[RESOLVED] Compilling abinit on CentOS

option, parallelism,...

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Junjie
Posts: 5
Joined: Sun Sep 12, 2010 6:39 pm

[RESOLVED] Compilling abinit on CentOS

Post by Junjie » Mon Sep 13, 2010 11:45 am

hi, there

I'm trying to compiling abinit on CentOS 5.5.

(1) the compiler: ifort 11.1
(2) the architecture: 64-bit HP Z400 workstation
(3) if the problems occur compiling in serial/in parallel: both
(4) the version of ABINIT : 6.2.3

(5) the relevant compiler error message

../configure FC=/opt/intel/Compiler/11.1/073/bin/intel64/ifort --disable-etsf-io

configure

Code: Select all

configure:  * new option --enable-gw-cutoff is available
configure:  * new option --enable-gw-optimal is available
configure:  * new option --enable-gw-wrapper is available
configure:  * new option --enable-linalg is available
configure:  * new option --enable-maintainer-checks is available
configure:  * --enable-gsl renamed --enable-math
configure:  * new option --enable-smp is available
configure:  * --enable-nightly renamed --enable-test-timeout
configure:  * --enable-papi renamed --enable-timer
configure:  * new option --enable-trio is available
configure:  * new option --enable-vdwxc is available
configure:  * --with-64bit-flags removed
configure:  * --with-ar-dbgflags removed
configure:  * --with-ar-optflags removed
configure:  * --with-cc-dbgflags removed
configure:  * --with-cc-ld-dbgflags removed
configure:  * --with-cc-ld-dbglibs removed
configure:  * --with-cc-ld-optflags removed
configure:  * --with-cc-ld-optlibs removed
configure:  * --with-cc-optflags removed
configure:  * --with-cpp-dbgflags removed
configure:  * --with-cpp-optflags removed
configure:  * --with-cxx-dbgflags removed
configure:  * --with-cxx-ld-dbgflags removed
configure:  * --with-cxx-ld-dbglibs removed
configure:  * --with-cxx-ld-optflags removed
configure:  * --with-cxx-ld-optlibs removed
configure:  * --with-cxx-optflags removed
configure:  * new option --with-dft-flavor is available
configure:  * new option --with-dft-includes is available
configure:  * new option --with-dft-libs is available
configure:  * --with-etsf-io-test-includes removed
configure:  * --with-etsf-io-test-libs removed
configure:  * --with-fc-dbgflags removed
configure:  * --with-fc-ld-dbgflags removed
configure:  * --with-fc-ld-dbglibs removed
configure:  * --with-fc-ld-optflags removed
configure:  * --with-fc-ld-optlibs removed
configure:  * --with-fc-optflags removed
configure:  * new option --with-fft-flavor is available
configure:  * --with-fftw-includes renamed --with-fft-includes
configure:  * --with-fftw-libs renamed --with-fft-libs
configure:  * new option --with-gpu-cflags is available
configure:  * new option --with-gpu-cppflags is available
configure:  * new option --with-gpu-flavor is available
configure:  * --with-cuda-includes renamed --with-gpu-includes
configure:  * new option --with-gpu-ldflags is available
configure:  * --with-cuda-libs renamed --with-gpu-libs
configure:  * new option --with-gpu-prefix is available
configure:  * --with-linalg-type renamed --with-linalg-flavor
configure:  * new option --with-math-flavor is available
configure:  * --with-gsl-includes renamed --with-math-includes
configure:  * --with-gsl-libs renamed --with-math-libs
configure:  * --with-mpi-runner removed
configure:  * --with-scalapack-includes removed
configure:  * --with-scalapack-libs removed
configure:  * --with-timeout renamed --with-test-timeout
configure:  * new option --with-timer-flavor is available
configure:  * --with-papi-includes renamed --with-timer-includes
configure:  * --with-papi-libs renamed --with-timer-libs
configure:  * new option --with-trio-flavor is available
configure:  * new option --with-trio-includes is available
configure:  * new option --with-trio-libs is available

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

configure: checking consistency of external prerequisite options
configure:  |---> all OK
configure:
configure: checking consistency of plug-in options
configure:  |---> all OK
configure:
configure: checking consistency of experimental options
configure:  |---> all OK
configure:
configure: parsing command-line options

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

configure: MPI support disabled from command-line
configure: GPU support disabled from command-line

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

checking for sh... /bin/sh
checking for mv... /bin/mv
checking for perl... /usr/bin/perl
checking for rm... /bin/rm
checking for dvips... no
checking for dvipdf... dvipdf
checking for latex... no
checking for markdown... no
checking for md5sum... md5sum
checking for patch... patch
checking for ps2pdf... ps2pdf
checking for tar... tar
checking for wget... 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 which type of compiler we have... gnu 4.1
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 4.1

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

checking whether we are using the GNU Fortran compiler... no
checking whether /opt/intel/Compiler/11.1/073/bin/intel64/ifort accepts -g... yes
checking which type of Fortran compiler we have... intel 11.1
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 /opt/intel/Compiler/11.1/073/bin/intel64/ifort... -v
checking for Fortran libraries of /opt/intel/Compiler/11.1/073/bin/intel64/ifort...  -L/opt/intel/Compiler/11.1/073/lib/intel64 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../.. -L/lib64 -L/lib -L/usr/lib64 -L/usr/lib -lifport -lifcore -limf -lsvml -lm -lipgo -lirc -lpthread -lirc_s -ldl
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... no
checking for python2.6-config... no
checking for python2.5-config... no
checking for python2.4-config... no
checking for Python CPPFLAGS...
checking for bzr... no
checking for Python NumPy headers... not found
checking numarray/arrayobject.h usability... no
checking numarray/arrayobject.h presence... no
checking for numarray/arrayobject.h... no

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

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

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

checking for cpp... cpp
checking for a true C preprocessor... 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... default/default/default
checking which fc hints to apply... intel/default/default
checking which ar hints to apply... none/none/none
checking which Fortran preprocessor to use...
checking which Fortran preprocessor flags to apply...
checking whether to wrap Fortran compiler calls... no

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

checking debugging status... enabled (using compiler defaults)
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
checking whether to activate design-by-contract debugging... no

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

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

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

checking for a 64-bit architecture... yes
checking whether to use 64-bit flags... no
checking for user-defined 64-bit flags...

