[gpfsug-discuss] SpectrumScale / AFM / Singularity soft lockups

Robert Horton robert.horton at icr.ac.uk
Thu Mar 18 15:47:07 GMT 2021


Hello,

We've recently started having an issue where processes running in a singularity container get stuck in a soft lockup and eventually the node needs to be forcibly rebooted. I have included a sample call trace below. Additionally, other (non-singularity) processes on other nodes accessing the same fileset seem to get into the same state. It's also an AFM IW fileset just to add to the complexity ;)

Does anyone have any thoughts on what might be happening / how to proceed? I'm not really sure if it's a GPFS issue or a Singularity / Kernel issue - although fact it seems to spread to other nodes would seem to suggest some GPFS involvement. It's possible the user is doing something inadvisable with Singularity (it's difficult to work out what's happening in the Nextflow pipeline) but even if they are it would be good to find a way of preventing them taking nodes down. I'm assuming the AFM is unlikely to be relevant - any views on that?

Thanks,
Rob

 Call Trace:
? _Z11kSFSGetattrP15KernelOperationP13gpfsVfsData_tP10gpfsNode_tiP10cxiVattr_tP12gpfs_iattr64+0x1e4/0x5d0 [mmfs26]
 _ZL17refreshCacheAttrsP13gpfsVfsData_tP15KernelOperationP9cxiNode_tP10pcacheAttriPcj+0x441/0x450 [mmfs26]
 _Z21pcacheHandleCollisionP13gpfsVfsData_tP15KernelOperationP10gpfsNode_tS4_PcPvP9MMFSVInfoiP10pcacheAttriS5_10PcacheModej+0xa21/0x11b0 [mmfs26]
 ? _ZN6ThCond6signalEv+0x82/0x190 [mmfs26]
  ? _ZN10MemoryPool6shFreeEPv9MallocUse+0x1a5/0x2a0 [mmfs26]
 ? _ZL14kSFSPcacheSendP13gpfsVfsData_tP15KernelOperation7FileUIDS3_PciiPPv+0x387/0x570 [mmfs26]
 ? _ZL17pcacheNeedRefresh10PcacheModejlijj+0x206/0x230 [mmfs26]
_Z12pcacheLookupP13gpfsVfsData_tP15KernelOperationP10gpfsNode_tPvPcP7FilesetjjjPS5_PS4_PyPjS9_+0x1dcf/0x25c0 [mmfs26]
? _Z15findFilesetByIdP15KernelOperationjjPP7Filesetj+0x4f/0xa0 [mmfs26]
 _Z10gpfsLookupP13gpfsVfsData_tPvP9cxiNode_tS1_S1_PcjPS1_PS3_PyP10cxiVattr_tPjP10ext_cred_tjS5_PiS4_SD_+0x65c/0xad0 [mmfs26]
gpfs_i_lookup+0x189/0x3f0 [mmfslinux]
 ? _Z8gpfsLinkP13gpfsVfsData_tP9cxiNode_tS2_PvPcjjP10ext_cred_t+0x6e0/0x6e0 [mmfs26]
 ? d_alloc_parallel+0x99/0x4a0
 ? _Z33gpfsIsCifsBypassTraversalCheckingv+0xe2/0x130 [mmfs26]
 __lookup_slow+0x97/0x150
 lookup_slow+0x35/0x50
  walk_component+0x1bf/0x330
 ? _ZL12gpfsGetattrxP13gpfsVfsData_tP9cxiNode_tP10cxiVattr_tP12gpfs_iattr64i+0x147/0x390 [mmfs26]
 path_lookupat.isra.49+0x75/0x200
  filename_lookup.part.63+0xa0/0x170
? strncpy_from_user+0x4f/0x1b0
 vfs_statx+0x73/0xe0
  __do_sys_newlstat+0x39/0x70
 ? syscall_trace_enter+0x1d3/0x2c0
 ? __audit_syscall_exit+0x249/0x2a0
  do_syscall_64+0x5b/0x1a0
 entry_SYSCALL_64_after_hwframe+0x65/0xca

--

Robert Horton | Research Data Storage Lead
The Institute of Cancer Research | 237 Fulham Road | London | SW3 6JB
T +44 (0)20 7153 5350 | E robert.horton at icr.ac.uk<mailto:robert.horton at icr.ac.uk> | W www.icr.ac.uk | Twitter @ICR_London
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The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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