Hello Gilles and all
Here is an update: looks like I have root-caused it:
Disabling MPI's signal handlers after MPI_Init() AND mentioning both the
PML AND BTL explicitly does generate a core dump. (Note that just
mentioning -mca pml ob1 alone does not do it, which I find strange) I
believe there was a similar post recently. To be more explicit, the
following command generates a core file
mpirun -np 2 -mca pml ob1 -mca btl self,sm ./btrtest
only if I have the following 4 lines after MPI_Init()
signal(SIGABRT, SIG_DFL);
signal(SIGBUS, SIG_DFL);
signal(SIGFPE, SIG_DFL);
signal(SIGSEGV, SIG_DFL);
So, whatever default MCA parameters OMPI is choosing seems to be incorrect,
on a machine that has the extra NICs, link off.
That still leaves open the question as to why the default signal handlers
are not required in the other cluster.
To investigate what parameters OMPI is choosing my default, I did the
following:
mpirun -np 2 -mca pml_base_verbose 100 -mca bml_base_verbose 100 -mca
btl_base_verboe 100 ./btrtest
which did not seem to return anything very insightful:
before MPI_Init : -1 -1
before MPI_Init : -1 -1
[smallMPI:15125] mca: base: components_register: registering framework bml
components
[smallMPI:15125] mca: base: components_register: found loaded component r2
[smallMPI:15125] mca: base: components_register: component r2 register
function successful
[smallMPI:15125] mca: base: components_open: opening bml components
[smallMPI:15125] mca: base: components_open: found loaded component r2
[smallMPI:15125] mca: base: components_open: component r2 open function
successful
[smallMPI:15126] mca: base: components_register: registering framework bml
components
[smallMPI:15126] mca: base: components_register: found loaded component r2
[smallMPI:15126] mca: base: components_register: component r2 register
function successful
[smallMPI:15126] mca: base: components_open: opening bml components
[smallMPI:15126] mca: base: components_open: found loaded component r2
[smallMPI:15126] mca: base: components_open: component r2 open function
successful
btrtest:15125 terminated with signal 11 at PC=7ff5d13927d8
SP=7ffe4fe833d8. Backtrace:
/lib64/libc.so.6(+0x3ba7d8)[0x7ff5d13927d8]
btrtest:15126 terminated with signal 11 at PC=7f568715c7d8
SP=7ffe5057b518. Backtrace:
/lib64/libc.so.6(+0x3ba7d8)[0x7f568715c7d8]
I'll be more than happy to run any command in this machine that might help
the developers narrow down the issue; please let me know.
Thank you
Durga
The surgeon general advises you to eat right, exercise regularly and quit
ageing.
On Wed, May 11, 2016 at 10:34 PM, dpchoudh . <dpcho...@gmail.com> wrote:
> Hello Gilles
>
> Thank you for your continued support. With your help, I have a better
> understanding of what is happening. Here are the details.
>
> 1. Yes, I am sure that ulimit -c is 'unlimited' (and for the test in
> question, I am running it on a single node, so there are no other nodes)
>
> 2. The command I am running is possibly the simplest MPI command:
> mpirun -np 2 <program>
>
> It looks to me, after running your test code, that what is crashing is
> MPI_Init() itself. The output from your code (I called it 'btrtest') is as
> follows:
>
> [durga@smallMPI ~]$ mpirun -np 2 ./btrtest
> before MPI_Init : -1 -1
> before MPI_Init : -1 -1
>
> btrtest:7275 terminated with signal 11 at PC=7f401f49e7d8
> SP=7ffec47e7578. Backtrace:
> /lib64/libc.so.6(+0x3ba7d8)[0x7f401f49e7d8]
>
> btrtest:7274 terminated with signal 11 at PC=7f1ba21897d8
> SP=7ffc516ac8d8. Backtrace:
> /lib64/libc.so.6(+0x3ba7d8)[0x7f1ba21897d8]
> -------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code. Per user-direction, the job has been aborted.
