[ccp4bb] CCP4I2: non standard ssh port for remote jobs

[Michael Weyand]

Dear CCP4I2 experts,

I'm trying to submit remote jobs via SSH within CCP4i2. Unfortunately,
we use a non standard SSH port.
So far, I'm not able to add any option within the CCP4I2 interface. For
job submission, I need something to do like

'ssh -p X -Y . ccp4i-specific-command ...'.

Is there any chance to enter this '-p' SSH option within CCP4i2? I tried
already to define a "ssh command" via "Preferences".
But so far without any success.

I'm also wondering why there is a sshkey file option. If an user already
uses a ssh-key for a client/server connection, why is necessary to
re-input the key file again?
Any ssh between client and server should work from scratch ...

Any hints are highly appreciated,
Michael



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Re: [ccp4bb] CCP4I2: non standard ssh port for remote jobs

[Christian Becke]

Dear Michael,

I've been playing around a bit with remote job submission via SSH in 
CCP4 7.0. I remember I had to patch some files and upgraded a python lib 
to add support for ED25519 keys and to allow passing non-standard ports 
through the GUI. I never got around to wrap this up and forward it to 
the CCP4 devs. If you think this is useful (and I can port the patches 
to CCP4 7.1), I could have another look and wrap this up so I can share it.


All the best,

Christian

Am 08.06.20 um 18:39 schrieb Michael Weyand:

Dear CCP4I2 experts,

I'm trying to submit remote jobs via SSH within CCP4i2. Unfortunately,
we use a non standard SSH port.
So far, I'm not able to add any option within the CCP4I2 interface. For
job submission, I need something to do like

'ssh -p X -Y . ccp4i-specific-command ...'.

Is there any chance to enter this '-p' SSH option within CCP4i2? I tried
already to define a "ssh command" via "Preferences".
But so far without any success.

I'm also wondering why there is a sshkey file option. If an user already
uses a ssh-key for a client/server connection, why is necessary to
re-input the key file again?
Any ssh between client and server should work from scratch ...

Any hints are highly appreciated,
Michael



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Re: [ccp4bb] CCP4I2: non standard ssh port for remote jobs

[Eugene Osipov]

Hi, Michael,
as a workaround you could create a tunnel (or port forwarding) from your
machine to the ssh server and bind port 22 on the local machine to the
non-standard ssh port of the remote host.
the command will look like this:
$ *ssh -L 127.0.0.1:22:remote-ssh-server:remote-ssh-port
remote-username@remote-ssh-server -p remote-ssh-port -i private-key*
Of course, it will require root privileges to bind port 22 and the command
won't work if port 22 is already occupied by running ssh server.
After that, you could submit your jobs to localhost - it will forward them
to remote ssh server.
I think the same thing is doable under Windows using  plink or cygwin.

Best wishes,


пн, 8 июн. 2020 г. в 18:40, Michael Weyand :

> Dear CCP4I2 experts,
>
> I'm trying to submit remote jobs via SSH within CCP4i2. Unfortunately,
> we use a non standard SSH port.
> So far, I'm not able to add any option within the CCP4I2 interface. For
> job submission, I need something to do like
>
> 'ssh -p X -Y . ccp4i-specific-command ...'.
>
> Is there any chance to enter this '-p' SSH option within CCP4i2? I tried
> already to define a "ssh command" via "Preferences".
> But so far without any success.
>
> I'm also wondering why there is a sshkey file option. If an user already
> uses a ssh-key for a client/server connection, why is necessary to
> re-input the key file again?
> Any ssh between client and server should work from scratch ...
>
> Any hints are highly appreciated,
> Michael
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>


-- 
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O&N2



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Re: [ccp4bb] CCP4I2: non standard ssh port for remote jobs

[Stuart McNicholas]

Dear Michael,
   I think that the port number is hardwired in CCP4i2 on line 439 of
$CCP4/share/ccp4i2/core/CCP4JobServer.py

transport = paramiko.Transport((sP.machine, 22))

also there are various calls to the "paramiko" library which handles ssh,
which do not pass a port number and so default to 22.

This is all bad.

I have attached a replacement for this file. Could you try making a backup
of the above file and copying the attached file in its place.
I have put a constant for the port number in the line

PARAMIKO_PORT=22

near the top of the file. Then change this port number for what is suitable
for you.

If this works, then I will make the port number an option in the program.
If not, then I will try something else.


