"a bites-like object is required, not 'str'" error

[jjuarez84]

Hi James,

I am having problems to run the quick-start examples for amber and gromacs (have not tested the rest). I keep getting this rather cryptic error: a bytes-like object is required, not 'str'

I am pasting the whole log file after executing this command in mypath/longbow-examples/quick_start/gromacs:
longbow --hosts mypath/hosts.conf mdrun_mpi -deffnm example

2017-10-31 17:52:56 - Welcome to Longbow!
2017-10-31 17:52:56 - This software was developed as part of the EPSRC-funded HECBioSim project (http://www.hecbiosim.ac.uk/)
2017-10-31 17:52:56 - HECBioSim facilitates high-end biomolecular simulation on resources such as ARCHER
2017-10-31 17:52:56 - Longbow is Copyright (C) of Science and Technology Facilities Council and The University of Nottingham.
2017-10-31 17:52:56 - Longbow was created by Dr James T. Gebbie-Rayet, Dr Gareth B. Shannon and Prof Charles A. Laughton.
2017-10-31 17:52:56 - Please cite our paper: Gebbie-Rayet, J, Shannon, G, Loeffler, H H and Laughton, C A 2016 Longbow: A Lightweight Remote Job Submission Tool. Journal of Open Research Software, 4: e1, DOI: http://dx.doi.org/10.5334/jors.95
2017-10-31 17:52:56 - Python version: 3.6
2017-10-31 17:52:56 - Longbow version: 1.5.0
2017-10-31 17:52:56 - Longbow Commandline: --hosts mypath/hosts.conf mdrun_mpi -deffnm example
2017-10-31 17:52:56 - hosts file is: 'mypath/hosts.conf'
2017-10-31 17:52:56 - Initialisation complete.
2017-10-31 17:52:56 - Loading configuration information from file 'mypath/hosts.conf'
2017-10-31 17:52:56 - Performing basic connection and environment tests for all machines referenced in jobs.
2017-10-31 17:53:03 - Test connection to 'remotehost' - passed
2017-10-31 17:53:06 - a bytes-like object is required, not 'str'
2017-10-31 17:53:06 - Good bye from Longbow!
2017-10-31 17:53:06 - Check out http://www.hecbiosim.ac.uk/ for other powerful biomolecular simulation software tools.

I downloaded Longbow v1.5.0 via pip and I am currently using python3.6.2

Many thanks!

Jordi

[jimboid]

Hi Jordi,

Yes that looks like a bug, it is unclear if this is related to python 3.6 due to the rather cryptic error message. Could you rerun the offending run with the debug command-line flag set:

longbow --debug --hosts mypath/hosts.conf mdrun_mpi -deffnm example

That should generate the full python traceback for the error, then could you paste it back here and I will then try and reproduce the error to fix it. Thanks for reporting this.

[jjuarez84]

Hi James,

From the traceback it seems that the issue is related with module not being installed in the computer I am using to run the tests.

