installation problem abinit 7.2.2

spaz · Post by **spaz** » Thu Aug 15, 2013 5:10 pm

dear all,
I am trying to install abinit 7.2.2 on opensuse 12.3 system. first i installed intel C and fortran compilers then mpich to /opt file. then added related paths to .bashrc then i confıgured the abinit "ac " file as here and coppied it to ~/.abinit/build file and coppied all fallbacks files to ~/.abinit/tarballs file.

when ı use

"./configure --prefix=/opt/abinit/mpich2"

command to confıgure abınıt it gives

"configure: error: the requested mkl+scalapack linear algebra flavor is not supported on this architecture"

error on screen. if i changed mkl+scalapack to custom this warning disappears. but this time i faced with the

"The error "HAVE_MPI1 and HAVE_MPI2 are both undefined" error. i read too much forum topics ("--with-mpi-level=2" or "--with-mpi-level=1" didnt worked )to solve this problem but nothing changed.

indium.ac file content:

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--enable-mpi=yes
--with-mpi-prefix=/opt/mpich2/intel
--with-trio-flavor="none"
--with-linalg-flavor="mkl+scalapack"
--with_linalg_libs="-L/opt/intel/Compiler/mkl/lib/intel64 -Wl,--start-group -lmkl_scalapack_lp64  -lmkl_blacs_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group
--with-dft-flavor="atompaw+bigdft+libxc"
--enable-gw-dpc="yes"
--enable-test-timeout="yes"
--enable-gui-build="no"

Post by **jbeuken** » Thu Aug 15, 2013 11:44 pm

Hi,

first of all, scalapack is not yet officially supported... :roll:

we have not yet tested intel 12 compiler under opensuse,
but we have a nightly bot that tests a configuration with "native" packages of opensuse 12.1

packages : fftw3, openmpi 1.4.3, gfortran 4.6.2, netcdf 4

and my build.ac file is

Code: Select all

enable_mpi="yes"
enable_mpi_io="yes"
with_mpi_prefix="/usr/lib64/mpi/gcc/openmpi"
with_trio_flavor="netcdf+etsf_io+fox"
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 -lfftw3f"
with_linalg_flavor="netlib"
with_linalg_libs="-L/usr/lib64 -llapack -lblas"
with_dft_flavor="atompaw+bigdft+libxc+wannier90"
enable_clib="yes"
enable_gw_dpc="yes"

and the command :

Code: Select all

./configure --with-config-file=./build.ac

to resolve your problem, can you send the config.log ?

regards

jmb

spaz · Post by **spaz** » Fri Aug 16, 2013 1:02 am

hi again,

iused the build.ac file as below:

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enable_mpi="yes"
enable_mpi_io="yes"
with_mpi_prefix="/opt/mpich2/intel"
#with_trio_flavor="netcdf+etsf_io+fox"
with_trio_flavor="none"
#with_netcdf_incs="-I/usr/include"
#with_netcdf_libs="-L/usr/lib64 -libnetcdf -lnetcdff"
with_fft_flavor="fftw3"
with_fft_incs="-I/usr/include"
with_fft_libs="-L/usr/lib64 -lfftw3 -lfftw3f"
with_linalg_flavor="netlib"
with_linalg_libs="-L/usr/lib64 -llapack -lblas"
with_dft_flavor="atompaw+bigdft+libxc+wannier90"
with_mpi_level="1"
with-tardir="/home/menderes/.abinit/tarballs"
enable_clib="yes"

with the command

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./configure --prefix=/opt/abinit/mpich2

./configure --prefix=/opt/abinit/mpich2

after this it gives the summary as here

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Summary of important options:

  * C compiler      : gnu version 4.7
  * Fortran compiler: gnu version 4.7
  * architecture    : unknown unknown (64 bits)