 ==============================================================================
 === Build flags                                                            ===
 ==============================================================================

configure: static builds may be performed

 ==============================================================================
 === Advanced compiler features                                             ===
 ==============================================================================

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 errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking mcheck.h usability... yes
checking mcheck.h presence... yes
checking for mcheck.h... yes
checking for abort... yes
checking size of char... 1
checking size of short... 2
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of unsigned int... 4
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking size of float... 4
checking size of double... 8
checking size of long double... 16
checking size of size_t... 8
checking size of ptrdiff_t... 8
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether the Fortran compiler provides the iso_c_binding module... yes
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()... no
checking whether the Fortran compiler accepts getenv()... yes
checking whether the Fortran compiler accepts getpid()... yes
checking whether the Fortran compiler accepts the null() intrinsic... 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 etime()... yes
checking whether to use C clock for timings... no

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

checking whether MPI is usable... no
checking whether to build MPI code... no
checking whether to activate GPU support... no
checking whether to use transferable I/O libraries... no
checking whether to use optimized timer libraries... no
checking whether to use optimized linear algebra libraries... yes
checking whether to activate ScaLAPACK support... no
checking for the requested linear algebra support... netlib
checking for zgemm in -lblas... no
checking for zhpev in -llapack... no
checking for the actual linear algebra support... none
checking whether to use optimized math libraries... no
checking whether to use optimized FFT libraries... no
checking whether to use DFT libraries... no

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

configure: using tarball repository /root/.abinit/tarballs
checking whether to enable the FOX plug-in... no
checking whether to build the FOX plug-in... no
checking for a source tarball of NETCDF... yes
configure: tarball MD5 check succeeded
configure: applying NetCDF tricks (vendor: intel, version: 11.1)
checking whether to enable the NETCDF plug-in... yes
checking whether to build the NETCDF plug-in... yes
checking whether to enable the ETSF_IO plug-in... no
checking whether to build the ETSF_IO plug-in... no
checking for a source tarball of LIBXC... yes
configure: tarball MD5 check succeeded
configure: applying LIBXC tricks
checking whether to enable the LIBXC plug-in... yes
checking whether to build the LIBXC plug-in... yes
checking for a source tarball of BIGDFT... yes
configure: tarball MD5 check succeeded
configure: applying BigDFT tricks (vendor: intel, version: 11.1)
checking whether to enable the BIGDFT plug-in... yes
checking whether to build the BIGDFT plug-in... yes
checking for a source tarball of WANNIER90... yes
configure: tarball MD5 check succeeded
configure: applying Wannier90 tricks (vendor: intel, version: 11.1)
checking whether to enable the WANNIER90 plug-in... yes
checking whether to build the WANNIER90 plug-in... yes

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

checking whether to build test timeout code... no
checking timeout for automatic tests... none

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

checking whether to enable bindings... no
checking whether to enable BSE unpacking... no
checking whether to enable CLib... no
checking whether to build exports... no
checking whether to accelerate 'make check'... no
checking whether to enable GW cut-off... no
checking whether to enable GW double-precision calculations... no
checking whether to enable optimal GW... no
checking whether to enable GW wrapper... no
checking whether to activate maintainer checks... no
checking whether to use macroave... yes
checking whether to read input from stdin... yes
checking whether to activate Symmetric Multi-Processing... no

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

configure: creating ./config.status
config.status: creating config.dump
config.status: creating config.mk
config.status: creating config.pc
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 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/01_qespresso_ext/Makefile
config.status: creating src/02_clib/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/15_gpu_toolbox/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/43_ptgroups/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/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: config.h is unchanged
config.status: executing depfiles commands
config.status: executing dump-optim commands
config.status: executing script-perms commands
config.status: executing long-lines commands

        +--------------------------------------------------------------+
        | 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.                                                   |
        +--------------------------------------------------------------+