Here is the full traceback
2017-11-01 10:33:42 - INFO - longbow - Welcome to Longbow!
2017-11-01 10:33:42 - INFO - longbow - This software was developed as part of the EPSRC-funded HECBioSim project (http://www.hecbiosim.ac.uk/)
2017-11-01 10:33:42 - INFO - longbow - HECBioSim facilitates high-end biomolecular simulation on resources such as ARCHER
2017-11-01 10:33:42 - INFO - longbow - Longbow is Copyright (C) of Science and Technology Facilities Council and The University of Nottingham.
2017-11-01 10:33:42 - INFO - longbow - Longbow was created by Dr James T. Gebbie-Rayet, Dr Gareth B. Shannon and Prof Charles A. Laughton.
2017-11-01 10:33:42 - INFO - longbow - Please cite our paper: Gebbie-Rayet, J, Shannon, G, Loeffler, H H and Laughton, C A 2016 Longbow: A Lightweight Remote Job Submission Tool. Journal of Open Research Software, 4: e1, DOI: http://dx.doi.org/10.5334/jors.95
2017-11-01 10:33:42 - INFO - longbow - Python version: 3.6
2017-11-01 10:33:42 - INFO - longbow - Longbow version: 1.5.0
2017-11-01 10:33:42 - INFO - longbow - Longbow Commandline: --debug --hosts mypaht/hosts.conf mdrun_mpi -deffnm example
2017-11-01 10:33:42 - INFO - longbow - hosts file is: 'mypath/hosts.conf'
2017-11-01 10:33:42 - INFO - longbow - Initialisation complete.
2017-11-01 10:33:42 - INFO - longbow.corelibs.configuration - Loading configuration information from file 'mypath/hosts.conf'
2017-11-01 10:33:42 - DEBUG - longbow.corelibs.configuration - Job 'LongbowJob' will be run in the 'remotepath/LongbowJob50515' directory on the remote resource.
2017-11-01 10:33:42 - INFO - longbow.corelibs.shellwrappers - Performing basic connection and environment tests for all machines referenced in jobs.
2017-11-01 10:33:42 - DEBUG - longbow.corelibs.shellwrappers - Testing connection to 'remotehost'
2017-11-01 10:33:42 - DEBUG - longbow.corelibs.shellwrappers - Sending the following to subprocess '['ssh', '-p 22', 'username@cluster.ed.ac.uk', 'ls']'
username@cluster.ed.ac.uk's password:
2017-11-01 10:33:49 - INFO - longbow.corelibs.shellwrappers - Test connection to 'cluster' - passed
2017-11-01 10:33:49 - DEBUG - longbow.corelibs.shellwrappers - Sending the following to subprocess '['ssh', '-p 22', 'username@cluster.ed.ac.uk', 'module avail']'
username@cluster.ed.ac.uk's password:
2017-11-01 10:33:55 - ERROR - longbow - a bytes-like object is required, not 'str'
Traceback (most recent call last):
File "mypath/miniconda3/lib/python3.6/site-packages/longbow/corelibs/shellwrappers.py", line 151, in checkconnections
sendtossh(jobs[item], ["module avail"])
File "mypath/miniconda3/lib/python3.6/site-packages/longbow/corelibs/shellwrappers.py", line 271, in sendtossh
"to be sure there are no connection issues.", shellout)
longbow.corelibs.exceptions.SSHError: SSH failed, make sure a normal terminal can connect to SSH to be sure there are no connection issues.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "mypath/miniconda3/lib/python3.6/site-packages/longbow/corelibs/entrypoints.py", line 224, in launcher
longbow(parameters)
File "mypath/miniconda3/lib/python3.6/site-packages/longbow/corelibs/entrypoints.py", line 269, in longbow
shellwrappers.checkconnections(jobs)
File "mypath/miniconda3/lib/python3.6/site-packages/longbow/corelibs/shellwrappers.py", line 159, in checkconnections
"bash: module: command not found" in err.stderr):
TypeError: a bytes-like object is required, not 'str'
2017-11-01 10:33:55 - INFO - longbow - Good bye from Longbow!
2017-11-01 10:33:55 - INFO - longbow - Check out http://www.hecbiosim.ac.uk/ for other powerful biomolecular simulation software tools.

[jimboid]

That looks like the bash command module is missing. Is this a machine that does not use linux modules? So if you ssh'd in and ran module avail, does this work?

Either way, there is still a bug here because it should have told you that there is an error with the modules and not that weird error about byte-like objects.

[jjuarez84]

Yes, this is a machine that does not use linux modules.

[jimboid]

I've seen this before on a number of smaller cluster type machines that are managed by the research group themselves. So what is happening is Longbow is trying to load up the linux module if the executable is not an absolute path (this poses problems when users add it to their bashrc, I have yet to find a robust workaround for that!).

If you specify the mdrun_mpi as an absolute path like this:

longbow --hosts mypath/hosts.conf /absolute/path/to/mdrun_mpi -deffnm example

Then it should disable the module load, and hopefully this should resolve the underlying issue with the modules, although I will still fix that error message so that it gives the proper one to the user.

[jjuarez84]

The call to module is still triggered. Note that the call to gromacs executable is 5.X style andmaybe that is an issue?

/absolute/path/to/gmx_mpi mdrun -deffnm example

[jimboid]

Actually, I just realised. This is related to a different part of the code, I misread the traceback. This is relating to the environment fix I implemented for those other small cluster machines I mentioned.

So on those machines, they were still using linux modules but the environment in /etc/profile was not loaded when using a non-login shell (which python subprocess doesn't). So I have a check that does this "module avail" and then sources the /etc/profile if this fails. This fixed a problem that was found at 5/6 different universities.

In your case, your machine is simply not using the linux module system, it also looks like the output of that check is somehow not decoded from bytes. This is definitely a bug in Longbow, I've just complete your slurm-gres request so will look at this now.

