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.846@xxxxxxxxxxx>
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@xxxxxxx
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
Re: Using multi-processor for model_free