ABINIT Discussion Forums

Hello Dear,

Please help me,

"OS OpenSUSE 11.4 32bit
in Computer Pentium Dual Core"

i use openmpi 1.6.2, extract and configure at /home/usrname/openmpi

Setting LD_LIBRARY_PATH="/openmpi/lib/" in .bashrc file

and configure abinit with this command ./configure --enable-mpi --with-mpi-level=2 FC=gfortran --with-mpi-prefix="/home/usrname/openmpi" --with-linalg-libs="-llapack -lbas"

give me this report

Summary of important options:

* C compiler : gnu version 4.5
* Fortran compiler: gnu version 4.5
* architecture : unknown unknown (32 bits)

* debugging : basic
* optimizations : standard

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

* TRIO flavor = netcdf-fallback+etsf_io-fallback
* TIMER flavor = abinit (libs: ignored)
* LINALG flavor = netlib-fallback (libs: internal)
* 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 i type make multi multi_nprocs=2
give me this report

==============================================================================
make[4]: Leaving directory `/home/arsyik/abinit/tests'
make[3]: Leaving directory `/home/arsyik/abinit/tests'
make[3]: Entering directory `/home/arsyik/abinit'
make[3]: Leaving directory `/home/arsyik/abinit'
make[2]: Leaving directory `/home/arsyik/abinit'
make[1]: Leaving directory `/home/arsyik/abinit'

finally i type sudo make install
and give me this
.......
/bin/mkdir -p '/usr/local/share/abinit-test/fox'
/usr/bin/install -c -m 644 fox/README fox/tests.cnf '/usr/local/share/abinit-test/fox'
make[3]: Leaving directory `/home/arsyik/abinit/tests'
make[2]: Leaving directory `/home/arsyik/abinit/tests'
make[1]: Leaving directory `/home/arsyik/abinit/tests'
make[1]: Entering directory `/home/arsyik/abinit'
make[2]: Entering directory `/home/arsyik/abinit'
make[2]: Nothing to be done for `install-exec-am'.
/usr/bin/install -c -d -m 755 /usr/local/lib/pkgconfig
/usr/bin/install -c -m 644 -m 644 config.pc \
/usr/local/lib/pkgconfig/abinit.pc
make[2]: Leaving directory `/home/arsyik/abinit'
make[1]: Leaving directory `/home/arsyik/abinit'

and i tried to run
mpirun -np 2 /usr/local/bin/abinit < tparal_1.files> tparal.log
or
mpirun -np 2 abinit < tparal_1.files> tparal.log

that's give the same error

[linux-u242.site:10094] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

orte_rml_base_select failed
--> Returned value -13 instead of ORTE_SUCCESS

--------------------------------------------------------------------------
[linux-u242.site:10094] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_system_init.c at line 42
[linux-u242.site:10094] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 52
--------------------------------------------------------------------------
Open RTE was unable to initialize properly. The error occured while
attempting to orte_init(). Returned value -13 instead of ORTE_SUCCESS.
--------------------------------------------------------------------------
How to fix it?

thanks in advance

Hi,

Several comments about your Abinit configure step
--with-mpi-prefix expects the root path where MPI has been installed i.e. a path with subdirs like bin, lib, include, ... If I understand /home/username/openmpi is the place where you built (compiled) openmpi and not where openmpi has been installed during the make install step. Seeing your LD_LIBRARY_PATH, I assume openmpi lives in /opempi (you should have /openmpi/bin/mpif90, /opempi/lib/, ...) and --with-mpi-prefix should equal /openmpi. Add PATH=/openmpi/bin:$PATH to help configure to find your mpi binaries in this unusual place.
Don't set FC=gfortran ... your fortran compiler is now mpif90. Try mpif90 -show, it should return the name of the backend gfortran compiler. Try which mpif90, it should return /openmpi/bin/mpif90
--with-mpi-level=2 is useless; openmpi is level 2 compliant.
--with-linalg-libs= .... first of all, it should be -lblas instead of -lbas and if your intention is to use the linear algebra libraries provided by Abinit, the option is useless

All this to say that Abinit should configure with a configure --enable-mpi --with-mpi-prefix=/openmpi and the mentioned environment variables.
Please mention the version of Abinit you're working on.

