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Subject: Re: [OMPI users] Segmentation fault in oob_tcp.c of openmpi-1.7.4a1r29646
From: tmishima_at_[hidden]
Date: 2013-11-13 21:39:34


Sorry for cross-post.

Nodefile is very simple which consists of 8 lines:

node08
node08
node08
node08
node08
node08
node08
node08

Therefore, NPROCS=8

My aim is to modify the allocation as you pointed out. According to Openmpi
FAQ,
proper subset of the hosts allocated to the Torque / PBS Pro job should be
allowed.

tmishima

> Please - can you answer my question on script2? What is the value of
NPROCS?
>
> Why would you want to do it this way? Are you planning to modify the
allocation?? That generally is a bad idea as it can confuse the system
>
>
> On Nov 13, 2013, at 5:55 PM, tmishima_at_[hidden] wrote:
>
> >
> >
> > Since what I really want is to run script2 correctly, please let us
> > concentrate script2.
> >
> > I'm not an expert of the inside of openmpi. What I can do is just
> > obsabation
> > from the outside. I doubt these lines are strange, especially the last
one.
> >
> > [node08.cluster:26952] mca:rmaps:rr: mapping job [56581,1]
> > [node08.cluster:26952] [[56581,0],0] Starting with 1 nodes in list
> > [node08.cluster:26952] [[56581,0],0] Filtering thru apps
> > [node08.cluster:26952] [[56581,0],0] Retained 1 nodes in list
> > [node08.cluster:26952] [[56581,0],0] Removing node node08 slots 0 inuse
0
> >
> > These lines come from this part of orte_rmaps_base_get_target_nodes
> > in rmaps_base_support_fns.c:
> >
> > } else if (node->slots <= node->slots_inuse &&
> > (ORTE_MAPPING_NO_OVERSUBSCRIBE &
> > ORTE_GET_MAPPING_DIRECTIVE(policy))) {
> > /* remove the node as fully used */
> > OPAL_OUTPUT_VERBOSE((5,
> > orte_rmaps_base_framework.framework_output,
> > "%s Removing node %s slots %d inuse
%d",
> > ORTE_NAME_PRINT(ORTE_PROC_MY_NAME),
> > node->name, node->slots, node->
> > slots_inuse));
> > opal_list_remove_item(allocated_nodes, item);
> > OBJ_RELEASE(item); /* "un-retain" it */
> >
> > I wonder why node->slots and node->slots_inuse is 0, which I can read
> > from the above line "Removing node node08 slots 0 inuse 0".
> >
> > Or I'm not sure but
> > "else if (node->slots <= node->slots_inuse &&" should be
> > "else if (node->slots < node->slots_inuse &&" ?
> >
> > tmishima
> >
> >> On Nov 13, 2013, at 4:43 PM, tmishima_at_[hidden] wrote:
> >>
> >>>
> >>>
> >>> Yes, the node08 has 8 slots but the process I run is also 8.
> >>>
> >>> #PBS -l nodes=node08:ppn=8
> >>>
> >>> Therefore, I think it should allow this allocation. Is that right?
> >>
> >> Correct
> >>
> >>>
> >>> My question is why scritp1 works and script2 does not. They are
> >>> almost same.
> >>>
> >>> #PBS -l nodes=node08:ppn=8
> >>> export OMP_NUM_THREADS=1
> >>> cd $PBS_O_WORKDIR
> >>> cp $PBS_NODEFILE pbs_hosts
> >>> NPROCS=`wc -l < pbs_hosts`
> >>>
> >>> #SCRITP1
> >>> mpirun -report-bindings -bind-to core Myprog
> >>>
> >>> #SCRIPT2
> >>> mpirun -machinefile pbs_hosts -np ${NPROCS} -report-bindings -bind-to
> > core
> >>
> >> This version is not only reading the PBS allocation, but also invoking
> > the hostfile filter on top of it. Different code path. I'll take a look
-
> > it should still match up assuming NPROCS=8. Any
> >> possibility that it is a different number? I don't recall, but isn't
> > there some extra lines in the nodefile - e.g., comments?
