make check fails (python yaml problem)

[Roger Mason]

libyaml-0.1.6_2 py27-yaml-3.11 bigdft 1.7.7 FreeBSD 10.2

cryptoperthite tests gmake check
Making check in DFT
gmake[1]: Entering directory '/home/rmason/Software/BigDFT/64-bit/tests/DFT'
Making check in cubic
gmake[2]: Entering directory '/home/rmason/Software/BigDFT/64-bit/tests/DFT/cubic'
gmake[3]: Entering directory '/home/rmason/Software/BigDFT/64-bit/tests/DFT/cubic/C-test'
gmake[3]: 'C.psp' is up to date.
gmake[3]: Leaving directory '/home/rmason/Software/BigDFT/64-bit/tests/DFT/cubic/C-test'
gmake[3]: Entering directory '/home/rmason/Software/BigDFT/64-bit/tests/DFT/cubic/C-test'
gmake[3]: 'C-test.post-in' is up to date.
gmake[3]: Leaving directory '/home/rmason/Software/BigDFT/64-bit/tests/DFT/cubic/C-test'
Input prepared in "C-test" directory, make C.run available
touch C.in
==============================================
Will run tests in parallel with 'mpirun -np 2'
==============================================
gmake[3]: Entering directory '/home/rmason/Software/BigDFT/64-bit/tests/DFT/cubic/C-test'
gmake[3]: 'C.out.out' is up to date.
gmake[3]: Leaving directory '/home/rmason/Software/BigDFT/64-bit/tests/DFT/cubic/C-test'
Tests have run in "C-test" directory, make C.check available
gmake[3]: Entering directory '/home/rmason/Software/BigDFT/64-bit/tests/DFT/cubic/C-test'
python /home/rmason/Software/BigDFT/64-bit/../bigdft-1.7.7/tests/fldiff_yaml.py -r C.out.ref.yaml -d log-C.yaml -t /home/rmason/Software/BigDFT/64-bit/../bigdft-1.7.7/tests/tols-BigDFT.yaml --label=C -o C.out.report.yaml
Traceback (most recent call last):
  File "/home/rmason/Software/BigDFT/64-bit/../bigdft-1.7.7/tests/fldiff_yaml.py", line 356, in <module>
    open(args.ref, "r").read(), Loader=yaml.CLoader)]
AttributeError: 'module' object has no attribute 'CLoader'
../Makefile:556: recipe for target 'C.out.report.yaml' failed
gmake[3]: *** [C.out.report.yaml] Error 1
gmake[3]: Leaving directory '/home/rmason/Software/BigDFT/64-bit/tests/DFT/cubic/C-test'
Makefile:759: recipe for target 'C.yaml-check' failed
gmake[2]: *** [C.yaml-check] Error 2
rm C.run
gmake[2]: Leaving directory '/home/rmason/Software/BigDFT/64-bit/tests/DFT/cubic'
Makefile:402: recipe for target 'check-recursive' failed
gmake[1]: *** [check-recursive] Error 1
gmake[1]: Leaving directory '/home/rmason/Software/BigDFT/64-bit/tests/DFT'
Makefile:420: recipe for target 'check-recursive' failed
gmake: *** [check-recursive] Error 1

[Luigi Genovese (luigi-genovese)]

This is not a bug, but a weakness of the present build system.

The " make check" command has to be launched from the tob builddir directory instaed that from test.
this will be corrected in the forthcoming release.

Many thanks

Luigi

[Roger Mason (rmason-8)]

Hello,

Luigi Genovese <email address hidden> writes:

> This is not a bug, but a weakness of the present build system.
>
> The " make check" command has to be launched from the tob builddir directory instaed that from test.
> this will be corrected in the forthcoming release.

I have the same problem running from the top build directory:

