SGE adator error: Cannot parse slots for queue

[arnikz]

Hi, I'm testing xenon-cli /snakemake integration and got the following error while submitting a single SGE job from the head (submit) node:

I'm passing the following cmd: xenon scheduler gridengine --location local://${PWD} submit...

gridengine adaptor: Cannot parse slots for queue "test.q", got "12,[@cores_36=36],[@cores_12=12],[@cores_48=48], \"
Error submitting jobscript (exit code 1):

Could you please help?

[sverhoeven]

This is a Xenon library problem.

Did you specify a queue yourself? Can you run qconf -sq test.q and post the output? So it can be made part of the Xenon testsuite.

[arnikz]

Thanks, I forgot to specify my queue explicitly. See the output for the test.q (some info replaced with xxx)

$ qconf -sq test.q
qname                 test.q
hostlist              xxx.compute.hpc xxx.compute.hpc
seq_no                100
load_thresholds       np_load_avg=1.05
suspend_thresholds    NONE
nsuspend              1
suspend_interval      00:05:00
priority              0
min_cpu_interval      00:05:00
processors            UNDEFINED
qtype                 BATCH INTERACTIVE
ckpt_list             NONE
pe_list               make smp mpi threaded
rerun                 FALSE
slots                 12,[@cores_36=36],[@cores_12=12],[@cores_48=48], \
                      [@cores_24=24],[@cores_40=40]
tmpdir                /tmp
shell                 /bin/bash
prolog                root@/opt/sge/umc_scripts/prologtest.sh
epilog                root@/opt/sge/umc_scripts/epilog.sh
shell_start_mode      posix_compliant
starter_method        NONE
suspend_method        NONE
resume_method         NONE
terminate_method      NONE
notify                00:00:60
owner_list            NONE
user_lists            xxx
xuser_lists           NONE
subordinate_list      NONE
complex_values        NONE
projects              NONE
xprojects             NONE
calendar              NONE
initial_state         disabled
s_rt                  INFINITY
h_rt                  2400:0:0
s_cpu                 INFINITY
h_cpu                 INFINITY
s_fsize               INFINITY
h_fsize               INFINITY
s_data                INFINITY
h_data                INFINITY
s_stack               INFINITY
h_stack               INFINITY
s_core                INFINITY
h_core                INFINITY
s_rss                 INFINITY
h_rss                 INFINITY
s_vmem                INFINITY
h_vmem                INFINITY

[sverhoeven]

Moved issue to Xenon at https://github.com/NLeSC/Xenon/issues/606