ABINIT Discussion Forums

Dear users and developers I try to install abinit 7.6.4 with intel compiler but I found this error:
Undefined symbols for architecture x86_64:
"_m_profiling_mp_abi_alloc_stat_", referenced from:
_drvaim_ in lib63_bader.a(drvaim.o)
_m_xmpi_mp_xmpi_distab_4d_ in lib12_hide_mpi.a(m_xmpi.o)
_m_xmpi_mp_xallgatherv_mpi_int1_dp1_ in lib12_hide_mpi.a(m_xmpi.o)
_m_xmpi_mp_xallgatherv_mpi_coeff2d_ in lib12_hide_mpi.a(m_xmpi.o)
_m_xmpi_mp_xallgatherv_mpi_coeff2d_indx_ in lib12_hide_mpi.a(m_xmpi.o)
_m_xmpi_mp_xgatherv_mpi_int1_dp1_ in lib12_hide_mpi.a(m_xmpi.o)
_addout_ in lib63_bader.a(addout.o)
...
"_m_profiling_mp_sz1_", referenced from:
_m_pawrhoij_mp_symrhoij_ in lib42_libpaw.a(m_pawrhoij.o)
"_m_profiling_mp_sz2_", referenced from:
_m_pawrhoij_mp_symrhoij_ in lib42_libpaw.a(m_pawrhoij.o)
ld: symbol(s) not found for architecture x86_64
make[5]: *** [aim] Error 1
make[5]: *** Waiting for unfinished jobs....
Undefined symbols for architecture x86_64:
"_m_profiling_mp_abi_alloc_stat_", referenced from:
_MAIN__ in anaddb-anaddb.o
_anaddb_dtset_clean_ in lib77_ddb.a(anaddb_dtset_clean.o)
_asria_calc_ in lib72_response.a(asria_calc.o)
_asrprs_ in lib72_response.a(asrprs.o)
_chneu9_ in lib72_response.a(chneu9.o)
_destroy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_copy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
...
"_m_profiling_mp_sz1_", referenced from:
_copy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_m_pawtab_mp_pawtab_bcast_ in lib42_libpaw.a(m_pawtab.o)
_complete_gkk_ in lib77_ddb.a(complete_gkk.o)
_m_pawrhoij_mp_symrhoij_ in lib42_libpaw.a(m_pawrhoij.o)
"_m_profiling_mp_sz2_", referenced from:
_copy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_get_all_gkq_ in lib77_ddb.a(get_all_gkq.o)
_m_pawtab_mp_pawtab_bcast_ in lib42_libpaw.a(m_pawtab.o)
_complete_gkk_ in lib77_ddb.a(complete_gkk.o)
_m_pawrhoij_mp_symrhoij_ in lib42_libpaw.a(m_pawrhoij.o)
"_m_profiling_mp_sz3_", referenced from:
_copy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_get_all_gkq_ in lib77_ddb.a(get_all_gkq.o)
"_m_profiling_mp_sz4_", referenced from:
_get_all_gkq_ in lib77_ddb.a(get_all_gkq.o)
"_m_profiling_mp_sz5_", referenced from:
_get_all_gkq_ in lib77_ddb.a(get_all_gkq.o)
"_m_profiling_mp_sz6_", referenced from:
_get_all_gkq_ in lib77_ddb.a(get_all_gkq.o)
ld: symbol(s) not found for architecture x86_64
make[5]: *** [anaddb] Error 1
Undefined symbols for architecture x86_64:
"_m_profiling_mp_abi_alloc_stat_", referenced from:
_MAIN__ in abinit-abinit.o
_chkinp_ in lib57_iovars.a(chkinp.o)
_destroy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_copy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_set_mpi_enreg_fft_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_driver_ in lib95_drive.a(driver.o)
_m_ab7_invars_mp_ab7_invars_set_flags_ in lib57_iovars.a(m_ab7_invars_f90.o)
...
"_m_profiling_mp_sz1_", referenced from:
_copy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_m_pawang_mp_pawang_init_ in lib42_libpaw.a(m_pawang.o)
_m_pawtab_mp_pawtab_bcast_ in lib42_libpaw.a(m_pawtab.o)
_respfn_ in lib95_drive.a(respfn.o)
_m_paw_an_mp_paw_an_gather_ in lib42_libpaw.a(m_paw_an.o)
_m_paw_an_mp_paw_an_copy_ in lib42_libpaw.a(m_paw_an.o)
_m_paw_an_mp_paw_an_gather_..0 in lib42_libpaw.a(m_paw_an.o)
...
"_m_profiling_mp_sz2_", referenced from:
_copy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_m_pawang_mp_pawang_init_ in lib42_libpaw.a(m_pawang.o)
_m_pawtab_mp_pawtab_bcast_ in lib42_libpaw.a(m_pawtab.o)
_respfn_ in lib95_drive.a(respfn.o)
_d2frnl_ in lib72_response.a(d2frnl.o)
_m_paw_an_mp_paw_an_gather_ in lib42_libpaw.a(m_paw_an.o)
_m_paw_an_mp_paw_an_gather_..0 in lib42_libpaw.a(m_paw_an.o)
...
"_m_profiling_mp_sz3_", referenced from:
_copy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_m_pawang_mp_pawang_init_ in lib42_libpaw.a(m_pawang.o)
_d2frnl_ in lib72_response.a(d2frnl.o)
_m_paw_an_mp_paw_an_gather_ in lib42_libpaw.a(m_paw_an.o)
