Tutorial ex. 3.1 takes forever. Wrong configuration?

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spamrefuse
Posts: 35
Joined: Wed Jan 20, 2010 3:08 am

Tutorial ex. 3.1 takes forever. Wrong configuration?

Post by spamrefuse » Thu May 20, 2010 4:27 am

Hi,

I have a sequential version of abinit compiled on an up-to-date
Linux Fedora 12 system (32bits). It's a 8-core CPU, hence fairly fast
for the moderate examples in the tutorial.

I can run the tutorial examples of chapters 1 and 2, all about hydrogen.
However, when I run example 3.1 from the tutorial, the calculation never
seems to finish (I've waited more than 24 hours, whereas all previous
tutorial examples finished within seconds).

I wonder if there's something wrong with my compilation configuration for
the abinit executable. This is what I do:

$ ./configure --prefix=/opt/abinit --disable-netcdf --disable-bigdft --disable-wannier90
<...snip...>
==============================================================================
=== Connectors ===
==============================================================================

checking whether MPI is usable... no
configure: disabling MPI support
checking whether to build MPI code... no
checking whether to use the CUDA Library... no
checking whether to use the FFTW library... no
checking whether to use the GNU Scientific Library... no
configure: applying linear algebra tricks (type: abinit)
checking whether to build the LINALG library... yes
checking whether to activate ScaLAPACK support... no
checking whether to use the PAPI library... no
<...snip...>
<see below for the full output>

$ make multi multi_nprocs=8

# make install



The library dependencies of the abinit executable:
$ ldd /opt/abinit/bin/abinit
linux-gate.so.1 => (0x00421000)
libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00983000)
libm.so.6 => /lib/libm.so.6 (0x00ab3000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x005eb000)
libc.so.6 => /lib/libc.so.6 (0x00110000)
/lib/ld-linux.so.2 (0x008f8000)



$ /opt/abinit/bin/abinit < t3x.files > log
<takes for ever......eventually I have to kill abinit>



The last couple of lines in the log file are these:

chkinp: machine precision is 2.2204460492503131E-16

chkinp: Checking input parameters for consistency.
dtsetcopy : copying area algalch the actual size ( 1) of the index ( 1) differs from its standard size ( 0)
dtsetcopy : copying area atvshift the actual size ( 0) of the index ( 3) differs from its standard size ( 2)
dtsetcopy : copying area kberry the actual size ( 20) of the index ( 2) differs from its standard size ( 1)



The last couple of lines in the t3x.out file are these:

== DATASET 1 ==================================================================

Exchange-correlation functional for the present dataset will be:
LDA: new Teter (4/93) with spin-polarized option - ixc=1
Citation for XC functional:


$ cat t3x_STATUS

Status file, with repetition rate 49, status number 10

Level abinit : call outvars(1



Any idea why abinit seems to "hang" on tutorial example 3.1?

Thank you!
Rob.





# THE FULL CONFIGURE OUTPUT

==============================================================================
=== 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 for a BSD-compatible install... /usr/bin/install -c
checking whether ln -s works... yes
checking for a sed that does not truncate output... /bin/sed
checking for gawk... (cached) gawk
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for a thread-safe mkdir -p... /bin/mkdir -p

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

configure: ABINIT version: 6.0.3
configure: M4 010413 - Autoconf 026300 - Automake 011100 - Libtool 020204
configure: reporting user interface changes:
configure: * new option --enable-cuda is available
configure: * --enable-debug has a new meaning
configure: please check that --enable-debug="yes" is OK for you
configure: * new option --enable-etsf-io-test is available
configure: * --enable-tricks renamed --enable-hints
configure: * --enable-etsf-xc renamed --enable-libxc
configure: * --enable-mpi has a new meaning
configure: please check that --enable-mpi="" is OK for you
configure: * --enable-mpi-io-buggy renamed --enable-mpi-io-test
configure: * --enable-optlevel renamed --enable-optim
configure: * --enable-xmlf90 removed
configure: * new option --with-cuda-includes is available
configure: * new option --with-cuda-libs is available
configure: * new option --with-etsf-io-test-includes is available
configure: * new option --with-etsf-io-test-libs is available
configure: * --with-etsf-xc-includes renamed --with-libxc-includes
configure: * --with-etsf-xc-libs renamed --with-libxc-libs
configure: * --with-mpi-cc-ldflags removed
configure: * --with-mpi-cc-libs removed
configure: * --with-mpi-cflags removed
configure: * --with-mpi-cppflags removed
configure: * --with-mpi-cxx-ldflags removed
configure: * --with-mpi-cxx-libs removed
configure: * --with-mpi-cxxflags removed
configure: * --with-mpi-fc-ldflags removed
configure: * --with-mpi-fc-libs removed
configure: * --with-mpi-fcflags removed
configure: * --with-mpi-prefix has a new meaning
configure: please check that --with-mpi-prefix="" is OK for you
configure: * --with-xmlf90-includes removed
configure: * --with-xmlf90-libs removed

