mailRe: Using multi-processor for model_free


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Posted by Mahdi, Sam on September 30, 2016 - 19:04:
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 <edward@xxxxxxxxxxxxx>
wrote:


On 30 September 2016 at 17:37, Mahdi, Sam <sam.mahdi.846@xxxxxxxxxxx>
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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