_m_paw_an_mp_paw_an_gather_..0 in lib42_libpaw.a(m_paw_an.o)
_m_paw_ij_mp_paw_ij_gather_ in lib42_libpaw.a(m_paw_ij.o)
_m_paw_ij_mp_paw_ij_copy_ in lib42_libpaw.a(m_paw_ij.o)
...
"_m_profiling_mp_sz4_", referenced from:
_m_paw_ij_mp_paw_ij_gather_ in lib42_libpaw.a(m_paw_ij.o)
_m_paw_ij_mp_paw_ij_copy_ in lib42_libpaw.a(m_paw_ij.o)
_m_paw_ij_mp_paw_ij_gather_..0 in lib42_libpaw.a(m_paw_ij.o)
_m_bandfft_kpt_mp_copy_bandfft_kpt_ in lib66_wfs.a(m_bandfft_kpt.o)
"_pseudo_pwscf_mp_betar_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_chi_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_pswfc_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_dft_", referenced from:
_upfheader2abi_ in lib57_iopsp_parser.a(upfheader2abi.o)
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_dion_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_ecutrho_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_ecutwfc_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_els_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_etotps_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_ikk2_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_isus_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_lchi_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_lll_", referenced from:
_upfheader2abi_ in lib57_iopsp_parser.a(upfheader2abi.o)
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_lmax_", referenced from:
_upfheader2abi_ in lib57_iopsp_parser.a(upfheader2abi.o)
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_mesh_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_mesh_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_rhoatom_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_pswfc_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_local_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_nlcc_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
...
"_pseudo_pwscf_mp_nbeta_", referenced from:
_upfheader2abi_ in lib57_iopsp_parser.a(upfheader2abi.o)
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_nlcc_", referenced from:
_upfheader2abi_ in lib57_iopsp_parser.a(upfheader2abi.o)
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_nqf_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_nqlc_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_ntwfc_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_pswfc_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_oc_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_psd_", referenced from:
_upfheader2abi_ in lib57_iopsp_parser.a(upfheader2abi.o)
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_pseudotype_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_qfcoef_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_qfunc_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_qqq_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_r_", referenced from:
_read_pseudo_mesh_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_rab_", referenced from:
_read_pseudo_mesh_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_rho_at_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_rhoatom_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_rho_atc_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_nlcc_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_rinner_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_vloc0_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_local_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_zp_", referenced from:
_upfheader2abi_ in lib57_iopsp_parser.a(upfheader2abi.o)
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_unlink_", referenced from:
_mlwfovlp_ in lib67_common.a(mlwfovlp.o)
ld: symbol(s) not found for architecture x86_64
make[5]: *** [abinit] Error 1
make[4]: *** [all-recursive] Error 1
make[3]: *** [all-recursive] Error 1
make[2]: *** [all] Error 2
make[1]: *** [multi] Error 2
make: *** [mj4] Error 2