  * debugging       : basic
  * optimizations   : standard

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

  * TRIO   flavor = none
  * TIMER  flavor = abinit (libs: ignored)
  * LINALG flavor = netlib-fallback (libs: ignored)
  * ALGO   flavor = none (libs: ignored)
  * FFT    flavor = fftw3 (libs: user-defined)
  * MATH   flavor = none (libs: ignored)
  * DFT    flavor = libxc-fallback+atompaw-fallback+bigdft-fallback+wannier90-fallback

then i did make mj4 and it ended with this message
"make[5]: Entering directory `/home/menderes/programs/abinit-7.2.2/src/11_memory_mpi'
gfortran -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -I/home/menderes/programs/abinit-7.2.2/fallbacks/exports/include -ffree-form -J/home/menderes/programs/abinit-7.2.2/src/mods -O2 -mtune=native -march=native -g -ffree-line-length-none -c -o m_profiling.o m_profiling.F90
m_profiling.F90:275: Error: Can't open included file 'mpif.h'
make[5]: *** [m_profiling.o] Error 1
make[5]: Leaving directory `/home/menderes/programs/abinit-7.2.2/src/11_memory_mpi'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory `/home/menderes/programs/abinit-7.2.2/src'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/menderes/programs/abinit-7.2.2'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/menderes/programs/abinit-7.2.2'
make[1]: *** [multi] Error 2
make[1]: Leaving directory `/home/menderes/programs/abinit-7.2.2':

Post by **pouillon** » Fri Aug 16, 2013 4:19 pm

Looks like the build system of Abinit did not find the mpif90 compiler wrapper, but since you forced enable_mpi to "yes", it has considered that you know what you're doing. You will find more information at the beginning of the configure output and in the "Multicore architecture support" section.

Please check the following:

/opt/mpich2/intel/bin/mpif90 exists and is executable;
/opt/mpich2/intel/lib exists and is in the $LD_LIBRARY_PATH variable.

spaz · Post by **spaz** » Fri Aug 16, 2013 6:17 pm

hii......

I began to build abinit from the beginning and to do that re-installed all intel fortran and C compilaer then mpich2 into /opt directory and all paths are defined as follows in .bashrc file

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# Intel Compilers
source /opt/intel/composer_xe_2013.0.079/bin/compilervars.sh intel64
source /opt/intel/composer_xe_2013.0.079/mkl/bin/mklvars.sh intel64
#

# Mpich2
ulimit -s unlimited
export OMP_NUM_THREADS=2
PATH=/opt/mpich2/intel/bin:$PATH
export PATH
LD_LIBRARY_PATH=/opt/mpich2/intel/lib64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH
#

then I configured the abinit with build.ac directory at ~/.abinit/build and copied all tarballs to ~/.abinit/tarballs directory\ then typed the command

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/configure --prefix=/opt/abinit/mpich2  --enable-mpi=yes –with-mpi-prefix=/opt/mpich2/intel –with-trio-flavor=”none” --with-linalg-flavor=”mkl+scalapack” --with-linalg-libs="-L/opt/intel/composer_xe_2013.0.079/mkl/lib/intel64 -Wl,--start-group -libmkl_scalapack_lp64  -libmkl_blacs_lp64 -libmkl_intel_lp64 
 -libmkl_sequential -libmkl_core -Wl,--end-group"
--with-dft-flavor=”atompaw+bigdft+libxc” --enable-gui-build=”no” --enable-gw-dpc=”yes” --enable-test-timeout=”yes”

then the summary is as follows

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Summary of important options:

  * C compiler      : intel version 13.0
  * Fortran compiler: intel version 13.0
  * architecture    : unknown unknown (64 bits)

  * debugging       : basic
  * optimizations   : standard

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

  * TRIO   flavor = none
  * TIMER  flavor = abinit (libs: ignored)
  * LINALG flavor = mkl+scalapack (libs: auto-detected)
  * ALGO   flavor = none (libs: ignored)
  * FFT    flavor = none (libs: ignored)
  * MATH   flavor = none (libs: ignored)
  * DFT    flavor = libxc-fallback+atompaw-fallback+bigdft-fallback+wannier90-fallback

Configuration complete.
You may now type "make" to build ABINIT.
(or, on a SMP machine, "make mj4", or "make multi multi_nprocs=<n>")

then typed `make`

after too many outputs.... I faced with this error message!!!!!
….............