Best wishes,
Stuart McNicholas

On Mon, 8 Jun 2020 at 17:40, Michael Weyand 
wrote:

> Dear CCP4I2 experts,
>
> I'm trying to submit remote jobs via SSH within CCP4i2. Unfortunately,
> we use a non standard SSH port.
> So far, I'm not able to add any option within the CCP4I2 interface. For
> job submission, I need something to do like
>
> 'ssh -p X -Y . ccp4i-specific-command ...'.
>
> Is there any chance to enter this '-p' SSH option within CCP4i2? I tried
> already to define a "ssh command" via "Preferences".
> But so far without any success.
>
> I'm also wondering why there is a sshkey file option. If an user already
> uses a ssh-key for a client/server connection, why is necessary to
> re-input the key file again?
> Any ssh between client and server should work from scratch ...
>
> Any hints are highly appreciated,
> Michael
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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from __future__ import print_function


"""
 CCP4JobServer.py: CCP4 GUI Project
 Copyright (C) 2016 STFC

 This library is free software: you can redistribute it and/or
 modify it under the terms of the GNU Lesser General Public License
 version 3, modified in accordance with the provisions of the 
 license to address the requirements of UK law.
 
 You should have received a copy of the modified GNU Lesser General 
 Public License along with this library.  If not, copies may be 
 downloaded from http://www.ccp4.ac.uk/ccp4license.php
 
 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU Lesser General Public License for more details.
"""

"""
   Liz Potterton Apr 2016 - Separate 'remote' server code out from CCP4JobController
"""
import os
import re
from PyQt4 import QtCore
from core.CCP4ErrorHandling import *

PARAMIKO_PORT=22

class CServerParams:
SAVELIST = ['machine', 'username', 'ccp4Dir', 'tempDir', 'mechanism', 'keyFilename', 'serverProcessId',
'remotePath', 'validate', 'customCodeFile', 'queueOptionsFile', 'sge_root', 'serverGroup']

def __init__(self, **kw):
self.jobId = kw.get('jobId', None)
self.password = kw.get('password', None)
self.jobNumber = None
self.projectId = None
self.projectName = None
self.projectDirectory = None
# pollFinish flags: 0=no poll (eg ssh expecting a signal) 1=poll for FINISHED file 2=poll qsub
#   3=custom poll (started in current i2 session) 4 = custom poll (from previous i2 session)
self.pollFinish = 0
self.pollReport = 0
for item in CServerParams.SAVELIST:
setattr(self, item, kw.get(item, None))
self.serverProcessId = None

def __str__(self):
tx = ''
for item in CServerParams.SAVELIST + ['jobNumber', 'projectName', 'projectDirectory', 'pollFinish', 'pollReport']:
tx = tx + item + ': ' + str(getattr(self, item)) + '\n'
return tx

@property
def remote_finished_tarball(self):
return self.remotePath + 'finished.ccp4db.zip'

@property
def remote_report_file(self):
if self.mechanism in ['ssh_shared', 'qsub_local', 'qsub_shared']:
return None
else:
if self.remotePath is None:
return 'work/project/CCP4_JOBS/job_' + self.jobNumber + '/program.xml'
else:
 

Re: [ccp4bb] CCP4I2: non standard ssh port for remote jobs

[Martin Noble]

Dear all,

This is a very good idea for development: with many of us port-forwarding to 
access resources from home, the capacity to specify a non-standard port for ssh 
connections in i2 can in principle allow submission from a home laptop to a 
work-based server…very efficient !

Please keep me in the loop if this fix has worked, and i may end up using it 
myself.

With best wishes,

Martin

On 9 Jun 2020, at 09:17, Stuart McNicholas 
<19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk>
 wrote:

⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.
Dear Michael,
   I think that the port number is hardwired in CCP4i2 on line 439 of 
$CCP4/share/ccp4i2/core/CCP4JobServer.py

transport = paramiko.Transport((sP.machine, 22))

also there are various calls to the "paramiko" library which handles ssh, which 
do not pass a port number and so default to 22.

This is all bad.

I have attached a replacement for this file. Could you try making a backup of 
the above file and copying the attached file in its place.
I have put a constant for the port number in the line

PARAMIKO_PORT=22

near the top of the file. Then change this port number for what is suitable for 
you.

If this works, then I will make the port number an option in the program. If 
not, then I will try something else.


Best wishes,
Stuart McNicholas

On Mon, 8 Jun 2020 at 17:40, Michael Weyand 
mailto:michael.wey...@uni-bayreuth.de>> wrote:
Dear CCP4I2 experts,

I'm trying to submit remote jobs via SSH within CCP4i2. Unfortunately,
we use a non standard SSH port.
So far, I'm not able to add any option within the CCP4I2 interface. For
job submission, I need something to do like

'ssh -p X -Y . ccp4i-specific-command ...'.

