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Subject: Re: [OMPI users] Segfault on any MPI communication on head node
From: Phillip Vassenkov (phillip.vassenkov_at_[hidden])
Date: 2011-10-03 17:44:20


I went into the directory that I used to install 1.4.3, did the following:
make clean
./configure --enable-debug
make -j8 all install

and it hangs at this when I try to run my code (I commented out all the
host name stuff, so it's just MPI code now)

[hostname:16574] [[17705,0],0] ORTE_ERROR_LOG: Buffer type (described vs
non-described) mismatch - operation not allowed in file
base/odls_base_default_fns.c at line 2600

I'm googling for more info but does anyone have any ideas?

On 9/28/11 8:30 PM, Jeff Squyres wrote:
> Use --enable-debug on your configure line. This will add in some debugging code to OMPI, and it'll compile everything with -g so that you can get stack traces.
>
> Beware that the extra debugging junk makes OMPI slightly slower; don't do any benchmarking with this install, etc.
>
>
> On Sep 28, 2011, at 6:27 PM, Phillip Vassenkov wrote:
>
>> I tried 1.4.4rc4, same problem. Where do I get a debugging version?
>>
>> On 9/28/11 8:32 AM, Jeff Squyres wrote:
>>> Agreed that the original program had the char*[20]/char[20] bug, but his segv is occurring before trying to use that array. So it's a bug - but he just hadn't hit it yet. :-)
>>>
>>> I'd still like to see a debugging version so that we can get a real stack trace, and/or try the latest 1.4.4 RC (posted yesterday).
>>>
>>>
>>> On Sep 27, 2011, at 3:08 PM, German Hoecht wrote:
>>>
>>>> char* name[20]; yields 20 (undefined) pointers to char, guess you mean
>>>> char name[20];
>>>>
>>>> So Brent's suggestion should work as well(?)
>>>>
>>>> To be safe I would also add:
>>>> gethostname(name,maxlen);
>>>> name[19] = '\0';
>>>> printf("Hello, world. I am %d of %d and host %s \n", rank, ...
>>>>
>>>> Cheers
>>>>
>>>> On 09/27/2011 07:40 PM, Phillip Vassenkov wrote:
>>>>> Thanks, but my main concern is the segfault :P I changed and as I
>>>>> expected it still segfaults.
>>>>>
>>>>> On 9/27/11 9:48 AM, Henderson, Brent wrote:
>>>>>> Here is another possibly non-helpful suggestion. :) Change:
>>>>>>
>>>>>> char* name[20];
>>>>>> int maxlen = 20;
>>>>>>
>>>>>> To:
>>>>>>
>>>>>> char name[256];
>>>>>> int maxlen = 256;
>>>>>>
>>>>>> gethostname() is supposed to properly truncate the hostname it returns
>>>>>> if the actual name is longer than the length provided, but since you
>>>>>> have at least one that is longer than 20 characters, I'm curious.
>>>>>>
>>>>>> Brent
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]]
>>>>>> On Behalf Of Jeff Squyres
>>>>>> Sent: Tuesday, September 27, 2011 6:29 AM
>>>>>> To: Open MPI Users
>>>>>> Subject: Re: [OMPI users] Segfault on any MPI communication on head node
>>>>>>
>>>>>> Hmm. It's not immediately clear to me what's going wrong here.
>>>>>>
>>>>>> I hate to ask, but could you install a debugging version of Open MPI
>>>>>> and capture a proper stack trace of the segv?
>>>>>>
>>>>>> Also, could you try the 1.4.4 rc and see if that magically fixes the
>>>>>> problem? (I'm about to post a new 1.4.4 rc later this morning, but
>>>>>> either the current one or the one from later today would be a good
>>>>>> datapoint)
>>>>>>
>>>>>>
>>>>>> On Sep 26, 2011, at 5:09 PM, Phillip Vassenkov wrote:
>>>>>>
>>>>>>> Yep, Fedora Core 14 and OpenMPI 1.4.3
>>>>>>>
>>>>>>> On 9/24/11 7:02 AM, Jeff Squyres wrote:
>>>>>>>> Are you running the same OS version and Open MPI version between the
>>>>>>>> head node and regular nodes?