Kind regards,

Alain

Hi,
Thanks for your reply

i'm using abinit 6.12.3 and openmpi 1.6.2

now i configure with this command
./configure --enable-mpi FC=mpif90 --with-mpi-prefix="/usr/lib/mpi/gcc/bin" --with-linalg-libs="-llapack -lblas"

and give this report
==============================================================================
=== Overall startup ===
==============================================================================

checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking target system type... i686-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make sets $(MAKE)... (cached) yes
checking whether ln -s works... yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for gawk... (cached) gawk
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
configure: not loading options (no config file available)

==============================================================================
=== Build-system information ===
==============================================================================

configure: ABINIT version 6.12.3
configure: M4 010416 - Autoconf 026800 - Automake 011100 - Libtool 020204
configure: reporting user interface changes:
configure: * new option --enable-gui is available
configure: * new option --enable-gw-openmp is available
configure: * new option --with-algo-flavor is available
configure: * new option --with-algo-incs is available
configure: * new option --with-algo-libs is available
configure: * --with-fallbacks-tardir removed

==============================================================================
=== Option consistency checking ===
==============================================================================

configure: checking consistency of library-related options
configure: |---> all OK
configure:
configure: checking consistency of experimental options
configure: |---> all OK
configure:
configure: |---> all OK
configure:
configure: parsing command-line options

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

configure: Initializing MPI support
configure: looking for MPI in /usr/lib/mpi/gcc/openmpi/bin
checking for a MPI C compiler... none found
checking for a MPI C++ compiler... none found
checking for a MPI Fortran compiler... none found
checking for a MPI runner... none found
configure: GPU support disabled from command-line

==============================================================================
=== Utilities ===
==============================================================================

checking for sh... /usr/bin/sh
checking for mv... /bin/mv
checking for perl... /usr/bin/perl
checking for rm... /bin/rm
checking for patch... patch
checking for tar... tar

==============================================================================
=== C support ===
==============================================================================

checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking which type of compiler we have... gnu 4.5
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether byte ordering is bigendian... no

==============================================================================
=== C++ support ===
==============================================================================

checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking which type of C++ compiler we have... gnu 4.5

==============================================================================
=== Fortran support ===
==============================================================================

checking for mpif90... /usr/lib/mpi/gcc/openmpi/bin/mpif90
checking whether we are using the GNU Fortran compiler... yes
checking whether mpif90 accepts -g... yes
checking which type of Fortran compiler we have... gnu 4.5
checking fortran 90 modules extension... mod
checking for Fortran flag to compile .F90 files... none
configure: determining Fortran module case
checking whether Fortran modules are upper-case... no
checking how to get verbose linking output from mpif90... -v
checking for Fortran libraries of mpif90... -L/usr/lib/mpi/gcc/openmpi/lib -L/usr/lib/gcc/i586-suse-linux/4.5 -L/usr/lib/gcc/i586-suse-linux/4.5/../../../../i586-suse-linux/lib -L/usr/lib/gcc/i586-suse-linux/4.5/../../.. -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -lnsl -lutil -lgfortran -lm -lpthread
checking for dummy main to link with Fortran libraries... unknown
configure: error: in `/home/arsyik/abinit':
configure: error: linking to Fortran libraries from C fails
See `config.log' for more details
arsyik@linux-u277:~/abinit>

What should i do next?

Thanks

This my configure log file.

configure: Initializing MPI support
configure: looking for MPI in /usr/lib/mpi/gcc/openmpi/bin
checking for a MPI C compiler... none found
checking for a MPI C++ compiler... none found
checking for a MPI Fortran compiler... none found
checking for a MPI runner... none found

configure cannot find the MPI executables and config.log shows that the MPI libraries cannot be located too. The --with-mpi-prefix option refers to the root of your MPI installation, configure expects to find the bin, lib, include subdirectories under the prefix path i.e. if you set --with-mpi-prefix=/xxx then you should find /xxx/bin/mpif90 executable and /xxx/lib/libmpi.so or /xxx/lib/libmpi.a.
So I assume that the right mpi-prefix for your system is /usr/lib/mpi/gcc/openmpi

Kind regards,

Alain

Dear arsylik,

I noticed that there could have a problem with your command (even with Alain's correction)

./configure --enable-mpi FC=mpif90 --with-mpi-prefix="/usr/lib/mpi/gcc/openmpi" --with-linalg-libs="-llapack -lblas"

if you want to use your own linalg libs, you need to add ( replace the LIBPATH by the right path ):



and , also, in your environment,



regards

jmb

Thanks for your reply

now i'm doing this
./configure --with-linalg-flavor=netlib --enable-mpi FC=mpif90 --with-mpi-prefix=/usr/lib/mpi/gcc/openmpi

make mj4
sudo make mj4 install

then i tried to running abinit with mpirun with this command
mpirun -n 2 /usr/local/bin/abinit < tparal_1.files >&log

and in output file show this

--------------------------------------------------------------------------------
------------- Echo of variables that govern the present computation ------------
--------------------------------------------------------------------------------
-
- outvars: echo of selected default values
- accesswff0 = 0 , fftalg0 =112 , wfoptalg0 = 0
-
- outvars: echo of global parameters not present in the input file
- nproc = 1
-
-outvars: echo values of preprocessed input variables --------

what should i do?
Thanks in advance

arsyik