issues with tests and xml

Marc Riera

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Jun 1, 2018, 10:48:47 PM6/1/18

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Hello,

I installed (hopefully properly) i-pi, but when I run the command:

nosetests -v

Some of the tests are failing (output below).

*********************************

(py27) [mrierari@russell i-pi]$ nosetests -v

Tests names of Atoms object. ... ERROR

Contraction with one bead. ... ok

Contraction with two beads. ... ok

Contraction with tree beads. ... ok

Contraction with four beads. ... ok

Depend: Slicing test ... ok

Depend: Addition test ... ok

Depend: Increment test ... ok

Depend: Dot test ... ok

Depend: Dot-f test ... ok

Depend: read-only flag ... ok

Client: startup without socket. ... ok

Driver: startup without socket. ... ok

InterfaceSocket: startup. ... ok

Socket client for ASE. ... SKIP

Tests that xyz files are read correctly. ... ERROR

Tests that xyz files with multiple frames are read correctly. ... ERROR

Tests that pdb files are read correctly. ... FAIL

Tests that pdb files with multiple frames are read correctly. ... FAIL

Tests that pdb files are printed correctly. ... FAIL

Tests that xyz files are printed correctly. ... FAIL

Tests that mode/xyz files are read correctly. ... ERROR

Tests that mode/xyz files with multiple frames are read correctly. ... ERROR

Tests that mode/pdb files are read correctly. ... FAIL

Tests that mode/pdb files with multiple frames are read correctly. ... FAIL

Tests that mode/pdb files are printed correctly. ... FAIL

Tests that mode/xyz files are printed correctly. ... FAIL

ipi.tests.test_runs.test_lj_gas ... running ../../drivers/driver.x

ok

ipi.tests.test_units.test_case_insensitive ... ok

ipi_tests.engine.test_initializer.test_init_file ... ERROR

Failure: ImportError (No module named mock) ... ERROR

ipi_tests.utils.io.backends.test_io_units.test_process_units_noobj ... ERROR

ipi_tests.utils.io.backends.test_io_units.test_process_units_object ... ERROR

ipi_tests.utils.io.backends.test_io_xyz.test_read_xyz ... ERROR

ipi_tests.utils.io.backends.test_io_xyz.test_iter_xyz ... ERROR

ipi_tests.utils.io.backends.test_io_xyz.test_print_xyz ... ERROR

doc: run make aux ... ok

doc: run make ...

********************************************

Also, and I guess that the above is one of the reasons, running

i-pi input.xml

for a slightly modified input.xml I took from : i-pi/examples/lammps/h2o-pimd

yields the error below

I realized that some other examples have the initialize insisde system, and they seem to load well with i-pi, but the manual (v1.0, page 52, section 5.1.2) states that initialize must be inside simulation.

**********************************

(py27) [mrierari@russell test]$ i-pi input.xml

Traceback (most recent call last):

File "/home/mrierari/codes/i-pi/bin/i-pi", line 105, in <module>

main(args[0], options)

File "/home/mrierari/codes/i-pi/bin/i-pi", line 48, in main

simulation = Simulation.load_from_xml(fn_input, request_banner=True, custom_verbosity=options.verbosity)

File "/home/mrierari/codes/i-pi/ipi/engine/simulation.py", line 78, in load_from_xml

input_simulation.parse(xmlrestart.fields[0][1])

File "/home/mrierari/codes/i-pi/ipi/utils/inputvalue.py", line 342, in parse

raise NameError("Tag name '" + f + "' is not a recognized property of '" + xml.name + "' objects")

NameError: Tag name 'initialize' is not a recognized property of 'simulation' objects

***********************************

******************** input.xml ***********

[100.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,100.0]

</cell>

</initialize>

<properties stride='1' filename='out'> [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_cv, potential, pressure_cv{megapascal}] </properties>

<trajectory filename='pos' stride='20'> positions </trajectory>

</output>

<total_steps>500000</total_steps>

<address>localhost</address>

</socket>

</forces>

</thermostat>

</ensemble>

</simulation>

**********************************************************8

I am pretty sure is some error in my configuration, but sincerely I don't know where to look at.

