Hi Edward,
So the GUI problems came from relax 2.2.5 The actual output is big, so I
will only post where the errors started
relax> monte_carlo.error_analysis()
relax> results.write(file='devnull', dir='pipe_name', compress_type=1,
force=True)
Opening the null device file for writing.
Traceback (most recent call last):
File
"/usr/local/Relax/relax-2.2.5/test_suite/system_tests/n_state_model.py",
line 733, in test_paramag_centre_fit
self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'paramag_centre_fit.py')
File
"/usr/local/Relax/relax-2.2.5/test_suite/system_tests/base_classes.py",
line 65, in script_exec
self.interpreter.run(script_file=script)
File "/usr/local/Relax/relax-2.2.5/prompt/interpreter.py", line 278, in
run
return run_script(intro=self.__intro_string, local=locals(),
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/usr/local/Relax/relax-2.2.5/prompt/interpreter.py", line 585, in
run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/usr/local/Relax/relax-2.2.5/prompt/interpreter.py", line 468, in
interact_script
exec_script(script_file, local)
File "/usr/local/Relax/relax-2.2.5/prompt/interpreter.py", line 341, in
exec_script
runpy.run_module(module, globals)
File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
fname, loader, pkg_name)
File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File
"/usr/local/Relax/relax-2.2.5/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py",
line 121, in <module>
print("A:\n" % cdp.align_tensors[0])
TypeError: not all arguments converted during string formatting
----------------------------------------------------------------------
Ran 284 tests in 279.175s
FAILED (errors=1)
##############
# Unit tests #
##############
.........................................................................................................................................................................................................E.E............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................E...................E........................................................................................................................................................................................................................................................................................................................................................................................
======================================================================
ERROR: test_read_protein_noe_data
(test_suite.unit_tests._generic_fns.test_sequence.Test_sequence)
Test the reading of the amino acid sequence out of a protein NOE data file.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/Relax/relax-2.2.5/test_suite/unit_tests/sequence_testing_base.py",
line 130, in test_read_protein_noe_data
self.sequence_fns.read(file='Ap4Aase.Noe.600.bz2',
dir=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'relaxation_data',
res_num_col=1, res_name_col=2)
File "/usr/local/Relax/relax-2.2.5/generic_fns/sequence.py", line 339, in
read
for mol_name, res_num, res_name, spin_num, spin_name in
read_spin_data(file=file, dir=dir, file_data=file_data,
spin_id_col=spin_id_col, mol_name_col=mol_name_col,
res_num_col=res_num_col, res_name_col=res_name_col,
spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep,
spin_id=spin_id):
File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 533, in
read_spin_data
file_data = extract_data(file, dir)
File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 141, in extract_data
file = open_read_file(file_name=file, dir=dir)
File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 345, in
open_read_file
compress_type, file_path = determine_compression(file_path)
File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 112, in
determine_compression
raise RelaxFileError(file_path)
RelaxFileError: RelaxError: The file
'/usr/local/Relax/relax-2.2.5/test_suite/shared_data/relaxation_data/Ap4Aase.Noe.600.bz2'
does not exist.
======================================================================
ERROR: test_read
(test_suite.unit_tests._generic_fns.test_relax_data.Test_relax_data)
Test the reading of relaxation data.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/Relax/relax-2.2.5/test_suite/unit_tests/relax_data_testing_base.py",
line 63, in test_read
sequence.read(file='Ap4Aase.Noe.600.bz2',
dir=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'relaxation_data',
res_num_col=1, res_name_col=2)
File "/usr/local/Relax/relax-2.2.5/generic_fns/sequence.py", line 339, in
read
for mol_name, res_num, res_name, spin_num, spin_name in
read_spin_data(file=file, dir=dir, file_data=file_data,
spin_id_col=spin_id_col, mol_name_col=mol_name_col,
res_num_col=res_num_col, res_name_col=res_name_col,
spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep,
spin_id=spin_id):
File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 533, in
read_spin_data
file_data = extract_data(file, dir)
File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 141, in extract_data
file = open_read_file(file_name=file, dir=dir)
File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 345, in
open_read_file
compress_type, file_path = determine_compression(file_path)
File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 112, in
determine_compression
raise RelaxFileError(file_path)
RelaxFileError: RelaxError: The file
'/usr/local/Relax/relax-2.2.5/test_suite/shared_data/relaxation_data/Ap4Aase.Noe.600.bz2'
does not exist.
======================================================================
ERROR: test_read_protein_noe_data
(test_suite.unit_tests._prompt.test_sequence.Test_sequence)
Test the reading of the amino acid sequence out of a protein NOE data file.
