Hi Troels,
I just created another bug report. I simply copy pasted the email, and
uploaded the script files there.
Sincerely,
Sam
On Mon, Sep 12, 2016 at 5:14 AM, Troels Emtekær Linnet <
tlin...@nmr-relax.com> wrote:
> Hi Sam.
>
> Can you produce another bug report.
>
> Please don't attach files to these mails as it will strain the
> mailinglists.
>
> Cheers
> Troels
>
>
> Den lørdag den 10. september 2016 skrev Mahdi, Sam <
> sam.mahdi....@my.csun.edu>:
>
>> Hi Troels,
>>
>> Additional question that I had, if you could also look into this as well
>> on Tuesday please. I have decided to try to write a script to automate this
>> whole process (since I won't be using the gui to do model free), and I've
>> come across a problem. I can successfully open up relax using openmpi, and
>> can load the pdb file, and assign all the spins and isotopes; however, it
>> appears it will only load one data file (the very first one I'll have
>> inputed in the script). I don't know if there is a problem with how I wrote
>> my script. Not only will it not load the rest of my data sets, it won't
>> actually run dAuvergne's protocol either, it'll just load the data set and
>> exit out of the program. Attached is the script I wrote for relax.
>>
>> This is the output once relax has loaded
>>
>> script = 'model_free_sample_script.py'
>> ------------------------------------------------------------
>> ----------------------------------------
>> from time import asctime, localtime
>> from auto_analyses.dauvergne_protocol import dAuvergne_protocol
>> DIFF_MODEL=['local_tm','sphere','prolate','oblate','ellipsoid','final']
>> MF_MODELS=['m0','m1','m2','m3','m4','m5','m6','m7','m8','m9']
>> LOCAL_TM_MODELS=['tm0','tm1','tm2','tm3','tm4','tm5','tm6','
>> tm7','tm7','tm8','tm9']
>> GRID_INC=11
>> MIN_ALGOR='newton'
>> MC_NUM=500
>> CONV_LOOP=True
>> pipe_bundle="mf(%s)"%asctime(localtime())
>> name="origin-"+pipe_bundle
>> pipe.create(name,'mf',bundle=pipe_bundle)
>> structure.read_pdb('2d9j.pdb',set_mol_name='hRGS7')
>> structure.load_spins('@N',ave_pos=True)
>> structure.load_spins('@NE1',ave_pos=True)
>> structure.load_spins('@H',ave_pos=True)
>> structure.load_spins('@HE1',ave_pos=True)
>> spin.isotope('15N',spin_id='@N*')
>> spin.isotope('1H',spin_id='@H*')
>> relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
>> file='R1_Agnes',res_num_col=1,data_col=2,error_col=3)
>> relax_data.read(ri_id='R2_Agnes',ri_type='R2',frq=599.642*1e6,
>> file='R2_Agnes',res_num_col=1,data_col=2,error_col=3)
>> relax_data.read(ri_id='ssNOE_Agnes',ri_type='NOE',frq=599.642*1e6,
>> file='ssNOE_Agnes',res_num_col=1,data_col=2,error_col=3)
>> relax_data.read(ri_id='R1_NMRFAM',ri_type='R1',frq=799.642*1e6,
>> file='R1_NMRFAM',res_num_col=1,data_col=2,error_col=3)
>> relax_data.read(ri_id='R2_NMRFAM',ri_type='R2',frq=799.642*1e6,
>> file='R2_NMRFAM',res_num_col=1,data_col=2,error_col=3)
>> relax_data.read(ri_id='ssNOE_NMRFAM',ri_type='NOE',frq=799.642*1e6,
>> file='ssNOE_NMRFAM',res_num_col=1,data_col=2,error_col=3)
>> interatom.define(spin_id1='@N',spin_id2='@H', direct_bond=True)
>> interatom.define(spin_id1='@NE1',spin_id2='@HE1', direct_bond=True)
>> interatom.set_dist(spin_id1='@N*',spin_id2='@H*',ave_dist=1.02*1e-10)
>> interatom.unit_vectors()
>> value.set(-172*1e-6,'csa',spin_id='@N*')
>> dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,di
>> ff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=
>> LOCAL_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_
>> sim_num=MC_NUM,conv_loop=CONV_LOOP)
>>
>> So it indicates that my script has loaded. However, after it loads the
>> spins from the pdb file, this is what happens after my first data set has
>> been loaded:
>>
>> relax> relax_data.read(ri_id='R1_Agnes', ri_type='R1', frq=599642000.0,
>> file='R1_Agnes', dir=None, spin_id_col=None, mol_name_col=None,
>> res_num_col=1, res_name_col=None, spin_num_col=None, spin_name_col=None,
>> data_col=2, error_col=3, sep=None, spin_id=None)
>> Opening the file 'R1_Agnes' for reading.
