ABINIT Discussion Forums

Hi,all
when I use intel 2016 to install abinit 8.0.8, then turn to GNU C and fortran.

that is :
Summary of important options:

* C compiler : gnu version 4.4
* Fortran compiler: gnu version 4.4
* architecture : intel xeon (64 bits)
and the configure :

./configure CC="mpicc" CXX="mpicxx" FC="mpiifort" \
--prefix=/public/software/abinit/808 \
--with-tardir=/public/software/abinit/tarballs \
--enable-64bit-flags="yes" \
--enable-mpi \
--with-mpi-prefix="/public/software/intel2016/compilers_and_libraries_2016.3.210/linux/mpi/intel64" \
--with-trio-flavor="netcdf+etsf_io" \
--with-fft-flavor="fftw3" \
--with-fft-libs="-L/public/software/intel2016/mkl/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group" \
--with-linalg-flavor="mkl" \
--with-linalg-libs="-L/public/software/intel2016/mkl/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group" \
--with-dft-flavor="atompaw+bigdft+libxc+wannier90" \
--enable-gw-dpc="yes"

how to resolve the problem?

Thanks!

Hello

What does mpiifort --version an mpicc --version return you ?
If Intel Ifort ou Intel ICC then we need to investigate more, otherwise, it means you intelmpi was not compile with intel compilers and so the default compiler for mpi is not intel.
Rebuilt you intelmpi or force the compiler to be ifort.

Cheers

Jordan

Jordan wrote:Hello

What does mpiifort --version an mpicc --version return you ?
If Intel Ifort ou Intel ICC then we need to investigate more, otherwise, it means you intelmpi was not compile with intel compilers and so the default compiler for mpi is not intel.
Rebuilt you intelmpi or force the compiler to be ifort.

Cheers

Jordan

Hi, Jordan

this is the mpiifort and mpicc version
[root@admin abinit]# mpicc -v
mpigcc for the Intel(R) MPI Library 5.1.3 for Linux*
Copyright(C) 2003-2015, Intel Corporation. All rights reserved.
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC)
[root@admin abinit]# mpiicc -v
mpiicc for the Intel(R) MPI Library 5.1.3 for Linux*
Copyright(C) 2003-2015, Intel Corporation. All rights reserved.
icc version 16.0.3 (gcc version 4.4.7 compatibility)
[root@admin abinit]# mpiifort -v
mpiifort for the Intel(R) MPI Library 5.1.3 for Linux*
Copyright(C) 2003-2015, Intel Corporation. All rights reserved.
ifort version 16.0.3

Thanks!

Hi,

So don't use mpicc but mpiicc.
Try without the --with-mpi-prefix, just keep the CC=mpiicc CXX=mpiicc and FC=mpiifort flags.
Something is messing up the configuration.

Cheers

Jordan

For IntelMPI compilers, mpicc, mpif90, mpicxx etc is just wrappers to the actual compilers. It means that the same commands can be used refer to either the gnu version of intel version, depending on the environmental variables. The default configuration is to link to the gnu versions, which is why you get gnu version in your output.

To direct IntelMPI to use intel compilers, just export theses environmental variables before building Abinit:
export I_MPI_CC=icc
export I_MPI_CXX=icpc
export I_MPI_F77=ifort
export I_MPI_F90=ifort

PS: It works for IntelMPI 2015, and I do not know whether it will work for the 2016 version.

Dear all,

I have gone through the configuration fine, but I have problem on the make part. It's abinit 8 on a ubuntu 16 machine
The problem is an undefined reference to `sfftw_execute_dft_' in src/52_fft_mpi_noabirule m_fftw3.F90:3246
Below you can find the lasts few lines on my terminal

Thanks in advance.

../../src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a(m_fftw3.o):/home/marco/CODES/abinit-8.0.8/tmp/src/52_fft_mpi_noabirule/../../../src/52_fft_mpi_noabirule/m_fftw3.F90:3246: more undefined references to `sfftw_execute_dft_' follow
collect2: error: ld returned 1 exit status
Makefile:3436: recipe for target 'abinit' failed
make[3]: *** [abinit] Error 1
make[3]: Leaving directory '/home/marco/CODES/abinit-8.0.8/tmp/src/98_main'
Makefile:930: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/marco/CODES/abinit-8.0.8/tmp/src'
Makefile:2238: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/marco/CODES/abinit-8.0.8/tmp'
Makefile:2167: recipe for target 'all' failed
make: *** [all] Error 2
marco@qmrcd:~/CODES/abinit-8.0.8/tmp$

Hi,

can you provide some more infos :

- version of os : 16.04 or 16.10
- dpkg --list
- cat ubuntu.ac

jmb

Absolutely:

