ABINIT Discussion Forums

I'm trying to compile abinit for parallel version but I'm getting this error:
checking whether to enable OpenMP support... no
checking whether to build MPI code... yes
checking whether the C compiler supports MPI... no
checking whether the C++ compiler supports MPI... no
checking whether the Fortran Compiler supports MPI... no
checking whether MPI is usable... no
configure: error: MPI support is broken - please fix your config parameters and/or MPI installation
....
Any comment!

Regards,
MH

need more infos !!!

your configure command ( ./configure and/or the config.log )
your environment ( env, PATH, which mpif90, mpif90 -show,… )

thx

I used what it mention at : http://www.abinit.org/documentation/bui ... pi-support
----------------------------------------------------------------------------------------------------
cd abinit-5.8.0
mkdir tmp-serial
cd tmp-serial
../configure \
--program-suffix="-seq" \
--disable-mpi
make
cd ..
mkdir tmp-scalapack
cd tmp-scalapack
../configure \
--program-suffix="-mpi" \
--enable-mpi \
--enable-scalapack \
--with-scalapack-libs="-lscalapack -lblacs" \
FC=gfortran
make
--------------------------------------------------------------------------------------------------

outdated !
please use a more recent version of abinit ( 7.10.2 )

I'm using it!
I just used the commands that mention on the link I posted. commands line do not depend on the version, right?

I just used the commands that mention on the link I posted. commands line do not depend on the version, right?

yes and no !

some configure options have been removed while others have been added …

concerning the MPI support, what are the results of theses commands :

I just used this command line :
./configure --enable-mpi --with-mpi-prefix="/usr/bin"
but I've got this error:

configure: error: MPI support is broken - please fix your config parameters and/or MPI installation
This error is weird because I'm using another code without any problems, so how MPI is broken??

I do not know what env is on the cluster.

jbeuken wrote:

I just used the commands that mention on the link I posted. commands line do not depend on the version, right?

yes and no !

some configure options have been removed while others have been added …

concerning the MPI support, what are the results of theses commands :