Is there any chance to enter this '-p' SSH option within CCP4i2? I tried
already to define a "ssh command" via "Preferences".
But so far without any success.

I'm also wondering why there is a sshkey file option. If an user already
uses a ssh-key for a client/server connection, why is necessary to
re-input the key file again?
Any ssh between client and server should work from scratch ...

Any hints are highly appreciated,
Michael



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Re: [ccp4bb] CCP4I2: non standard ssh port for remote jobs

[Stuart McNicholas]

My idea seemingly hasn't worked for me. I'll keep trying.

On Tue, 9 Jun 2020 at 09:17, Stuart McNicholas 
wrote:

> Dear Michael,
>I think that the port number is hardwired in CCP4i2 on line 439 of
> $CCP4/share/ccp4i2/core/CCP4JobServer.py
>
> transport = paramiko.Transport((sP.machine, 22))
>
> also there are various calls to the "paramiko" library which handles ssh,
> which do not pass a port number and so default to 22.
>
> This is all bad.
>
> I have attached a replacement for this file. Could you try making a backup
> of the above file and copying the attached file in its place.
> I have put a constant for the port number in the line
>
> PARAMIKO_PORT=22
>
> near the top of the file. Then change this port number for what is
> suitable for you.
>
> If this works, then I will make the port number an option in the program.
> If not, then I will try something else.
>
>
> Best wishes,
> Stuart McNicholas
>
> On Mon, 8 Jun 2020 at 17:40, Michael Weyand <
> michael.wey...@uni-bayreuth.de> wrote:
>
>> Dear CCP4I2 experts,
>>
>> I'm trying to submit remote jobs via SSH within CCP4i2. Unfortunately,
>> we use a non standard SSH port.
>> So far, I'm not able to add any option within the CCP4I2 interface. For
>> job submission, I need something to do like
>>
>> 'ssh -p X -Y . ccp4i-specific-command ...'.
>>
>> Is there any chance to enter this '-p' SSH option within CCP4i2? I tried
>> already to define a "ssh command" via "Preferences".
>> But so far without any success.
>>
>> I'm also wondering why there is a sshkey file option. If an user already
>> uses a ssh-key for a client/server connection, why is necessary to
>> re-input the key file again?
>> Any ssh between client and server should work from scratch ...
>>
>> Any hints are highly appreciated,
>> Michael
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>>
>



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Re: [ccp4bb] CCP4I2: non standard ssh port for remote jobs

[Stuart McNicholas]

Apologies, it did work for me, I think. I just hadn't set my username.

On Tue, 9 Jun 2020 at 09:45, Stuart McNicholas 
wrote:

> My idea seemingly hasn't worked for me. I'll keep trying.
>
> On Tue, 9 Jun 2020 at 09:17, Stuart McNicholas <
> stuart.mcnicho...@york.ac.uk> wrote:
>
>> Dear Michael,
>>I think that the port number is hardwired in CCP4i2 on line 439 of
>> $CCP4/share/ccp4i2/core/CCP4JobServer.py
>>
>> transport = paramiko.Transport((sP.machine, 22))
>>
>> also there are various calls to the "paramiko" library which handles ssh,
>> which do not pass a port number and so default to 22.
>>
>> This is all bad.
>>
>> I have attached a replacement for this file. Could you try making a
>> backup of the above file and copying the attached file in its place.
>> I have put a constant for the port number in the line
>>
>> PARAMIKO_PORT=22
>>
>> near the top of the file. Then change this port number for what is
>> suitable for you.
>>
>> If this works, then I will make the port number an option in the program.
>> If not, then I will try something else.
>>
>>
>> Best wishes,
>> Stuart McNicholas
>>
>> On Mon, 8 Jun 2020 at 17:40, Michael Weyand <
>> michael.wey...@uni-bayreuth.de> wrote:
>>
>>> Dear CCP4I2 experts,
>>>
>>> I'm trying to submit remote jobs via SSH within CCP4i2. Unfortunately,
>>> we use a non standard SSH port.
>>> So far, I'm not able to add any option within the CCP4I2 interface. For
>>> job submission, I need something to do like
>>>
>>> 'ssh -p X -Y . ccp4i-specific-command ...'.
>>>
>>> Is there any chance to enter this '-p' SSH option within CCP4i2? I tried
>>> already to define a "ssh command" via "Preferences".
>>> But so far without any success.
>>>
>>> I'm also wondering why there is a sshkey file option. If an user already
>>> uses a ssh-key for a client/server connection, why is necessary to
>>> re-input the key file again?
>>> Any ssh between client and server should work from scratch ...
>>>
>>> Any hints are highly appreciated,
>>> Michael
>>>
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>>
>>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
>>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>>>
>>



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Re: [ccp4bb] CCP4I2: non standard ssh port for remote jobs

[Michael Weyand]

Dear Stuart,

yes, you are right. I also submitted successfully a first Phaser job to
our number cruncher.
Thanks a lot for this fast work around.

