ABINIT Discussion Forums

hi
I am trying to install on HPCC with config: 1 Sun* Fire X4270 with Intel Xeon Nehalam* processors with total 16 cores,
Intel® Fortran Composer XE 2013 for Linux
I used

1) export FC=ifort
2) export PATH=/usr/lib64/openmpi/1.2.7-gcc/bin/:$PATH
3) export LD_LIBRARY_PATH=/usr/lib64/openmpi/1.2.7-gcc/lib:$LD_LIBRARY_PATH
4) ./configure --with-config-file=./build.ac

build.ac file contains:
prefix="${HOME}/abinit"
enable_mpi="yes"
enable_mpi_io="yes"
with_mpi_prefix="/usr/lib64/openmpi/1.2.7-gcc/bin/"



5) make multi multi_nprocs=16

At the end i got following error:
make[3]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5/fallbacks'
Making all in src
make[3]: Entering directory `/home/gurinder/abinit/abinit-7.0.5/src'
Making all in incs
make[4]: Entering directory `/home/gurinder/abinit/abinit-7.0.5/src/incs'
There is no buildable file here
make[4]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5/src/incs'
Making all in mods
make[4]: Entering directory `/home/gurinder/abinit/abinit-7.0.5/src/mods'
There is no buildable file here
make[4]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5/src/mods'
Making all in 01_interfaces_ext
make[4]: Entering directory `/home/gurinder/abinit/abinit-7.0.5/src/01_interfaces_ext'
ifort -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -I/home/gurinder/abinit/abinit-7.0.5/fallbacks/exports/include -I/home/gurinder/abinit/abinit-7.0.5/fallbacks/exports/include -free -module /home/gurinder/abinit/abinit-7.0.5/src/mods -O2 -xHost -g -extend-source -vec-report0 -noaltparam -nofpscomp -c -o m_iso_c_bindings.o m_iso_c_bindings.F90
config.h(642): #error: "HAVE_MPI1 and HAVE_MPI2 are both undefined"

make[4]: *** [m_iso_c_bindings.o] Error 1
make[4]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5/src/01_interfaces_ext'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5/src'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5'
make: *** [multi] Error 2


Please help me.
Janpreet Sidhu

Your config.log shows that the MPI library had not been detected correctly.
Use an MPI library compiled with ifort if you want to compile abinit with ifort.
Note, moreover, that with_mpi_prefix should point to the installation directory of the MPI library, not to the bin dir.

Hi Janpreet Sidhu,
The error "HAVE_MPI1 and HAVE_MPI2 are both undefined" occurs when there is a conflict between "built-in" (that is those came in your Linux distribution) and installed by you libraries, I guess. It happens also during unsuccessfully repeated installation efforts when Abinit cannot define which libraries to choose.
I have faced with this error and I tried to:
- do installation from clean situation (remove package), even to reinstall MPI (I use OpenMPI, using Intel compilers).
- indicate the library path (you installed Intel Fortran compiler, why did not indicate also CC=icc, CXX=icpc after installing Intel C compilers too?)
Cheers,
Tuan

gmatteo wrote:Your config.log shows that the MPI library had not been detected correctly.
Use an MPI library compiled with ifort if you want to compile abinit with ifort.
Note, moreover, that with_mpi_prefix should point to the installation directory of the MPI library, not to the bin dir.

hi Gmatteo
thanks
i change the path accordingly as below:

1) export FC=ifort
2) export PATH=/home/gurinder/mpich-install/bin:$PATH
3) export LD_LIBRARY_PATH=/home/gurinder/mpich-install/lib:$LD_LIBRARY_PATH
4) ./configure --with-config-file=./build.ac

build.ac file contains:
prefix="${HOME}/abinit"
enable_mpi="yes"
enable_mpi_io="yes"
with_mpi_prefix="/home/gurinder/mpich-install/"

this solve the problem "HAVE_MPI1 and HAVE_MPI2 are both undefined".But i ran into new one:

