[gpaw-users] GPAW compilation - sysroot error

[SKLENARD Benoit 242444]

Dear Rogério,

As a workaround you can add the following hack in your setup.py:

vars = get_config_vars()
tmp = vars['LDFLAGS'].split()
del tmp[-1]
vars['LDFLAGS'] = ' '.join(tmp)

Kind regards,

Benoît


De : gpaw-users-bounces at listserv.fysik.dtu.dk <gpaw-users-bounces at listserv.fysik.dtu.dk> De la part de Rogério Gouvêa via gpaw-users
Envoyé : mercredi 24 juillet 2019 22:57
À : gpaw-users at listserv.fysik.dtu.dk
Objet : [gpaw-users] GPAW compilation - sysroot error

When I try to compile I am get the following error:

$ python setup.py install --user
....
mpicc -DNPY_NO_DEPRECATED_API=7 -D_GNU_SOURCE=1 -DPARALLEL=1 -DGPAW_INTERPRETER=1 -Wall -Wno-unknown-pragmas -std=c99 -fPIC -I/home/efracio/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/home/efracio/anaconda3/envs/myenv/include -I/home/efracio/anaconda3/include/python3.7m -I/home/efracio/anaconda3/include/python3.7m -o build/temp.linux-x86_64-3.7/c/xc/libvdwxc.o -c c/xc/libvdwxc.c
mpicc -o build/bin.linux-x86_64-3.7//gpaw-python build/temp.linux-x86_64-3.7/c/_gpaw.o build/temp.linux-x86_64-3.7/c/bc.o build/temp.linux-x86_64-3.7/c/blacs.o build/temp.linux-x86_64-3.7/c/blas.o build/temp.linux-x86_64-3.7/c/bmgs/bmgs.o build/temp.linux-x86_64-3.7/c/cerf.o build/temp.linux-x86_64-3.7/c/elpa.o build/temp.linux-x86_64-3.7/c/fftw.o build/temp.linux-x86_64-3.7/c/lapack.o build/temp.linux-x86_64-3.7/c/lcao.o build/temp.linux-x86_64-3.7/c/lfc.o build/temp.linux-x86_64-3.7/c/lfc2.o build/temp.linux-x86_64-3.7/c/localized_functions.o build/temp.linux-x86_64-3.7/c/mlsqr.o build/temp.linux-x86_64-3.7/c/mpi.o build/temp.linux-x86_64-3.7/c/operators.o build/temp.linux-x86_64-3.7/c/plane_wave.o build/temp.linux-x86_64-3.7/c/plt.o build/temp.linux-x86_64-3.7/c/point_charges.o build/temp.linux-x86_64-3.7/c/spline.o build/temp.linux-x86_64-3.7/c/symmetry.o build/temp.linux-x86_64-3.7/c/tetra.o build/temp.linux-x86_64-3.7/c/transformers.o build/temp.linux-x86_64-3.7/c/utilities.o build/temp.linux-x86_64-3.7/c/wigner_seitz.o build/temp.linux-x86_64-3.7/c/woperators.o build/temp.linux-x86_64-3.7/c/xc/ensemble_gga.o build/temp.linux-x86_64-3.7/c/xc/libvdwxc.o build/temp.linux-x86_64-3.7/c/xc/libxc.o build/temp.linux-x86_64-3.7/c/xc/m06l.o build/temp.linux-x86_64-3.7/c/xc/pbe.o build/temp.linux-x86_64-3.7/c/xc/pw91.o build/temp.linux-x86_64-3.7/c/xc/revtpss.o build/temp.linux-x86_64-3.7/c/xc/revtpss_c_pbe.o build/temp.linux-x86_64-3.7/c/xc/rpbe.o build/temp.linux-x86_64-3.7/c/xc/tpss.o build/temp.linux-x86_64-3.7/c/xc/vdw.o build/temp.linux-x86_64-3.7/c/xc/xc.o build/temp.linux-x86_64-3.7/c/xc/xc_mgga.o  -L/home/efracio/lapack-3.8.0 -L/home/efracio/blas/BLAS-3.8.0 -L/home/efracio/anaconda3/lib/python3.7/config-3.7m-x86_64-linux-gnu -lblas -llapack -L. -lpython3.7m -lpthread -ldl -lutil -lrt -lm  /home/efracio/anaconda3/envs/myenv/lib/libxc.a -L/home/efracio/anaconda3/lib -Wl,-rpath=/home/efracio/anaconda3/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Xlinker -export-dynamic
/usr/bin/ld: this linker was not configured to use sysroots
collect2: ld returned 1 exit status
Traceback (most recent call last):
  File "setup.py", line 264, in <module>
    'Topic :: Scientific/Engineering :: Physics'])
  File "/home/efracio/anaconda3/lib/python3.7/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/home/efracio/anaconda3/lib/python3.7/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/home/efracio/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/home/efracio/anaconda3/lib/python3.7/distutils/command/install.py", line 545, in run
    self.run_command('build')
  File "/home/efracio/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/home/efracio/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/home/efracio/anaconda3/lib/python3.7/distutils/command/build.py", line 135, in run
    self.run_command(cmd_name)
  File "/home/efracio/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/home/efracio/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "setup.py", line 215, in run
    assert error == 0
AssertionError

I think if I could eliminate the option --sysroot=/ from the command line it would compile fine. Any idea on how to do this?

Confs:
gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
anaconda Command line client (version 1.7.2)
Python 3.7.1 (from anaconda since system's version is too old)

Thanks in advance.
--

Rogério Gouvêa
Phd student on Materials Science - UFRGS


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