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/opt/mpich2/intel/bin/mpif90 -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -I/home/menderes/programs/abinit-7.2.2/fallbacks/exports/include   -free -module /home/menderes/programs/abinit-7.2.2/src/mods  -O2 -xHost -g -extend-source -vec-report0 -noaltparam -nofpscomp   -c -o xdefineoff.o xdefineoff.F90
rm -f lib51_manage_mpi.a
ar rc lib51_manage_mpi.a clnmpi_atom.o clnmpi_grid.o clnmpi_img.o clnmpi_pert.o distrb2.o get_npert_rbz.o herald.o initmpi_atom.o initmpi_band.o initmpi_grid.o initmpi_img.o initmpi_pert.o initmpi_seq.o initmpi_world.o leave_test.o mpi_enreg_tools.o m_io_redirect.o m_wffile.o m_xredistribute.o pawbcast.o pawrad_bcast.o pawtab_bcast.o pre_gather.o pre_scatter.o pspheads_comm.o xdefineoff.o interfaces_51_manage_mpi.o 
ranlib lib51_manage_mpi.a
make[3]: Leaving directory `/home/menderes/programs/abinit-7.2.2/src/51_manage_mpi'
Making all in 52_fft_mpi_noabirule
make[3]: Entering directory `/home/menderes/programs/abinit-7.2.2/src/52_fft_mpi_noabirule'
/opt/mpich2/intel/bin/mpif90 -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -I/home/menderes/programs/abinit-7.2.2/fallbacks/exports/include   -free -module /home/menderes/programs/abinit-7.2.2/src/mods  -O2 -xHost -g -extend-source -vec-report0 -noaltparam -nofpscomp   -c -o interfaces_52_fft_mpi_noabirule.o interfaces_52_fft_mpi_noabirule.F90
/opt/mpich2/intel/bin/mpif90 -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -I/home/menderes/programs/abinit-7.2.2/fallbacks/exports/include   -free -module /home/menderes/programs/abinit-7.2.2/src/mods  -O2 -xHost -g -extend-source -vec-report0 -noaltparam -nofpscomp   -c -o accrho.o accrho.F90
accrho.F90(76): error #6401: The attributes of this name conflict with those made accessible by a USE statement.   [MPI_COMM]
        integer            :: md1,md2proc,md3,mpi_comm,nproc,iproc,paral_kgb
----------------------------------------------^
accrho.F90(224): error #6405: The same named entity from different modules and/or program units cannot be referenced.   [MPI_COMM]
                          MPI_double_precision,mpi_comm,ierr)
-----------------------------------------------^
accrho.F90(224): error #6478: A type-name must not be used as a variable.   [MPI_COMM]
                          MPI_double_precision,mpi_comm,ierr)
-----------------------------------------------^
compilation aborted for accrho.F90 (code 1)
make[3]: *** [accrho.o] Error 1
make[3]: Leaving directory `/home/menderes/programs/abinit-7.2.2/src/52_fft_mpi_noabirule'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/menderes/programs/abinit-7.2.2/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/menderes/programs/abinit-7.2.2'
make: *** [all] Error 2

Post by **jbeuken** » Fri Aug 16, 2013 10:11 pm

Hi,

some questions and suggestions...

