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 >> > > _______________________________________________ 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