This is my simple configuration :
./configure FC=ifort CC=icc --enable-64bit-flags
please can you help me??
because I found no problem with gnu fortran but I found the error above with intel compiler..
thanks thanks a lots for your patience and to help me
Dearly lorenzo
I added my config.log

Hi,

it seems that your build system is for building 32-bit target
some thing missing ( lib ) for 64bit target ( intel 14 is 64bit version )

some "details" in your config.log

...
configure:3637: checking build system type
configure:3651: result: i386-apple-darwin13.2.0
configure:3671: checking host system type
configure:3684: result: i386-apple-darwin13.2.0
configure:3704: checking target system type
configure:3717: result: i386-apple-darwin13.2.0
...
configure:20379: checking for a 64-bit architecture
configure:20381: result:
configure:20383: checking whether to use 64-bit flags
configure:20385: result: yes
…
Undefined symbols for architecture x86_64:
"_foobar", referenced from:
_main in iccrLaMDV.o
(maybe you meant: _foobar_)
ld: symbol(s) not found for architecture x86_64
…

my 50¢

jmb

Dear jmb can you help me to solve this problem.
Another problem found with intel compiler:
I compiled openmpi 1.8.1 with intel compiler without problem but when i try to configure abinit 7.6.4 with:
./configure --enable-64bit-flags="yes" --with-mpi-prefix=/Users/lorenzodona/Documents/openmpi-1.8.1 --enable-mpi="yes" --enable-mpi-io="yes"

i found this problem during configuration:
==============================================================================
=== Multicore architecture support ===
==============================================================================

checking whether to enable OpenMP support... no
checking whether to build MPI code... yes
checking whether the C compiler supports MPI... no
checking whether the C++ compiler supports MPI... no
checking whether the Fortran Compiler supports MPI... yes
checking whether MPI is usable... no
configure: error: MPI support is broken - please fix your config parameters and/or MPI installation

Please can you help me to install abinit with intel compiler...
thanks thanks a lot.

Hi,

I need config.log to see the problem...

but 2 thinks :

before to run configure, setting these env variables :

1) export FC_LDFLAGS_EXTRA = -Wl,-search_paths_first

2) export PATH=/Users/lorenzodona/Documents/openmpi-1.8.1/bin:$PATH

can help sometime…

by the way, have you resolved the 64bits issue ? if yes, how ?

jmb

Dear jmb thanks to help me really a lot
NO I am not able to solve the 64 bit issue i also used FC="ifort -m64" and fort -m32 but the problem is always the same a lot of d: symbol(s) not found for architecture x86_64
Please can you help me to solce this big problem and now I try for opempi like you told me.
Dearly lorenzo
Thanks thanks a lot

Dear jmb I tried also with mpich 3.0.4 compiled with intel compiler and i export the env variables but i found the same problem
checking whether to enable OpenMP support... no
checking whether to build MPI code... yes
checking whether the C compiler supports MPI... no
checking whether the C++ compiler supports MPI... yes
checking whether the Fortran Compiler supports MPI... yes
checking whether MPI is usable... no
configure: error: MPI support is broken - please fix your config parameters and/or MPI installation

I give you my config.log

Hi,
very strange "checking whether the C compiler supports MPI… no" !

how two you install mpich 3 ?
have you run "make check" after compiling mpich3 ?

can you send the results of these commands :


jmb

Hi and thanks to help me.
I installed mpich in this way:
./configure FC=ifort CC=icc CXX=icpc F77=ifort --prefix=/Users/lorenzodona/Desktop/mpich-3.0.4/exec/

after make check I found:
MacBook-Pro-di-Lorenzo-Dona:mpich-3.0.4 lorenzodona$ make check

make check-recursive
Making check in src/mpl
/Applications/Xcode.app/Contents/Developer/usr/bin/make strsep
CC strsep.o
CCLD strsep
ld: warning: ignoring file ./.libs/libmpl.a, file was built for archive which is not the architecture being linked (i386): ./.libs/libmpl.a
Undefined symbols for architecture i386:
"_MPL_strsep", referenced from:
_main in strsep.o
ld: symbol(s) not found for architecture i386
make[3]: *** [strsep] Error 1
make[2]: *** [check-am] Error 2
make[1]: *** [check-recursive] Error 1
make: *** [check] Error 2

