[Chimera-users] open amber trajectory error

[Greg Couch]

One more thing.

You might be running out of temporary disk space.  Run the 'df' command 
in a shell to see which filesystems are full.  If the filesystem with 
the trajectories has extra space, but / or /var is full, then set the 
TMPDIR environment variable to a directory on that filesystem before 
running chimera, so the temporary files get created on the other disk.

      HTH,

     Greg

On 9/19/2014 9:34 AM, Greg Couch wrote:
> While the traceback was not in the trajectory code, the clue is:
>
>     OSError: [Errno 28] No space left on device
>
> You ran out of disk space.  So if you free up some space by deleting 
> some files or moving them to a different disk, you should be alright.
>
>     HTH,
>
>      Greg
>
> On 9/19/2014 7:37 AM, Renato Freitas wrote:
>> I am trying to open a zipped amber trajectory with chimera but I am 
>> getting the following error:
>>
>> #################################
>> Traceback (most recent call last):
>>   File 
>> "/home/disk0/rfreitas/softwares/chimera/share/chimera/triggerSet.py", 
>> line 83, in invoke
>>     self._funcData, triggerData)
>>   File 
>> "/home/disk0/rfreitas/softwares/chimera/share/DBPuppet/__init__.py", 
>> line 329, in portOnTop
>>     self.remove_webinfo(self.listen_port)
>>   File 
>> "/home/disk0/rfreitas/softwares/chimera/share/DBPuppet/__init__.py", 
>> line 369, in remove_webinfo
>>     with lock:
>>   File 
>> "/home/disk0/rfreitas/softwares/chimera/lib/python2.7/site-packages/filelock.py", 
>> line 120, in __enter__
>>     self.acquire()
>>   File 
>> "/home/disk0/rfreitas/softwares/chimera/lib/python2.7/site-packages/filelock.py", 
>> line 32, in acquire
>>     self._createFile()
>>   File 
>> "/home/disk0/rfreitas/softwares/chimera/lib/python2.7/site-packages/filelock.py", 
>> line 86, in _createFile
>>     os.write(self.fd, "%d\n" % os.getpid())
>> OSError: [Errno 28] No space left on device
>> Error processing trigger "Focus In":
>> OSError: [Errno 28] No space left on device
>>
>>   File 
>> "/home/disk0/rfreitas/softwares/chimera/lib/python2.7/site-packages/filelock.py", 
>> line 86, in _createFile
>>     os.write(self.fd, "%d\n" % os.getpid())
>>
>> See reply log for Python traceback.
>> ################################################
>>
>> if I unzip the file, I can open it without problems. Since I have 
>> many files to look and they are very big (> 300 MB zipped) I don't 
>> want to unzip every file whenever I have to look at the trajectory.
>> Any help will be appreciated.
>>
>> thanks,
>>
>> Renato
>>
>>
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>
>
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