I am using a conda environment for python 2.7, and I made sure that PYTHONPATH contains the path to the installed libraries:

(py27) [mrierari@russell test]$ echo $PYTHONPATH

/home/mrierari/codes/miniconda3/envs/py27/lib/python2.7/site-packages/:/home/mrierari/codes/i-pi:/home/mrierari/codes/miniconda3/envs/py27/

I would appreciate any hint on what am I doing wrong.

Thanks!

Marc

venkat kapil

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Jun 2, 2018, 12:24:00 PM6/2/18

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1) Thanks for pointing them out. We have found the source of the failures and are working making them work. Just FYI these issues are harmless.
2) Some of the examples are outdated and we should purge them. You can try h2o-pimd.1 which should work fine.

Marc Riera

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Jun 2, 2018, 12:26:59 PM6/2/18

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Thanks a lot!

Marc

CHAITANYA JITENDRA SHAH

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Jun 17, 2023, 3:29:25 PM6/17/23

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Hello Venkat and Marc

I recently came to know about I-Pi and since it could be very useful in my project, I am trying to install it.

I am following the steps given in the manual. But after completion of the installation, when I run the command: nosetests -v,

I get lot of errors. Unlike Marc's case, I mostly get errors and only some of the tests turn out to be ok.

Can you please help me in finding what is going wrong? I am very new to installations and stuff, so please be patient.

Here is the output I get:

Intermediate function to run the examples (by calling Runner_examples) which makes ... ERROR
Intermediate function to run the regression test (by calling Runner) and makes ... ERROR
This function recursively searches for test ... ERROR
This function recursively searches for test ... ERROR
This function looks for the existence of test_settings.dat file. ... ERROR
Modify xml to run dummy tests ... ERROR
Tests names of Atoms object. ... ok
ipi_tests.unit_tests.engine.test_initializer.test_init_file ... ERROR
ipi_tests.unit_tests.engine.test_properties.test_Trajectories_print_traj ... ERROR
Failure: ModuleNotFoundError (No module named 'pytest_mock') ... ERROR
ipi_tests.unit_tests.utils.io.backends.test_io_units.test_process_units_noobj ... ERROR
ipi_tests.unit_tests.utils.io.backends.test_io_units.test_process_units_object ... ERROR
ipi_tests.unit_tests.utils.io.backends.test_io_xyz.test_read_xyz ... ERROR
ipi_tests.unit_tests.utils.io.backends.test_io_xyz.test_iter_xyz ... ERROR
ipi_tests.unit_tests.utils.io.backends.test_io_xyz.test_print_xyz ... ERROR
Test contraction to `n` replicas with original positions `q`. ... ERROR

Depend: Slicing test ... ok
Depend: Addition test ... ok
Depend: Increment test ... ok
Depend: Dot test ... ok
Depend: Dot-f test ... ok
Depend: read-only flag ... ok

Tests that xyz files are read correctly. ... ok
Tests that xyz files with multiple frames are read correctly. ... ok
Tests that pdb files are read correctly. ... ok
Tests that pdb files with multiple frames are read correctly. ... ok
Tests that pdb files are printed correctly. ... ok
Tests that xyz files are printed correctly. ... ok
Tests that mode/xyz files are read correctly. ... ok
Tests that mode/xyz files with multiple frames are read correctly. ... ok
Tests that mode/pdb files are read correctly. ... ok
Tests that mode/pdb files with multiple frames are read correctly. ... ok
Tests that mode/pdb files are printed correctly. ... ok
Tests that mode/xyz files are printed correctly. ... ok
ipi_tests.unit_tests.utils.test_units.test_case_insensitive ... ok

======================================================================
ERROR: Intermediate function to run the examples (by calling Runner_examples) which makes
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