On 2019-05-14 09:24, Jason Bacon wrote:
On 2018-12-16 09:02, Jason Bacon wrote:
Good morning,
We've been running 17.02.11 for a long time and upon testing an
upgrade to the 18 series, we discovered a regression. It appeared
somewhere between 17.02.11 and 17.11.7.
Everything works fine under 17.02.11.
Under later versions, everything is fine if I don't use srun or if I
use TaskPlugin=task/none.
Just wondering if someone can suggest where to look in the source
code for this. If I can just pinpoint where the problem is, I'm sure
I can come up with a solution pretty quickly. I've poked around a
bit but have not spotted anything yet. If this doesn't look familiar
to anyone, I'll dig deeper and figure it out eventually. Just don't
want to duplicate someone's effort if this is something that's been
fixed already on other platforms.
Below is output from a failed srun and successful sbatch --array and
openmpi jobs.
Thanks,
Jason
Failing job:
FreeBSD login.wren bacon ~ 474: srun hostname
srun: error: slurm_receive_msgs: Zero Bytes were transmitted or received
srun: error: Task launch for 82.0 failed on node compute-001: Zero
Bytes were transmitted or received
srun: error: Application launch failed: Zero Bytes were transmitted
or received
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
srun: error: Timed out waiting for job step to complete
Tail of slurmctld log:
[2018-12-01T16:29:09.873] debug2: got 1 threads to send out
[2018-12-01T16:29:09.874] debug2: Tree head got back 0 looking for 2
[2018-12-01T16:29:09.874] debug3: Tree sending to compute-001
[2018-12-01T16:29:09.874] debug3: Tree sending to compute-002
[2018-12-01T16:29:09.874] debug2: slurm_connect failed: Connection
refused
[2018-12-01T16:29:09.874] debug2: Error connecting slurm stream
socket at 192.168.1.13:6818: Connection refused
[2018-12-01T16:29:09.874] debug3: connect refused, retrying
[2018-12-01T16:29:09.874] debug4: orig_timeout was 10000 we have 0
steps and a timeout of 10000
[2018-12-01T16:29:10.087] debug2: Processing RPC:
MESSAGE_NODE_REGISTRATION_STATUS from uid=0
[2018-12-01T16:29:10.087] debug2: Tree head got back 1
[2018-12-01T16:29:10.087] debug2: _slurm_rpc_node_registration
complete for compute-002 usec=97
[2018-12-01T16:29:10.917] debug2: slurm_connect failed: Connection
refused
[2018-12-01T16:29:10.917] debug2: Error connecting slurm stream
socket at 192.168.1.13:6818: Connection refused
[2018-12-01T16:29:11.976] debug2: slurm_connect failed: Connection
refused
[2018-12-01T16:29:11.976] debug2: Error connecting slurm stream
socket at 192.168.1.13:6818: Connection refused
[2018-12-01T16:29:12.007] debug2: Testing job time limits and
checkpoints
[2018-12-01T16:29:13.011] debug2: slurm_connect failed: Connection
refused
[2018-12-01T16:29:13.011] debug2: Error connecting slurm stream
socket at 192.168.1.13:6818: Connection refused
Successful sbatch --array:
#!/bin/sh -e
#SBATCH --array=1-8
hostname
FreeBSD login.wren bacon ~ 462: more slurm-69_8.out
cpu-bind=MASK - compute-002, task 0 0 [64261]: mask 0x8 set
compute-002.wren
Successful openmpi:
#!/bin/sh -e
#SBATCH --ntasks=8
mpirun --report-bindings ./mpi-bench 3
FreeBSD login.wren bacon ~/Data/mpi-bench/trunk 468: more slurm-81.out
cpu-bind=MASK - compute-001, task 0 0 [64589]: mask 0xf set
CPU 0 is set
CPU 1 is set
CPU 2 is set
CPU 3 is set
CPU 0 is set
CPU 1 is set
[compute-001.wren:64590] MCW rank 0 bound to socket 0[core 0[hwt 0]],
socket 0[core 1[hwt 0]]: [B/B][./.]
[compute-001.wren:64590] MCW rank 1 bound to socket 1[core 2[hwt 0]],
socket 1[core 3[hwt 0]]: [./.][B/B]
[compute-001.wren:64590] MCW rank 2 bound to socket 0[core 0[hwt 0]],
socket 0[core 1[hwt 0]]: [B/B][./.]
