Compilation of Abinit-8.10.1 fails on SL 7.6

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letuan
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Joined: Fri Jan 25, 2013 4:00 pm
Location: Hanoi
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Compilation of Abinit-8.10.1 fails on SL 7.6

Post by letuan » Sat Jan 05, 2019 6:09 pm

I am facing with this error many times in my Scientific Linux v.7.6 distro and I cannot fix it :

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make[3]: Entering directory `/home/letuan/Programs/abinit-8.10.1/src/98_main'
/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I../..  -I../../src/incs -I../../src/incs -I/home/letuan/Programs/abinit-8.10.1/fallbacks/exports/include  -I/home/letuan/Programs/abinit-8.10.1/fallbacks/exports/include -I/home/letuan/Programs/abinit-8.10.1/fallbacks/exports/include   -ffree-form -J/home/letuan/Programs/abinit-8.10.1/src/mods    -g -O3 --free-line-length-none  -g -O3 --free-line-length-none -c -o abinit-abinit.o `test -f 'abinit.F90' || echo './'`abinit.F90
/usr/local/bin/mpif90 -ffree-form -J/home/letuan/Programs/abinit-8.10.1/src/mods    -g -O3 --free-line-length-none  -g -O3 --free-line-length-none   -o abinit abinit-abinit.o  ../../src/95_drive/lib95_drive.a ../../src/94_scfcv/lib94_scfcv.a ../../src/79_seqpar_mpi/lib79_seqpar_mpi.a ../../src/78_effpot/lib78_effpot.a ../../src/78_eph/lib78_eph.a ../../src/77_ddb/lib77_ddb.a ../../src/77_suscep/lib77_suscep.a ../../src/72_response/lib72_response.a ../../src/71_bse/lib71_bse.a ../../src/71_wannier/lib71_wannier.a ../../src/70_gw/lib70_gw.a ../../src/69_wfdesc/lib69_wfdesc.a ../../src/68_dmft/lib68_dmft.a  ../../src/68_recursion/lib68_recursion.a ../../src/68_rsprc/lib68_rsprc.a  ../../src/67_common/lib67_common.a ../../src/66_vdwxc/lib66_vdwxc.a ../../src/66_wfs/lib66_wfs.a ../../src/66_nonlocal/lib66_nonlocal.a ../../src/65_paw/lib65_paw.a  ../../src/64_psp/lib64_psp.a ../../src/62_iowfdenpot/lib62_iowfdenpot.a ../../src/62_wvl_wfs/lib62_wvl_wfs.a ../../src/62_poisson/lib62_poisson.a ../../src/62_cg_noabirule/lib62_cg_noabirule.a ../../src/62_ctqmc/lib62_ctqmc.a ../../src/61_occeig/lib61_occeig.a ../../src/59_ionetcdf/lib59_ionetcdf.a ../../src/57_iovars/lib57_iovars.a ../../src/57_iopsp_parser/lib57_iopsp_parser.a ../../src/56_recipspace/lib56_recipspace.a ../../src/56_xc/lib56_xc.a ../../src/56_mixing/lib56_mixing.a ../../src/56_io_mpi/lib56_io_mpi.a ../../src/55_abiutil/lib55_abiutil.a ../../src/54_spacepar/lib54_spacepar.a ../../src/53_ffts/lib53_ffts.a  ../../src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a ../../src/51_manage_mpi/lib51_manage_mpi.a ../../src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a ../../src/46_diago/lib46_diago.a ../../src/45_xgTools/lib45_xgTools.a ../../src/45_geomoptim/lib45_geomoptim.a ../../src/44_abitypes_defs/lib44_abitypes_defs.a ../../src/44_abitools/lib44_abitools.a ../../src/43_wvl_wrappers/lib43_wvl_wrappers.a ../../src/43_ptgroups/lib43_ptgroups.a ../../src/42_parser/lib42_parser.a ../../src/42_nlstrain/lib42_nlstrain.a ../../src/42_libpaw/lib42_libpaw.a ../../src/41_xc_lowlevel/lib41_xc_lowlevel.a ../../src/41_geometry/lib41_geometry.a ../../src/32_util/lib32_util.a ../../src/29_kpoints/lib29_kpoints.a ../../src/28_numeric_noabirule/lib28_numeric_noabirule.a ../../src/27_toolbox_oop/lib27_toolbox_oop.a ../../src/21_hashfuncs/lib21_hashfuncs.a ../../src/18_timing/lib18_timing.a ../../src/17_libtetra_ext/lib17_libtetra_ext.a ../../src/16_hideleave/lib16_hideleave.a  ../../src/14_hidewrite/lib14_hidewrite.a ../../src/12_hide_mpi/lib12_hide_mpi.a ../../src/11_memory_mpi/lib11_memory_mpi.a ../../src/10_dumpinfo/lib10_dumpinfo.a ../../src/10_defs/lib10_defs.a ../../src/02_clib/lib02_clib.a  -L/home/letuan/Programs/abinit-8.10.1/fallbacks/exports/lib -lwannier90 -L/home/letuan/Programs/abinit-8.10.1/fallbacks/exports/lib -lnetcdf -L/home/letuan/Programs/abinit-8.10.1/fallbacks/exports/lib -lxcf90 -lxc -llapack  -lblas -lrt -L/usr/local/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../.. -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran -lm -lquadmath -lpthread -L/usr/local/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../.. -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran -lm -lquadmath -lpthread
../../src/12_hide_mpi/lib12_hide_mpi.a(m_xmpi.o): In function `__m_xmpi_MOD_xmpi_init':
/home/letuan/Programs/abinit-8.10.1/src/12_hide_mpi/m_xmpi.F90:638: undefined reference to `mpi_attr_get_'
collect2: error: ld returned 1 exit status
make[3]: *** [abinit] Error 1
make[3]: Leaving directory `/home/letuan/Programs/abinit-8.10.1/src/98_main'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/letuan/Programs/abinit-8.10.1/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/letuan/Programs/abinit-8.10.1'
make: *** [all] Error 2