> -------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun detected that one or more processes exited with non-zero status,
> thus causing
> the job to be terminated. The first process to do so was:
>
> Process name: [[7936,1],1]
> Exit code: 1
> --------------------------------------------------------------------------
>
> So obviously the code does not make it past MPI_Init()
>
> This is an issue that I have been observing for quite a while in different
> forms and have reported on the forum a few times also. Let me elaborate:
>
> Both my 'well-behaving' and crashing clusters run CentOS 7 (the crashing
> one has the latest updates, the well-behaving one does not as I am not
> allowed to apply updates on that). They both have OMPI, from the master
> branch, compiled from the source. Both consist of 64 bit Dell servers,
> although not identical models (I doubt if that matters)
>
> The only significant difference between the two is this:
>
> The well behaved one (if it does core dump, that is because there is a bug
> in the MPI app) has very simple network hardware: two different NICs (one
> Broadcom GbE, one proprietary NIC that is currently being exposed as an IP
> interface). There is no RDMA capability there at all.
>
> The crashing one have 4 different NICs:
> 1. Broadcom GbE
> 2. Chelsio T3 based 10Gb iWARP NIC
> 3. QLogic 20Gb Infiniband (PSM capable)
> 4. LSI logic Fibre channel
>
> In this situation, WITH ALL BUT THE GbE LINK DOWN (the GbE connects the
> machine to the WAN link), it seems just the presence of these NICs matter.
>
> Here are the various commands and outputs:
>
> [durga@smallMPI ~]$ mpirun -np 2 ./btrtest
> before MPI_Init : -1 -1
> before MPI_Init : -1 -1
>
> btrtest:10032 terminated with signal 11 at PC=7f6897c197d8
> SP=7ffcae2b2ef8. Backtrace:
> /lib64/libc.so.6(+0x3ba7d8)[0x7f6897c197d8]
>
> btrtest:10033 terminated with signal 11 at PC=7fb035c3e7d8
> SP=7ffe61a92088. Backtrace:
> /lib64/libc.so.6(+0x3ba7d8)[0x7fb035c3e7d8]
> -------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code. Per user-direction, the job has been aborted.
> -------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun detected that one or more processes exited with non-zero status,
> thus causing
> the job to be terminated. The first process to do so was:
>
> Process name: [[9294,1],0]
> Exit code: 1
> --------------------------------------------------------------------------
>
> [durga@smallMPI ~]$ mpirun -np 2 -mca pml ob1 ./btrtest
> before MPI_Init : -1 -1
> before MPI_Init : -1 -1
>
> btrtest:10076 terminated with signal 11 at PC=7fa92d20b7d8
> SP=7ffebb106028. Backtrace:
> /lib64/libc.so.6(+0x3ba7d8)[0x7fa92d20b7d8]
>
> btrtest:10077 terminated with signal 11 at PC=7f5012fa57d8
> SP=7ffea4f4fdf8. Backtrace:
> /lib64/libc.so.6(+0x3ba7d8)[0x7f5012fa57d8]
> -------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code. Per user-direction, the job has been aborted.
> -------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun detected that one or more processes exited with non-zero status,
> thus causing
> the job to be terminated. The first process to do so was:
>
> Process name: [[9266,1],0]
> Exit code: 1
> --------------------------------------------------------------------------
>
> [durga@smallMPI ~]$ mpirun -np 2 -mca pml ob1 -mca btl self,sm ./btrtest
> before MPI_Init : -1 -1
> before MPI_Init : -1 -1
>
> btrtest:10198 terminated with signal 11 at PC=400829 SP=7ffe6e148870.
> Backtrace:
>
> btrtest:10197 terminated with signal 11 at PC=400829 SP=7ffe87be6cd0.
