paths.

Cheers,

Jim

Post by **jbeuken** » Wed Feb 06, 2019 12:11 pm

ok ! PATHs seems to exist...
I do not understand why the netcdf is badly detected...

can you try with this config ? ( I added -lxcf90 and -latompaw )

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prefix="/usr/local"
with_trio_flavor="netcdf"
with_netcdf_incs="-I/usr/lib/netcdf/include"
with_netcdf_libs="-L/usr/lib/netcdf/lib -lnetcdff -lnetcdf"
with_fft_flavor="fftw3"
with_fft_incs="-I/usr/include"
with_fft_libs="-L/usr/lib/x86-64-linux-gnu -lfftw3 -lfftw3f"
with_linalg_flavor="atlas"
with_linalg_inc="-I/usr/include"
with_linalg_libs="-L/usr/lib/x86_64-linux-gnu -llapack -lf77blas -lcblas -latlas"
with_dft_flavor="atompaw+bigdft+libxc+wannier90"
with_atompaw_bins="/usr/local/bin"
with_atompaw_incs="-I/usr/local/include"
with_atompaw_libs="-L/usr/local/lib -latompaw"
with_bigdft_incs="-I/usr/local/include"
with_bigdft_libs="-L/usr/local/lib -lbigdft -lPSolver-1 -labinit"
with_libxc_incs="-I/usr/lib/libxc/include"
with_libxc_libs="-L/usr/lib/libxc/lib -lxcf90 -lxc"
with_wannier90_bins="-L/usr/local/bin"
with_wannier90_libs="-L/usr/local/lib -lwannier"

and send me the config.log

jmb

JimEvans · Post by **JimEvans** » Thu Feb 07, 2019 1:16 am

Thank you very much! Here are the config log and output.

out.log: Output; (18.16 KiB) Downloaded 323 times

config.log: Config.log; (119.83 KiB) Downloaded 340 times

Post by **jbeuken** » Thu Feb 07, 2019 2:43 pm

Hi,

Clearly, there is a problem with your netcdf installation...

in config.log :

gfortran -o conftest -g -ffree-line-length-none -I/usr/lib/netcdf/include conftest.F90 -L/usr/lib/netcdf/lib -lnetcdff -lnetcdf -L/usr/lib/gcc/x86_64-linux-gnu/8 -L/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/8/../../../../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/8/../../.. -lgfortran -lm -lquadmath >&5
/usr/bin/ld: /usr/lib/netcdf/lib/libnetcdf.a(liboc_la-ocinternal.o): in function `ocinitialize':
/home/jim/netcdf-4.1.1/build/libncdap3/oc/../../../libncdap3/oc/ocinternal.c:167: undefined reference to `curl_version_info'
/usr/bin/ld: /usr/lib/netcdf/lib/libnetcdf.a(liboc_la-http.o): in function `ocsetcurlproperties':
/home/jim/netcdf-4.1.1/build/libncdap3/oc/../../../libncdap3/oc/http.c:283: undefined reference to `curl_easy_strerror'
/usr/bin/ld: /usr/lib/netcdf/lib/libnetcdf.a(liboc_la-http.o): in function `ocfetchhttpcode':
/home/jim/netcdf-4.1.1/build/libncdap3/oc/../../../libncdap3/oc/http.c:27: undefined reference to `curl_easy_getinfo'
/usr/bin/ld: /usr/lib/netcdf/lib/libnetcdf.a(liboc_la-http.o): in function `ocfetchurl_file':
/home/jim/netcdf-4.1.1/build/libncdap3/oc/../../../libncdap3/oc/http.c:44: undefined reference to `curl_easy_setopt'
/usr/bin/ld: /home/jim/netcdf-4.1.1/build/libncdap3/oc/../../../libncdap3/oc/http.c:49: undefined reference to `curl_easy_setopt'
/usr/bin/ld: /home/jim/netcdf-4.1.1/build/libncdap3/oc/../../../libncdap3/oc/http.c:54: undefined reference to `curl_easy_setopt'
...
/usr/bin/ld: /usr/lib/netcdf/lib/libnetcdf.a(liboc_la-curlfunctions.o):/home/jim/netcdf-4.1.1/build/libncdap3/oc/../../../libncdap3/oc/curlfunctions.c:88: more undefined references to `curl_easy_setopt' follow
collect2: error: ld returned 1 exit status

it seems that curl lib is missing !
in my installation , there are these two libs :