/home/gurinder/abinit/abinit-7.0.5/config/wrappers/wrap-mpifc -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -I/home/gurinder/abinit/abinit-7.0.5/fallbacks/exports/include -free -module /home/gurinder/abinit/abinit-7.0.5/src/mods -O2 -xHost -g -extend-source -vec-report0 -noaltparam -nofpscomp -c -o back.o back.F90
/home/gurinder/abinit/abinit-7.0.5/config/wrappers/wrap-mpifc -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -I/home/gurinder/abinit/abinit-7.0.5/fallbacks/exports/include -free -module /home/gurinder/abinit/abinit-7.0.5/src/mods -O2 -xHost -g -extend-source -vec-report0 -noaltparam -nofpscomp -c -o back_wf.o back_wf.F90
/home/gurinder/abinit/abinit-7.0.5/config/wrappers/wrap-mpifc -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -I/home/gurinder/abinit/abinit-7.0.5/fallbacks/exports/include -free -module /home/gurinder/abinit/abinit-7.0.5/src/mods -O2 -xHost -g -extend-source -vec-report0 -noaltparam -nofpscomp -c -o forw.o forw.F90
/home/gurinder/abinit/abinit-7.0.5/config/wrappers/wrap-mpifc -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -I/home/gurinder/abinit/abinit-7.0.5/fallbacks/exports/include -free -module /home/gurinder/abinit/abinit-7.0.5/src/mods -O2 -xHost -g -extend-source -vec-report0 -noaltparam -nofpscomp -c -o forw_wf.o forw_wf.F90
/home/gurinder/abinit/abinit-7.0.5/config/wrappers/wrap-mpifc -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -I/home/gurinder/abinit/abinit-7.0.5/fallbacks/exports/include -free -module /home/gurinder/abinit/abinit-7.0.5/src/mods -O2 -xHost -g -extend-source -vec-report0 -noaltparam -nofpscomp -c -o m_sgfft.o m_sgfft.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[4]: *** [accrho.o] Error 1
make[4]: *** Waiting for unfinished jobs....
applypot.F90(78): error #6401: The attributes of this name conflict with those made accessible by a USE statement. [MPI_COMM]
integer :: max1o,max2o,max3o,m1o,m2o,m3o,mpi_comm,nproc,iproc
-------------------------------------------------^
applypot.F90(251): error #6405: The same named entity from different modules and/or program units cannot be referenced. [MPI_COMM]
MPI_double_precision,mpi_comm,ierr)
-----------------------------------------------^
applypot.F90(251): error #6478: A type-name must not be used as a variable. [MPI_COMM]
MPI_double_precision,mpi_comm,ierr)
-----------------------------------------------^
applypot.F90(431): error #6405: The same named entity from different modules and/or program units cannot be referenced. [MPI_COMM]
MPI_double_precision,mpi_comm,ierr)
-----------------------------------------------^
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[4]: *** [applypot.o] Error 1
make[4]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5/src/52_fft_mpi_noabirule'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5/src'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5'
make: *** [multi] Error 2

Here i am using mpich installed localy. This library is not compiled with ifort. I have to re-compile this library with ifort or there is any other reason?

Janpreet Sidhu

letuan wrote:Hi Janpreet Sidhu,
The error "HAVE_MPI1 and HAVE_MPI2 are both undefined" occurs when there is a conflict between "built-in" (that is those came in your Linux distribution) and installed by you libraries, I guess. It happens also during unsuccessfully repeated installation efforts when Abinit cannot define which libraries to choose.
I have faced with this error and I tried to:
- do installation from clean situation (remove package), even to reinstall MPI (I use OpenMPI, using Intel compilers).
- indicate the library path (you installed Intel Fortran compiler, why did not indicate also CC=icc, CXX=icpc after installing Intel C compilers too?)
Cheers,
Tuan

Hi Tuan Thanks
I do installation from clean situation but stil not reinstall MPI using Intel compiler.I have installed only intel fortran compiler to overcome the error i got by using
C compiler : gnu version 4.1
Fortran compiler: gnu version 4.1
architecture : intel xeon (64 bits)

And when i made then got error :

checking for Fortran flag to compile .f90 files... unknown
configure: error: Fortran could not compile .f90 files
make[2]: *** [stamps/libxc-config-stamp] Error 1
make[2]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5/fallbacks'
make[1]: [all-local] Error 2 (ignored)
Checking build of libxc fallback
test -e stamps/libxc-install-stamp
make[1]: *** [all-local] Error 1
make[1]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5/fallbacks'
make: *** [multi] Error 2

Thats why i use only intel fortran compiler .Is it necessary to install Intel C compiler also ?
I make some changes as in above post but still got errors.