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

make
make  all-recursive
make[1]: Entering directory `/opt/abinit-6.2.3/tmp'
Making all in prereqs
make[2]: Entering directory `/opt/abinit-6.2.3/tmp/prereqs'
Making all in linalg
make[3]: Entering directory `/opt/abinit-6.2.3/tmp/prereqs/linalg'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/opt/abinit-6.2.3/tmp/prereqs/linalg'
make[3]: Entering directory `/opt/abinit-6.2.3/tmp/prereqs'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/opt/abinit-6.2.3/tmp/prereqs'
make[2]: Leaving directory `/opt/abinit-6.2.3/tmp/prereqs'
Making all in plugins
make[2]: Entering directory `/opt/abinit-6.2.3/tmp/plugins'
Making all in netcdf
make[3]: Entering directory `/opt/abinit-6.2.3/tmp/plugins/netcdf'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/netcdf'
Making all in libxc
make[3]: Entering directory `/opt/abinit-6.2.3/tmp/plugins/libxc'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/libxc'
Making all in bigdft
make[3]: Entering directory `/opt/abinit-6.2.3/tmp/plugins/bigdft'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/bigdft'
Making all in wannier90
make[3]: Entering directory `/opt/abinit-6.2.3/tmp/plugins/wannier90'
make -f ../../../plugins/wannier90/wannier90.mk
make[4]: Entering directory `/opt/abinit-6.2.3/tmp/plugins/wannier90'
wannier90-1.2 has been uncompressed.
mkdir tmp
mkdir: cannot create directory `tmp': File exists
make[4]: [configure-stamp] Error 1 (ignored)
echo "F90 = /opt/intel/Compiler/11.1/073/bin/intel64/ifort" > wannier90-1.2/make.sys
echo "FCOPTS =  -free -g -extend-source -vec-report0  -O2" >> wannier90-1.2/make.sys
echo "LDOPTS =  -free -g -extend-source -vec-report0  -O2 -static-libgcc -static-intel " >> wannier90-1.2/make.sys
echo "LIBS = -L/opt/abinit-6.2.3/tmp/prereqs/linalg -llapack -lblas -L/opt/abinit-6.2.3/tmp/prereqs/linalg -llapack -lblas  -lsvml" >> wannier90-1.2/make.sys
touch configure-stamp
wannier90-1.2 has been configured.
cd wannier90-1.2 && make wannier lib
make[5]: Entering directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2'
(cd src ; make prog)
make[6]: Entering directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/src'
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0  -O2 -c transport.F90
transport.F90(57): error #7013: This module file was not generated by any release of this compiler.   [W90_CONSTANTS]
  use w90_constants,  only : dp
------^
transport.F90(65): error #6683: A kind type parameter must be a compile-time constant.   [DP]
  complex(kind=dp), parameter :: eta=(0.d0,0.0005d0)
---------------^
transport.F90(80): error #6683: A kind type parameter must be a compile-time constant.   [DP]
  real(kind=dp), allocatable :: hr_one_dim(:,:,:)
------------^
transport.F90(81): error #6683: A kind type parameter must be a compile-time constant.   [DP]
  real(kind=dp), allocatable :: hB0(:,:)
------------^
transport.F90(82): error #6683: A kind type parameter must be a compile-time constant.   [DP]
  real(kind=dp), allocatable :: hB1(:,:)
------------^
transport.F90(83): error #6683: A kind type parameter must be a compile-time constant.   [DP]
  real(kind=dp), allocatable :: hL0(:,:)
------------^
transport.F90(84): error #6683: A kind type parameter must be a compile-time constant.   [DP]
  real(kind=dp), allocatable :: hL1(:,:)
------------^
transport.F90(85): error #6683: A kind type parameter must be a compile-time constant.   [DP]
  real(kind=dp), allocatable :: hR0(:,:)
------------^
transport.F90(86): error #6683: A kind type parameter must be a compile-time constant.   [DP]
  real(kind=dp), allocatable :: hR1(:,:)
------------^
transport.F90(87): error #6683: A kind type parameter must be a compile-time constant.   [DP]
  real(kind=dp), allocatable :: hC(:,:)
------------^
transport.F90(88): error #6683: A kind type parameter must be a compile-time constant.   [DP]
  real(kind=dp), allocatable :: hLC(:,:)
------------^
transport.F90(89): error #6683: A kind type parameter must be a compile-time constant.   [DP]
  real(kind=dp), allocatable :: hCR(:,:)
------------^
transport.F90(99): error #7013: This module file was not generated by any release of this compiler.   [W90_IO]
    use w90_io,         only : stdout,io_stopwatch
--------^
transport.F90(106): error #6683: A kind type parameter must be a compile-time constant.   [DP]
    real(kind=dp),allocatable,dimension(:,:)     :: signatures
--------------^
transport.F90(160): error #6580: Name in only-list does not exist.   [DP]
    use w90_constants,   only : dp, eps8
--------------------------------^
transport.F90(160): error #6580: Name in only-list does not exist.   [EPS8]
    use w90_constants,   only : dp, eps8
------------------------------------^
transport.F90(161): error #6580: Name in only-list does not exist.   [IO_ERROR]
    use w90_io,          only : io_error, io_stopwatch, stdout
--------------------------------^
transport.F90(161): error #6580: Name in only-list does not exist.   [IO_STOPWATCH]
    use w90_io,          only : io_error, io_stopwatch, stdout
------------------------------------------^
transport.F90(161): error #6580: Name in only-list does not exist.   [STDOUT]
    use w90_io,          only : io_error, io_stopwatch, stdout
--------------------------------------------------------^
transport.F90(162): error #7013: This module file was not generated by any release of this compiler.   [W90_PARAMETERS]
    use w90_parameters,  only : one_dim_dir,real_lattice,num_wann, &
--------^
transport.F90(246): error #6580: Name in only-list does not exist.   [DP]
    use w90_constants,   only : dp
--------------------------------^
transport.F90(247): error #6580: Name in only-list does not exist.   [IO_STOPWATCH]
    use w90_io,          only : io_stopwatch,stdout
--------------------------------^
transport.F90(247): error #6580: Name in only-list does not exist.   [STDOUT]
    use w90_io,          only : io_stopwatch,stdout
---------------------------------------------^
transport.F90(248): error #6580: Name in only-list does not exist.   [NUM_WANN]
    use w90_parameters,  only : num_wann,mp_grid,timing_level,real_lattice,&
--------------------------------^
transport.F90(248): error #6580: Name in only-list does not exist.   [MP_GRID]
    use w90_parameters,  only : num_wann,mp_grid,timing_level,real_lattice,&
-----------------------------------------^
transport.F90(248): error #6580: Name in only-list does not exist.   [TIMING_LEVEL]
    use w90_parameters,  only : num_wann,mp_grid,timing_level,real_lattice,&
-------------------------------------------------^
transport.F90(248): error #6580: Name in only-list does not exist.   [REAL_LATTICE]
    use w90_parameters,  only : num_wann,mp_grid,timing_level,real_lattice,&
--------------------------------------------------------------^
transport.F90(249): error #6580: Name in only-list does not exist.   [HR_CUTOFF]
                                hr_cutoff,dist_cutoff,dist_cutoff_mode, &
--------------------------------^
transport.F90(249): error #6580: Name in only-list does not exist.   [DIST_CUTOFF]
                                hr_cutoff,dist_cutoff,dist_cutoff_mode, &
------------------------------------------^
transport.F90(249): error #6580: Name in only-list does not exist.   [DIST_CUTOFF_MODE]
                                hr_cutoff,dist_cutoff,dist_cutoff_mode, &
------------------------------------------------------^
(3321): catastrophic error: Too many errors, exiting
compilation aborted for transport.F90 (code 1)
make[6]: *** [transport.o] Error 1
make[6]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/src'
make[5]: *** [wannier] Error 2
make[5]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2'
make[4]: *** [build-stamp] Error 2
make[4]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/wannier90'
make[3]: *** [package-ready] Error 2
make[3]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/wannier90'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/opt/abinit-6.2.3/tmp'
make: *** [all] Error 2


Any comments are appreciated.

Thanks.

Junjie

User avatar
pouillon
Posts: 651
Joined: Wed Aug 19, 2009 10:08 am
Location: Spain
Contact:

Re: Compilling abinit on CentOS

Post by pouillon » Mon Sep 13, 2010 2:46 pm

Looks like there is a problem in the compilation of Wannier 90.

