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 > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users