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

configure: checking consistency of external prerequisite options
configure: |---> all OK
configure:
configure: checking consistency of plug-in options
configure: |---> disabling ETSF I/O support (as you don't want NetCDF)
configure:
configure: parsing command-line options

==============================================================================
=== Connector startup ===
==============================================================================

configure: Initializing MPI support
checking for mpirun... no
checking for mpiexec... no
checking for dmpirun... no
configure: compiler checks deferred

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

checking for sh... /bin/sh
checking for perl... /usr/bin/perl
checking for rm... /bin/rm
checking for mv... /bin/mv
checking for tar... /bin/tar
checking for latex... /bin/false
checking for dvips... /bin/false
checking for dvipdf... /usr/bin/dvipdf
checking for ps2pdf... /usr/bin/ps2pdf
checking for markdown... no
checking for wget... /usr/bin/wget
configure: using internal version of MarkDown

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

checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 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 which type of compiler we have... gnu 4.4
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking for abort... yes
checking size of int... 4
checking size of unsigned int... 4
checking size of float... 4
checking size of double... 8
checking size of long... 4
checking size of unsigned long... 4
checking size of long long... 8
checking size of unsigned long long... 8
checking size of size_t... 4
checking size of ptrdiff_t... 4
checking for an ANSI C-conforming const... yes
checking for size_t... 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 4.4

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

checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
configure: Fortran source will be preprocessed using C preprocessor
checking which type of Fortran compiler we have... gnu 4.4
checking fortran 90 modules extension... mod
checking for Fortran flag to compile .F90 files... none
checking whether the Fortran compiler accepts exit()... yes
checking whether the Fortran compiler accepts flush()... yes
checking whether the Fortran compiler accepts flush_()... no
checking whether the Fortran compiler accepts gamma()... yes
checking whether the Fortran compiler accepts get_environment_variable... yes
checking whether the Fortran compiler accepts quadruple integers... no
checking whether the Fortran compiler accepts long lines... no
checking whether the Fortran compiler accepts the null() intrinsic... yes
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran... -L/usr/lib/gcc/i686-redhat-linux/4.4.3 -L/usr/lib/gcc/i686-redhat-linux/4.4.3/../../.. -lgfortranbegin -lgfortran -lm
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore

==============================================================================
=== Python support ===
==============================================================================

checking for python... python
checking for python-config... python-config
checking for Python CPPFLAGS... -I/usr/include/python2.6 -I/usr/include/python2.6
checking for bzr... bzr
checking for Python NumPy headers... found

==============================================================================
=== Libraries and linking ===
==============================================================================

checking for ar... ar
checking for ranlib... ranlib

==============================================================================
=== Hints ===
==============================================================================

checking for cpp... cpp
checking which cpp hints to apply... default/default/default
checking which cc hints to apply... gnu/default/default
checking which xpp hints to apply... none/none/none
checking which cxx hints to apply... gnu/default/default
checking which fpp hints to apply... none/none/none
checking which fc hints to apply... gnu/default/default
checking which ar hints to apply... none/none/none

==============================================================================
=== Debugging ===
==============================================================================

checking debugging status... enabled (custom flags are allowed)
configure: setting C debug flags to '-g'
configure: setting C++ debug flags to '-g'
configure: setting Fortran debug flags to '-g'
checking whether to activate debug mode in source files... no

==============================================================================
=== Optimizations ===
==============================================================================

checking optimization status... enabled (profile mode: standard)
checking which cc optimizations to apply... gnu/default/default
checking which cxx optimizations to apply... gnu/default/default
checking which fc optimizations to apply... gnu/default/default
checking whether to apply per-directory optimizations... yes

==============================================================================
=== 64-bit support ===
==============================================================================

checking for a 64-bit architecture... unknown
checking whether to use 64-bit flags... no
checking for user-defined 64-bit flags... none