>> RelaxWarning: The sequence data in the line ['Residue', 'R1', 'Error'] is
>> invalid, the residue number data 'Residue' is invalid.
>> RelaxWarning: The sequence data in the line ['1'] is invalid, the data is
>> missing.
>> RelaxWarning: The sequence data in the line ['2'] is invalid, the data is
>> missing.
>> RelaxWarning: The sequence data in the line ['3'] is invalid, the data is
>> missing.
>> RelaxWarning: The sequence data in the line ['4'] is invalid, the data is
>> missing.
>> RelaxWarning: The sequence data in the line ['5'] is invalid, the data is
>> missing.
>> RelaxWarning: The sequence data in the line ['6'] is invalid, the data is
>> missing.
>> RelaxWarning: The sequence data in the line ['7'] is invalid, the data is
>> missing.
>> RelaxWarning: The sequence data in the line ['8'] is invalid, the data is
>> missing.
>> RelaxWarning: The sequence data in the line ['9'] is invalid, the data is
>> missing.
>> RelaxWarning: The sequence data in the line ['10'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['11'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['16'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['17'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['18'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['21'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['22'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['23'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['26'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['27'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['28'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['31'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['40'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['46'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['58'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['61'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['62'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['63'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['73'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['76'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['79'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['81'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['82'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['85'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['94'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['97'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['99'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['106'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['115'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['121'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['126'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['127'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['134'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['135'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['136'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['137'] is invalid, the data
>> is missing.
>> RelaxWarning: The sequence data in the line ['139'] is invalid, the data
>> is missing.
>>
>> RelaxError: The spin ID '#hRGS7:12' corresponds to multiple spins,
>> including '#hRGS7:12@N' and '#hRGS7:12@H'.
>> crowlab: [~/relax-4.0.2]>
>>
>> As you can see, I have all 6 data sets set to load, but only the very
>> first one appears to do so, and after it loads, it just exits out of relax.
>> Again, I don't know if this is a problem with how I wrote the script. The
>> Relax_script1 is the one that I load up to run the whole thing. The model
>> free script.py is just the script it reads once relax has opened up.
>> Again, I can see all the spins are properly loaded, and the isotopes are
>> set. It just everything after the first data set that doesn't load. Thanks
>> again in advance.
>>
>> Sincerely,
>> Sam
>>
>> On Thu, Sep 8, 2016 at 10:15 AM, Mahdi, Sam <sam.mahdi....@my.csun.edu>
>> wrote:
>>
>>> Hi Troels,
>>>
>>> Thank you so much. If there is any extra info you need please let me
>>> know.
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Thu, Sep 8, 2016 at 9:12 AM, Troels Emtekær Linnet <
>>> tlin...@nmr-relax.com> wrote:
>>>
>>>> Hi Sam.
>>>>
>>>> I will have some time on Tuesday, and then I will look at it.
>>>>
>>>> Best
>>>> Troels
>>>>
>>>>
>>>> Den onsdag den 7. september 2016 skrev Mahdi, Sam <
>>>> sam.mahdi....@my.csun.edu>:
>>>>
>>>>> Hello Troels,
>>>>>
>>>>> I uploaded all the files, and even added in the entire output that i
>>>>> recieved using model free in script mode. I didn't know if all the files
>>>>> uploaded need to have that link, so only the initial files that were
>>>>> uploaded it, have it.
>>>>> Thank you in advance for your help!
>>>>> Sincerely,
>>>>> Sam
>>>>>
>>>>> On Wed, Sep 7, 2016 at 12:41 AM, Troels Emtekær Linnet <
>>>>> tlin...@nmr-relax.com> wrote:
>>>>>
>>>>>> Hi Sam.
>>>>>>
>>>>>> You should be able to upload more files after the initial upload.
>>>>>> In the comment thread, please also make a link to this discussion.
>>>>>>
>>>>>> https://mail.gna.org/public/relax-users/2016-09/threads.html#00001
>>>>>>
>>>>>> Best
>>>>>> Troels
>>>>>>
>>>>>>
>>>>>>
>>>>>> 2016-09-06 19:10 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>>>>>>
>>>>>>> Thank you for your reply. When I come to upload my data though, I
>>>>>>> see there are only 4 available slots I can upload my data. I have a
>>>>>>> total
>>>>>>> of 6 data files however, that need to be uploaded (3 of each
>>>>>>> frequency). I
>>>>>>> also need to upload the relax -i of 2 different computers, and the
>>>>>>> script
>>>>>>> file I've been using for a total of 9 files that need to be uploaded. Is
>>>>>>> there a way to increase the amount I can upload, or can I upload more
>>>>>>> after
>>>>>>> the initial submission?
