Hi All,
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 application is https://www.broadinstitute.org/igv/
Could you please advise, what causes this behaviour and what to do? The server¹s OS is CentOS 6, I am using X2go packages from EPEL, and the desktop the user uses is GNOME. Thank you very much in advance!
-- Grigory Shamov
Westgrid/ComputeCanada Site Lead University of Manitoba E2-588 EITC Building, (204) 474-9625