==============================================================================
=== Connectors ===
==============================================================================

checking whether MPI is usable... no
configure: disabling MPI support
checking whether to build MPI code... no
checking whether to use the CUDA Library... no
checking whether to use the FFTW library... no
checking whether to use the GNU Scientific Library... no
configure: applying linear algebra tricks (type: abinit)
checking whether to build the LINALG library... yes
checking whether to activate ScaLAPACK support... no
checking whether to use the PAPI library... no

==============================================================================
=== Plug-ins ===
==============================================================================

configure: using tarball repository /home/lahaye/.abinit/tarballs
checking whether to enable the FOX plug-in... no
checking whether to build the FOX plug-in... no
checking whether to enable the NETCDF plug-in... no
checking whether to build the NETCDF plug-in... no
checking whether to enable the ETSF_IO plug-in... no
checking whether to build the ETSF_IO plug-in... no
checking whether to enable the ETSF_IO_TEST plug-in... no
checking whether to build the ETSF_IO_TEST plug-in... no
checking for a source tarball of LIBXC... yes
configure: applying LIBXC tricks
checking whether to enable the LIBXC plug-in... yes
checking whether to build the LIBXC plug-in... yes
checking whether to enable the BIGDFT plug-in... no
checking whether to build the BIGDFT plug-in... no
checking whether to enable the WANNIER90 plug-in... no
checking whether to build the WANNIER90 plug-in... no

==============================================================================
=== Nightly builds ===
==============================================================================

checking whether to build Nightly code... no

==============================================================================
=== Experimental developments ===
==============================================================================

checking whether to enable bindings... no
checking whether to use C clock for timings... no
checking whether to enable error handlers... no
checking whether to build exports... no
checking whether to enable GW double-precision calculations... no
checking whether to test abirules...
checking whether to use macroave... yes
checking whether to read input from stdin... yes

==============================================================================
=== Output ===
==============================================================================

configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.dump
config.status: creating config.pc
config.status: creating config.py
config.status: creating config.sh
config.status: creating config/wrappers/wrap-fc
config.status: creating src/incs/Makefile
config.status: creating src/mods/Makefile
config.status: creating src/16_hideleave/m_build_info.F90
config.status: creating src/98_main/abinis
config.status: creating src/98_main/abinip
config.status: creating tests/tests.env
config.status: creating tests/tests-install.env
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/01_gsl_ext/Makefile
config.status: creating src/01_interfaces_ext/Makefile
config.status: creating src/01_macroavnew_ext/Makefile
config.status: creating src/10_defs/Makefile
config.status: creating src/12_hide_mpi/Makefile
config.status: creating src/14_hidewrite/Makefile
config.status: creating src/16_hideleave/Makefile
config.status: creating src/18_timing/Makefile
config.status: creating src/27_toolbox_oop/Makefile
config.status: creating src/28_numeric_noabirule/Makefile
config.status: creating src/32_contract/Makefile
config.status: creating src/32_util/Makefile
config.status: creating src/42_geometry/Makefile
config.status: creating src/42_nlstrain/Makefile
config.status: creating src/42_parser/Makefile
config.status: creating src/45_psp_parser/Makefile
config.status: creating src/47_xml/Makefile
config.status: creating src/49_gw_toolbox_oop/Makefile
config.status: creating src/50_abitypes_defs/Makefile
config.status: creating src/51_manage_cuda/Makefile
config.status: creating src/51_manage_mpi/Makefile
config.status: creating src/52_fft_mpi_noabirule/Makefile
config.status: creating src/53_abiutil/Makefile
config.status: creating src/53_ffts/Makefile
config.status: creating src/53_spacepar/Makefile
config.status: creating src/56_recipspace/Makefile
config.status: creating src/56_xc/Makefile
config.status: creating src/57_iovars/Makefile
config.status: creating src/59_io_mpi/Makefile
config.status: creating src/61_ionetcdf/Makefile
config.status: creating src/62_cg_noabirule/Makefile
config.status: creating src/62_iowfdenpot/Makefile
config.status: creating src/62_occeig/Makefile
config.status: creating src/62_poisson/Makefile
config.status: creating src/62_wvl_wfs/Makefile
config.status: creating src/63_bader/Makefile
config.status: creating src/64_atompaw/Makefile
config.status: creating src/65_nonlocal/Makefile
config.status: creating src/65_psp/Makefile
config.status: creating src/66_paw/Makefile
config.status: creating src/66_wfs/Makefile
config.status: creating src/67_common/Makefile
config.status: creating src/68_dmft/Makefile
config.status: creating src/68_gw/Makefile
config.status: creating src/68_recursion/Makefile
config.status: creating src/68_rsprc/Makefile
config.status: creating src/69_bse/Makefile
config.status: creating src/72_geomoptim/Makefile
config.status: creating src/72_response/Makefile
config.status: creating src/77_ddb/Makefile
config.status: creating src/77_lwf/Makefile
config.status: creating src/77_suscep/Makefile
config.status: creating src/79_seqpar_mpi/Makefile
config.status: creating src/83_cut3d/Makefile
config.status: creating src/93_rdm/Makefile
config.status: creating src/95_drive/Makefile
config.status: creating src/98_main/Makefile
config.status: creating src/libs/Makefile
config.status: creating tests/Nightly/Makefile
config.status: creating prereqs/Makefile
config.status: creating prereqs/linalg/Makefile
config.status: creating plugins/Makefile
config.status: creating plugins/bigdft/Makefile
config.status: creating plugins/etsf_io/Makefile
config.status: creating plugins/etsf_io_test/Makefile
config.status: creating plugins/fox/Makefile
config.status: creating plugins/libxc/Makefile
config.status: creating plugins/netcdf/Makefile
config.status: creating plugins/wannier90/Makefile
config.status: creating bindings/Makefile
config.status: creating bindings/parser/Makefile
config.status: creating doc/Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing script-perms commands