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ii  libcurl3-gnutls:amd64                      7.58.0-2ubuntu3.6                            amd64        easy-to-use client-side URL transfer library (GnuTLS flavour)
ii  libcurl4-gnutls-dev:amd64                  7.58.0-2ubuntu3.6                            amd64        development files and documentation for libcurl (GnuTLS flavour)

then, I think you must install these two librairies...

but what disturbs me, is the presence of the folder "/usr/lib/netcdf" !
I think there is perhaps a conflict between the installed ubuntu libraries ( libnetcdf-dev and libnetcdf13 ) and the installation in the folder "/usr/lib/netcdf" which is not standard.

Finally, if you try to use the installed ubuntu libraries, the fortran components of netcdf are missing :

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ii  libnetcdff-dev                             4.4.4+ds-3                                   amd64        creation, access, and sharing of scientific data in Fortran
ii  libnetcdff6                                4.4.4+ds-3                                   amd64        Fortran interface for scientific data access to large binary data

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apt install libnetcdff-dev libnetcdff6

After the installation of the fortran components, can you retry with this netcdf configuration :

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with_trio_flavor="netcdf"
with_netcdf_incs="-I/usr/include"
with_netcdf_libs="-L/usr/lib -lnetcdff -lnetcdf"

jmb

JimEvans · Post by **JimEvans** » Sun Feb 17, 2019 2:24 am

This seems to do the trick with netcdf.

So I spent the last week recompiling the libxc, bigdft, etc libraries and making sure everything was in /usr/local. However the configure script is still choking on libxc.

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checking whether to select a fallback for libxc... no
checking xc.h usability... yes
checking xc.h presence... yes
checking for xc.h... yes
checking xc_funcs.h usability... yes
checking xc_funcs.h presence... yes
checking for xc_funcs.h... yes
checking for Fortran module includes... none required (cached)
checking whether LibXC has Fortran support... yes
checking whether this is LibXC version 2.2->4.2... no
configure: WARNING: package: libxc - preq= - working=no - incs=-I/usr/local/include libs=-L/usr/local/lib -lxcf90 -lxc -lxcf03

Could this be because I am trying to use libxc-4.3.0 instead of 4.2? Config and log files below:

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prefix="/usr/local"
with_trio_flavor="netcdf"
with_netcdf_incs="-I/usr/include"
with_netcdf_libs="-L/usr/lib -lnetcdff -lnetcdf"
with_fft_flavor="fftw3"
with_fft_incs="-I/usr/include"
with_fft_libs="-L/usr/lib/x86-64-linux-gnu -lfftw3 -lfftw3f"
with_linalg_flavor="atlas"
with_linalg_inc="-I/usr/include"
with_linalg_libs="-L/usr/lib/x86_64-linux-gnu -llapack -lf77blas -lcblas -latlas"
with_dft_flavor="atompaw+bigdft+libxc+wannier90"
with_atompaw_bins="/usr/local/bin"
with_atompaw_incs="-I/usr/local/include"
with_atompaw_libs="-L/usr/local/lib -latompaw"
with_bigdft_incs="-I/usr/local/include"
with_bigdft_libs="-L/usr/local/lib -lbigdft -lPSolver -labinit"
enable_fallbacks=yes
with_libxc_incs="-I/usr/local/include"
with_libxc_libs="-L/usr/local/lib -lxcf90 -lxc -lxcf03"
with_wannier90_bins="-L/usr/local/bin"
with_wannier90_libs="-L/usr/local/lib -lwannier"

config.log: configure log file; (121.8 KiB) Downloaded 291 times

I am inexperienced installing things in a Linux/Unix environment. I feel like I'm missing something fundamental in making these libraries...

Cheers,

Jim

JimEvans · Post by **JimEvans** » Mon Feb 18, 2019 9:56 pm

My problem with libxc WAS that I was using 4.3.0 instead of 4.2.*. I am still not having any luck with bigDFT and wannier90, but I don't think I need those yet. If I do, I will be back

Thanks for your help!

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