Code: Select all

env
which mpif90

mpif90:
/usr/local/openmpi/bin/mpif90


env:
MKLROOT=/opt/intel/composer_xe_2011_sp1.10.319/mkl
LESSKEY=/etc/lesskey.bin
NNTPSERVER=news
MANPATH=/opt/intel/composer_xe_2011_sp1.10.319/man/en_US:/opt/intel/composer_xe_2011_sp1.10.319/man/en_US:/opt/intel/composer_xe_2011_sp1.10.319/man/en_US:/usr/local/man:/usr/share/man:
XDG_SESSION_ID=22748
HOSTNAME=whisper
XKEYSYMDB=/usr/X11R6/lib/X11/XKeysymDB
INTEL_LICENSE_FILE=/opt/intel/composer_xe_2011_sp1.10.319/licenses:/opt/intel/licenses:/home/mhammouri/intel/licenses
HOST=whisper
TERM=vt100
SHELL=/bin/bash
PROFILEREAD=true
HISTSIZE=1000
SSH_CLIENT=172.16.117.71 49194 22
LIBRARY_PATH=/opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64:/opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/intel64:/opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64:/opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64:/opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/intel64
FPATH=/opt/intel/composer_xe_2011_sp1.10.319/mkl/include:/opt/intel/composer_xe_2011_sp1.10.319/mkl/include
MORE=-sl
SSH_TTY=/dev/pts/16
JRE_HOME=/usr/lib64/jvm/jre
USER=mhammouri
LS_COLORS=no=00:fi=00:di=01;34:ln=00;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=41;33;01:ex=00;32:*.cmd=00;32:*.exe=01;32:*.com=01;32:*.bat=01;32:*.btm=01;32:*.dll=01;32:*.tar=00;31:*.tbz=00;31:*.tgz=00;31:*.rpm=00;31:*.deb=00;31:*.arj=00;31:*.taz=00;31:*.lzh=00;31:*.lzma=00;31:*.zip=00;31:*.zoo=00;31:*.z=00;31:*.Z=00;31:*.gz=00;31:*.bz2=00;31:*.tb2=00;31:*.tz2=00;31:*.tbz2=00;31:*.xz=00;31:*.avi=01;35:*.bmp=01;35:*.fli=01;35:*.gif=01;35:*.jpg=01;35:*.jpeg=01;35:*.mng=01;35:*.mov=01;35:*.mpg=01;35:*.pcx=01;35:*.pbm=01;35:*.pgm=01;35:*.png=01;35:*.ppm=01;35:*.tga=01;35:*.tif=01;35:*.xbm=01;35:*.xpm=01;35:*.dl=01;35:*.gl=01;35:*.wmv=01;35:*.aiff=00;32:*.au=00;32:*.mid=00;32:*.mp3=00;32:*.ogg=00;32:*.voc=00;32:*.wav=00;32:
LD_LIBRARY_PATH=/usr/local/openmpi/lib64:/opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64:/opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/intel64:/opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64:/opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64:/opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/intel64:/opt/intel/composer_xe_2011_sp1.10.319/debugger/lib/intel64:/opt/intel/composer_xe_2011_sp1.10.319/mpirt/lib/intel64
XNLSPATH=/usr/share/X11/nls
HYDRA_HOST_FILE=/usr/local/mpich2/share/machines.LINUX
CPATH=/opt/intel/composer_xe_2011_sp1.10.319/mkl/include:/opt/intel/composer_xe_2011_sp1.10.319/mkl/include
HOSTTYPE=x86_64
CONFIG_SITE=/usr/share/site/x86_64-unknown-linux-gnu
FROM_HEADER=
PAGER=less
CSHEDIT=emacs
XDG_CONFIG_DIRS=/etc/xdg
NLSPATH=/opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/intel64/locale/%l_%t/%N:/opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64/locale/%l_%t/%N:/opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/intel64/locale/%l_%t/%N:/opt/intel/composer_xe_2011_sp1.10.319/debugger/intel64/locale/%l_%t/%N
MINICOM=-c on
MAIL=/var/mail/mhammouri
PATH=/usr/local/openmpi/bin:.:/opt/intel/composer_xe_2011_sp1.10.319/bin/intel64:/home/mhammouri/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib64/jvm/jre/bin:/opt/intel/composer_xe_2011_sp1.10.319/mpirt/bin/intel64:/usr/local/mpich2/bin
CPU=x86_64
JAVA_BINDIR=/usr/lib64/jvm/jre/bin
INPUTRC=/home/mhammouri/.inputrc
PWD=/home/mhammouri/mhmood/abinit/abinit-7
JAVA_HOME=/usr/lib64/jvm/jre
LANG=en_US.UTF-8
PYTHONSTARTUP=/etc/pythonstart
GPG_TTY=/dev/pts/16
QT_SYSTEM_DIR=/usr/share/desktop-data
SHLVL=1
HOME=/home/mhammouri
SDL_AUDIODRIVER=pulse
ALSA_CONFIG_PATH=/etc/alsa-pulse.conf
LESS_ADVANCED_PREPROCESSOR=no
OSTYPE=linux
LS_OPTIONS=-N --color=tty -T 0
XCURSOR_THEME=DMZ
WINDOWMANAGER=/usr/bin/startkde
G_FILENAME_ENCODING=@locale,UTF-8,ISO-8859-15,CP1252
LESS=-M -I -R
MACHTYPE=x86_64-suse-linux
LOGNAME=mhammouri
CVS_RSH=ssh
XDG_DATA_DIRS=/usr/share
SSH_CONNECTION=172.16.117.71 49194 128.123.210.194 22
LESSOPEN=lessopen.sh %s
XDG_RUNTIME_DIR=/run/user/mhammouri
INCLUDE=/opt/intel/composer_xe_2011_sp1.10.319/mkl/include:/opt/intel/composer_xe_2011_sp1.10.319/mkl/include
LESSCLOSE=lessclose.sh %s %s
G_BROKEN_FILENAMES=1
JAVA_ROOT=/usr/lib64/jvm/jre
COLORTERM=1
_=/usr/bin/env
OLDPWD=/home/mhammouri

ok…

mpif90:
/usr/local/openmpi/bin/mpif90

then, at least, the configure command must be :



we progress…

Still have problems ...