> >>
> >>
> >>> Myprog
> >>>
> >>> tmishima
> >>>
> >>>> I guess here's my confusion. If you are using only one node, and
that
> >>> node has 8 allocated slots, then we will not allow you to run more
than
> > 8
> >>> processes on that node unless you specifically provide
> >>>> the --oversubscribe flag. This is because you are operating in a
> > managed
> >>> environment (in this case, under Torque), and so we treat the
> > allocation as
> >>> "mandatory" by default.
> >>>>
> >>>> I suspect that is the issue here, in which case the system is
behaving
> > as
> >>> it should.
> >>>>
> >>>> Is the above accurate?
> >>>>
> >>>>
> >>>> On Nov 13, 2013, at 4:11 PM, Ralph Castain <rhc_at_[hidden]> wrote:
> >>>>
> >>>>> It has nothing to do with LAMA as you aren't using that mapper.
> >>>>>
> >>>>> How many nodes are in this allocation?
> >>>>>
> >>>>> On Nov 13, 2013, at 4:06 PM, tmishima_at_[hidden] wrote:
> >>>>>
> >>>>>>
> >>>>>>
> >>>>>> Hi Ralph, this is an additional information.
> >>>>>>
> >>>>>> Here is the main part of output by adding "-mca rmaps_base_verbose
> >>> 50".
> >>>>>>
> >>>>>> [node08.cluster:26952] [[56581,0],0] plm:base:setup_vm
> >>>>>> [node08.cluster:26952] [[56581,0],0] plm:base:setup_vm creating
map
> >>>>>> [node08.cluster:26952] [[56581,0],0] plm:base:setup_vm only HNP in
> >>>>>> allocation
> >>>>>> [node08.cluster:26952] mca:rmaps: mapping job [56581,1]
> >>>>>> [node08.cluster:26952] mca:rmaps: creating new map for job
[56581,1]
> >>>>>> [node08.cluster:26952] mca:rmaps:ppr: job [56581,1] not using ppr
> >>> mapper
> >>>>>> [node08.cluster:26952] [[56581,0],0] rmaps:seq mapping job
[56581,1]
> >>>>>> [node08.cluster:26952] mca:rmaps:seq: job [56581,1] not using seq
> >>> mapper
> >>>>>> [node08.cluster:26952] mca:rmaps:resilient: cannot perform initial
> > map
> >>> of
> >>>>>> job [56581,1] - no fault groups
> >>>>>> [node08.cluster:26952] mca:rmaps:mindist: job [56581,1] not using
> >>> mindist
> >>>>>> mapper
> >>>>>> [node08.cluster:26952] mca:rmaps:rr: mapping job [56581,1]
> >>>>>> [node08.cluster:26952] [[56581,0],0] Starting with 1 nodes in list
> >>>>>> [node08.cluster:26952] [[56581,0],0] Filtering thru apps
> >>>>>> [node08.cluster:26952] [[56581,0],0] Retained 1 nodes in list
> >>>>>> [node08.cluster:26952] [[56581,0],0] Removing node node08 slots 0
> >>> inuse 0
> >>>>>>
> >>>>>> From this result, I guess it's related to oversubscribe.
