Subject: x2goagent exhaust all Sysv5 shared memory segments when running Java GUI app

From: Grigory Shamov <[email-masked]>
Date: Mon, 18 Jul 2016 15:34:46 +0000

Package: x2goagent
Version: 3.5.0.32

We have encountered a strange problem: x2goagent on the server  would eat
up all the System5 shared memory segments when running a particular Java
GUI application. After that any other processes doing shared memory would
naturally fail. 

When the user connects, everything is as usual; then when Java program is
opened and starts working (dataset is loaded, some graphics based on it
displayed, several threads started to process the data) it quickly uses
over 4K of the shared memory segments.

In the output 'lsof -u user' there is about 4K lines of the sort:

x2goagent 29374 auser  DEL    REG                0,4           402984941
/SYSV00000000
x2goagent 29374 auser  DEL    REG                0,4           403017710
/SYSV00000000
x2goagent 29374 auser  DEL    REG                0,4           403050479
/SYSV00000000

In Œipcs¹ output there is about 4K lines of this sort:

------ Shared Memory Segments --------
key        shmid      owner      perms      bytes      nattch     status

0x00000000 339708005 auser 600        4331520    1          dest
0x00000000 339740774 auser 600        4331520    1          dest
0x00000000 339773543 auser 600        4331520    1          dest

The Java application is IGV: https://www.broadinstitute.org/igv/

Could you please advise, what causes this behaviour and what to do?

The server¹s OS is CentOS 6.6, I am using X2go packages rebuilt from from
EPEL sources. 
The desktop environment is GNOME. Thank you very much in advance!

-- 
Grigory Shamov

Westgrid/ComputeCanada Site Lead
University of Manitoba
E2-588 EITC Building,
(204) 474-9625