> Backtrace:
> ./btrtest[0x400829]
> /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f9473bbeb15]
> ./btrtest[0x4006d9]
> ./btrtest[0x400829]
> /lib64/libc.so.6(__libc_start_main+0xf5)[0x7fdfe2d8eb15]
> ./btrtest[0x4006d9]
> after MPI_Init : -1 -1
> after MPI_Init : -1 -1
> -------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code. Per user-direction, the job has been aborted.
> -------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun detected that one or more processes exited with non-zero status,
> thus causing
> the job to be terminated. The first process to do so was:
>
> Process name: [[9384,1],1]
> Exit code: 1
> --------------------------------------------------------------------------
>
>
> [durga@smallMPI ~]$ ulimit -a
> core file size (blocks, -c) unlimited
> data seg size (kbytes, -d) unlimited
> scheduling priority (-e) 0
> file size (blocks, -f) unlimited
> pending signals (-i) 216524
> max locked memory (kbytes, -l) unlimited
> max memory size (kbytes, -m) unlimited
> open files (-n) 1024
> pipe size (512 bytes, -p) 8
> POSIX message queues (bytes, -q) 819200
> real-time priority (-r) 0
> stack size (kbytes, -s) 8192
> cpu time (seconds, -t) unlimited
> max user processes (-u) 4096
> virtual memory (kbytes, -v) unlimited
> file locks (-x) unlimited
> [durga@smallMPI ~]$
>
>
> I do realize that my setup is very unusual (I am a quasi-developer of MPI
> whereas most other folks in this list are likely end-users), but somehow
> just disabling this 'execinfo' MCA would allow me to make progress (and
> also find out why/where MPI_Init() is crashing!). Is there any way I can do
> that?
>
> Thank you
> Durga
>
> The surgeon general advises you to eat right, exercise regularly and quit
> ageing.
>
> On Wed, May 11, 2016 at 8:58 PM, Gilles Gouaillardet <gil...@rist.or.jp>
> wrote:
>
>> Are you sure ulimit -c unlimited is *really* applied on all hosts
>>
>>
>> can you please run the simple program below and confirm that ?
>>
>>
>> Cheers,
>>
>>
>> Gilles
>>
>>
>> #include <sys/time.h>
>> #include <sys/resource.h>
>> #include <poll.h>
>> #include <stdio.h>
>>
>> int main(int argc, char *argv[]) {
>> struct rlimit rlim;
>> char * c = (char *)0;
>> getrlimit(RLIMIT_CORE, &rlim);
>> printf ("before MPI_Init : %d %d\n", rlim.rlim_cur, rlim.rlim_max);
>> MPI_Init(&argc, &argv);
>> getrlimit(RLIMIT_CORE, &rlim);
>> printf ("after MPI_Init : %d %d\n", rlim.rlim_cur, rlim.rlim_max);
>> *c = 0;
>> MPI_Finalize();
>> return 0;
>> }
>>
>>
>> On 5/12/2016 4:22 AM, dpchoudh . wrote:
>>
>> Hello Gilles
>>
>> Thank you for the advice. However, that did not seem to make any
>> difference. Here is what I did (on the cluster that generates .btr files
>> for core dumps):
>>
>> [durga@smallMPI git]$ ompi_info --all | grep opal_signal
>> MCA opal base: parameter "opal_signal" (current value:
>> "6,7,8,11", data source: default, level: 3 user/all, type: string)
>> [durga@smallMPI git]$
>>
>>
>> According to <bits/signum.h>, signals 6.7,8,11 are this:
>>
>> #define SIGABRT 6 /* Abort (ANSI). */
>> #define SIGBUS 7 /* BUS error (4.2 BSD). */
>> #define SIGFPE 8 /* Floating-point exception (ANSI). */
>> #define SIGSEGV 11 /* Segmentation violation (ANSI). */
>>
>> And thus I added the following just after MPI_Init()
>>
>> MPI_Init(&argc, &argv);
>> signal(SIGABRT, SIG_DFL);
>> signal(SIGBUS, SIG_DFL);
>> signal(SIGFPE, SIG_DFL);
>> signal(SIGSEGV, SIG_DFL);
>> signal(SIGTERM, SIG_DFL);
>>
>> (I added the 'SIGTERM' part later, just in case it would make a
>> difference; i didn't)
>>
>> The resulting code still generates .btr files instead of core files.
