[gpaw-users] GPAW compilation - sysroot error

[Rogério Gouvêa]

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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