[compute-001.wren:64590] MCW rank 3 bound to socket 1[core 2[hwt 0]],
socket 1[core 3[hwt 0]]: [./.][B/B]
FreeBSD login.wren bacon ~ 474: srun hostname
srun: error: slurm_receive_msgs: Zero Bytes were transmitted or received
srun: error: Task launch for 82.0 failed on node compute-001: Zero
Bytes were transmitted or received
srun: error: Application launch failed: Zero Bytes were transmitted
or received
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
srun: error: Timed out waiting for job step to complete
'Been busy upgrading our CentOS clusters, but finally got a chance to
dig into this.
I couldn't find any clues in the logs, but I noticed that slurmd was
dying every time I use srun, so I manually ran it under GDB:
root@compute-001:~ # gdb slurmd
GNU gdb 6.1.1 [FreeBSD]
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and
you are
welcome to change it and/or distribute copies of it under certain
conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB. Type "show warranty" for
details.
This GDB was configured as "amd64-marcel-freebsd"...(no debugging
symbols found)...
(gdb) run -D
Starting program: /usr/local/sbin/slurmd -D
(no debugging symbols found)...(no debugging symbols found)...slurmd:
debug: Log file re-opened
slurmd: debug: CPUs:4 Boards:1 Sockets:2 CoresPerSocket:2
ThreadsPerCore:1
slurmd: Message aggregation disabled
slurmd: debug: CPUs:4 Boards:1 Sockets:2 CoresPerSocket:2
ThreadsPerCore:1
slurmd: topology NONE plugin loaded
slurmd: route default plugin loaded
slurmd: CPU frequency setting not configured for this node
slurmd: debug: Resource spec: No specialized cores configured by
default on this node
slurmd: debug: Resource spec: Reserved system memory limit not
configured for this node
slurmd: task affinity plugin loaded with CPU mask
000000000000000000000000000000000000000000000000000000000000000f
slurmd: debug: Munge authentication plugin loaded
slurmd: debug: spank: opening plugin stack /usr/local/etc/plugstack.conf
slurmd: Munge cryptographic signature plugin loaded
slurmd: slurmd version 18.08.7 started
slurmd: debug: Job accounting gather LINUX plugin loaded
slurmd: debug: job_container none plugin loaded
slurmd: debug: switch NONE plugin loaded
slurmd: slurmd started on Tue, 14 May 2019 09:17:12 -0500
slurmd: CPUs=4 Boards=1 Sockets=2 Cores=2 Threads=1 Memory=16344
TmpDisk=15853 Uptime=2815493 CPUSpecList=(null) FeaturesAvail=(null)
FeaturesActive=(null)
slurmd: debug: AcctGatherEnergy NONE plugin loaded
slurmd: debug: AcctGatherProfile NONE plugin loaded
slurmd: debug: AcctGatherInterconnect NONE plugin loaded
slurmd: debug: AcctGatherFilesystem NONE plugin loaded
slurmd: debug: _handle_node_reg_resp: slurmctld sent back 8 TRES.
slurmd: launch task 33.0 request from UID:2001 GID:2001
HOST:192.168.0.20 PORT:244
slurmd: debug: Checking credential with 336 bytes of sig data
slurmd: task affinity : enforcing 'verbose,cores' cpu bind method
slurmd: debug: task affinity : before lllp distribution cpu bind
method is 'verbose,cores' ((null))
slurmd: lllp_distribution jobid [33] binding:
verbose,cores,one_thread, dist 1
slurmd: _task_layout_lllp_cyclic
/usr/local/lib/slurm/task_affinity.so: Undefined symbol "slurm_strlcpy"
Program exited with code 01.
(gdb)
Looks like a simply build issue. Seems a little odd that the build
succeeded with an undefined symbol, but should be pretty easy to track
down in any case.
Here's the culprit:
In src/common/slurm_xlator.h, strlcpy is unconditionally defined as
slurm_strlcpy:
/* strlcpy.[ch] functions */
#define strlcpy slurm_strlcpy
But in src/common/strlcpy.c, the definition of strlcpy() and the
slurm_strlcpy alias are masked by
#if (!HAVE_STRLCPY)
So this will cause failures on platforms that already have an strlcpy()
function.
Here's a quick fix:
--- src/common/slurm_xlator.h.orig 2019-04-12 04:20:25 UTC
+++ src/common/slurm_xlator.h
@@ -299,7 +299,9 @@
* The header file used only for #define values. */
/* strlcpy.[ch] functions */
+#if (!HAVE_STRLCPY) // Match this to src/common/strlcpy.c
#define strlcpy slurm_strlcpy
+#endif
/* switch.[ch] functions
* None exported today.
--
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