>>
>> It looks like the 'execinfo' MCA component is being used as the backtrace
>> mechanism:
>>
>> [durga@smallMPI git]$ ompi_info | grep backtrace
>> MCA backtrace: execinfo (MCA v2.1.0, API v2.0.0, Component
>> v3.0.0)
>>
>> However, I could not find any way to choose 'none' instead of 'execinfo'
>>
>> And the strange thing is, on the cluster where regular core dump is
>> happening, the output of
>> $ ompi_info | grep backtrace
>> is identical to the above. (Which kind of makes sense because they were
>> created from the same source with the same configure options.)
>>
>> Sorry to harp on this, but without a core file it is hard to debug the
>> application (e.g. examine stack variables).
>>
>> Thank you
>> Durga
>>
>>
>> The surgeon general advises you to eat right, exercise regularly and quit
>> ageing.
>>
>> On Wed, May 11, 2016 at 3:37 AM, Gilles Gouaillardet <
>> <gilles.gouaillar...@gmail.com>gilles.gouaillar...@gmail.com> wrote:
>>
>>> Durga,
>>>
>>> you might wanna try to restore the signal handler for other signals as
>>> well
>>> (SIGSEGV, SIGBUS, ...)
>>> ompi_info --all | grep opal_signal
>>> does list the signal you should restore the handler
>>>
>>>
>>> only one backtrace component is built (out of several candidates :
>>> execinfo, none, printstack)
>>> nm -l libopen-pal.so | grep backtrace
>>> will hint you which component was built
>>>
>>> your two similar distros might have different backtrace component
>>>
>>>
>>>
>>> Gus,
>>>
>>> btr is a plain text file with a back trace "ala" gdb
>>>
>>>
>>>
>>> Nathan,
>>>
>>> i did a 'grep btr' and could not find anything :-(
>>> opal_backtrace_buffer and opal_backtrace_print are only used with stderr.
>>> so i am puzzled who creates the tracefile name and where ...
>>> also, no stack is printed by default unless opal_abort_print_stack is
>>> true
>>>
>>> Cheers,
>>>
>>> Gilles
>>>
>>>
>>> On Wed, May 11, 2016 at 3:43 PM, dpchoudh . < <dpcho...@gmail.com>
>>> dpcho...@gmail.com> wrote:
>>> > Hello Nathan
>>> >
>>> > Thank you for your response. Could you please be more specific? Adding
>>> the
>>> > following after MPI_Init() does not seem to make a difference.
>>> >
>>> > MPI_Init(&argc, &argv);
>>> > signal(SIGABRT, SIG_DFL);
>>> > signal(SIGTERM, SIG_DFL);
>>> >
>>> > I also find it puzzling that nearly identical OMPI distro running on a
>>> > different machine shows different behaviour.
>>> >
>>> > Best regards
>>> > Durga
>>> >
>>> > The surgeon general advises you to eat right, exercise regularly and
>>> quit
>>> > ageing.
>>> >
>>> > On Tue, May 10, 2016 at 10:02 AM, Hjelm, Nathan Thomas <
>>> hje...@lanl.gov>
>>> > wrote:
>>> >>
>>> >> btr files are indeed created by open mpi's backtrace mechanism. I
>>> think we
>>> >> should revisit it at some point but for now the only effective way i
>>> have
>>> >> found to prevent it is to restore the default signal handlers after
>>> >> MPI_Init.
>>> >>
>>> >> Excuse the quoting style. Good sucks.
>>> >>
>>> >>
>>> >> ________________________________________
>>> >> From: users on behalf of dpchoudh .