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


# END CONFIGURE OUTPUT

spamrefuse
Posts: 35
Joined: Wed Jan 20, 2010 3:08 am

Re: Tutorial ex. 3.1 takes forever. Wrong configuration?

Post by spamrefuse » Thu May 20, 2010 5:39 pm

Here is some more info on this problem:

When I compile abinit 5.8.4p in a similar fashion

$ ./configure --prefix=/opt/abinit --disable-netcdf --disable-bigdft --disable-wannier90 --disable-libxc
<snip>
$ make
<snip>
# make install

and run abinit on Tutorial example 3.1, it finishes in seconds.

For some reason, compiling 6.0.3 generates an executable
which hangs on this very same example.

Any ideas what's wrong here?
Or what else I can do to resolve this?

Rob.

mverstra
Posts: 655
Joined: Wed Aug 19, 2009 12:01 pm

Re: Tutorial ex. 3.1 takes forever. Wrong configuration?

Post by mverstra » Tue May 25, 2010 9:50 am

Hello Rob,

the courageous thing to do would be to run the debugger. In 10 seconds it will tell you where the code is stopping.

1) make sure you have gdb installed (sudo yum install gdb)

2) go to the tutorial directory with the t3x.files file

3)

Code: Select all

gdb ../<path>/abinit
run < t3x.files
.
.
.

once it hangs you can hit control-C and it should tell you in which routine you are stalling, as well as give you the very last bits of stdout. The log file may not have everything because the system needs to buffer a certain amount of text before writing it to the log, which of course never happens.

You can also try

valgrind ../<path>/abinit < t3x.files

and wait a while to see if valgrind complains about somthing in particular at the stalling bit. Then kill it of course. No use waiting more than a minute or 2 for the tutorial examples.

Did you change the input variables in t31.in? In a few cases, eg if you don't have a value for ecut, there are platforms where I have seen a hang instead of the error message you should be getting.

I don't think your configure is the problem, but we'll see.

have fun

Matthieu
Matthieu Verstraete
University of Liege, Belgium

mverstra
Posts: 655
Joined: Wed Aug 19, 2009 12:01 pm

Re: Tutorial ex. 3.1 takes forever. Wrong configuration?

Post by mverstra » Tue May 25, 2010 9:54 am

Hi again - I notice the previous thread has the same content, and you have already used the debugger to good effect and gotten an answer from Matteo. Any reason for the second post?
Matthieu Verstraete
University of Liege, Belgium

sathishpon
Posts: 1
Joined: Sun Jul 25, 2010 9:52 am

Re: Tutorial ex. 3.1 takes forever. Wrong configuration?