My suggestion:

Code: Select all

cd /opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/src/
make constants.o
cd .. &&  make
cd .. && touch build-stamp && make
cd ../.. && make multi_dual
Yann Pouillon
Simune Atomistics
Donostia-San Sebastián, Spain

Junjie
Posts: 5
Joined: Sun Sep 12, 2010 6:39 pm

Re: Compilling abinit on CentOS

Post by Junjie » Tue Sep 14, 2010 11:33 am

Thanks a lot for you suggetion.

cd /opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/src/
make constants.o
cd .. && make

then error

(cd src ; make prog)
make[1]: Entering directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/src'
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c transport.F90
transport.F90(57): error #7013: This module file was not generated by any release of this compiler. [W90_CONSTANTS]
use w90_constants, only : dp
------^
transport.F90(65): error #6683: A kind type parameter must be a compile-time constant. [DP]
complex(kind=dp), parameter :: eta=(0.d0,0.0005d0)
---------------^
transport.F90(80): error #6683: A kind type parameter must be a compile-time constant. [DP]
real(kind=dp), allocatable :: hr_one_dim(:,:,:)
------------^
transport.F90(81): error #6683: A kind type parameter must be a compile-time constant. [DP]
real(kind=dp), allocatable :: hB0(:,:)
------------^
transport.F90(82): error #6683: A kind type parameter must be a compile-time constant. [DP]
real(kind=dp), allocatable :: hB1(:,:)
------------^
transport.F90(83): error #6683: A kind type parameter must be a compile-time constant. [DP]
real(kind=dp), allocatable :: hL0(:,:)
------------^
transport.F90(84): error #6683: A kind type parameter must be a compile-time constant. [DP]
real(kind=dp), allocatable :: hL1(:,:)
------------^
transport.F90(85): error #6683: A kind type parameter must be a compile-time constant. [DP]
real(kind=dp), allocatable :: hR0(:,:)
------------^
transport.F90(86): error #6683: A kind type parameter must be a compile-time constant. [DP]
real(kind=dp), allocatable :: hR1(:,:)
------------^
transport.F90(87): error #6683: A kind type parameter must be a compile-time constant. [DP]
real(kind=dp), allocatable :: hC(:,:)
------------^
transport.F90(88): error #6683: A kind type parameter must be a compile-time constant. [DP]
real(kind=dp), allocatable :: hLC(:,:)
------------^
transport.F90(89): error #6683: A kind type parameter must be a compile-time constant. [DP]
real(kind=dp), allocatable :: hCR(:,:)
------------^
transport.F90(99): error #7013: This module file was not generated by any release of this compiler. [W90_IO]
use w90_io, only : stdout,io_stopwatch
--------^
transport.F90(106): error #6683: A kind type parameter must be a compile-time constant. [DP]
real(kind=dp),allocatable,dimension(:,:) :: signatures
--------------^
transport.F90(160): error #6580: Name in only-list does not exist. [DP]
use w90_constants, only : dp, eps8
--------------------------------^
transport.F90(160): error #6580: Name in only-list does not exist. [EPS8]
use w90_constants, only : dp, eps8
------------------------------------^
transport.F90(161): error #6580: Name in only-list does not exist. [IO_ERROR]
use w90_io, only : io_error, io_stopwatch, stdout
--------------------------------^
transport.F90(161): error #6580: Name in only-list does not exist. [IO_STOPWATCH]
use w90_io, only : io_error, io_stopwatch, stdout
------------------------------------------^
transport.F90(161): error #6580: Name in only-list does not exist. [STDOUT]
use w90_io, only : io_error, io_stopwatch, stdout
--------------------------------------------------------^
transport.F90(162): error #7013: This module file was not generated by any release of this compiler. [W90_PARAMETERS]
use w90_parameters, only : one_dim_dir,real_lattice,num_wann, &
--------^
transport.F90(246): error #6580: Name in only-list does not exist. [DP]
use w90_constants, only : dp
--------------------------------^
transport.F90(247): error #6580: Name in only-list does not exist. [IO_STOPWATCH]
use w90_io, only : io_stopwatch,stdout
--------------------------------^
transport.F90(247): error #6580: Name in only-list does not exist. [STDOUT]
use w90_io, only : io_stopwatch,stdout
---------------------------------------------^
transport.F90(248): error #6580: Name in only-list does not exist. [NUM_WANN]
use w90_parameters, only : num_wann,mp_grid,timing_level,real_lattice,&
--------------------------------^
transport.F90(248): error #6580: Name in only-list does not exist. [MP_GRID]
use w90_parameters, only : num_wann,mp_grid,timing_level,real_lattice,&
-----------------------------------------^
transport.F90(248): error #6580: Name in only-list does not exist. [TIMING_LEVEL]
use w90_parameters, only : num_wann,mp_grid,timing_level,real_lattice,&
-------------------------------------------------^
transport.F90(248): error #6580: Name in only-list does not exist. [REAL_LATTICE]
use w90_parameters, only : num_wann,mp_grid,timing_level,real_lattice,&
--------------------------------------------------------------^
transport.F90(249): error #6580: Name in only-list does not exist. [HR_CUTOFF]
hr_cutoff,dist_cutoff,dist_cutoff_mode, &
--------------------------------^
transport.F90(249): error #6580: Name in only-list does not exist. [DIST_CUTOFF]
hr_cutoff,dist_cutoff,dist_cutoff_mode, &
------------------------------------------^
transport.F90(249): error #6580: Name in only-list does not exist. [DIST_CUTOFF_MODE]
hr_cutoff,dist_cutoff,dist_cutoff_mode, &
------------------------------------------------------^
(3321): catastrophic error: Too many errors, exiting
compilation aborted for transport.F90 (code 1)
make[1]: *** [transport.o] Error 1
make[1]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/src'
make: *** [wannier] Error 2

User avatar
jbeuken
Posts: 365
Joined: Tue Aug 18, 2009 9:24 pm
Contact:

Re: Compilling abinit on CentOS

Post by jbeuken » Tue Sep 14, 2010 7:21 pm

Hi Junjie

there is the same "machine/OS/compiler" combinaison on our test farm ( coba2_intel11 : http://buildbot.abinit.org/waterfall )

then I can test your commands ( ./configure and make )
the output of configure is the same and my compilation of Abinit is ok...