[jimboid]

Hi Jordi,

So I think I have found the offending code that caused the weird error message in the first place. Are you comfortable with testing out development copies of Longbow?

If you go here https://github.com/HECBioSim/Longbow/tree/release-prep this is the release-prep branch for v1.5.1. If you download the zip file by clicking the "clone or download" button on the right, then unpack the zip. Then uninstall the old Longbow using "pip uninstall longbow" then change into the newly downloaded directory and do "pip install . --user" or without the --user if that is how you normally do it.

Doing longbow --version should show v1.5.1-dev

This version should contain this fix, and also the slurm-gres from the other ticket (instructions on how to use it are in that ticket, I'll need to document it still).

Hopefully this should let you get past the issue you are having here, I'm not sure yet if you can get away with doing:

longbow --hosts mypath/hosts.conf mdrun_mpi -deffnm example

you might still need to do the absolute path to the executable:

longbow --hosts mypath/hosts.conf /absolute/path/to/mdrun_mpi -deffnm example

If this works, we could look at trying to come up with a smarter solution for disabling modules than having to specify the path, although this is only generally an issue on a small number of machines.

[jjuarez84]

Ok, I am little bit confused.

I donwloaded the development version and run longbow and the error has disapeared, however, it does not look as it is actually working. This is the tracebak I get using this command.

longbow --verbose --hosts /mypath/hosts.conf /mypath/mdrun_mpi -s example.tpr -deffnm output

2017-11-07 10:42:08 - This software was developed as part of the EPSRC-funded HECBioSim project (http://www.hecbiosim.ac.uk/)
2017-11-07 10:42:08 - HECBioSim facilitates high-end biomolecular simulation on resources such as ARCHER
2017-11-07 10:42:08 - Longbow is Copyright (C) of Science and Technology Facilities Council and The University of Nottingham.
2017-11-07 10:42:08 - Longbow was created by Dr James T. Gebbie-Rayet, Dr Gareth B. Shannon and Prof Charles A. Laughton.
2017-11-07 10:42:08 - Please cite our paper: Gebbie-Rayet, J, Shannon, G, Loeffler, H H and Laughton, C A 2016 Longbow: A Lightweight Remote Job Submission Tool. Journal of Open Research Software, 4: e1, DOI: http://dx.doi.org/10.5334/jors.95
2017-11-07 10:42:08 - Python version: 3.6
2017-11-07 10:42:08 - Longbow version: 1.5.1-dev
2017-11-07 10:42:08 - Longbow Commandline: --verbose --hosts ./mypathhosts.conf /mypath/mdrun_mpi -s example.tpr -deffnm output
2017-11-07 10:42:08 - hosts file is: '/mypath/hosts.conf'
2017-11-07 10:42:08 - Initialisation complete.
2017-11-07 10:42:08 - Loading configuration information from file '/mypath/hosts.conf'
2017-11-07 10:42:08 - Performing basic connection and environment tests for all machines referenced in jobs.
2017-11-07 10:42:12 - Test connection to 'remotehost' - passed
2017-11-07 10:42:15 - The environment on host 'remotehost' is 'SLURM'
2017-11-07 10:42:15 - The handler on host 'remotehost' is 'mpirun'
2017-11-07 10:42:15 - Testing the executables defined for each job.
2017-11-07 10:42:15 - Checking executable '/mypath/mdrun_mpi' on 'remotehost'
2017-11-07 10:42:19 - Executable check - passed.
2017-11-07 10:42:19 - Processing job/s and detecting files that require upload.
2017-11-07 10:42:19 - '/mypath/mdrun_mpi'
2017-11-07 10:42:19 - Good bye from Longbow!
2017-11-07 10:42:19 - Check out http://www.hecbiosim.ac.uk/ for other powerful biomolecular simulation software tools.

But nothing appears in the remote host queue nor any files are transferred. What am I doing wrong?
Thanks

[jimboid]

Hi,

Can you change the --verbose for --debug please. There is still a problem here, a full debug traceback should give me some more information to see what is failing.

[jimboid]

But nothing appears in the remote host queue nor any files are transferred. What am I doing wrong?

You are not doing anything wrong, I think you have just found some bugs in our code which we don't see getting triggered on most HPC machines. I'm grateful that you have reported them so that these can be fixed and new unit tests written to help prevent them re-occurring.