Troubleshooting Common Problems

This section provides information to help you diagnose and respond to the cause of common problems.

• Problem — The output file for your job says, Warning: no access to tty; thus no job control in this shell....

  • Possible cause — One or more of your login files contain an stty command. These commands are useful only if a terminal is present.

  • Possible solution — No terminal is associated with batch jobs. You must remove all stty commands from your login files, or you must bracket such commands with an if statement. The if statement should check for a terminal before processing. The following example shows an if statement:

    /bin/csh: stty -g # checks terminal status if ($status == 0) # succeeds if a terminal is present <put all stty commands in here> endif

• Problem — The job standard error log file says `tty`:Ambiguous. However, no reference to tty exists in the user's shell that is called in the job script.

  • Possible cause — shell_start_mode is, by default, posix_compliant. Therefore all job scripts run with the shell that is specified in the queue definition. The scripts do not run with the shell that is specified on the first line of the job script.

  • Possible solution — Use the -S flag to the qsub command, or change shell_start_mode to unix_behavior.

• Problem — You can run your job script from the command line, but the job script fails when you run it using the qsub command.

  • Possible cause — Process limits might be being set for your job. To test whether limits are being set, write a test script that performs limit and limit -h functions. Run both functions interactively, at the shell prompt and using the qsub command, to compare the results.

  • Possible solution — Remove any commands in configuration files that sets limits in your shell.

• Problem — Execution hosts report a load of 99.99.

  1. Possible cause — The sge_execd daemon is not running on the host.

     Possible solution — As root, start up the sge_execd daemon on the execution host by running the sge-root/cell/common/sgeexecd script.

  2. Possible cause — A default domain is incorrectly specified.

     Possible solution — As the grid engine system administrator, run the qconf -mconf command and change the default_domain variable to none.

  3. Possible cause — The sge_qmaster host sees the name of the execution host as different from the name that the execution host sees for itself.

     Possible solution — If you are using DNS to resolve the host names of your compute cluster, configure /etc/hosts and NIS to return the fully qualified domain name (FQDN) as the primary host name. Of course, you can still define and use the short alias name, for example, 168.0.0.1 myhost.dom.com myhost.

     If you are not using DNS, make sure that all of your /etc/hosts files and your NIS table are consistent, for example, 168.0.0.1 myhost.corp myhost or 168.0.0.1 myhost

• Problem — Every 30 seconds a warning that is similar to the following message is printed to cell/spool/host/messages:

  Tue Jan 23 21:20:46 2001|execd|meta|W|local configuration meta not defined - using global configuration

  But cell/common/local_conf contains a file for each host, with FQDN.

  • Possible cause — The host name resolving at your machine meta returns the short name, but at your master machine, meta with FQDN is returned.

  • Possible solution — Make sure that all of your /etc/hosts files and your NIS table are consistent in this respect. In this example, a line such as the following text could erroneously be included in the /etc/hosts file of the host meta:

    168.0.0.1 meta meta.your.domain

    The line should instead be:

    168.0.0.1 meta.your.domain meta.

• Problem — Occasionally you see CHECKSUM ERROR, WRITE ERROR, or READ ERROR messages in the messages files of the daemons.

  • Possible cause — As long as these messages do not appear in a one-second interval, you need not do anything. These messages typically can appear between 1 and 30 times a day.

• Problem — Jobs finish on a particular queue and return the following message in qmaster/messages:

  Wed Mar 28 10:57:15 2001|qmaster|masterhost|I|job 490.1 finished on host exechost

  Then you see the following error messages in the execution host's exechost/messages file:

  Wed Mar 28 10:57:15 2001|execd|exechost|E|can't find directory "active_jobs/490.1" for reaping job 490.1

  Wed Mar 28 10:57:15 2001|execd|exechost|E|can't remove directory "active_jobs/490.1": opendir(active_jobs/490.1) failed: Input/output error

  • Possible cause — The sge-root directory, which is automounted, is being unmounted, causing the sge_execd daemon to lose its current working directory.

  • Possible solution — Use a local spool directory for your sge_execd host. Set the parameter execd_spool_dir, using QMON or the qconf command.

• Problem — When submitting interactive jobs with the qrsh utility, you get the following error message:

  % qrsh -l mem_free=1G error: error: no suitable queues

  However, queues are available for submitting batch jobs with the qsub command. These queues can be queried using qhost -l mem_free=1G and qstat -f -l mem_free=1G.

  • Possible cause — The message error: no suitable queues results from the -w e submit option, which is active by default for interactive jobs such as qrsh. Look for -w e on the qrsh(1) man page. This option causes the submit command to fail if the sge_qmaster does not know for sure that the job is dispatchable according to the current cluster configuration. The intention of this mechanism is to decline job requests in advance, in case the requests can't be granted.