> >>>>>> So I added "-oversubscribe" and rerun, then it worked well as show
> >>> below:
> >>>>>>
> >>>>>> [node08.cluster:27019] [[56774,0],0] Starting with 1 nodes in list
> >>>>>> [node08.cluster:27019] [[56774,0],0] Filtering thru apps
> >>>>>> [node08.cluster:27019] [[56774,0],0] Retained 1 nodes in list
> >>>>>> [node08.cluster:27019] AVAILABLE NODES FOR MAPPING:
> >>>>>> [node08.cluster:27019] node: node08 daemon: 0
> >>>>>> [node08.cluster:27019] [[56774,0],0] Starting bookmark at node
> > node08
> >>>>>> [node08.cluster:27019] [[56774,0],0] Starting at node node08
> >>>>>> [node08.cluster:27019] mca:rmaps:rr: mapping by slot for job
> > [56774,1]
> >>>>>> slots 1 num_procs 8
> >>>>>> [node08.cluster:27019] mca:rmaps:rr:slot working node node08
> >>>>>> [node08.cluster:27019] mca:rmaps:rr:slot node node08 is full -
> >>> skipping
> >>>>>> [node08.cluster:27019] mca:rmaps:rr:slot job [56774,1] is
> >>> oversubscribed -
> >>>>>> performing second pass
> >>>>>> [node08.cluster:27019] mca:rmaps:rr:slot working node node08
> >>>>>> [node08.cluster:27019] mca:rmaps:rr:slot adding up to 8 procs to
> > node
> >>>>>> node08
> >>>>>> [node08.cluster:27019] mca:rmaps:base: computing vpids by slot for
> > job
> >>>>>> [56774,1]
> >>>>>> [node08.cluster:27019] mca:rmaps:base: assigning rank 0 to node
> > node08
> >>>>>> [node08.cluster:27019] mca:rmaps:base: assigning rank 1 to node
> > node08
> >>>>>> [node08.cluster:27019] mca:rmaps:base: assigning rank 2 to node
> > node08
> >>>>>> [node08.cluster:27019] mca:rmaps:base: assigning rank 3 to node
> > node08
> >>>>>> [node08.cluster:27019] mca:rmaps:base: assigning rank 4 to node
> > node08
> >>>>>> [node08.cluster:27019] mca:rmaps:base: assigning rank 5 to node
> > node08
> >>>>>> [node08.cluster:27019] mca:rmaps:base: assigning rank 6 to node
> > node08
> >>>>>> [node08.cluster:27019] mca:rmaps:base: assigning rank 7 to node
> > node08
> >>>>>>
> >>>>>> I think something is wrong with treatment of oversubscription,
which
> >>> might
> >>>>>> be
> >>>>>> related to "#3893: LAMA mapper has problems"
> >>>>>>
> >>>>>> tmishima
> >>>>>>
> >>>>>>> Hmmm...looks like we aren't getting your allocation. Can you
rerun
> >>> and
> >>>>>> add -mca ras_base_verbose 50?
> >>>>>>>
> >>>>>>> On Nov 12, 2013, at 11:30 PM, tmishima_at_[hidden] wrote:
> >>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> Hi Ralph,
> >>>>>>>>
> >>>>>>>> Here is the output of "-mca plm_base_verbose 5".
> >>>>>>>>
> >>>>>>>> [node08.cluster:23573] mca:base:select:( plm) Querying
component
> >>> [rsh]
> >>>>>>>> [node08.cluster:23573] [[INVALID],INVALID] plm:rsh_lookup on
> >>>>>>>> agent /usr/bin/rsh path NULL
> >>>>>>>> [node08.cluster:23573] mca:base:select:( plm) Query of
component
> >>> [rsh]
> >>>>>> set
> >>>>>>>> priority to 10
> >>>>>>>> [node08.cluster:23573] mca:base:select:( plm) Querying
component
> >>>>>> [slurm]
> >>>>>>>> [node08.cluster:23573] mca:base:select:( plm) Skipping
component
> >>>>>> [slurm].
