6.12.1 make fails with 'ld ... File format not recognized'

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danieruz
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Joined: Fri Mar 09, 2012 2:16 pm

6.12.1 make fails with 'ld ... File format not recognized'

Post by danieruz » Fri Mar 09, 2012 2:30 pm

Greetings,

I'm attempting to build abinit 6.12.1 from source for our cluster. While running make, linking fails with the error I've pasted at the bottom of this post. Here are some useful notes:

-we've successfully compiled and used 6.10.2 on the same system and environment
-I can successfully compile if I disable mpi
-looking at the first libtool line in the output below, I can see that -rpath is being passed as an argument twice, both times with the same path, so perhaps there is a problem in the abinit config file??
-export FC=ifort CC=icc CXX=icpc

Can anyone offer insight and or suggestions on how to resolve this?

Regards,
Daniel

libtool: link: mpif90 -free -g -extend-source -vec-report0 -noaltparam -nofpscomp -O2 -g -I/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks/exports/include -rpath /lap/libfftw/3.3.0/lib -rpath /lap/libfftw/3.3.0/lib/openmpi -o atompaw atompaw_prog.o -L/lap/libfftw/3.3.0/lib -L/lap/libfftw/3.3.0/lib/openmpi ./.libs/libatompaw.a -L/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks/exports/lib -lmkl_scalapack_lp64 -lmkl_blacs_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core /afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks/exports/lib/libnetcdf.a /lap/openmpi/1.5.4/intel-12.1/lib/libmpi_f90.so /lap/openmpi/1.5.4/intel-12.1/lib/libmpi_f77.so /lap/openmpi/1.5.4/intel-12.1/lib/libmpi.so -ldl -lnsl -lutil /afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks/exports/lib/libxc.a -pthread -rpath /lap/openmpi/1.5.4/intel-12.1/lib -rpath /lap/openmpi/1.5.4/intel-12.1/lib
ifort: command line warning #10006: ignoring unknown option '-rpath'
ifort: command line warning #10006: ignoring unknown option '-rpath'
ifort: command line remark #10010: option '-pthread' is deprecated and will be removed in a future release. See '-help deprecated'
ifort: command line warning #10006: ignoring unknown option '-rpath'
ifort: command line warning #10006: ignoring unknown option '-rpath'
ipo: warning #11010: file format not recognized for /lap/libfftw/3.3.0/lib
ipo: warning #11010: file format not recognized for /lap/libfftw/3.3.0/lib/openmpi
ipo: warning #11010: file format not recognized for /lap/openmpi/1.5.4/intel-12.1/lib
ipo: warning #11010: file format not recognized for /lap/openmpi/1.5.4/intel-12.1/lib
ld: /lap/libfftw/3.3.0/lib: No such file: File format not recognized
make[6]: *** [atompaw] Error 1
make[6]: Leaving directory `/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks/sources/atompaw-3.0.1.3/src'
make[5]: *** [all-recursive] Error 1
make[5]: Leaving directory `/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks/sources/atompaw-3.0.1.3'
make[4]: *** [all] Error 2
make[4]: Leaving directory `/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks/sources/atompaw-3.0.1.3'
make[3]: *** [stamps/atompaw-build-stamp] Error 2
make[3]: Leaving directory `/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks'
make[2]: [all-local] Error 2 (ignored)
Checking build of atompaw fallback
test -e stamps/atompaw-install-stamp
make[2]: *** [all-local] Error 1
make[2]: Leaving directory `/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks'
make[1]: *** [multi] Error 2
make[1]: Leaving directory `/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel'
make: *** [mj4] Error 2
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pouillon
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Re: 6.12.1 make fails with 'ld ... File format not recognize

Post by pouillon » Fri Mar 09, 2012 3:03 pm

This is an ifort-related problem. For now, just reconfigure Abnit with the following:

Code: Select all

../configure --with-dft-flavor="bigdft+libxc+wannier90" ...
Yann Pouillon
Simune Atomistics
Donostia-San Sebastián, Spain
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danieruz
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Joined: Fri Mar 09, 2012 2:16 pm

Re: 6.12.1 make fails with 'ld ... File format not recognize

Post by danieruz » Fri Mar 09, 2012 3:06 pm

thanks for the quick reply, I'll come back with the result.
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danieruz
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Re: 6.12.1 make fails with 'ld ... File format not recognize

Post by danieruz » Fri Mar 09, 2012 3:51 pm

Hi,

I passed the argument you specified to configure, ran make clean then make mj4 and receive the error below. It looks like it's attempting to use the fallback, but is still dying with the same error.