>>> >> Sent: Monday, May 09, 2016 2:59:37 PM
>>> >> To: Open MPI Users
>>> >> Subject: Re: [OMPI users] No core dump in some cases
>>> >>
>>> >> Hi Gus
>>> >>
>>> >> Thanks for your suggestion. But I am not using any resource manager
>>> (i.e.
>>> >> I am launching mpirun from the bash shell.). In fact, both of the two
>>> >> clusters I talked about run CentOS 7 and I launch the job the same
>>> way on
>>> >> both of these, yet one of them creates standard core files and the
>>> other
>>> >> creates the 'btr; files. Strange thing is, I could not find anything
>>> on the
>>> >> .btr (= Backtrace?) files on Google, which is any I asked on this
>>> forum.
>>> >>
>>> >> Best regards
>>> >> Durga
>>> >>
>>> >> The surgeon general advises you to eat right, exercise regularly and
>>> quit
>>> >> ageing.
>>> >>
>>> >> On Mon, May 9, 2016 at 12:04 PM, Gus Correa
>>> >> <g...@ldeo.columbia.edu<mailto: <g...@ldeo.columbia.edu>
>>> g...@ldeo.columbia.edu>> wrote:
>>> >> Hi Durga
>>> >>
>>> >> Just in case ...
>>> >> If you're using a resource manager to start the jobs (Torque, etc),
>>> >> you need to have them set the limits (for coredump size, stacksize,
>>> locked
>>> >> memory size, etc).
>>> >> This way the jobs will inherit the limits from the
>>> >> resource manager daemon.
>>> >> On Torque (which I use) I do this on the pbs_mom daemon
>>> >> init script (I am still before the systemd era, that lovely POS).
>>> >> And set the hard/soft limits on /etc/security/limits.conf as well.
>>> >>
>>> >> I hope this helps,
>>> >> Gus Correa
>>> >>
>>> >> On 05/07/2016 12:27 PM, Jeff Squyres (jsquyres) wrote:
>>> >> I'm afraid I don't know what a .btr file is -- that is not something
>>> that
>>> >> is controlled by Open MPI.
>>> >>
>>> >> You might want to look into your OS settings to see if it has some
>>> kind of
>>> >> alternate corefile mechanism...?
>>> >>
>>> >>
>>> >> On May 6, 2016, at 8:58 PM, dpchoudh .
>>> >> <dpcho...@gmail.com<mailto: <dpcho...@gmail.com>dpcho...@gmail.com>>
>>> wrote:
>>> >>
>>> >> Hello all
>>> >>
>>> >> I run MPI jobs (for test purpose only) on two different 'clusters'.
>>> Both
>>> >> 'clusters' have two nodes only, connected back-to-back. The two are
>>> very
>>> >> similar, but not identical, both software and hardware wise.
>>> >>
>>> >> Both have ulimit -c set to unlimited. However, only one of the two
>>> creates
>>> >> core files when an MPI job crashes. The other creates a text file
>>> named
>>> >> something like
>>> >>
>>> >>
>>> <program_name_that_crashed>.80s-<a-number-that-looks-like-a-PID>,<hostname-where-the-crash-happened>.btr
>>> >>
>>> >> I'd much prefer a core file because that allows me to debug with a lot
>>> >> more options than a static text file with addresses. How do I get a
>>> core
>>> >> file in all situations? I am using MPI source from the master branch.
>>> >>
>>> >> Thanks in advance
>>> >> Durga
>>> >>
>>> >> The surgeon general advises you to eat right, exercise regularly and
>>> quit
>>> >> ageing.
>>> >> _______________________________________________
>>> >> users mailing list
>>> >> us...@open-mpi.org<mailto: <us...@open-mpi.org>us...@open-mpi.org>
>>> >> Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users
>>> >> Link to this post:
>>> >> http://www.open-mpi.org/community/lists/users/2016/05/29124.php
>>> >>
>>> >>
>>> >>
>>> >> _______________________________________________
>>> >> users mailing list
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>>> >>
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>>> >
>>> >
>>> >
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>>
>>
>>
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>
>