Hello jbeuken,
I thought I have the parallel version of abinit. I tried to test a simple parallel job by following the simple run that already mention at the website of abinit, I got these lines from the output file which indicates I do not have the parallel version yet:
=== Multicore ===
Parallel build : no
Parallel I/O : no
openMP support : no
GPU support : no
===============
Going back to your last post, I used this command :
./configure --enable-mpi --with-mpi-prefix="/usr/local/openmpi"
and after it finished I got this summery :
==============================================================================
=== Final remarks ===
==============================================================================


+--------------------------------------------------------------+
| About the Intel Fortran compiler |
+--------------------------------------------------------------+
| Your compiler will work properly only if the LD_LIBRARY_PATH |
| and INTEL_LICENSE_FILE environment variables are correctly |
| set-up. Please make sure that this is the case before |
| building ABINIT. |
| |
| In most cases it means sourcing a script in the Intel |
| compiler install directory, e.g.: |
| |
| . /opt/intel/fc/9.1/bin/ifortvars.sh |
| |
| for a Bourne-like shell (do not forget the leading dot), or |
| |
| source /opt/intel/fc/9.1/bin/ifortvars.csh |
| |
| for a C-like shell. |
| |
| If you do not know what this is all about, please refer to |
| the Intel documentation or ask your system administrator. |
| |
| Please note that the same holds for the Intel C and C++ |
| compilers. |
+--------------------------------------------------------------+


Summary of important options:

* C compiler : gnu version 4.6
* Fortran compiler: intel version 12.1
* architecture : amd opteron (64 bits)

* debugging : basic
* optimizations : standard

* OpenMP enabled : no (collapse: ignored)
* MPI enabled : yes
* MPI-IO enabled : auto
* GPU enabled : no (flavor: none)

* TRIO flavor = none
* TIMER flavor = abinit (libs: ignored)
* LINALG flavor = netlib (libs: auto-detected)
* ALGO flavor = none (libs: ignored)
* FFT flavor = none (libs: ignored)
* MATH flavor = none (libs: ignored)
* DFT flavor = none

Configuration complete.
You may now type "make" to build ABINIT.
(or, on a SMP machine, "make mj4", or "make multi multi_nprocs=<n>")
===========================================
Then I typed "make".
But It seems no parallel run is there.
What do you think?

The log file you posted is from the configure step.

As you can read :
* MPI enabled : yes means that your abinit will support MPI jobs, ie parallel jobs.
The compilation, however, is build in sequential, meaning that only one core will build abinit. This is due to the fact that you use "make" only.
If you want to speed up the compilation and use several cores to build abinit then use
[code]
make multi multi_nprocs=X
[code]
where X is the number of cores you want to use (typically at least the number of core you CPU has).

Jordan

Thank you Jordan for your reply, I still have the problem:
This is what I did in detail:
1) unzip abinit-7.10.2
2) go inside the folder and type: ./configure --enable-mpi --with-mpi-prefix="/usr/local/openmpi"
3) after it finished I typed : make multi multi_nprocs=64

Then, I went to "src/98_main" directory and copied abinit executable
I made a new directory and I copied tbasepar_1.in & tbasepar_1.files and run them on 2, 10, and 16 processors, but all cases failed.
take a look at the log file.
What do think now?

I tried to type : make install, this is what I've got:
:
:
:
:
test -z "/usr/local/bin" || /bin/mkdir -p "/usr/local/bin"
/usr/bin/install -c abinit aim anaddb band2eps bsepostproc conducti cut3d fftprof ioprof kss2wfk lapackprof mrgddb mrggkk mrgscr optic ujdet vdw_kernelgen macroave '/usr/local/bin'
/usr/bin/install: cannot create regular file `/usr/local/bin/abinit': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/aim': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/anaddb': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/band2eps': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/bsepostproc': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/conducti': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/cut3d': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/fftprof': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/ioprof': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/kss2wfk': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/lapackprof': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/mrgddb': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/mrggkk': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/mrgscr': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/optic': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/ujdet': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/vdw_kernelgen': Permission denied
/usr/bin/install: cannot create regular file `/usr/local/bin/macroave': Permission denied
make[3]: *** [install-binPROGRAMS] Error 1
make[2]: *** [install-am] Error 2
make[1]: *** [install-recursive] Error 1
make: *** [install-recursive] Error 1


any help guys!

No one is here to help me?

Hi,

you don't had permission to write in the /usr/local/bin :

/usr/bin/install: cannot create regular file `/usr/local/bin/abinit': Permission denied

try with :

I'm not a root user!

add to your configure line

you should have permissions for this "prefix" directory.

