Bug #2909
closedUploading images unstable and then creating processing db error
0%
Description
［Uploading images］Ｓｔｏｐ：
Starting image 24 ( skip:0, remain:914 ) file: 14aug21z_Image_023
... Reading original image: /home/fuchiyu/Documents/STIVsingleparticle2012Apr/Image_023.mrc
Traceback (most recent call last):
File "/usr/bin/appion/imageloader.py", line 582, in <module>
imgLoop.run()
File "/usr/bin/appion/imageloader.py", line 237, in run
imgdata, results = self.loopProcessImage(info)
File "/usr/lib/python2.6/site-packages/appionlib/appionLoop2.py", line 139, in loopProcessImage
return self.processImage(imgdata)
File "/usr/bin/appion/imageloader.py", line 327, in processImage
imgdata = self.makeImageData(imagearray,imginfo)
File "/usr/bin/appion/imageloader.py", line 550, in makeImageData
self.publish(imgdata)
File "/usr/bin/appion/imageloader.py", line 344, in publish
data.insert(force=dbforce)
File "/usr/lib/python2.6/site-packages/sinedon/data.py", line 390, in insert
db.insert(self, **kwargs)
File "/usr/lib/python2.6/site-packages/sinedon/dbdatakeeper.py", line 253, in insert
self._insert(newdata, force=force)
File "/usr/lib/python2.6/site-packages/sinedon/dbdatakeeper.py", line 287, in _insert
return self.recursiveInsert(newdata, force=force)
File "/usr/lib/python2.6/site-packages/sinedon/dbdatakeeper.py", line 280, in recursiveInsert
dbid = self.flatInsert(newdata, force=force)
File "/usr/lib/python2.6/site-packages/sinedon/dbdatakeeper.py", line 297, in flatInsert
definition, formatedData = sqldict.dataSQLColumns(newdata, fail)
File "/usr/lib/python2.6/site-packages/sinedon/sqldict.py", line 1515, in dataSQLColumns
result = type2columns(key, value, value_type, data_instance)
File "/usr/lib/python2.6/site-packages/sinedon/sqldict.py", line 1584, in type2columns
column_dict = value_dict = saveMRC(value, key, path, filename)
File "/usr/lib/python2.6/site-packages/sinedon/sqldict.py", line 1456, in saveMRC
pyami.mrc.write(object, fullname)
File "/usr/lib/python2.6/site-packages/pyami/mrc.py", line 524, in write
appendArray(a, fobj)
File "/usr/lib/python2.6/site-packages/pyami/mrc.py", line 593, in appendArray
b[start:end].tofile(f)
ValueError: 4194304 requested and 2806528 written
[New Project "creating processing" db error ]
Error: CREATE TABLE IF NOT EXISTS ApAppionJobData ( `DEF_id` int(20) NOT NULL auto_increment, `DEF_timestamp` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP on update CURRENT_TIMESTAMP , `REF|ApPathData|path` int(20) null , `name` text null , `jobtype` text null , `REF|ApPathData|dmfpath` int(20) null , `REF|ApPathData|clusterpath` int(20) null , `REF|leginondata|SessionData|session` int(20) null , `cluster` text null , `clusterjobid` int(20) null , `status` varchar(1) null , `user` text null , PRIMARY KEY (`DEF_id`), KEY `DEF_timestamp` (`DEF_timestamp`), KEY `REF|ApPathData|clusterpath` (`REF|ApPathData|clusterpath`), KEY `REF|leginondata|SessionData|session` (`REF|leginondata|SessionData|session`), KEY `REF|ApPathData|dmfpath` (`REF|ApPathData|dmfpath`), KEY `clusterjobid` (`clusterjobid`), KEY `status` (`status`), KEY `jobtype_10` (`jobtype`(10)) ) ;Error writing file './ap9/ApAppionJobData.frm' (Errcode: 28)
Should I check the database (rebuild/restart) or Appion installed.
Thanks help to figure it out!
Files
Updated by Anchi Cheng over 10 years ago
I Googled "mysql error 28" and got several results. The majority of them is because /tmp or other places it needs to write like the one indicated in your error where mysql is (/var/lib/mysql on my CentOS 6 installation) ran out of space. You can try some of the solutions from them to repair the tables, but above all check the space available on your database server and where the image is to be uploaded.
During the upload, the mrc file is copied, not moved. You can remove the original file afterwards, but it will needs the space for both during the process if you are in fact doing it on the same computer.
Updated by Anchi Cheng about 9 years ago
- Status changed from New to Won't Fix or Won't Do
- Show in known bugs changed from Yes to No