...
Making all in wannier90
make[3]: Entering directory `/home/buildbot/ABINIT/coba2_intel11/beuken_6.2.2-public/plugins/wannier90'
make -f ../../plugins/wannier90/wannier90.mk
make[4]: Entering directory `/home/buildbot/ABINIT/coba2_intel11/beuken_6.2.2-public/plugins/wannier90'
gzip -cd /home/buildbot/.abinit/tarballs/wannier90-1.2.tar.gz | tar xf -
cd wannier90-1.2 && patch -p1 < /home/buildbot/ABINIT/coba2_intel11/beuken_6.2.2-public/plugins/wannier90/wannier90-1.2-0001.patch
patching file src/disentangle.F90
patching file src/overlap.F90
patching file src/parameters.F90
patching file src/plot.F90
patching file src/wannier_lib.F90
cd wannier90-1.2 && patch -p1 < /home/buildbot/ABINIT/coba2_intel11/beuken_6.2.2-public/plugins/wannier90/wannier90-1.2-0002.patch
patching file src/transport.F90
touch uncompress-stamp
wannier90-1.2 has been uncompressed.
mkdir tmp
echo "F90 = /opt/intel/Compiler/11.1/056/bin/intel64/ifort" > wannier90-1.2/make.sys
echo "FCOPTS = -free -g -extend-source -vec-report0 -O2" >> wannier90-1.2/make.sys
echo "LDOPTS = -free -g -extend-source -vec-report0 -O2 -static-libgcc -static-intel " >> wannier90-1.2/make.sys
echo "LIBS = -L/home/buildbot/ABINIT/coba2_intel11/beuken_6.2.2-public/prereqs/linalg -llapack -lblas -L/home/buildbot/ABINIT/coba2_intel11/beuken_6.2.2-public/prereqs/linalg -llapack -lblas -lsvml" >> wannier90-1.2/make.sys
touch configure-stamp
wannier90-1.2 has been configured.
cd wannier90-1.2 && make wannier lib
make[5]: Entering directory `/home/buildbot/ABINIT/coba2_intel11/beuken_6.2.2-public/plugins/wannier90/wannier90-1.2'
(cd src ; make prog)
make[6]: Entering directory `/home/buildbot/ABINIT/coba2_intel11/beuken_6.2.2-public/plugins/wannier90/wannier90-1.2/src'
/opt/intel/Compiler/11.1/056/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c constants.F90
/opt/intel/Compiler/11.1/056/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c io.F90
/opt/intel/Compiler/11.1/056/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c utility.F90
/opt/intel/Compiler/11.1/056/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c parameters.F90
/opt/intel/Compiler/11.1/056/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c hamiltonian.F90
/opt/intel/Compiler/11.1/056/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c overlap.F90
/opt/intel/Compiler/11.1/056/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c kmesh.F90
/opt/intel/Compiler/11.1/056/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c disentangle.F90
/opt/intel/Compiler/11.1/056/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c wannierise.F90
/opt/intel/Compiler/11.1/056/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c plot.F90
/opt/intel/Compiler/11.1/056/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c transport.F90
/opt/intel/Compiler/11.1/056/bin/intel64/ifort wannier_prog.F90 -free -g -extend-source -vec-report0 -O2 -static-libgcc -static-intel constants.o io.o utility.o parameters.o hamiltonian.o overlap.o kmesh.o disentangle.o wannierise.o plot.o transport.o -L/home/buildbot/ABINIT/coba2_intel11/beuken_6.2.2-public/prereqs/linalg -llapack -lblas -L/home/buildbot/ABINIT/coba2_intel11/beuken_6.2.2-public/prereqs/linalg -llapack -lblas -lsvml -o ../wannier90.x
make[6]: Leaving directory `/home/buildbot/ABINIT/coba2_intel11/beuken_6.2.2-public/plugins/wannier90/wannier90-1.2/src'
(cd src ; make libs)
...


I remark that, in your wannier compilation section, the patches are missing...
perhaps, have you make a lot of "make"...
can you try :

Code: Select all

cd plugins/wannier90/
make clean
make


and post the output...