If it's helpful, here is the complete configure call:

Code: Select all

./configure --with-dft-flavor="bigdft+libxc+wannier90" --prefix=/lap/abinit/6.12.1 --with-math-flavor=gsl --with-linalg-flavor=scalapack+mkl --with-fft-flavor=fftw3 --with-fft-incs="-I/lap/libfftw/3.3.0/include" --enable-mpi



Code: Select all

libtool: link: ar cru .libs/libwannier90.a  constants.o disentangle.o hamiltonian.o io.o kmesh.o overlap.o 
parameters.o plot.o transport.o utility.o wannierise.o wannier_lib.o
libtool: link: ranlib .libs/libwannier90.a
libtool: link: ( cd ".libs" && rm -f "libwannier90.la" && ln -s "../libwannier90.la" "libwannier90.la" )
mpif90 -DHAVE_CONFIG_H -I. -I..   -I/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fall
backs/exports/include  -free -g -extend-source -vec-report0 -noaltparam -nofpscomp  -O2 -g -I/afs/hpc2n.umu
.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks/exports/include -c -o wannier_prog.o wannier
_prog.F90
/bin/bash ../libtool --tag=FC   --mode=link mpif90  -free -g -extend-source -vec-report0 -noaltparam -nofpscomp  -O2 -g -I/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks/exports/include  -L/lap/libfftw/3.3.0/lib -Wl,-rpath,/lap/libfftw/3.3.0/lib -L/lap/libfftw/3.3.0/lib/openmpi -Wl,-rpath,/lap/libfftw/3.3.0/lib/openmpi -o wannier90.x wannier_prog.o libwannier90.la -lmkl_scalapack_lp64  -lmkl_blacs_lp64  -lmkl_intel_lp64  -lmkl_intel_lp64 -lmkl_sequential -lmkl_core   -L/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks/exports/lib -letsf_io_low_level -letsf_io_utils -letsf_io 
libtool: link: mpif90 -free -g -extend-source -vec-report0 -noaltparam -nofpscomp -O2 -g -I/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks/exports/include -rpath /lap/libfftw/3.3.0/lib -rpath /lap/libfftw/3.3.0/lib/openmpi -o wannier90.x wannier_prog.o  -L/lap/libfftw/3.3.0/lib -L/lap/libfftw/3.3.0/lib/openmpi ./.libs/libwannier90.a -L/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks/exports/lib -lmkl_scalapack_lp64 -lmkl_blacs_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -letsf_io_low_level -letsf_io_utils -letsf_io
ifort: command line warning #10006: ignoring unknown option '-rpath'
ifort: command line warning #10006: ignoring unknown option '-rpath'
ipo: warning #11010: file format not recognized for /lap/libfftw/3.3.0/lib
ipo: warning #11010: file format not recognized for /lap/libfftw/3.3.0/lib/openmpi
ld: /lap/libfftw/3.3.0/lib: No such file: File format not recognized
make[6]: *** [wannier90.x] Error 1
make[6]: Leaving directory `/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks/sources/wannier90-1.2.0.1/src'
make[5]: *** [all-recursive] Error 1
make[5]: Leaving directory `/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks/sources/wannier90-1.2.0.1'
make[4]: *** [all] Error 2
make[4]: Leaving directory `/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks/sources/wannier90-1.2.0.1'
make[3]: *** [stamps/wannier90-build-stamp] Error 2
make[3]: Leaving directory `/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks'
make[2]: [all-local] Error 2 (ignored)
Checking build of wannier90 fallback
test -e stamps/wannier90-install-stamp
make[2]: *** [all-local] Error 1
make[2]: Leaving directory `/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel/fallbacks'
make[1]: *** [multi] Error 2
make[1]: Leaving directory `/afs/hpc2n.umu.se/lap/abinit/6.12.1/src/abinit-6.12.1/abisko-intel'
make: *** [mj4] Error 2
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pouillon
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Re: 6.12.1 make fails with 'ld ... File format not recognize

Post by pouillon » Fri Mar 09, 2012 5:12 pm

Then, assuming you'll not use BigDFT nor Wannier functions, just reduce further the option:

Code: Select all

--with-dft-flavor="libxc"


When I have time, I'll see whether rebuilding the tarball with a more recent version of Libtool fixes the problem.
Yann Pouillon
Simune Atomistics
Donostia-San Sebastián, Spain
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danieruz
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Joined: Fri Mar 09, 2012 2:16 pm

Re: 6.12.1 make fails with 'ld ... File format not recognize

Post by danieruz » Mon Mar 12, 2012 2:22 pm

Hi pouillon,
Compiling without bigdft and wannier90 succeeded. I'll let our users know that for the time being, we don't have support for them in 6.12.1. Hopefully they don't need them just now ;)

Thanks for your help, and if you do find a solution, I would be glad to hear about it.

Regards,
Daniel
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