> >>>>>>>> Query failed to return a module
> >>>>>>>> [node08.cluster:23573] mca:base:select:( plm) Querying
component
> >>> [tm]
> >>>>>>>> [node08.cluster:23573] mca:base:select:( plm) Query of
component
> >>> [tm]
> >>>>>> set
> >>>>>>>> priority to 75
> >>>>>>>> [node08.cluster:23573] mca:base:select:( plm) Selected
component
> >>> [tm]
> >>>>>>>> [node08.cluster:23573] plm:base:set_hnp_name: initial bias 23573
> >>>>>> nodename
> >>>>>>>> hash 85176670
> >>>>>>>> [node08.cluster:23573] plm:base:set_hnp_name: final jobfam 59480
> >>>>>>>> [node08.cluster:23573] [[59480,0],0] plm:base:receive start comm
> >>>>>>>> [node08.cluster:23573] [[59480,0],0] plm:base:setup_job
> >>>>>>>> [node08.cluster:23573] [[59480,0],0] plm:base:setup_vm
> >>>>>>>> [node08.cluster:23573] [[59480,0],0] plm:base:setup_vm creating
> > map
> >>>>>>>> [node08.cluster:23573] [[59480,0],0] plm:base:setup_vm only HNP
in
> >>>>>>>> allocation
> >>>>>>>>
> >>>>>>
> >>>
> >
--------------------------------------------------------------------------
> >>>>>>>> All nodes which are allocated for this job are already filled.
> >>>>>>>>
> >>>>>>
> >>>
> >
--------------------------------------------------------------------------
> >>>>>>>>
> >>>>>>>> Here, openmpi's configuration is as follows:
> >>>>>>>>
> >>>>>>>> ./configure \
> >>>>>>>> --prefix=/home/mishima/opt/mpi/openmpi-1.7.4a1-pgi13.10 \
> >>>>>>>> --with-tm \
> >>>>>>>> --with-verbs \
> >>>>>>>> --disable-ipv6 \
> >>>>>>>> --disable-vt \
> >>>>>>>> --enable-debug \
> >>>>>>>> CC=pgcc CFLAGS="-tp k8-64e" \
> >>>>>>>> CXX=pgCC CXXFLAGS="-tp k8-64e" \
> >>>>>>>> F77=pgfortran FFLAGS="-tp k8-64e" \
> >>>>>>>> FC=pgfortran FCFLAGS="-tp k8-64e"
> >>>>>>>>
> >>>>>>>>> Hi Ralph,
> >>>>>>>>>
> >>>>>>>>> Okey, I can help you. Please give me some time to report the
> >>> output.
> >>>>>>>>>
> >>>>>>>>> Tetsuya Mishima
> >>>>>>>>>
> >>>>>>>>>> I can try, but I have no way of testing Torque any more - so
all
> > I
> >>>>>> can
> >>>>>>>> do
> >>>>>>>>> is a code review. If you can build --enable-debug and add -mca
> >>>>>>>>> plm_base_verbose 5 to your cmd line, I'd appreciate seeing the
> >>>>>>>>>> output.
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> On Nov 12, 2013, at 9:58 PM, tmishima_at_[hidden] wrote:
> >>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> Hi Ralph,
> >>>>>>>>>>>
> >>>>>>>>>>> Thank you for your quick response.
> >>>>>>>>>>>
> >>>>>>>>>>> I'd like to report one more regressive issue about Torque
> > support
> >>> of
> >>>>>>>>>>> openmpi-1.7.4a1r29646, which might be related to "#3893: LAMA
> >>> mapper
> >>>>>>>>>>> has problems" I reported a few days ago.
> >>>>>>>>>>>
> >>>>>>>>>>> The script below does not work with openmpi-1.7.4a1r29646,
> >>>>>>>>>>> although it worked with openmpi-1.7.3 as I told you before.
> >>>>>>>>>>>
> >>>>>>>>>>> #!/bin/sh
> >>>>>>>>>>> #PBS -l nodes=node08:ppn=8
> >>>>>>>>>>> export OMP_NUM_THREADS=1
> >>>>>>>>>>> cd $PBS_O_WORKDIR
> >>>>>>>>>>> cp $PBS_NODEFILE pbs_hosts
> >>>>>>>>>>> NPROCS=`wc -l < pbs_hosts`
> >>>>>>>>>>> mpirun -machinefile pbs_hosts -np ${NPROCS} -report-bindings
> >>>>>> -bind-to
> >>>>>>>>> core
> >>>>>>>>>>> Myprog
> >>>>>>>>>>>
> >>>>>>>>>>> If I drop "-machinefile pbs_hosts -np ${NPROCS} ", then it
> > works
> >>>>>>>> fine.