----------------------------------------------------------------------
relax> sequence.read(file='Ap4Aase.Noe.600.bz2',
dir='/usr/local/Relax/relax-2.2.5/test_suite/shared_data/relaxation_data',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, sep=None, spin_id=None)
Traceback (most recent call last):
File
"/usr/local/Relax/relax-2.2.5/test_suite/unit_tests/sequence_testing_base.py",
line 130, in test_read_protein_noe_data
self.sequence_fns.read(file='Ap4Aase.Noe.600.bz2',
dir=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'relaxation_data',
res_num_col=1, res_name_col=2)
File "/usr/local/Relax/relax-2.2.5/prompt/uf_objects.py", line 221, in
__call__
self._backend(*new_args, **uf_kargs)
File "/usr/local/Relax/relax-2.2.5/generic_fns/sequence.py", line 339, in
read
for mol_name, res_num, res_name, spin_num, spin_name in
read_spin_data(file=file, dir=dir, file_data=file_data,
spin_id_col=spin_id_col, mol_name_col=mol_name_col,
res_num_col=res_num_col, res_name_col=res_name_col,
spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep,
spin_id=spin_id):
File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 533, in
read_spin_data
file_data = extract_data(file, dir)
File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 141, in extract_data
file = open_read_file(file_name=file, dir=dir)
File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 345, in
open_read_file
compress_type, file_path = determine_compression(file_path)
File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 112, in
determine_compression
raise RelaxFileError(file_path)
RelaxFileError: RelaxError: The file
'/usr/local/Relax/relax-2.2.5/test_suite/shared_data/relaxation_data/Ap4Aase.Noe.600.bz2'
does not exist.
======================================================================
ERROR: test_read
(test_suite.unit_tests._prompt.test_relax_data.Test_relax_data)
Test the reading of relaxation data.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/Relax/relax-2.2.5/test_suite/unit_tests/relax_data_testing_base.py",
line 63, in test_read
sequence.read(file='Ap4Aase.Noe.600.bz2',
dir=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'relaxation_data',
res_num_col=1, res_name_col=2)
File "/usr/local/Relax/relax-2.2.5/generic_fns/sequence.py", line 339, in
read
for mol_name, res_num, res_name, spin_num, spin_name in
read_spin_data(file=file, dir=dir, file_data=file_data,
spin_id_col=spin_id_col, mol_name_col=mol_name_col,
res_num_col=res_num_col, res_name_col=res_name_col,
spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep,
spin_id=spin_id):
File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 533, in
read_spin_data
file_data = extract_data(file, dir)
File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 141, in extract_data
file = open_read_file(file_name=file, dir=dir)
File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 345, in
open_read_file
compress_type, file_path = determine_compression(file_path)
File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 112, in
determine_compression
raise RelaxFileError(file_path)
RelaxFileError: RelaxError: The file
'/usr/local/Relax/relax-2.2.5/test_suite/shared_data/relaxation_data/Ap4Aase.Noe.600.bz2'
does not exist.
----------------------------------------------------------------------
Ran 1253 tests in 10.734s
FAILED (errors=4)
That was for relax 2.2.5
This is the output for relax 4.0.2 It seemed to run and finish, but it gave
a bunch of errors that stated
(python:28738): IBUS-WARNING **: Create input context failed: Timeout was
reached.
This warning basically takes up the entire terminal. Followed by this
Ran 83 tests in 296.397s
OK
===============================
= Software verification tests =
===============================
..
----------------------------------------------------------------------
Ran 2 tests in 0.184s
OK
===================================
= Summary of the relax test suite =
===================================
Optional packages/modules
=========================
Tests skipped due to missing optional packages/modules/software:
------------------------------------------------------------------------------------------------------------------------
Module/package/software System test count Unit test
count GUI test count Verification test count
------------------------------------------------------------------------------------------------------------------------
Art Palmer's Modelfree4 software 2
0 0 0
Dasha model-free software 1
0 0 0
------------------------------------------------------------------------------------------------------------------------
Synopsis
========
System/functional tests
..................................................................... [ OK ]
Unit tests
..................................................................................
[ OK ]
GUI tests
...................................................................................
[ OK ]
Software verification tests
................................................................. [ OK ]
Synopsis
....................................................................................
[ OK ]
crowlab: [~/relax-4.0.2]>
On Fri, Sep 30, 2016 at 9:26 AM, Edward d'Auvergne <[email protected]>
wrote:
> On 30 September 2016 at 17:37, Mahdi, Sam <[email protected]>
> wrote:
> > Hi Edward,
> >
> > I also wanted to add, for running a multi-processor platform problem. I
> > installed openmpi from the fedora package list, not from the site
> itself. I
> > installed both openmpi, mpi4py, and the openmpi devel. I did not modify
> > anything. I can also successfully open relax using mpirun in a single
> > processor mode (as in I can load the module, and do mpirun relax and
> it'll
> > work). Do I actually have to do some modifications to openmpi for relax?
> The
> > other computer I was able to successfully run multi-processor on, already
> > had openmpi installed and set up, so I only downloaded mpi4py on that
> > computer. So I don't know what their setting or configuration was.
>
> Hi Sam,
>
> This sounds like a Fedora OpenMPI misconfiguration. I guess on the
> computer that you see no output with relax, you would also see no
> output with:
>
> [edward@localhost ~]$ mpirun -np 5 echo "hello"
> hello
> hello
> hello
> hello
> hello
> [edward@localhost ~]$
>
> In any case, this has nothing to do with relax. And without a local
> login to your computer, there is not much anyone can do about it. Do
> you have a system administrator there who can help you? Oh, another
> good and quick test is:
>
> [edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
> --multi="mpi4py" -v
> relax 4.0.2
> [edward@localhost ~]$
>
> You should only see a single version number printed. This tests both
> your OpenMPI configuration and the mpi4py Python package. If you do
> not see these exact same results, you have some configuration work in
> front of you ;)
>
> Regards,
>
> Edward
>
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