Hi Edward,
So I ran the the mpirun commands you suggested. The echo world works fine.
I get the same results you did. For the relax one, this is the output I
recieved
[~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax 4.0.2
Usage: relax [options] [script_file]
RelaxError: incorrect number of arguments
Usage: relax [options] [script_file]
Usage: relax [options] [script_file]
RelaxError: incorrect number of arguments
RelaxError: incorrect number of arguments
Usage: relax [options] [script_file]
RelaxError: incorrect number of arguments
Usage: relax [options] [script_file]
RelaxError: incorrect number of arguments
I know sometimes its 2 hyphens instead of one. So I added an extra one for
the -v and obtained this output
crowlab: [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" --v relax
4.0.2
Usage: relax [options] [script_file]
RelaxError: ambiguous option: --v (--verification-tests, --version?)
Usage: relax [options] [script_file]
RelaxError: ambiguous option: --v (--verification-tests, --version?)
Usage: relax [options] [script_file]
RelaxError: ambiguous option: --v (--verification-tests, --version?)
Usage: relax [options] [script_file]
RelaxError: ambiguous option: --v (--verification-tests, --version?)
Usage: relax [options] [script_file]
RelaxError: ambiguous option: --v (--verification-tests, --version?)
crowlab: [~/relax-4.0.2]>
Also, the reason its ./relax is because I have relax 2.2.5 installed, and I
have that set up as an Alias, so if I just type relax, it'll open up relax
2.2.5. So I went to the actual relax-4.0.2. directory instead of indicating
its path and just typed ./relax. (By I, I mean the administrator of this
computer, I do not have root access to this computer).
Sincerely,
Sam
On Fri, Sep 30, 2016 at 10:03 AM, Mahdi, Sam <sam.mahdi....@my.csun.edu>
wrote:
> 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 <edw...@nmr-relax.com>
> wrote:
>
>> On 30 September 2016 at 17:37, Mahdi, Sam <sam.mahdi....@my.csun.edu>
>> 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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