- Ubuntu 16.04
- dpkg --list (see attachment)
- cat .abinit/build/ubuntu.ac
prefix="/usr/local"
enable_mpi="yes"
enable_mpi_io="yes"
with_mpi_prefix="/usr"
with_netcdf_incs="-I/usr/include"
with_netcdf_libs="-L/usr/lib64 -lnetcdf -lnetcdff"
with_fft_flavor="fftw3"
with_fft_incs="-I/usr/include/"
with_fft_libs="-L/usr/lib64 -lfftw3"
with_linalg_flavor="atlas"
with_linalg_libs="-L/usr/lib64 -llapack -lf77blas -lcblas -latlas"
with_dft_flavor="atompaw+bigdft+libxc+wannier90"
enable_gw_dpc="yes"
enable_maintainer_checks="no"
- end of .abinit/build/ubuntu.ac

BR
MDG

Hi

forgot to attach "dpkg -l" ?


your ac file :

prefix="/usr/local"
enable_mpi="yes"
enable_mpi_io="yes"
with_mpi_prefix="/usr"
with_netcdf_incs="-I/usr/include"
with_netcdf_libs="-L/usr/lib64 -lnetcdf -lnetcdff"
with_fft_flavor="fftw3"
with_fft_incs="-I/usr/include/"
with_fft_libs="-L/usr/lib64 -lfftw3"
with_linalg_flavor="atlas"
with_linalg_libs="-L/usr/lib64 -llapack -lf77blas -lcblas -latlas"
with_dft_flavor="atompaw+bigdft+libxc+wannier90"
enable_gw_dpc="yes"
enable_maintainer_checks="no"

a little remark : install a fresh ubuntu 16.04 and the /usr/lib64 doesn't exist...

you can see in the config.log

configure:28447: /usr/bin/mpif90 -o conftest -g -ffree-line-length-none conftest.F90 -L/usr/lib64 -llapack -lf77blas -lcblas -latlas -L/usr/lib/openmpi/lib -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../../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/5/../../.. -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lquadmath -lpthread >&5
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lf77blas
/usr/bin/ld: cannot find -lcblas
/usr/bin/ld: cannot find -latlas

but the build system is able to find automatically the libs fftw3, atlas...


to use netcdf , add with_trio_flavor
and, last but not least , forgot -lfftw3f in with_fft_libs

then , my .ac file is



and the tail of the output of my ./configure command :



compilation ok for me...

regards

thank you,

the dpkg.in is now here.
I inserted the << with_netcdf_incs="-I/usr/include" >> line to my .ac file.
I also included the compilers:

>> FC=/usr/bin/mpif90
>> CC=/usr/bin/mpicc
>> CXX=/usr/bin/mpicc

but still, the configuration crashes with the following error message.

checking for netcdf.h... yes
checking for Fortran module includes... unknown

+--------------------------------------------------------------+
| Connector detection failure |
+--------------------------------------------------------------+
| The build system of Abinit has not been able to detect |
| one or more requested external packages, probably because |
| you did not provide sufficient information. This means |
| that the build cannot proceed, and the configure script |
| will thus abort now with an error. |
| |
| To address this issue, you may: |
| |
| * make sure that the prerequisites of the external |
| packages are available and enabled, e.g. |
| --with-dft-flavor="libxc+bigdft" or |
| --with-trio-flavor="netcdf+etsf_io" |
| |
| * use the --with-*-bins, --with-*-incs, and |
| --with-*-libs options of configure to provide |
| additional information; please see the section related |
| to connectors in |
| ~abinit/doc/build/config-template.ac for available |
| options and details; |
| |
| * disable the corresponding extensions, by using the |
| associated --with-*-flavor="none" options of |
| configure; please see the section associated to |
| connectors in ~abinit/doc/build/config-template.ac for |
| details. |
| |
+--------------------------------------------------------------+

configure: error: external netcdf support does not work
marco@qmrcd:~/CODES/abinit-8.0.8/tmp$

please read carefully my post...

I didn't speak about "with_netcdf_incs="-I/usr/include"

but about :

1) replace everywhere "/usr/lib64" by "/usr/lib" in your ac file
2) add -lfftw3f then replace

with_fft_libs="-L/usr/lib64 -lfftw3"

by

with_fft_libs="-L/usr/lib64 -lfftw3 -lfftw3f "

3) you forgot alos to install fortran netcdf



in fact, you can use my ac file...

Touche'

It now indeed works. The only difference I can say wrt your output is:
* LINALG flavor = netlib-fallback (libs: ignored)
instead of:
* LINALG flavor = atlas (libs: user-defined)
I have no idea if this could lead to problems in the future.

BTW also the compliation went through.

Thanks a lot

MDG