Note you don't need to "make install" to use abinit.

The seg fault you got in your log file might come from the linear algebra library you use.
Which one do you use ? the lapack-fallback ? atlas ? mkl ? acml ?... ?
With what compiler ?
What kind of CPU (brand and model)?
What supercomputer ?

these are some info about my machine :
Linux version 3.1.10-1.9-desktop (geeko@buildhost) (gcc version 4.6.2 (SUSE Linux) ) #1 SMP PREEMPT
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
Vendor ID: AuthenticAMD
CPU family: 21
For math libraries i do not know which one i have but i can tell I'm using siesta and quantum espresso, and i was able to compile abinit for the serial version.

Ok,

I don't have much ideas but as you use intel12, I would suggest to compile abinit with the MKL library (for example with --with-linalg-flavor="mkl" --with-linalg-incs="-I$MKLROOT/include/intel64/lp64" --with-linalg_libs="-L$MKLROOT/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group" --with-fft-flavor=fftw3 --with-fft-libs="-L$MKLROOT/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group")
I would also add FCFLAGS_EXTRA="-traceback" on you configure line.

This should 1) use MKLlibrary and avoid old netlib bugs, 2) if the segfaul occures, it shoud give the file and subroutine where it happens.
When you do the ./configure, at the end, please check that you do have mkl and fftw3 for the linalg flavor and fft flavor respectively.
Please don't forget to "make clean" before "make"
and before the make command terminates, be sure that you do have the -traceback option in the compilation lines.
If everything is fine, then rerun the test which failed.

PS : You should adapt the --with-*-* I gave to fit you system. You can also look inside abinit/doc/build/config-examples for some examples (Note that in a .ac file, the "-" are replaced by "_"

Why did you assume I'm using intel 12

if i just follow what is mention in this video : https://www.youtube.com/watch?v=DppLQ-KQA68
will solve my problem?

I tried this :
./configure --with-linalg-flavor="mkl" --with-linalg-incs="-I$opt/intel/composer_xe_2011_sp1.10.319/mkl/include/intel64/lp64" --with-linalg_libs="-L$opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group" --with-fft-flavor=fftw3 --with-fft-libs="-L$opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,FCFLAGS_EXTRA="-traceback",--end-group"

and this is the result:
checking for the requested linear algebra support... mkl
checking whether to select a fallback for linear algebra... no
checking for BLAS support in specified libraries... yes
checking for AXPBY support in specified BLAS libraries... yes
checking for gemm3m in specified libraries... yes
checking for mkl_imatcopy in specified libraries... yes
checking for mkl_omatcopy in specified libraries... yes
checking for mkl_omatadd in specified libraries... yes
checking for LAPACK support in specified libraries... yes
checking for LAPACKE C API support in specified libraries... no
checking for BLACS support in specified libraries... no
checking for ScaLAPACK support in specified libraries... no
checking for ELPA support in specified libraries... no
checking for PLASMA support in specified libraries... no
checking for MAGMA (version>=1.1.0) support in specified libraries... no
checking whether we have a serial linear algebra support... yes
checking whether we have a MPI linear algebra support... no
checking whether we have a GPU linear algebra support... no
checking for the actual linear algebra support... mkl
checking for the requested FFT support... fftw3
checking for the actual FFT support... broken

+--------------------------------------------------------------+
| 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: the specified FFT libraries do not work

You can try the video but it assumes you have a package manager.

Your command is wrong you have
--with-fft-libs="-L$opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,FCFLAGS_EXTRA="-traceback",--end-group"

Which should be
--with-fft-libs="-L$opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group" FCFLAGS_EXTRA="-traceback"

I said intel12 because I must have seen it in you previsous attached file

if use this command line:
./configure --with-linalg-flavor="mkl" --with-linalg-incs="-I$opt/intel/composer_xe_2011_sp1.10.319/mkl/include/intel64/lp64" --with-linalg_libs="-L$opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group" --with-fft-flavor=fftw3 --with-fft-libs="-L$mhmood/fftw-3.3.4 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group"FCFLAGS_EXTRA="-traceback"
do I need to make build.ac? becuase when i used the above lines it came with no mpi.
And it is ok to uncomment the netcdf lines?