> >>>>>>>>>>> Since this happens without lama request, I guess it's not the
> >>>>>> problem
> >>>>>>>>>>> in lama itself. Anyway, please look into this issue as well.
> >>>>>>>>>>>
> >>>>>>>>>>> Regards,
> >>>>>>>>>>> Tetsuya Mishima
> >>>>>>>>>>>
> >>>>>>>>>>>> Done - thanks!
> >>>>>>>>>>>>
> >>>>>>>>>>>> On Nov 12, 2013, at 7:35 PM, tmishima_at_[hidden]
wrote:
> >>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Dear openmpi developers,
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> I got a segmentation fault in traial use of
> >>> openmpi-1.7.4a1r29646
> >>>>>>>>> built
> >>>>>>>>>>> by
> >>>>>>>>>>>>> PGI13.10 as shown below:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> [mishima_at_manage testbed-openmpi-1.7.3]$ mpirun -np 4
> >>>>>> -cpus-per-proc
> >>>>>>>> 2
> >>>>>>>>>>>>> -report-bindings mPre
> >>>>>>>>>>>>> [manage.cluster:23082] MCW rank 2 bound to socket 0[core 4
> > [hwt
> >>>>>> 0]],
> >>>>>>>>>>> socket
> >>>>>>>>>>>>> 0[core 5[hwt 0]]: [././././B/B][./././././.]
> >>>>>>>>>>>>> [manage.cluster:23082] MCW rank 3 bound to socket 1[core 6
> > [hwt
> >>>>>> 0]],
> >>>>>>>>>>> socket
> >>>>>>>>>>>>> 1[core 7[hwt 0]]: [./././././.][B/B/./././.]
> >>>>>>>>>>>>> [manage.cluster:23082] MCW rank 0 bound to socket 0[core 0
> > [hwt
> >>>>>> 0]],
> >>>>>>>>>>> socket
> >>>>>>>>>>>>> 0[core 1[hwt 0]]: [B/B/./././.][./././././.]
> >>>>>>>>>>>>> [manage.cluster:23082] MCW rank 1 bound to socket 0[core 2
> > [hwt
> >>>>>> 0]],
> >>>>>>>>>>> socket
> >>>>>>>>>>>>> 0[core 3[hwt 0]]: [././B/B/./.][./././././.]
> >>>>>>>>>>>>> [manage:23082] *** Process received signal ***
> >>>>>>>>>>>>> [manage:23082] Signal: Segmentation fault (11)
> >>>>>>>>>>>>> [manage:23082] Signal code: Address not mapped (1)
> >>>>>>>>>>>>> [manage:23082] Failing at address: 0x34
> >>>>>>>>>>>>> [manage:23082] *** End of error message ***
> >>>>>>>>>>>>> Segmentation fault (core dumped)
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> [mishima_at_manage testbed-openmpi-1.7.3]$ gdb mpirun
core.23082
> >>>>>>>>>>>>> GNU gdb (GDB) CentOS (7.0.1-42.el5.centos.1)
> >>>>>>>>>>>>> Copyright (C) 2009 Free Software Foundation, Inc.
> >>>>>>>>>>>>> ...
> >>>>>>>>>>>>> Core was generated by `mpirun -np 4 -cpus-per-proc 2
> >>>>>>>> -report-bindings
> >>>>>>>>>>>>> mPre'.
> >>>>>>>>>>>>> Program terminated with signal 11, Segmentation fault.
