Compilation of Abinit-8.10.1 fails on SL 7.6

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Compilation of Abinit-8.10.1 fails on SL 7.6

Postby letuan » Sat Jan 05, 2019 7:09 pm

I am facing with this error many times in my Scientific Linux v.7.6 distro and I cannot fix it :
Code: Select all
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:
Code: Select all
./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
Code: Select all
-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
letuan
 
Posts: 25
Joined: Fri Jan 25, 2013 5:00 pm

Re: Compilation of Abinit-8.10.1 fails on SL 7.6

Postby admin » Wed Jan 30, 2019 10:48 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

Code: Select all
which mpif90
mpif90 -show
mpif90 --version
nm /usr/local/lib/lib*.* | grep mpi_attr_get_


regards

jmb
User avatar
admin
Site Admin
 
Posts: 21
Joined: Thu Sep 17, 2009 9:49 am

Re: Compilation of Abinit-8.10.1 fails on SL 7.6

Postby 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
letuan
 
Posts: 25
Joined: Fri Jan 25, 2013 5:00 pm


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