jmb
------
Jean-Michel Beuken
Computer Scientist

Junjie
Posts: 5
Joined: Sun Sep 12, 2010 6:39 pm

Re: Compilling abinit on CentOS

Post by Junjie » Wed Sep 15, 2010 10:44 am

Dear jmb

Here is the result

cd plugins/wannier90/
make clean
make

make -f ../../../plugins/wannier90/wannier90.mk
make[1]: Entering directory `/opt/abinit-6.2.3/tmp/plugins/wannier90'
gzip -cd /root/.abinit/tarballs/wannier90-1.2.tar.gz | tar xf -
cd wannier90-1.2 && patch -p1 < /opt/abinit-6.2.3/tmp/../plugins/wannier90/wannier90-1.2-0001.patch
patching file src/disentangle.F90
patching file src/overlap.F90
patching file src/parameters.F90
patching file src/plot.F90
patching file src/wannier_lib.F90
cd wannier90-1.2 && patch -p1 < /opt/abinit-6.2.3/tmp/../plugins/wannier90/wannier90-1.2-0002.patch
patching file src/transport.F90
touch uncompress-stamp
wannier90-1.2 has been uncompressed.
mkdir tmp
echo "F90 = /opt/intel/Compiler/11.1/073/bin/intel64/ifort" > wannier90-1.2/make.sys
echo "FCOPTS = -free -g -extend-source -vec-report0 -O2" >> wannier90-1.2/make.sys
echo "LDOPTS = -free -g -extend-source -vec-report0 -O2 -static-libgcc -static-intel " >> wannier90-1.2/make.sys
echo "LIBS = -L/opt/abinit-6.2.3/tmp/prereqs/linalg -llapack -lblas -L/opt/abinit-6.2.3/tmp/prereqs/linalg -llapack -lblas -lsvml" >> wannier90-1.2/make.sys
touch configure-stamp
wannier90-1.2 has been configured.
cd wannier90-1.2 && make wannier lib
make[2]: Entering directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2'
(cd src ; make prog)
make[3]: Entering directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/src'
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c constants.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c io.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c utility.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c parameters.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c hamiltonian.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c overlap.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c kmesh.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c disentangle.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c wannierise.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c plot.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c transport.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort wannier_prog.F90 -free -g -extend-source -vec-report0 -O2 -static-libgcc -static-intel constants.o io.o utility.o parameters.o hamiltonian.o overlap.o kmesh.o disentangle.o wannierise.o plot.o transport.o -L/opt/abinit-6.2.3/tmp/prereqs/linalg -llapack -lblas -L/opt/abinit-6.2.3/tmp/prereqs/linalg -llapack -lblas -lsvml -o ../wannier90.x
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(dgesvd.o): In function `dgesvd_':
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/dgesvd.f:216: undefined reference to `_gfortran_concat_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/dgesvd.f:380: undefined reference to `_gfortran_concat_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(dlamch.o): In function `dlamc2_':
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/dlamch.f:444: undefined reference to `_gfortran_pow_r8_i4'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/dlamch.f:465: undefined reference to `_gfortran_pow_r8_i4'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/dlamch.f:544: undefined reference to `_gfortran_st_write'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/dlamch.f:544: undefined reference to `_gfortran_transfer_integer'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/dlamch.f:544: undefined reference to `_gfortran_st_write_done'
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(dlamch.o): In function `dlamch_':
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/dlamch.f:104: undefined reference to `_gfortran_pow_r8_i4'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/dlamch.f:107: undefined reference to `_gfortran_pow_r8_i4'
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(dormbr.o): In function `dormbr_':
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/dormbr.f:184: undefined reference to `_gfortran_concat_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/dormbr.f:192: undefined reference to `_gfortran_concat_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/dormbr.f:187: undefined reference to `_gfortran_concat_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/dormbr.f:195: undefined reference to `_gfortran_concat_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(dormlq.o): In function `dormlq_':
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/dormlq.f:167: undefined reference to `_gfortran_concat_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(dormlq.o):/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/dormlq.f:193: more undefined references to `_gfortran_concat_string' follow
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(ilaenv.o): In function `ilaenv_':
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/ilaenv.f:353: undefined reference to `_gfortran_compare_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/ilaenv.f:418: undefined reference to `_gfortran_compare_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/ilaenv.f:418: undefined reference to `_gfortran_compare_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/ilaenv.f:418: undefined reference to `_gfortran_compare_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/ilaenv.f:418: undefined reference to `_gfortran_compare_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(ilaenv.o):/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/ilaenv.f:418: more undefined references to `_gfortran_compare_string' follow
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(ilaenv.o): In function `ilaenv_':
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/ilaenv.f:135: undefined reference to `_gfortran_copy_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/ilaenv.f:187: undefined reference to `_gfortran_copy_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/ilaenv.f:188: undefined reference to `_gfortran_copy_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/ilaenv.f:189: undefined reference to `_gfortran_copy_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/ilaenv.f:203: undefined reference to `_gfortran_compare_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/ilaenv.f:204: undefined reference to `_gfortran_compare_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/ilaenv.f:204: undefined reference to `_gfortran_compare_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/ilaenv.f:204: undefined reference to `_gfortran_compare_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/ilaenv.f:204: undefined reference to `_gfortran_compare_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(ilaenv.o):/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/ilaenv.f:204: more undefined references to `_gfortran_compare_string' follow
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(xerbla.o): In function `xerbla_':
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/xerbla.f:40: undefined reference to `_gfortran_st_write'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/xerbla.f:40: undefined reference to `_gfortran_string_len_trim'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/xerbla.f:40: undefined reference to `_gfortran_transfer_character'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/xerbla.f:40: undefined reference to `_gfortran_transfer_integer'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/xerbla.f:40: undefined reference to `_gfortran_st_write_done'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/xerbla.f:42: undefined reference to `_gfortran_stop_numeric'
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(zgesvd.o): In function `zgesvd_':
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/zgesvd.f:224: undefined reference to `_gfortran_concat_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/zgesvd.f:377: undefined reference to `_gfortran_concat_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(zhseqr.o): In function `zhseqr_':
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/zhseqr.f:337: undefined reference to `_gfortran_concat_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(zunmbr.o): In function `zunmbr_':
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/zunmbr.f:189: undefined reference to `_gfortran_concat_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/zunmbr.f:197: undefined reference to `_gfortran_concat_string'
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(zunmbr.o):/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/zunmbr.f:192: more undefined references to `_gfortran_concat_string' follow
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(dlartg.o): In function `dlartg_':
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/dlartg.f:85: undefined reference to `_gfortran_pow_r8_i4'
/opt/abinit-6.2.3/tmp/prereqs/linalg/liblapack.a(zlartg.o): In function `zlartg_':
/opt/abinit-6.2.3/tmp/prereqs/linalg/lapack/zlartg.f:96: undefined reference to `_gfortran_pow_r8_i4'
ld: ../wannier90.x: hidden symbol `__intel_cpu_indicator_init' in /opt/intel/Compiler/11.1/073/lib/intel64/libirc.a(cpu_disp.o) is referenced by DSO
ld: final link failed: Nonrepresentable section on output
make[3]: *** [prog] Error 1
make[3]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/src'
make[2]: *** [wannier] Error 2
make[2]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2'
make[1]: *** [build-stamp] Error 2
make[1]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/wannier90'
make: *** [package-ready] Error 2

User avatar
pouillon
Posts: 651
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Location: Spain
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Re: Compilling abinit on CentOS

Post by pouillon » Wed Sep 15, 2010 2:44 pm

Your source tree has been partially built using gfortran. However you cannot change compilers in the middle of a build.

I suggest you remove your build dir and restart from scratch.
Yann Pouillon
Simune Atomistics
Donostia-San Sebastián, Spain

Junjie
Posts: 5
Joined: Sun Sep 12, 2010 6:39 pm

Re: Compilling abinit on CentOS

Post by Junjie » Wed Sep 15, 2010 4:18 pm

Dear jmb,

Thanks a lot for you kindly help.