and the other thinks are:
MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ env
MKLROOT=/opt/intel/composer_xe_2013_sp1.3.166/mkl
MANPATH=/opt/intel/composer_xe_2013_sp1.3.166/man/en_US:/opt/intel/composer_xe_2013_sp1.3.166/man/en_US:/opt/intel/composer_xe_2013_sp1.3.166/man:/opt/intel/composer_xe_2013_sp1.3.166/man/en_US:/opt/intel/composer_xe_2013_sp1.3.166/man/en_US:/opt/intel/composer_xe_2013_sp1.3.166/man:/opt/intel/composer_xe_2013_sp1.3.166/man:/usr/share/man:/usr/local/share/man:/opt/X11/share/man:/Applications/Xcode.app/Contents/Developer/usr/share/man:/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/share/man::
TERM_PROGRAM=Apple_Terminal
INTEL_LICENSE_FILE=/opt/intel/composer_xe_2013_sp1.3.166/licenses:/opt/intel/licenses:/Users/lorenzodona/intel/licenses:/Users/Shared/Library/Application Support/Intel/Licenses:/opt/intel/composer_xe_2013_sp1.3.166/licenses:/opt/intel/licenses:/Users/lorenzodona/intel/licenses:/Users/Shared/Library/Application Support/Intel/Licenses
IPPROOT=/opt/intel/composer_xe_2013_sp1.3.166/ipp
SHELL=/bin/bash
TERM=xterm-256color
TMPDIR=/var/folders/dp/24y8tzl14llgc7r_ly2c45780000gn/T/
LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.3.166/compiler/lib:/opt/intel/composer_xe_2013_sp1.3.166/ipp/../compiler/lib:/opt/intel/composer_xe_2013_sp1.3.166/ipp/lib:/opt/intel/composer_xe_2013_sp1.3.166/compiler/lib:/opt/intel/composer_xe_2013_sp1.3.166/mkl/lib:/opt/intel/composer_xe_2013_sp1.3.166/tbb/lib:/opt/intel/composer_xe_2013_sp1.3.166/compiler/lib:/opt/intel/composer_xe_2013_sp1.3.166/ipp/../compiler/lib:/opt/intel/composer_xe_2013_sp1.3.166/ipp/lib:/opt/intel/composer_xe_2013_sp1.3.166/compiler/lib:/opt/intel/composer_xe_2013_sp1.3.166/mkl/lib:/opt/intel/composer_xe_2013_sp1.3.166/tbb/lib
CRY2K9_ROOT=/Users/lorenzodona/Crystal09
Apple_PubSub_Socket_Render=/tmp/launch-76ZwBo/Render
TERM_PROGRAM_VERSION=326
TERM_SESSION_ID=6DB814BC-B2F2-46D9-9A40-9F7E3EC2DE3F
CRY2K9_ARCH=Mac_ifort
USER=lorenzodona
CRY2K9_EXEDIR=/Users/lorenzodona/Crystal09/bin/Mac_ifort
CPATH=/opt/intel/composer_xe_2013_sp1.3.166/ipp/include:/opt/intel/composer_xe_2013_sp1.3.166/mkl/include:/opt/intel/composer_xe_2013_sp1.3.166/tbb/include:/opt/intel/composer_xe_2013_sp1.3.166/ipp/include:/opt/intel/composer_xe_2013_sp1.3.166/mkl/include:/opt/intel/composer_xe_2013_sp1.3.166/tbb/include
SSH_AUTH_SOCK=/tmp/launch-LDsXmR/Listeners
__CF_USER_TEXT_ENCODING=0x1F5:0:4
NLSPATH=/opt/intel/composer_xe_2013_sp1.3.166/compiler/lib/locale/en_US/%N:/opt/intel/composer_xe_2013_sp1.3.166/ipp/lib/locale/en_US/%N:/opt/intel/composer_xe_2013_sp1.3.166/mkl/lib/locale/%l_%t/%N:/opt/intel/composer_xe_2013_sp1.3.166/debugger/gdb/intel64_mic/py27/share/locale/%l_%t/%N:/opt/intel/composer_xe_2013_sp1.3.166/debugger/gdb/intel64/py27/share/locale/%l_%t/%N:/opt/intel/composer_xe_2013_sp1.3.166/compiler/lib/locale/en_US/%N:/opt/intel/composer_xe_2013_sp1.3.166/ipp/lib/locale/en_US/%N:/opt/intel/composer_xe_2013_sp1.3.166/mkl/lib/locale/%l_%t/%N:/opt/intel/composer_xe_2013_sp1.3.166/debugger/gdb/intel64_mic/py27/share/locale/%l_%t/%N:/opt/intel/composer_xe_2013_sp1.3.166/debugger/gdb/intel64/py27/share/locale/%l_%t/%N
PATH=/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/opt/intel/composer_xe_2013_sp1.3.166/bin/ia32:/opt/intel/composer_xe_2013_sp1.3.166/mpirt/bin/ia32:/opt/intel/composer_xe_2013_sp1.3.166/debugger/gdb/intel64_mic/py27/bin:/opt/intel/composer_xe_2013_sp1.3.166/debugger/gdb/intel64/py27/bin:/opt/intel/composer_xe_2013_sp1.3.166/bin:/opt/intel/composer_xe_2013_sp1.3.166/bin/ia32:/opt/intel/composer_xe_2013_sp1.3.166/mpirt/bin/ia32:/opt/intel/composer_xe_2013_sp1.3.166/debugger/gdb/intel64_mic/py27/bin:/opt/intel/composer_xe_2013_sp1.3.166/debugger/gdb/intel64/py27/bin:/opt/intel/composer_xe_2013_sp1.3.166/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:./:/Users/lorenzodona/Crystal09/bin/Mac_ifort/v1_0_1:/Users/lorenzodona/Crystal09/bin/Mac_ifort:/Users/lorenzodona/Crystal09/utils09:/Users/lorenzodona/Crystal09/crgra2006
__CHECKFIX1436934=1
GRA6_EXEDIR=/Users/lorenzodona/Crystal09/crgra2006/bin/Mac-ifort
CRY2K9_TEST=/Users/lorenzodona/Crystal09/testcase/inputs
PWD=/Users/lorenzodona
VERSION=v1_0_1
LANG=it_IT.UTF-8
CRY2K9_BIN=bin
SHLVL=1
HOME=/Users/lorenzodona
CRY2K9_UTILS=/Users/lorenzodona/Crystal09/utils09
DYLD_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.3.166/compiler/lib:/opt/intel/composer_xe_2013_sp1.3.166/compiler/lib/ia32:/opt/intel/composer_xe_2013_sp1.3.166/ipp/../compiler/lib:/opt/intel/composer_xe_2013_sp1.3.166/ipp/lib:/opt/intel/composer_xe_2013_sp1.3.166/compiler/lib:/opt/intel/composer_xe_2013_sp1.3.166/mkl/lib:/opt/intel/composer_xe_2013_sp1.3.166/tbb/lib:/opt/intel/composer_xe_2013_sp1.3.166/compiler/lib:/opt/intel/composer_xe_2013_sp1.3.166/compiler/lib/ia32:/opt/intel/composer_xe_2013_sp1.3.166/ipp/../compiler/lib:/opt/intel/composer_xe_2013_sp1.3.166/ipp/lib:/opt/intel/composer_xe_2013_sp1.3.166/compiler/lib:/opt/intel/composer_xe_2013_sp1.3.166/mkl/lib:/opt/intel/composer_xe_2013_sp1.3.166/tbb/lib
LOGNAME=lorenzodona
CRY2K9_SCRDIR=/Users/lorenzodona/Crystal09/tempdir
CRY2K6_GRA=/Users/lorenzodona/Crystal09/crgra2006
DISPLAY=/tmp/launch-kRG117/org.macosforge.xquartz:0
INCLUDE=/opt/intel/composer_xe_2013_sp1.3.166/mkl/include:/opt/intel/composer_xe_2013_sp1.3.166/mkl/include
_=/usr/bin/env

MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ which icc
/opt/intel/composer_xe_2013_sp1.3.166/bin/ia32/icc

MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ which ifort
/opt/intel/composer_xe_2013_sp1.3.166/bin/ia32/ifort

MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ which mpicc
/opt/local/bin/mpicc

MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ which mpif90
/opt/local/bin/mpif90

MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ mpicc -show
/usr/bin/clang -I/opt/local/include/openmpi-mp -L/opt/local/lib/openmpi-mp -lmpi

MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ mpicc --version
Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.2.0
Thread model: posix

MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ mpif90 -show
/opt/local/bin/gfortran-mp-4.8 -I/opt/local/include/openmpi-mp -Wl,-commons,use_dylibs -Wl,-commons,use_dylibs -I/opt/local/lib/openmpi-mp -L/opt/local/lib/openmpi-mp -lmpi_usempi -lmpi_mpifh -lmpi

MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ mpif90 --version
GNU Fortran (MacPorts gcc48 4.8.2_0) 4.8.2
Copyright (C) 2013 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING

I thank you so much for this big big help.
Dearly lorenzo

I recompiled now both openmpi 1.8.1 and mpich3.0.4 and I have passed all the tests
but abinit say that
checking whether to enable OpenMP support... no
checking whether to build MPI code... yes
checking whether the C compiler supports MPI... no
checking whether the C++ compiler supports MPI... no
checking whether the Fortran Compiler supports MPI... yes
checking whether MPI is usable... no
configure: error: MPI support is broken - please fix your config parameters and/or MPI installation

thaks a lot again excuse if I bother you.