Post by sathishpon » Sun Jul 25, 2010 10:13 am

Hello,
I too have the same problem from tutorial example 3.1 onwards, the execution of abinit hangs. My system is suse linux 32bit installed in X86_64 intel core2 duo machines. I have tried different configure option ranging from

./configure

./configure --enable-mpi --enable-mpi-io=yes --enable-mpi-trace=yes

./configure --enable-mpi --enable-mpi-io=yes --enable-mpi-trace=yes --enable-bigdft=yes --enable-etsf-xc=yes --enable-netcdf=yes --enable-wannier90=yes --enable-xmlf90=yes --enable-fox=yes --with-mpi-prefix=/usr/local

./configure --enable-mpi -enable-mpi-fft=yes --enable-mpi-io=yes --enable-mpi-trace=yes --enable-bigdft=yes --enable-etsf-xc=yes --enable-netcdf=yes --enable-wannier90=yes --enable-xmlf90=yes --enable-fox=yes --enable-fft=yes --with-fft-libs="-l/usr/local/lib/" --enable-bse-unpacked=yes --enable-dft=yes --enable-gw-cutoff=yes --enable-gw-optimal=yes --enable-gw-wrapper=yes --enable-linalg=yes --with-linalg-libs="-L/home/user/SW/ATLAS/ATLAS_BLD/lib -latlas -lcblas -lf77blas -lf77refblas -llapack -lptcblas -lptf77blas -ltstatlas" --enable-optlevel=standard --with-mpi-prefix=/usr/local

./configure --enable-mpi -enable-mpi-fft=yes --enable-mpi-io=yes --enable-mpi-trace=yes --enable-bigdft=yes --enable-etsf-xc=yes --enable-netcdf=yes --enable-wannier90=yes --enable-xmlf90=yes --enable-fox=yes --enable-fft=yes --with-fft-libs="-l/usr/local/lib/" --enable-bse-unpacked=yes --enable-dft=yes --enable-gw-cutoff=yes --enable-gw-optimal=yes --enable-gw-wrapper=yes --enable-linalg=yes --with-linalg-libs="-L/opt/intel/Compiler/11.1/072/mkl/lib/32 -lmkl_scalapack_core -lmkl_blacs -lmkl_blacs_intempi -lmkl_blacs_openmpi -lmkl_blas95 -lmkl_intel -lmkl_intel_thread -lmkl_lapack95 -lmkl_solver -lmkl_solver_sequential -lmkl_cdft_core -lmkl_core -lmkl_gf -lmkl_gnu_thread -lmkl_sequential -lmkl_pgi_thread" --enable-optlevel=standard --with-mpi-prefix=/usr/local

I compiled the code with default gcc, gfortran compilers and openmpi libraries.

finally, I tried the gdb advice given in this thread and got the following result where the execution hung again.

================================================================================
== DATASET 1 ==================================================================

dtsetcopy : copying area algalch the actual size ( 1) of the index ( 1) differs f rom its standard size ( 0)
dtsetcopy : copying area atvshift the actual size ( 0) of the index ( 3) differs f rom its standard size ( 2)
dtsetcopy : copying area kberry the actual size ( 20) of the index ( 2) differs f rom its standard size ( 1)
dtsetcopy : copying area nband the actual size ( 2) of the index ( 1) differs f rom its standard size ( 1)
dtsetcopy : copying area mixalch the actual size ( 1) of the index ( 1) differs f rom its standard size ( 0)
dtsetcopy : copying area mixalch the actual size ( 1) of the index ( 2) differs f rom its standard size ( 0)
dtsetcopy : copying area shiftk the actual size ( 8) of the index ( 2) differs f rom its standard size ( 1)
getdim_nloc : enter
pspheads(1)%nproj(0:3)= 1 1 0 0

getdim_nloc : deduce lmnmax = 4, lnmax = 2,
lmnmaxso= 4, lnmaxso= 2.
Exchange-correlation functional for the present dataset will be:
LDA: new Teter (4/93) with spin-polarized option - ixc=1
Citation for XC functional:
S. Goedecker, M. Teter, J. Huetter, PRB 54, 1703 (1996)