I have re-compilled and got following errors

rm -Rf tmp
mkdir tmp
cd tmp
../configure FC=/opt/intel/Compiler/11.1/073/bin/intel64/ifort --disable-etsf-io
cd /opt/abinit-6.2.3/tmp/plugins/wannier90
make

make -f ../../../plugins/wannier90/wannier90.mk
make[1]: Entering directory `/opt/abinit-6.2.3/tmp/plugins/wannier90'
gzip -cd /root/.abinit/tarballs/wannier90-1.2.tar.gz | tar xf -
cd wannier90-1.2 && patch -p1 < /opt/abinit-6.2.3/tmp/../plugins/wannier90/wannier90-1.2-0001.patch
patching file src/disentangle.F90
patching file src/overlap.F90
patching file src/parameters.F90
patching file src/plot.F90
patching file src/wannier_lib.F90
cd wannier90-1.2 && patch -p1 < /opt/abinit-6.2.3/tmp/../plugins/wannier90/wannier90-1.2-0002.patch
patching file src/transport.F90
touch uncompress-stamp
wannier90-1.2 has been uncompressed.
mkdir tmp
echo "F90 = /opt/intel/Compiler/11.1/073/bin/intel64/ifort" > wannier90-1.2/make.sys
echo "FCOPTS = -free -g -extend-source -vec-report0 -O2" >> wannier90-1.2/make.sys
echo "LDOPTS = -free -g -extend-source -vec-report0 -O2 -static-libgcc -static-intel " >> wannier90-1.2/make.sys
echo "LIBS = -L/opt/abinit-6.2.3/tmp/prereqs/linalg -llapack -lblas -L/opt/abinit-6.2.3/tmp/prereqs/linalg -llapack -lblas -lsvml" >> wannier90-1.2/make.sys
touch configure-stamp
wannier90-1.2 has been configured.
cd wannier90-1.2 && make wannier lib
make[2]: Entering directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2'
(cd src ; make prog)
make[3]: Entering directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/src'
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c constants.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c io.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c utility.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c parameters.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c hamiltonian.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c overlap.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c kmesh.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c disentangle.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c wannierise.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c plot.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort -free -g -extend-source -vec-report0 -O2 -c transport.F90
/opt/intel/Compiler/11.1/073/bin/intel64/ifort wannier_prog.F90 -free -g -extend-source -vec-report0 -O2 -static-libgcc -static-intel constants.o io.o utility.o parameters.o hamiltonian.o overlap.o kmesh.o disentangle.o wannierise.o plot.o transport.o -L/opt/abinit-6.2.3/tmp/prereqs/linalg -llapack -lblas -L/opt/abinit-6.2.3/tmp/prereqs/linalg -llapack -lblas -lsvml -o ../wannier90.x
ld: cannot find -llapack
make[3]: *** [prog] Error 1
make[3]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/src'
make[2]: *** [wannier] Error 2
make[2]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2'
make[1]: *** [build-stamp] Error 2
make[1]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/wannier90'
make: *** [package-ready] Error 2

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jbeuken
Posts: 365
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Re: Compilling abinit on CentOS

Post by jbeuken » Wed Sep 15, 2010 6:39 pm

ok !! the compilation of wannier plugins works
the error msg concerning lapack is normal
now

Code: Select all

cd /opt/abinit-6.2.3/tmp/
make


jmb
------
Jean-Michel Beuken
Computer Scientist

Junjie
Posts: 5
Joined: Sun Sep 12, 2010 6:39 pm

Re: Compilling abinit on CentOS

Post by Junjie » Thu Sep 16, 2010 1:12 pm

Dear jmb,

This time, "make" spent a lot of time. It is really a good impovement.

However, there is still errors after make.

cd wannier90-1.2 && make wannier lib
make[5]: Entering directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2'
(cd src ; make prog)
make[6]: Entering directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/src'
/opt/intel/Compiler/11.1/073/bin/intel64/ifort wannier_prog.F90 -free -g -extend-source -vec-report0 -O2 -static-libgcc -static-intel constants.o io.o utility.o parameters.o hamiltonian.o overlap.o kmesh.o disentangle.o wannierise.o plot.o transport.o -L/opt/abinit-6.2.3/tmp/prereqs/linalg -llapack -lblas -L/opt/abinit-6.2.3/tmp/prereqs/linalg -llapack -lblas -lsvml -o ../wannier90.x
ld: ../wannier90.x: hidden symbol `__intel_cpu_indicator_init' in /opt/intel/Compiler/11.1/073/lib/intel64/libirc.a(cpu_disp.o) is referenced by DSO
ld: final link failed: Nonrepresentable section on output
make[6]: *** [prog] Error 1
make[6]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/src'
make[5]: *** [wannier] Error 2
make[5]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2'
make[4]: *** [build-stamp] Error 2
make[4]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/wannier90'
make[3]: *** [package-ready] Error 2
make[3]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins/wannier90'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/opt/abinit-6.2.3/tmp/plugins'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/opt/abinit-6.2.3/tmp'
make: *** [all] Error 2

hatuey
Posts: 14
Joined: Tue Mar 23, 2010 3:35 pm

Re: Compilling abinit on CentOS

Post by hatuey » Thu Nov 18, 2010 1:47 pm

Hello,

I am facing the same problem here.

Any ideas?

Regards,

Hatuey

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pouillon
Posts: 651
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Re: Compilling abinit on CentOS

Post by pouillon » Thu Nov 18, 2010 7:12 pm

It could come from some mixing between 32-bit and 64-bit libraries, but I'm not completely sure. You should at least check your LD_LIBRARY_PATH.
Yann Pouillon
Simune Atomistics
Donostia-San Sebastián, Spain

hatuey
Posts: 14
Joined: Tue Mar 23, 2010 3:35 pm

Re: Compilling abinit on CentOS

Post by hatuey » Thu Nov 18, 2010 10:23 pm

Hello,

I do not have any LD_LIBRARY_PATH in my bashrc.

Which would be the ideal setting for LD_LIBRARY_PATH?