The compilation was with GNU compilers (v. 4.8.5). The similar compilation on OpenSuSE Leap 42 subsystem for Windows 10 went smoothly, without any difficulty.
This is the compilation receipt for Abinit:

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./configure --with-dft-flavor="libxc+atompaw+wannier90" --enable-mpi --enable-mpi-io="yes" F77=/usr/local/bin/mpif77 FC=/usr/local/bin/mpif90 CC=/usr/local/bin/mpicc CXX=/usr/local/bin/mpic++ --with-mpi-incs="-I/usr/local/include" --with-mpi-libs="-L/usr/local/lib -lmpi" --with-fft-incs="-I/usr/include" --with-fft-libs="-L/usr/lib64 -lfftw3l" --with-math-flavor="none" --enable-optim="aggressive" --with-trio-flavor="netcdf" --with-enable-64bit-flags="yes" FCFLAGS="-g -O3 --free-line-length-none"

(The key

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-free-line-length-none
was introduced for overcoming the break at the step with "27_toolbox_oop" compilation.)

Any help will be highly appreciated.
Le Tuan,
Dept. of Electronic Materials,
Hanoi Uni. of Sci. and Technol., Vietnam

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admin
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Posts: 33
Joined: Thu Sep 17, 2009 9:49 am

Re: Compilation of Abinit-8.10.1 fails on SL 7.6

Post by admin » Wed Jan 30, 2019 9:48 pm

Hi,

2 remarks :
- gnu 4.8.5 is obsolete and it is no more supported with ABINIT
- it seems you compile yourself the MPI package ( /usr/local/ ) : right ?

what the outputs of theses commands

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which mpif90
mpif90 -show
mpif90 --version
nm /usr/local/lib/lib*.* | grep mpi_attr_get_


regards

jmb

letuan
Posts: 29
Joined: Fri Jan 25, 2013 4:00 pm
Location: Hanoi
Contact:

Re: Compilation of Abinit-8.10.1 fails on SL 7.6

Post by letuan » Fri Apr 26, 2019 8:48 am

Dear JMB,
Yes, I compile openmpi v. 4.0 and fftw v. 3.3.8 for all computers before installing Abinit. The computers are on various platforms: Ubuntu v. 18.04 and OpenSuSE in Linux Subsystems for MS Windows 10 (for the first Abinit installation failed), on true SL, CentOS and OpenSuSE Leap and TumbleWeed distributions, etc, with also some versions of GNU C and Fortran compilers. Because our students's machines are not with the same OS.
From this forum I have got a lot.
Regards,
Le Tuan,
Dept. of Electronic Materials,
Hanoi Uni. of Sci. and Technol., Vietnam

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