Janpreet Sidhu

See viewtopic.php?f=3&t=2067

Hi Janpreet Sidhu,
Did you issue the command right after installation of Intel Fortran compiler (there is instruction in messages at the end of the installation)? For example, in my machine with Intel Parallel Studio XE 2013 Update 3 (compilers' version 13.1) I used . Without this step you probably cannot have Intel compilers to work correctly.
Experienced users gave me an advice that using Intel's mathematical library MKL accelerated abinit running at least to 25%, so I recommend to use also C compilers from Intel.
Cheers,
Tuan.

Hi Pouillon
thanks

when i configure with



this solve above problem but there is again error :



/home/gurinder/abinit/abinit-7.0.5/config/wrappers/wrap-mpifc -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -I/home/gurinder/abinit/abinit-7.0.5/fallbacks/exports/include -free -module /home/gurinder/abinit/abinit-7.0.5/src/mods -O2 -xHost -g -extend-source -vec-report0 -noaltparam -nofpscomp -c -o prep_nonlop.o prep_nonlop.F90
0_10711

: catastrophic error: **Internal compiler error: internal abort** Please report this error along with the circumstances in which it occurred in a Software Problem Report. Note: File and line given may not be explicit cause of this error.
compilation aborted for prep_fourwf.F90 (code 1)
make[4]: *** [prep_fourwf.o] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5/src/66_wfs'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5/src'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/gurinder/abinit/abinit-7.0.5'
make: *** [multi] Error 2

Is this a compiler error?? Can we overcome this?
Thanks in advance.

Janpreet

Hi again,
Please, look at the last messages in my topic viewtopic.php?f=3&t=2071
And you will find out the solution.
Tuan.

Hi again,
Please, look at the last messages in my topic viewtopic.php?f=3&t=2071
And you will find out the solution.
Tuan.

Hi Tuan
thanks again
Now i do as:
export FC=ifort
export PATH=/home/gurinder/mpich-install/bin:$PATH
export LD_LIBRARY_PATH=/home/gurinder/mpich-install/lib:$LD_LIBRARY_PATH
./configure --with-mpi-level=1 --with-config-file=./build.ac

build.ac file:

prefix="${HOME}/a"
enable_mpi="yes"
enable_mpi_io="yes"
with_mpi_prefix="/home/gurinder/mpich-install"
FCFLAGS="-O1"

then
make install

installation run upto last .But when i run simple test this stops and error in log file is:

wfconv: 4 bands initialized randomly with npw= 1960, for ikpt= 48
wfconv: 4 bands initialized randomly with npw= 1959, for ikpt= 49
wfconv: 4 bands initialized randomly with npw= 1957, for ikpt= 50
newkpt: loop on k-points done in parallel
leave_test : synchronization done...
pareigocc : MPI_ALLREDUCE

setup2: Arith. and geom. avg. npw (full set) are 1962.059 1962.049
initro : for itypat= 1, take decay length= 1.2500,
initro : indeed, coreel= 78.0000, nval= 4 and densty= 0.0000E+00.

================================================================================

getcut: wavevector= 0.0000 0.0000 0.0000 ngfft= 36 36 36
ecut(hartree)= 30.000 => boxcut(ratio)= 2.06487

ewald : nr and ng are 3 and 11

ITER STEP NUMBER 1
vtorho : nnsclo_now= 2, note that nnsclo,dbl_nnsclo,istep= 0 0 1
forrtl: severe (174): SIGSEGV, segmentation fault occurred


what is wrong here ? please help me.
input file is attached.
Janpreet

Hi Janpreet,
Obviously, you have compiled your abinit package
I guess the problem is in the lack of memory in your system? Try to decrease ecut in input file, for example, ecut=20.
And I don't understand why you do have "max_nprocs=1" in your input file?
I use "make check" right after abinit installation for checking and comparing with the "default" calculation data given by abinit creators.
Tuan

hii to all
Belated Thanks to all
finally abinit get installed

Janpreet