  • Possible solution — In this case, mem_free is configured to be a consumable resource, but you have not specified the amount of memory that is to be available at each host. The memory load values are deliberately not considered for this check because memory load values vary. Thus they can't be seen as part of the cluster configuration. You can do one of the following:

    • Omit this check generally by explicitly overriding the qrsh default option -w e with the -w n option. You can also put this command into sge-root/cell/common/sge_request.

    • If you intend to manage mem_free as a consumable resource, specify the mem_free capacity for your hosts in complex_values of host_conf by using qconf -me hostname.

    • If you don't intend to manage mem_free as a consumable resource, make it a nonconsumable resource again in the consumable column of complex(5) by using qconf -mc hostname.

• Problem — qrsh won't dispatch to the same node it is on. From a qsh shell you get a message such as the following:

  host2 [49]% qrsh -inherit host2 hostname error: executing task of job 1 failed: host2 [50]% qrsh -inherit host4 hostname host4

  • Possible cause — gid_range is not sufficient. gid_range should be defined as a range, not as a single number. The grid engine system assigns each job on a host a distinct gid.

  • Possible solution — Adjust the gid_range with the qconf -mconf command or with QMON. The suggested range is as follows:

    gid_range 20000-20100

• Problem — qrsh -inherit -V does not work when used inside a parallel job. You get the following message:

  cannot get connection to "qlogin_starter"

  • Possible cause — This problem occurs with nested qrsh calls. The problem is caused by the -V option. The first qrsh -inherit call sets the environment variable TASK_ID. TASK_ID is the ID of the tightly integrated task within the parallel job. The second qrsh -inherit call uses this environment variable for registering its task. The command fails as it tries to start a task with the same ID as the already-running first task.

  • Possible solution — You can either unset TASK_ID before calling qrsh -inherit, or use the -v option instead of -V. This option exports only the environment variables that you really need.

• Problem — qrsh does not seem to work at all. Messages like the following are generated:

  host2$ qrsh -verbose hostname local configuration host2 not defined - using global configuration waiting for interactive job to be scheduled ... Your interactive job 88 has been successfully scheduled. Establishing /share/gridware/utilbin/solaris64/rsh session to host exehost ... rcmd: socket: Permission denied /share/gridware/utilbin/solaris64/rsh exited with exit code 1 reading exit code from shepherd ... error: error waiting on socket for client to connect: Interrupted system call error: error reading return code of remote command cleaning up after abnormal exit of /share/gridware/utilbin/solaris64/rsh host2$

  • Possible cause — Permissions for qrsh are not set properly.

  • Possible solution — Check the permissions of the following files, which are located in sge-root/utilbin/. Note that rlogin and rsh must be setuid and owned by root.

    -r-s--x--x 1 root root 28856 Sep 18 06:00 rlogin* -r-s--x--x 1 root root 19808 Sep 18 06:00 rsh* -rwxr-xr-x 1 sgeadmin adm 128160 Sep 18 06:00 rshd*

    ---

    Note –

    The sge-root directory also needs to be NFS-mounted with the setuid option. If sge-root is mounted with nosuid from your submit client, qrsh and associated commands will not work.

    ---

• Problem – When you try to start a distributed make, qmake exits with the following error message:

  qrsh_starter: executing child process qmake failed: No such file or directory

  • Possible cause — The grid engine system starts an instance of qmake on the execution host. If the grid engine system environment, especially the PATH variable, is not set up in the user's shell resource file (.profile or .cshrc), this qmake call fails.

  • Possible solution — Use the -v option to export the PATH environment variable to the qmake job. A typical qmake call is as follows:

    qmake -v PATH -cwd -pe make 2-10 --

• Problem — When using the qmake utility, you get the following error message:

  waiting for interactive job to be scheduled ...timeout (4 s) expired while waiting on socket fd 5 Your "qrsh" request could not be scheduled, try again later.

  • Possible cause — The ARCH environment variable might be set incorrectly in the shell from which qmake was called.

  • Possible solution – Set the ARCH variable correctly to a supported value that matches an available host in your cluster, or else specify the correct value at submit time, for example, qmake -v ARCH=solaris64 ...

• Problem — If the following job is assigned to a SuSE Linux system, the -cwd option does not work and the cwd-test is created on the user's home directory.

  qsub -l arch=lx24-x86 -cwd -b y -o /dev/null -e /dev/null -V "hostname | tee -a cwd-test"

  • Possible cause — On SuSE Linux systems, the /etc/csh.login file includes the cd command to change its current working directory to the user's home directory. Shells usually source system-wide profile files. For (t)csh on Linux, the system-wide file is /etc/csh.login.

  • Possible solution – Use the -noshell option. In this case, there is no intermediate shell that can source the profile file, and therefore neither ~/.login nor ~/.cshrc are sourced.

    When using a batch script, use the PWD environment variable to change the current working directory inside the batch script before executing any programs.

    Another workaround is for users to use neither tcsh nor csh. Because the cd command only appears in /etc/csh.login, the issue would not happen.