Question: Get 0 byte in file size randomly when uploading files
1
gravatar for gongbinsheng
17 months ago by
gongbinsheng10
United States
gongbinsheng10 wrote:

We recently set up a Galaxy server on our cluster. Briefly, the Galaxy server is installed in one server node and jobs are set to run through qsub (to SGE cluster), with the proftpd FTP server and postgres Database set up. We are experiencing randomly issues when uploading files from either website or FTP. Sometime the file upload is good, but sometime it shows zero in size, even though Galaxy consider it is successful (Green in history). When check the file size on the storage, sometime the file size is correct, but show 0 in the webpage, sometime the file size is 0. Everything seems to be happened randomly. We didn't get error massages in the log file and when we track the qsub, even the jobs of uploading files were submit to the same computation node, some are good and some are zero. The issue only happens when uploading files and no matter the files are big or small (we tried files are 1kb 1GB and 10GB), no matter the file format (we tried fasta and fastq) and no matter the file are gzipped or not. Does anyone have any idea about this issue? Thanks!

ADD COMMENTlink modified 17 months ago • written 17 months ago by gongbinsheng10

Hello, As a baseline to start troubleshooting it would be helpful to know:

1) The master release of Galaxy you are running (15_07 or 15_10 or an older release)? Or is the install tracking a different branch?

2) If the configuration for ProFTPd follows these guidelines https://wiki.galaxyproject.org/Admin/Config/ProFTPd_with_AD

3) Any modifications to the ProFTPd config that have been made that deviate from 2 above

4) This occurs with all upload methods (local file browsing upload, FTP upload, URL, pasted data entry)? Or just certain types? I believe that you stated that this is occurring with file browsing and FTP, but it would be good to confirm that.

5) Is this a new issue or has it always been present since the server was set up? If this is a new issue, when did it start? Specifically, were other configuration or hardware changes performed around the same time? 

Thank you! Jen, Galaxy team

ADD REPLYlink modified 17 months ago • written 17 months ago by Jennifer Hillman Jackson22k
0
gravatar for gongbinsheng
17 months ago by
gongbinsheng10
United States
gongbinsheng10 wrote:

Hi Jen,

Thanks for your reply. We are running 15.05.

$ git log
commit 7144ed8f72994473606d2943f9a4f35a6b4eb739
Merge: f6b894a 8f175ef
Author: Dannon Baker <dannon.baker@gmail.com>
Date:   Fri Jul 24 10:37:18 2015 -0400

    Merge branch 'release_15.05'

For the ProFTPd setup, we actually followed the instruction from https://wiki.galaxyproject.org/Admin/Config/UploadviaFTP?action=show&redirect=Admin%2FConfig%2FUpload+via+FTP

The issue occurs with both local file browsing upload and FTP upload. We didn't test URL and pasted data.

The issue occurs since the server was set up.

 

Thank you!

Binsheng

 

ADD COMMENTlink written 17 months ago by gongbinsheng10
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