Regards,

Hatuey

hatuey
Posts: 14
Joined: Tue Mar 23, 2010 3:35 pm

Re: Compilling abinit on CentOS

Post by hatuey » Thu Nov 18, 2010 10:44 pm

Hi,

I found the following using echo $LD_LIBRARY_PATH:
/opt/intel/lib/intel64:/opt/intel/composerxe-2011.0.084/compiler/lib/intel64:/opt/intel/composerxe-2011.0.084/mpirt/lib/intel64:/opt/intel/composerxe-2011.0.084/ipp/../compiler/lib/intel64:/opt/intel/composerxe-2011.0.084/ipp/lib/intel64:/opt/intel/composerxe-2011.0.084/compiler/lib/intel64:/opt/intel/composerxe-2011.0.084/mkl/lib/intel64:/opt/intel/composerxe-2011.0.084/tbb/lib/intel64//cc4.1.0_libc2.4_kernel2.6.16.21

Regards,

Hatuey

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Alain_Jacques
Posts: 279
Joined: Sat Aug 15, 2009 9:34 pm
Location: Université catholique de Louvain - Belgium

Re: Compilling abinit on CentOS

Post by Alain_Jacques » Fri Nov 19, 2010 7:41 pm

Hello Hatuey,

LD_LIBRARY_PATH is fine; it means that you have correctly sourced the compilers paths.

What kind of processor do you have in your Linux box? - your can check with a

Code: Select all

cat /proc/cpuinfo
No need to dump the full listing, only if it is an Intel CPU or not.

And a suggestion to go through the error. After make failed,

Code: Select all

cd /opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/src
/opt/intel/Compiler/11.1/073/bin/intel64/ifort wannier_prog.F90 -free -g -extend-source -vec-report0 -O2 -static-libgcc -static-intel constants.o io.o utility.o parameters.o hamiltonian.o overlap.o kmesh.o disentangle.o wannierise.o plot.o transport.o -L/opt/abinit-6.2.3/tmp/prereqs/linalg -llapack -lblas -L/opt/abinit-6.2.3/tmp/prereqs/linalg -llapack -lblas -o ../wannier90.x

i.e. reissue the failing link command without the -lsvml. Tell me if it goes through and produces the ../wannier90.x file. Unfortunately, even if it is successful, you won't be able to restart the original make as is but it will give me a clue on how to solve this issue.

Kind regards,

Alain

hatuey
Posts: 14
Joined: Tue Mar 23, 2010 3:35 pm

Re: Compilling abinit on CentOS

Post by hatuey » Mon Nov 22, 2010 4:51 pm

Hello Alain,

Thank you by your replay.

Following your suggestion, I compiled the wannier plugin without any problem.

The output of the command cat /proc/cpuinfo was:

processor : 23
vendor_id : AuthenticAMD
cpu family : 16
model : 8
model name : Six-Core AMD Opteron(tm) Processor 8431
stepping : 0
cpu MHz : 2411.145
cache size : 512 KB
physical id : 4
siblings : 6
core id : 5
cpu cores : 6
apicid : 37
fpu : yes
fpu_exception : yes
cpuid level : 5
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc nonstop_tsc pni cx16 popcnt lahf_lm cmp_legacy svm extapic cr8_legacy altmovcr8 abm sse4a misalignsse 3dnowprefetch osvw
bogomips : 4821.54
TLB size : 1024 4K pages
clflush size : 64
cache_alignment : 64
address sizes : 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate [8]

Regards,

Hatuey

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Alain_Jacques
Posts: 279
Joined: Sat Aug 15, 2009 9:34 pm
Location: Université catholique de Louvain - Belgium

Re: Compilling abinit on CentOS

Post by Alain_Jacques » Mon Nov 22, 2010 8:18 pm

Hello Hatuey,

Nice to know that you managed to have passed through the error by removing the call to lsvml.

First ... why did I asked about your processor. There is a long story of suspicion that Intel cripples its compilers - and in particular the SMall Vector Library - when used in combination with AMD processors. You have an AMD processor - and quite a nice one - but it is not the origin of your problem here.
So what's the problem and why removing -lsvml cures it? In the very specific 11.1.073 release of its compilers, Intel introduced a feature - actually a bug - that pushes the compiler driver to automatically link libsvml even if this library is not explicitly specified during the link. In the wannier90 line, there is an extra -static-intel ... -lsvml so the linker is asked to link dynamically and statically the libsvml library at the same time. And of course this leads to a error.

Now how to finish the wannier90 plugin and resume abinit compilation? More a dirty hack than a clean patch but it should do the job. I assume that you are at the point of Abinit make where wannier90 failed (in the directory structure you mentioned earlier, with an Intel toolchain correctly "sourced") and that you applied the -lsvml recipe to link wannier90.x i.e. that you managed to build the /opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/wannier90.x binary. What's still missing at this point is the wannier90 library so let's try to build it ...

Code: Select all

cd /opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/
make lib

This should produce the /opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/libwannier.a library. Although I think it won't be the case, if you encounter other linking errors, cd to src and reissue the last failing command by removing the offending -lsvml.
Now copy the results in the parent directory and add a few stamp files to trick Abinit makefiles into believing they have completed Wannier90 by themselves (otherwise, Abinit will try to rebuild the library and fail on the same error again and again).

Code: Select all

cp /opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/wannier90.x /opt/abinit-6.2.3/tmp/plugins/wannier90/
cp /opt/abinit-6.2.3/tmp/plugins/wannier90/wannier90-1.2/libwannier.a /opt/abinit-6.2.3/tmp/plugins/wannier90/
cd /opt/abinit-6.2.3/tmp/plugins/wannier90
touch uncompress-stamp
touch configure-stamp
touch build-stamp
touch package-ready

Resume Abinit make hopefully this time up to the end ...

Code: Select all

cd /opt/abinit-6.2.3/tmp
make


Kind regards,

Alain

hatuey
Posts: 14
Joined: Tue Mar 23, 2010 3:35 pm

Re: Compilling abinit on CentOS

Post by hatuey » Tue Nov 23, 2010 7:40 pm

Dear Alain,

Thank you by your help!

Instead what you suggested, I simple remove the -lsvml directive from the configure file and then did a clean configure and a clean make.

Now I have the serial abinit code running in my box.


Best regards, and one more time: thank you.

Hatuey

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