>>>>>>>
>>>>>>> On Mon, Sep 5, 2016 at 2:46 AM, Troels Emtekær Linnet <
>>>>>>> tlin...@nmr-relax.com> wrote:
>>>>>>>
>>>>>>>> Hi Sam.
>>>>>>>>
>>>>>>>> To solve this problem, it would be easier to have access to some of
>>>>>>>> your data.
>>>>>>>> Can you upload to: https://gna.org/bugs/?group=relax
>>>>>>>>
>>>>>>>> Take each of your data files, and delete all data, except 2 spins.
>>>>>>>> Also provide your script file, or a description of which button you
>>>>>>>> press in the GUI.
>>>>>>>>
>>>>>>>> Please also provide information about your system with:
>>>>>>>> relax -i
>>>>>>>>
>>>>>>>> Then I will make a tutorial for you. To be added here:
>>>>>>>> http://wiki.nmr-relax.com/Category:Tutorials
>>>>>>>>
>>>>>>>> If there is a problem in relax, I will write a systemtest which
>>>>>>>> will solve the problem.
>>>>>>>> And the problem will never return.
>>>>>>>>
>>>>>>>> If this a user error, the tutorial should help to prevent this, and
>>>>>>>> would be the first step before
>>>>>>>> adding/modifying the manual.
>>>>>>>>
>>>>>>>> Regarding using mpirun.
>>>>>>>> Have a look at this page. Maybe it helps.
>>>>>>>> http://wiki.nmr-relax.com/OpenMPI
>>>>>>>>
>>>>>>>>
>>>>>>>> Cheers.
>>>>>>>>
>>>>>>>>
>>>>>>>> 2016-09-03 4:13 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>>>>>>>>
>>>>>>>>> Hello everyone,
>>>>>>>>>
>>>>>>>>> So I was able to set up and run the dauvergne_protocol
>>>>>>>>> successfully by
>>>>>>>>> using the script in the wiki. The problem I have come across now
>>>>>>>>> is the
>>>>>>>>> program doesn't seem to read my data. Using the gui interface I
>>>>>>>>> was able to
>>>>>>>>> successfully load my data and run it. When I upload my data using
>>>>>>>>> the
>>>>>>>>> script command:
>>>>>>>>> relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
>>>>>>>>> file='R1_Agnes',res_num_col=1,data_col=2,error_col=3)
>>>>>>>>>
>>>>>>>>> The output file simply gives errors for amino acids I don't have
>>>>>>>>> data for:
>>>>>>>>> RelaxWarning: The sequence data in the line ['1'] is invalid, the
>>>>>>>>> data is
>>>>>>>>> missing.
>>>>>>>>>
>>>>>>>>> This is fine as relax just ignores these values and continues its
>>>>>>>>> calculations. I only receive this warning for values I don't have
>>>>>>>>> data for.
>>>>>>>>> This is the same thing I got when using the gui interface (the gui
>>>>>>>>> however
>>>>>>>>> showed my values that I have data for and the residue it
>>>>>>>>> corresponds to,
>>>>>>>>> using the script I don't receive such an output, I don't know
>>>>>>>>> whether this
>>>>>>>>> is normal or not). However, since I don't get this warning for
>>>>>>>>> every amino
>>>>>>>>> acid, I assume this means it has read the values for the other
>>>>>>>>> amino acids.
>>>>>>>>> All of my data is the same, relax warnings only pop up for amino
>>>>>>>>> acids that
>>>>>>>>> I don't have data for. The problem is, when I enter the dAuvergne
>>>>>>>>> protocol,
>>>>>>>>> I get the protocol working, it starts running local_tm however it
>>>>>>>>> appears
>>>>>>>>> none of my data has been uploaded:
>>>>>>>>> RelaxWarning: The spin '#hRGS7:2@N' has been deselected because
>>>>>>>>> of missing
>>>>>>>>> relaxation data
>>>>>>>>> RelaxWarning: The spin '#hRGS7:3@N' has been deselected because
>>>>>>>>> of missing
>>>>>>>>> relaxation data
>>>>>>>>>
>>>>>>>>> And I get that warning for every single amino acid. From the
>>>>>>>>> output, it
>>>>>>>>> appears to have read the file since it knows exactly which amino
>>>>>>>>> acids I
>>>>>>>>> don't have data for, but I don't know why when it comes to running
>>>>>>>>> the
>>>>>>>>> protocol, it tells me I havn't inputed any data. I have typed
>>>>>>>>> everything
>>>>>>>>> directly according to the script from the wiki. From running the
>>>>>>>>> protoco,
>>>>>>>>> it appears everything has properly been uploaded, structure data,
>>>>>>>>> magnetic
>>>>>>>>> dipole interactions, csa, the data pipe, the analysis variables,
>>>>>>>>> the python
>>>>>>>>> module imports, and setting up the spins from the pdb file. It
>>>>>>>>> appears the
>>>>>>>>> only error is from loading the actual relaxation data.