> >>>>>>>>>>>>> #0 0x00002b5f861c9c4f in recv_connect
> > (mod=0x5f861ca20b00007f,
> >>>>>>>>>>> sd=32767,
> >>>>>>>>>>>>> hdr=0x1ca20b00007fff25) at ./oob_tcp.c:631
> >>>>>>>>>>>>> 631 peer = OBJ_NEW(mca_oob_tcp_peer_t);
> >>>>>>>>>>>>> (gdb) where
> >>>>>>>>>>>>> #0 0x00002b5f861c9c4f in recv_connect
> > (mod=0x5f861ca20b00007f,
> >>>>>>>>>>> sd=32767,
> >>>>>>>>>>>>> hdr=0x1ca20b00007fff25) at ./oob_tcp.c:631
> >>>>>>>>>>>>> #1 0x00002b5f861ca20b in recv_handler (sd=1778385023,
> >>>>>> flags=32767,
> >>>>>>>>>>>>> cbdata=0x8eb06a00007fff25) at ./oob_tcp.c:760
> >>>>>>>>>>>>> #2 0x00002b5f848eb06a in event_process_active_single_queue
> >>>>>>>>>>>>> (base=0x5f848eb27000007f, activeq=0x848eb27000007fff)
> >>>>>>>>>>>>> at ./event.c:1366
> >>>>>>>>>>>>> #3 0x00002b5f848eb270 in event_process_active
> >>>>>>>>>>> (base=0x5f848eb84900007f)
> >>>>>>>>>>>>> at ./event.c:1435
> >>>>>>>>>>>>> #4 0x00002b5f848eb849 in opal_libevent2021_event_base_loop
> >>>>>>>>>>>>> (base=0x4077a000007f, flags=32767) at ./event.c:1645
> >>>>>>>>>>>>> #5 0x00000000004077a0 in orterun (argc=7,
> > argv=0x7fff25bbd4a8)
> >>>>>>>>>>>>> at ./orterun.c:1030
> >>>>>>>>>>>>> #6 0x00000000004067fb in main (argc=7,
argv=0x7fff25bbd4a8)
> >>>>>>>>>>> at ./main.c:13
> >>>>>>>>>>>>> (gdb) quit
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> The line 627 in orte/mca/oob/tcp/oob_tcp.c is apparently
> >>>>>>>> unnecessary,
> >>>>>>>>>>> which
> >>>>>>>>>>>>> causes the segfault.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> 624 /* lookup the corresponding process
*/>>>>>>>>>>>>> 625 peer = mca_oob_tcp_peer_lookup(mod, &hdr->origin);
> >>>>>>>>>>>>> 626 if (NULL == peer) {
> >>>>>>>>>>>>> 627 ui64 = (uint64_t*)(&peer->name);
> >>>>>>>>>>>>> 628 opal_output_verbose(OOB_TCP_DEBUG_CONNECT,
> >>>>>>>>>>>>> orte_oob_base_framework.framework_output,
> >>>>>>>>>>>>> 629 "%s
> > mca_oob_tcp_recv_connect:
> >>>>>>>>>>>>> connection from new peer",
> >>>>>>>>>>>>> 630 ORTE_NAME_PRINT
> >>>>>>>>> (ORTE_PROC_MY_NAME));
> >>>>>>>>>>>>> 631 peer = OBJ_NEW(mca_oob_tcp_peer_t);
> >>>>>>>>>>>>> 632 peer->mod = mod;
> >>>>>>>>>>>>> 633 peer->name = hdr->origin;
> >>>>>>>>>>>>> 634 peer->state = MCA_OOB_TCP_ACCEPTING;
> >>>>>>>>>>>>> 635 ui64 = (uint64_t*)(&peer->name);
> >>>>>>>>>>>>> 636 if (OPAL_SUCCESS !=
> >>> opal_hash_table_set_value_uint64
> >>>>>>>>>>> (&mod->
> >>>>>>>>>>>>> peers, (*ui64), peer)) {
> >>>>>>>>>>>>> 637 OBJ_RELEASE(peer);
> >>>>>>>>>>>>> 638 return;
> >>>>>>>>>>>>> 639 }
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Please fix this mistake in the next release.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Regards,
> >>>>>>>>>>>>> Tetsuya Mishima
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>> users mailing list
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> >>>>>>>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> >>>>>>>>>>>>
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