To ask for the SSH port setting within the final user/password window
would be extremely helpful to avoid a fixed port setting.
An egoistic dream on my side, but  I support several groups with
different SSH ports by ONE CCP4 installation ... ;-)

Kind regards and thanks again,
Michael


Am 09.06.20 um 10:49 schrieb Stuart McNicholas:
> Apologies, it did work for me, I think. I just hadn't set my username.
>
> On Tue, 9 Jun 2020 at 09:45, Stuart McNicholas
> mailto:stuart.mcnicho...@york.ac.uk>>
> wrote:
>
> My idea seemingly hasn't worked for me. I'll keep trying.
>
> On Tue, 9 Jun 2020 at 09:17, Stuart McNicholas
>  > wrote:
>
> Dear Michael,
>    I think that the port number is hardwired in CCP4i2 on
> line 439 of $CCP4/share/ccp4i2/core/CCP4JobServer.py
>
>         transport = paramiko.Transport((sP.machine, 22))
>
> also there are various calls to the "paramiko" library which
> handles ssh, which do not pass a port number and so default to 22.
>
> This is all bad.
>
> I have attached a replacement for this file. Could you try
> making a backup of the above file and copying the attached
> file in its place.
> I have put a constant for the port number in the line
>
> PARAMIKO_PORT=22
>
> near the top of the file. Then change this port number for
> what is suitable for you.
>
> If this works, then I will make the port number an option in
> the program. If not, then I will try something else.
>
>
> Best wishes,
> Stuart McNicholas
>
> On Mon, 8 Jun 2020 at 17:40, Michael Weyand
>  > wrote:
>
> Dear CCP4I2 experts,
>
> I'm trying to submit remote jobs via SSH within CCP4i2.
> Unfortunately,
> we use a non standard SSH port.
> So far, I'm not able to add any option within the CCP4I2
> interface. For
> job submission, I need something to do like
>
> 'ssh -p X -Y . ccp4i-specific-command ...'.
>
> Is there any chance to enter this '-p' SSH option within
> CCP4i2? I tried
> already to define a "ssh command" via "Preferences".
> But so far without any success.
>
> I'm also wondering why there is a sshkey file option. If
> an user already
> uses a ssh-key for a client/server connection, why is
> necessary to
> re-input the key file again?
> Any ssh between client and server should work from scratch ...
>
> Any hints are highly appreciated,
> Michael
>
> 
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
> This message was issued to members of
> www.jiscmail.ac.uk/CCP4BB
> , a mailing list hosted
> by www.jiscmail.ac.uk , terms &
> conditions are available at
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>




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Re: [ccp4bb] [EXTERNAL] [ccp4bb] CCP4I2: non standard ssh port for remote jobs

[Edward Berry]

>>> Michael Weyand  06/08/20 12:40 PM >>>
Dear CCP4I2 experts,

I'm trying to submit remote jobs via SSH within CCP4i2. Unfortunately,
we use a non standard SSH port.
So far, I'm not able to add any option within the CCP4I2 interface. For
job submission, I need something to do like

'ssh -p X -Y . ccp4i-specific-command ...'.

Is there any chance to enter this '-p' SSH option within CCP4i2? I tried
already to define a "ssh command" via "Preferences".
But so far without any success.
==
Not sure if this is applicable, but you can set an alias name
to be equivalent to a real host with a non-standard port.
Something like: 

in ~/.ssh/config or /etc/ssh/ssh_config:


Host oswego
   hostname sanpablo

   hostkeyalias "[sanpablo]:8123"

   port 8123



"hostkeyalias" refers to one key in ~/.ssh/known_hosts that looks like:
[sanpablo]:8101,[192.168.2.4]:8123 ecdsa-sha2-nist
I'm not sure if I entered that or it was made the first time I logged in and 
said "yes".

So I or a program I'm running can issue "ssh oswego" and get connected to port 
8123 on sanpablo without needing to enter a password.

I'm also wondering why there is a sshkey file option. If an user already
uses a ssh-key for a client/server connection, why is necessary to
re-input the key file again?
Any ssh between client and server should work from scratch ...

Any hints are highly appreciated,
Michael



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