- which version of mpich2 ?
- minimum intel version usable is 13.0.1 or >= 13.1.2
- "--with_trio_flavor = netcdf+etsf_io" is mandatory
- try first : --with-linalg-flavor=”mkl”

I made a test with mpich2 1.5 , intel 12.1.4 and this build.ac :

Code: Select all

enable_gw_dpc = yes
enable_mpi = yes
enable_mpi_io = yes
fcflags_opt_77_ddb = -O1 -xHost -g -extend-source -vec-report0 -noaltparam -nofpscomp
with_dft_flavor = none
with_trio_flavor = netcdf+etsf_io
with_mpi_prefix = /usr/local/mpich2_ifort12
with_fft_flavor = fftw3
with_fft_libs = -L/opt/intel/composerxe/mkl/lib/intel64 -Wl,--start-group  -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group
with_linalg_flavor = mkl
with_linalg_libs = -L/opt/intel/composerxe/mkl/lib/intel64 -Wl,--start-group  -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group
status = certified

and it works ( compilation complete successfully and make Tfast succeeded )

( REM : there is a problem with -O2 to compile src/77_ddb/nmsq_pure_gkk_sumfs.F90 )

regards

jmb

spaz · Post by **spaz** » Fri Aug 16, 2013 10:23 pm

mpich2 version is 3.0.4
intel version is l_ccompxe_intel64_2013.0.079

i will tried your way but nothing changed still it gives same error

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-----------------------------------------------^
applypot.F90(431): error #6478: A type-name must not be used as a variable.   [MPI_COMM]
                          MPI_double_precision,mpi_comm,ierr)
-----------------------------------------------^
compilation aborted for applypot.F90 (code 1)
make[5]: *** [applypot.o] Error 1
make[5]: Leaving directory `/home/menderes/programs/abinit-7.2.2/src/52_fft_mpi_noabirule'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory `/home/menderes/programs/abinit-7.2.2/src'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/menderes/programs/abinit-7.2.2'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/menderes/programs/abinit-7.2.2'
make[1]: *** [multi] Error 2
make[1]: Leaving directory `/home/menderes/programs/abinit-7.2.2'
make: *** [mj4] Error 2

spaz · Post by **spaz** » Sat Aug 17, 2013 11:59 am

hi Pouillon !

==============================================================================
=== Multicore architecture startup ===
==============================================================================

configure: Initializing MPI support
configure: looking for MPI in /opt/mpich2/intel
checking for a MPI C compiler... /opt/mpich2/intel/bin/mpicc
checking for a MPI C++ compiler... /opt/mpich2/intel/bin/mpicxx
checking for a MPI Fortran compiler... /opt/mpich2/intel/bin/mpif90
checking for a MPI runner... /opt/mpich2/intel/bin/mpirun
configure: GPU support disabled from command-line

i followed your way to solve the problem and know all mpi and intel compilers are recognized by the abinit package but there are still some problems which I couldn't understand

here is the config.log file..... i'll be glad if you can help me thx for your time

Post by **jbeuken** » Wed Aug 21, 2013 9:28 pm

Hi,

Code: Select all

-----------------------------------------------^
applypot.F90(431): error #6478: A type-name must not be used as a variable.   [MPI_COMM]
                          MPI_double_precision,mpi_comm,ierr)
-----------------------------------------------^
compilation aborted for applypot.F90 (code 1)

ha ! I remember : this problem is corrected in the last released version 7.4.1 !

mpi_comm is use by mpich3
if you replace mpi_comm by mpicomm in src/applypot.F90 and src/accrho.F90 ( as done in 7.4.1 ) , the compilation will succeed...

PS : intel 13.0.0 is not recommended : use 13.0.1 or >= 13.1.2

regards

spaz · Post by **spaz** » Fri Aug 23, 2013 12:07 am

thx for help

after too many different combinations of compilers and versions of abinit i succeded to buil abinit without error and can compile it parallel

initially i changed mpich2 version to mpich2-1.4.1p1 and reinstall all of the intel compilers and mpich2 then configured abinit with above build file.

Post by **jbeuken** » Fri Aug 23, 2013 8:48 pm

Hi,

an error "ssh: Could not resolve hostname.........." .

this is not a abinit problem...

and i learn an important thing about failures, " Failures help us to learn more about what we are doing"

+1 or like 8-)

jmb

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