>>>>>>>>>
>>>>>>>>> On a completely unrelated side note, I have been attempting to run
>>>>>>>>> relax on
>>>>>>>>> multiple processors. I have tried 2 different computers, both
>>>>>>>>> fedora linux.
>>>>>>>>> I have mpi4py and openmpi downloaded on both. On one, I can get
>>>>>>>>> relax on
>>>>>>>>> multiple cores working (havn't been able to successfully run it
>>>>>>>>> due to
>>>>>>>>> being unable to upload any data properly). On the other however, I
>>>>>>>>> type in
>>>>>>>>> the mpirun -np --multi='mpi4py' script, but I get no output. I can
>>>>>>>>> see that
>>>>>>>>> it's running in the background (top command), but nothing pops up,
>>>>>>>>> no text
>>>>>>>>> command, nothing. I typed the same mpirun with the --gui, but that
>>>>>>>>> opened
>>>>>>>>> up nothing. On a uni-processor (typing in the exact same command
>>>>>>>>> without
>>>>>>>>> indicating how many cores i.e. no -np --multi='mpi4py') it works
>>>>>>>>> just fine,
>>>>>>>>> so I don't think its my openmpi that's an issue. I don't know
>>>>>>>>> whether this
>>>>>>>>> is an issue with my mpi4py or a personal computer issue (since on
>>>>>>>>> the other
>>>>>>>>> computer relax runs just fine on multiple cores).
>>>>>>>>>
>>>>>>>>> Sincerely,
>>>>>>>>> Sam
>>>>>>>>>
>>>>>>>>> P.S. when I do enter the top command to see what's running. My
>>>>>>>>> master shows
>>>>>>>>> mpirun, and the 3 slaves display python when I put -np 4, so I know
>>>>>>>>> something is running in the background. I have 8 cores.
>>>>>>>>>
>>>>>>>>> On Wed, Aug 31, 2016 at 6:49 PM, Mahdi, Sam <
>>>>>>>>> sam.mahdi....@my.csun.edu>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> > Hello everyone,
>>>>>>>>> >
>>>>>>>>> > I am attempting to run relax on a multi-processor mode. I have
>>>>>>>>> been able
>>>>>>>>> > to successfully set-up relax to operate in a multi-processor
>>>>>>>>> mode by using
>>>>>>>>> > the mpirun -np #ofprocessors /location/of/relax --multi='mpi4py'
>>>>>>>>> >
>>>>>>>>> > The problem I encounter is when using the --tee log
>>>>>>>>> dauvergne_protocol.py
>>>>>>>>> > command. I receive this error
>>>>>>>>> > RelaxError: the script file 'dauvergne_protocol.py' does not
>>>>>>>>> exist
>>>>>>>>> >
>>>>>>>>> > I located the script file and tried to direct to it's path
>>>>>>>>> > mpirun /usr/local/Relax/relax-2.2.5/relax --multi='mpi4py'
>>>>>>>>> --tee log
>>>>>>>>> > /usr/local/Relax/relax-2.2.5/auto-analyses/dauvergne_protocol.py
>>>>>>>>> >
>>>>>>>>> > But i received this error
>>>>>>>>> > RelaxError: the script file '/usr/local/Relax/relax-2.2.5/
>>>>>>>>> > auto-analyses/dauvergne_protocol.py' does not exist.
>>>>>>>>> >
>>>>>>>>> > Even though I have the script, it doesn't seem to be able to
>>>>>>>>> locate it.
>>>>>>>>> >
>>>>>>>>> > On a side note, in the manual, one dash doesn't actually run the
>>>>>>>>> command.
>>>>>>>>> > I.e. in the manual it displays -multi='mpi4py' . What it should
>>>>>>>>> be is
>>>>>>>>> > --multi='mpi4py' . The same goes for -tee. It should be --tee.
>>>>>>>>> >
>>>>>>>>> > Sincerely,
>>>>>>>>> > Sam
>>>>>>>>> >
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>
>>
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