Unit cell volume ucvol= 2.6374446E+02 bohr^3
Angles (23,13,12)= 6.00000000E+01 6.00000000E+01 6.00000000E+01 degrees

getcut: wavevector= 0.0000 0.0000 0.0000 ngfft= 20 20 20
ecut(hartree)= 8.000 => boxcut(ratio)= 2.18216
- pspatm: opening atomic psp file /home/user/SW/espresso-4.1.1/2_ab-init/abinit-6.2.1/tests /Psps_for_tests/14si.pspnc
Troullier-Martins psp for element Si Thu Oct 27 17:31:21 EDT 1994
14.00000 4.00000 940714 znucl, zion, pspdat
1 1 2 2 2001 0.00000 pspcod,pspxc,lmax,lloc,mmax,r2well
0 5.907 14.692 1 2.0872718 l,e99.0,e99.9,nproj,rcpsp
0.00000000 0.00000000 0.00000000 0.00000000 rms, ekb1, ekb2, epsatm
1 2.617 4.181 1 2.0872718 l,e99.0,e99.9,nproj,rcpsp
0.00000000 0.00000000 0.00000000 0.00000000 rms, ekb1, ekb2, epsatm
2 0.000 0.000 0 2.0872718 l,e99.0,e99.9,nproj,rcpsp
0.00000000 0.00000000 0.00000000 0.00000000 rms, ekb1, ekb2, epsatm
1.80626423934776 0.22824404341771 1.17378968127746 rchrg,fchrg,qchrg
pspatm: epsatm= 1.43386982
--- l ekb(1:nproj) -->
0 3.287949
1 1.849886
pspatm: atomic psp has been read and splines computed

2.29419171E+01 ecore*ucvol(ha*bohr**3)
wfconv: 5 bands initialized randomly with npw= 283, for ikpt= 1
wfconv: 5 bands initialized randomly with npw= 289, for ikpt= 2

setup2: Arith. and geom. avg. npw (full set) are 284.500 284.488
symatm: atom number 1 is reached starting at atom
1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2
1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2
symatm: atom number 2 is reached starting at atom
2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1
2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1
initro : for itypat= 1, take decay length= 1.1000,
initro : indeed, coreel= 10.0000, nval= 4 and densty= 0.0000E+00.

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

getcut: wavevector= 0.0000 0.0000 0.0000 ngfft= 20 20 20
ecut(hartree)= 8.000 => boxcut(ratio)= 2.18216
scfcv : before setvtr, energies%e_hartree= 0.0000000000000000

ewald : nr and ng are 3 and 11
mklocl_recipspace : will add potential with strength vprtrb(:)= 0.0000000000000000 0.0000000000000000
setvtr : istep,n1xccc,moved_rhor= 1 2501 0
scfcv : after setvtr, energies%e_hartree= 0.0000000000000000

ITER STEP NUMBER 1
vtorho : nnsclo_now= 2, note that nnsclo,dbl_nnsclo,istep= 0 0 1

Non-SCF iterations; k pt # 1 k= -0.25000 0.50000 0.00000 band residuals:
res: 2.20E-02 2.77E-02 2.68E-02 4.76E-02 1.55E-02


-------------------------------------------------------------------------------------

I even tried to compile with available intel ifort and icc compiler but the 'make' failed giving error about no intel fast memcpy


Any hints on troubleshooting will be greatly appreciated.

Thanks,
Sathish

Ngeah
Posts: 7
Joined: Wed Aug 18, 2010 1:44 am

Re: Tutorial ex. 3.1 takes forever. Wrong configuration?

Post by Ngeah » Wed Aug 18, 2010 2:28 am

sathishpon wrote:Hello,
I too have the same problem from tutorial example 3.1 onwards, the execution of abinit hangs. My system is suse linux 32bit installed in X86_64 intel core2 duo machines. I have tried different configure option ranging from



I had the same problem as well here at my school. Since I'm the only person on campus using ABINIT, I had to go back and forth with our IT guy to figure out what was wrong with it, so I don't have 100% of the details. As far as I understand, ABINIT is kind of picky when it comes to which version of GCC you're using, and if you don't have the right one, it causes issues. When we updated to the "newest" version of GCC (Red Hat's auto update), it didn't work, but there's a newer version of GCC availible that isn't availible on the auto update. After we installed it, the problem was fixed.

Also, after you do the "make" command, you can test to see whether or not it was a valid installation by running the internal tests.

make testin_1 (This test worked for me every time)
make testin_2 (The rest of the tests failed until I got things sorted out.)
make testin_3

make testin_bigdft
make testin_etst-io
make testin_libxc
make testin_wannier90

Check out the installation notes on the website and the README file for more info
~abinit/tests/built-in/README

I hope that helped.

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