Sounds like you need to look at how you installed it.

I did so with this command:
./steam -command update -game ship -dir theship

Thus, I have folders like such:
./theship/bin
./theship/ship/bin

The engine_i686.so file resides in theship/bin (again, "theship" is because of 
what i specified as the dir in my steam command).

So if you used "steam -command update -game ship -dir ." then your files might 
be in unexpected places.

-Joe

On Jul 26, 2012, at 3:30 PM, Saul Rennison wrote:

> I'm pretty sure that The Ship utilises its own engine. The CS:S engine
> lives in /steam/css/bin/, and I'm not sure where tf goes (possibly
> /steam/orangebox/bin).
> 
> Either way, you're fine putting the engine there (have you checked whether
> it works?)
> 
> 
> Kind regards,
> *Saul Rennison*
> 
> 
> On 26 July 2012 21:25, doc <[email protected]> wrote:
> 
>> Through the power of "dicking around" I have realized it goes in the
>> /steam/bin/ folder.
>> 
>> I'm testing it now but just so I can get confirmation - wouldn't this mess
>> up any other server I'm running, like CS:S, TF2, etc?
>> 
>> On Thu, Jul 26, 2012 at 12:56 PM, doc <[email protected]> wrote:
>> 
>>> The only thing I have my bin folder is server_i486.so
>>> 
>>> I was going to find a hex editor and poke around - it doesn't sound like
>>> exact rocket science, I only point this out because the prefix is
>>> different, I might be in the wrong folder?
>>> 
>>> I have server_i486, and you gave me engine_i686, I'm sure it's some
>>> misunderstanding on my part but it should just go in my /steam/ship/bin/
>>> folder right? (the 686 is the wrong version for my server I guess but the
>>> name differences is what confuse me)
>>> 
>>> 
>>> On Thu, Jul 26, 2012 at 6:24 AM, Joe Love <[email protected]> wrote:
>>> 
>>>> Actually, I just went through this process, with good results.  Course,
>>>> then I failed to follow through and actually run a server.
>>>> 
>>>> I managed to track down one of the guys running a linux Ship server,
>>>> Feldi, who had a modified linux (i686 only) binary.  Quick binary diff
>>>> between the release and the one he had which worked revealed just a
>> master
>>>> server change:
>>>> 
>>>> (This is a diff on the text output from UltraEdit, but it should be
>>>> enough information to go on to make your own binary changes.)
>>>> 
>>>> < 0037c900h: 32 30 37 2E 31 37 33 2E 31 37 37 2E 31 31 3A 32 ;
>>>> 207.173.177.11:2
>>>> < 0037c910h: 37 30 33 30 20 32 30 37 2E 31 37 33 2E 31 37 37 ; 7030
>>>> 207.173.177
>>>> < 0037c920h: 2E 31 32 3A 32 37 30 33 30 00 00 00 00 00 80 00 ;
>>>> .12:27030.....?.
>>>> ---
>>>>> 0037c900h: 36 39 2E 32 38 2E 31 35 31 2E 31 37 38 3A 32 37 ;
>>>> 69.28.151.178:27
>>>>> 0037c910h: 30 33 38 20 36 39 2E 32 38 2E 31 35 33 2E 38 32 ; 038
>>>> 69.28.153.82
>>>>> 0037c920h: 3A 32 37 30 33 38 00 00 00 00 00 00 00 00 80 00 ;
>>>> :27038........?.
>>>> 
>>>> So, replacing the servers makes it work.  You're on your own for finding
>>>> the location in the i486 binary if you need to use that, but most people
>>>> nowadays seem to be utilizing the i686 binary.
>>>> 
>>>> If you're not interested in finding a hex editor and just want to
>>>> download it, I have posted it here:
>>>> 
>>>> http://www.gameowls.com/lyfe/ship/bin/engine_i686.so
>>>> 
>>>> Just find your existing engine_i686.so, rename it, and drop an updated
>>>> one in place.
>>>> 
>>>> -Joe
>>>> 
>>>> On Jul 25, 2012, at 10:23 PM, doc wrote:
>>>> 
>>>>> http://forums.blazinggriffin.com/viewtopic.php?f=10&t=26
>>>>> 
>>>>> This is as far as I got. Valve changed you connect to the master
>>>> servers a
>>>>> long while back, the devs never updated it for linux, and the only
>>>> solution
>>>>> was on a forum long dead.
>>>>> 
>>>>> The only other option I have is to try running wine :(
>>>>> 
>>>>> On Wed, Jul 25, 2012 at 8:12 PM, doc <[email protected]> wrote:
>>>>> 
>>>>>> Is there anyone who runs a Ship server on linux?
>>>>>> The problem I'm running into is that it just "freezes", stops before
>> it
>>>>>> gets very far.
>>>>>> 
>>>>>> I've done some research but the best I can find is threads leading
>>>> nowhere
>>>>>> and some strange report that it needs updated binaries, something
>> about
>>>>>> master servers? Stumped.
>>>>>> 
>>>>>> Startup line:
>>>>>> ./srcds_run -game ship +map batavier +maxplayers 18 -autoupdate
>>>>>> 
>>>>>> Console output:
>>>>>> http://pastebin.com/nhrBii8v
>>>>>> 
>>>>>> Last 5 lines before the freeze:
>>>>>> Server logging enabled.
>>>>>> Server logging data to file logs/L0725001.log
>>>>>> L 07/25/2012 - 22:04:23: Log file started (file "logs/L0725001.log")
>>>> (game
>>>>>> "/usr/steam/ship") (version "3062")
>>>>>> Summary:  1278 resources total 60.70 Mb, 90.44 % of capacity
>>>>>> The nav mesh needs a full nav_analyze
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>> _______________________________________________
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>>>> please visit:
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>>>> 
>>>> 
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>>>> 
>>> 
>>> 
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