[ase-users] AssertionError while installing GPAW

[Ask Hjorth Larsen]

Hi

2017-05-25 8:33 GMT+02:00 Nam Tran via ase-users
<ase-users at listserv.fysik.dtu.dk>:
> Dear ASE users
>
>
> I have successfully installed ASE on my HPC account using anaconda2.
>
> Now I am trying to install GPAW. I have edited the customize.py file to use
> intel MKL library.
>
> But I faced an "AssertionError" that I don't know how to fix.
>
>
> Traceback (most recent call last):
>
>   File "setup.py", line 249, in <module>
>
>     'Topic :: Scientific/Engineering :: Physics'])
>
>   File "/home/vnt981/anaconda2/lib/python2.7/distutils/core.py", line 151,
> in setup
>
>     dist.run_commands()
>
>   File "/home/vnt981/anaconda2/lib/python2.7/distutils/dist.py", line 953,
> in run_commands
>
>     self.run_command(cmd)
>
>   File "/home/vnt981/anaconda2/lib/python2.7/distutils/dist.py", line 972,
> in run_command
>
>     cmd_obj.run()
>
>   File "/home/vnt981/anaconda2/lib/python2.7/distutils/command/install.py",
> line 563, in run
>
>     self.run_command('build')
>
>   File "/home/vnt981/anaconda2/lib/python2.7/distutils/cmd.py", line 326, in
> run_command
>
>     self.distribution.run_command(command)
>
>   File "/home/vnt981/anaconda2/lib/python2.7/distutils/dist.py", line 972,
> in run_command
>
>     cmd_obj.run()
>
>   File "/home/vnt981/anaconda2/lib/python2.7/distutils/command/build.py",
> line 127, in run
>
>     self.run_command(cmd_name)
>
>   File "/home/vnt981/anaconda2/lib/python2.7/distutils/cmd.py", line 326, in
> run_command
>
>     self.distribution.run_command(command)
>
>   File "/home/vnt981/anaconda2/lib/python2.7/distutils/dist.py", line 972,
> in run_command
>
>     cmd_obj.run()
>
>   File "setup.py", line 200, in run
>
>     assert error == 0
>
> AssertionError
>
>
>
> If you are familiar with the problem please help me.
>
> Any comments will be appreciated, thanks in advance.
>
> Here I attached my customize.py and error log

These lines indicate the problem:

build/temp.linux-x86_64-2.7/c/cerf.o: In function `itpp_cerf_rybicki':
/home/vnt981/Softwares/gpaw/c/cerf.c:194: undefined reference to `__svml_exp2'
build/temp.linux-x86_64-2.7/c/plane_wave.o: In function `plane_wave_grid':
/home/vnt981/Softwares/gpaw/c/plane_wave.c:36: undefined reference to
`__libm_sse2_sincos'
build/temp.linux-x86_64-2.7/c/utilities.o: In function
`utilities_gaussian_wave':
c/utilities.c:(.text+0x160e): undefined reference to `__libm_sse2_sincos'
c/utilities.c:(.text+0x2091): undefined reference to `__libm_sse2_sincos'
build/temp.linux-x86_64-2.7/c/utilities.o: In function `hartree':
c/utilities.c:(.text+0x2f7c): undefined reference to `__svml_pow2'
c/utilities.c:(.text+0x301b): undefined reference to `__svml_pow2'
c/utilities.c:(.text+0x3082): undefined reference to `__svml_pow2'
c/utilities.c:(.text+0x30f6): undefined reference to `__svml_pow2'
build/temp.linux-x86_64-2.7/c/utilities.o: In function `localize':
c/utilities.c:(.text+0x36ff): undefined reference to `__libm_sse2_sincos'
collect2: ld returned 1 exit status

You link to some libraries that need __svml_pow2 and other things, but
not to whichever library provides those.

The solution is to link also to the libraries that provide those symbols.

The __svml_pow2 probably comes from MKL's libsvml, so make sure to
link to that (-lsvml).

You may wish to write the list of libraries in the "libraries" list
and not extra_link_args.

Also __libm_sse2_sincos probably comes from libm (-lm).

If there are further problems: To see which symbols are present in a
library, run "nm" on it (probably together with grep).  Since MKL has
a complete jumble of libraries, this is probably a mind-wracking
exercise.  Best of luck!

(Adding gpaw-users mailing list; this is not related to ASE)

Best regards
Ask

>
>
> Best Regards
>
>
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