cryptoperthite 64-bit gmake check
Making check in flib
gmake[1]: Entering directory '/home/rmason/Software/BigDFT/64-bit/flib'
Making check in src
gmake[2]: Entering directory '/home/rmason/Software/BigDFT/64-bit/flib/src'
test -e "../../includes" || /usr/bin/install -c -d -m 755 ../../includes
for mod in "yaml_strings.mod dictionaries.mod dictionaries_base.mod f_enums.mod f_precisions.mod yaml_output.mod yaml_parse.mod metadata_interfaces.mod module_f_malloc.mod dynamic_memory.mod randomdata.mod memory_profiling.mod f_utils.mod f_input_file.mod f_refcnts.mod f_trees.mod exception_callbacks.mod time_profiling.mod" ; do \
  /usr/bin/install -c -m 644 $mod ../../includes ; \
done
gmake[2]: Leaving directory '/home/rmason/Software/BigDFT/64-bit/flib/src'
Making check in tests
gmake[2]: Entering directory '/home/rmason/Software/BigDFT/64-bit/flib/tests'
gmake yaml_test
gmake[3]: Entering directory '/home/rmason/Software/BigDFT/64-bit/flib/tests'
gmake[3]: 'yaml_test' is up to date.
gmake[3]: Leaving directory '/home/rmason/Software/BigDFT/64-bit/flib/tests'
export PYTHONPATH=/opt/lib/root:/opt/lib/root: ; \
export LD_LIBRARY_PATH=:/opt/local/lib:/opt/lib/root:/opt/lib:/opt/local/lib:/opt/lib/root:/opt/lib ; \
python ../../../bigdft-1.7.7/tests/fldiff_yaml.py --label yaml_test -t ../../../bigdft-1.7.7/tests/tols-BigDFT.yaml \
        -r /home/rmason/Software/BigDFT/64-bit/../bigdft-1.7.7/flib/tests/yaml_test.ref.yaml -d yaml_test.out.yaml --output yaml_test.report.yaml
Traceback (most recent call last):
  File "../../../bigdft-1.7.7/tests/fldiff_yaml.py", line 356, in <module>
    open(args.ref, "r").read(), Loader=yaml.CLoader)]
AttributeError: 'module' object has no attribute 'CLoader'
Makefile:628: recipe for target 'yaml_test.report.yaml' failed
gmake[2]: *** [yaml_test.report.yaml] Error 1
gmake[2]: Leaving directory '/home/rmason/Software/BigDFT/64-bit/flib/tests'
Makefile:397: recipe for target 'check-recursive' failed
gmake[1]: *** [check-recursive] Error 1
gmake[1]: Leaving directory '/home/rmason/Software/BigDFT/64-bit/flib'
Makefile:532: recipe for target 'check-recursive' failed
gmake: *** [check-recursive] Error 1

Cheers,
Roger

[Luigi Genovese (luigi-genovese)]

It seems that the code did not installed PyYaml.

The command:

export PYTHONPATH=/opt/lib/root:/opt/lib/root: ; \
export LD_LIBRARY_PATH=:/opt/local/lib:/opt/lib/root:/opt/lib:/opt/local/lib:/opt/lib/root:/opt/lib ;

which is now launched as make is ran from the builddir, does not contain the output of

ls -d $(abs_top_builddir)/PyYAML-3.10/build/lib.*

Do you have a clue on why pyaml did not compile on your build?
Also, the code should have added the
<top_builddir>/yaml-0.1.4/src/.libs

directory to the LD_LIBRARY_PATH.

Note that there is not need of pyyaml to run the code, but only to verify the tests.

Do not hesitate

Many thanks

Luigi

[Roger Mason (rmason-8)]

Hi Luigi,

Luigi Genovese <email address hidden> writes:

> The command:
>
> export PYTHONPATH=/opt/lib/root:/opt/lib/root: ; \
> export
> LD_LIBRARY_PATH=:/opt/local/lib:/opt/lib/root:/opt/lib:/opt/local/lib:/opt/lib/root:/opt/lib
> ;
>
> which is now launched as make is ran from the builddir, does not contain
> the output of
>
> ls -d $(abs_top_builddir)/PyYAML-3.10/build/lib.*
>
> Do you have a clue on why pyaml did not compile on your build?
> Also, the code should have added the
> <top_builddir>/yaml-0.1.4/src/.libs
>
> directory to the LD_LIBRARY_PATH.

The relevant lines are commented out in the builddir Makefile:

# This is required for testing.
#LD_LIBRARY_PATH := ${LD_LIBRARY_PATH}:$(abs_top_builddir)/yaml-0.1.4/src/.libs

# Required by tests
#PYTHONPATH := ${PYTHONPATH}:`ls -d
#$(abs_top_builddir)/PyYAML-3.10/build/lib.*`

I have no idea why this happened.

Cheers,
Roger

[Roger Mason (rmason-8)]

Hi Luigi,

Luigi Genovese <email address hidden> writes:

> Do you have a clue on why pyaml did not compile on your build?

It looks like it is necessary to configure with --enable-internal-yaml
in order to get PyYAML and libYAML built. I have not yet run the tests
but will report back when I have done so.

Cheers,
Roger