Hi,

your environment is not set correctly !

I suppose you install the "m_fcompxe_2013_sp1.3.166" package for ifort ( and perhaps m_ccompxe_2013_sp1.3.166 for icc )

( the output of env command is truncated )

but

MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ which icc
/opt/intel/composer_xe_2013_sp1.3.166/bin/ia32/icc

MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ which ifort
/opt/intel/composer_xe_2013_sp1.3.166/bin/ia32/ifort

the problem with the "Undefined symbols for architecture x86_64" must be resolved with the intel64 ( no doubt , you use ia32 ) -> see below

MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ which mpicc
/opt/local/bin/mpicc

MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ which mpif90
/opt/local/bin/mpif90

you see that the mpif90 and mpicc are not the cmd from your mpich3 or openmpi !
as I already said, you need to add paths for the binaries of MPICH3 in PATH variable before /opt/local/bin :

MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ mpicc -show
/usr/bin/clang -I/opt/local/include/openmpi-mp -L/opt/local/lib/openmpi-mp -lmpi

MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ mpicc --version
Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.2.0
Thread model: posix

you see that you use the mpi from Apple which is a 64 bits version : not icc 14 !

MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ mpif90 -show
/opt/local/bin/gfortran-mp-4.8 -I/opt/local/include/openmpi-mp -Wl,-commons,use_dylibs -Wl,-commons,use_dylibs -I/opt/local/lib/openmpi-mp -L/opt/local/lib/openmpi-mp -lmpi_usempi -lmpi_mpifh -lmpi

MacBook-Pro-di-Lorenzo-Dona:~ lorenzodona$ mpif90 --version
GNU Fortran (MacPorts gcc48 4.8.2_0) 4.8.2
Copyright (C) 2013 Free Software Foundation, Inc.

same with fortran : it's the GNU gfortran not ifort !!!

after installation of intel compilers, you need to "add" these compilers in your environment, for compiling any softwares like mpich3, openmpi and abinit :


( have you read the INSTALL note ?!? )

after recompiling MPICH3 and/or openmpi,
you can rerun the set of commands that I send previously and check that everything it's ok

after, you can retry to compile abinit

jmb

Hi I recompiled mpich and openmpi with fort intel64
which ifort
/opt/intel/composer_xe_2013_sp1.3.166/bin/intel64/ifort
MacBook-Pro-di-Lorenzo-Dona:abinit-7.6.4 lorenzodona$ which mpif90
/Users/lorenzodona/Documents/mpich-3.1/exec/bin/mpif90
MacBook-Pro-di-Lorenzo-Dona:abinit-7.6.4 lorenzodona$ mpif90 --version
ifort (IFORT) 14.0.3 20140415
Copyright (C) 1985-2014 Intel Corporation. All rights reserved.
MacBook-Pro-di-Lorenzo-Dona:abinit-7.6.4 lorenzodona$ mpif90 -v
mpif90 for MPICH version 3.1
ifort version 14.0.3
but in the configuration:
=== Multicore architecture support ===
==============================================================================

checking whether to enable OpenMP support... no
checking whether to build MPI code... yes
checking whether the C compiler supports MPI... no
checking whether the C++ compiler supports MPI... no
checking whether the Fortran Compiler supports MPI... no
checking whether MPI is usable... no
configure: error: MPI support is broken - please fix your config parameters and/or MPI installation

the error is the same i also recompiled openmpi e mpich whit intel 64 and after make check i found no errors.
when i compiled abinit with FC=ifort CC=icc CXX=icpc without parallel the error Undefined symbols for architecture x86_64" is the same
I have the same error .
Please can you help me again.
I do like you told me.
Thanks a lot

when you are in the abinit tree, have you make
before to run



?

Hi
Yes of course before recompile abinit i did make clean and after the configuration but the problem is always the same
Or mpi is broken but not Because i compiled it with intel64 and passed all tests or if i compile abinit without parallel i found ld symbol not found for architecture 86x64
Please can you tell me something more to do to compile abinit with intel??
Thanks a lot for your big patinece with me