>>>>>>>>
>>>>>>>> On Sep 23, 2011, at 5:27 PM, Vassenkov, Phillip wrote:
>>>>>>>>
>>>>>>>>> Hey all,
>>>>>>>>> I've been racking my brains over this for several days and was
>>>>>>>>> hoping anyone could enlighten me. I'll describe only the relevant
>>>>>>>>> parts of the network/computer systems. There is one head node and a
>>>>>>>>> multitude of regular nodes. The regular nodes are all identical to
>>>>>>>>> each other. If I run an mpi program from one of the regular nodes
>>>>>>>>> to any other regular nodes, everything works. If I include the head
>>>>>>>>> node in the hosts file, I get segfaults which I'll paste below
>>>>>>>>> along with sample code. The machines are all networked via
>>>>>>>>> infiniband and Ethernet. The issue only arises when mpi
>>>>>>>>> communication occurs. By this I mean, MPi_Init might succeed but
>>>>>>>>> the segfault always occurs on MPI_Barrier or MPI_send/recv. I found
>>>>>>>>> a work around by disabling the openib btl and enforcing that
>>>>>>>>> communications go over infiniband(if I don't force infiniband,
>>>>>>>>> it'll go over Ethernet). This command works when the head node is
>>>>>>>>> included in the hosts file:
>>>>>>>>> mpirun --hostfile hostfile --mca btl ^openib --mca
>>>>>>>>> btl_tcp_if_include ib0 -np 2 ./b.out
>>>>>>>>>
>>>>>>>>> Sample Code:
>>>>>>>>> #include "mpi.h"
>>>>>>>>> #include<stdio.h>
>>>>>>>>> int main(int argc, char *argv[])
>>>>>>>>> {
>>>>>>>>> int rank, nprocs;
>>>>>>>>> char* name[20];
>>>>>>>>> int maxlen = 20;
>>>>>>>>> MPI_Init(&argc,&argv);
>>>>>>>>> MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
>>>>>>>>> MPI_Comm_rank(MPI_COMM_WORLD,&rank);
>>>>>>>>> MPI_Barrier(MPI_COMM_WORLD);
>>>>>>>>> gethostname(name,maxlen);
>>>>>>>>> printf("Hello, world. I am %d of %d and host %s \n", rank,
>>>>>>>>> nprocs,name);
>>>>>>>>> fflush(stdout);
>>>>>>>>> MPI_Finalize();
>>>>>>>>> return 0;
>>>>>>>>>
>>>>>>>>> }
>>>>>>>>>
>>>>>>>>> Segfault:
>>>>>>>>> [pastec:19917] *** Process received signal ***
>>>>>>>>> [pastec:19917] Signal: Segmentation fault (11)
>>>>>>>>> [pastec:19917] Signal code: Address not mapped (1)
>>>>>>>>> [pastec:19917] Failing at address: 0x8
>>>>>>>>> [pastec:19917] [ 0] /lib64/libpthread.so.0() [0x34a880eeb0]
>>>>>>>>> [pastec:19917] [ 1] /usr/lib64/libmthca-rdmav2.so(+0x36aa)
>>>>>>>>> [0x7eff6430b6aa]
>>>>>>>>> [pastec:19917] [ 2]
>>>>>>>>> /usr/lib64/openmpi/lib/openmpi/mca_btl_openib.so(+0x133c9)
>>>>>>>>> [0x7eff66a163c9]
>>>>>>>>> [pastec:19917] [ 3]
>>>>>>>>> /usr/lib64/openmpi/lib/openmpi/mca_btl_openib.so(+0x1eb70)
>>>>>>>>> [0x7eff66a21b70]
>>>>>>>>> [pastec:19917] [ 4]
>>>>>>>>> /usr/lib64/openmpi/lib/openmpi/mca_btl_openib.so(+0x1ec89)
>>>>>>>>> [0x7eff66a21c89]
>>>>>>>>> [pastec:19917] [ 5]
>>>>>>>>> /usr/lib64/openmpi/lib/openmpi/mca_btl_openib.so(+0x1403d)
>>>>>>>>> [0x7eff66a1703d]
>>>>>>>>> [pastec:19917] [ 6]
>>>>>>>>> /usr/lib64/openmpi/lib/openmpi/mca_pml_ob1.so(+0x120e6)
>>>>>>>>> [0x7eff676670e6]
>>>>>>>>> [pastec:19917] [ 7]
>>>>>>>>> /usr/lib64/openmpi/lib/openmpi/mca_pml_ob1.so(+0x6273)
>>>>>>>>> [0x7eff6765b273]
>>>>>>>>> [pastec:19917] [ 8]
>>>>>>>>> /usr/lib64/openmpi/lib/openmpi/mca_coll_tuned.so(+0x1b2f)
>>>>>>>>> [0x7eff65539b2f]
>>>>>>>>> [pastec:19917] [ 9]
>>>>>>>>> /usr/lib64/openmpi/lib/openmpi/mca_coll_tuned.so(+0xa5cf)
>>>>>>>>> [0x7eff655425cf]
>>>>>>>>> [pastec:19917] [10]
>>>>>>>>> /usr/lib64/openmpi/lib/libmpi.so.0(MPI_Barrier+0x9e) [0x3a54c4c94e]
>>>>>>>>> [pastec:19917] [11] ./b.out(main+0x6e) [0x400a42]
>>>>>>>>> [pastec:19917] [12] /lib64/libc.so.6(__libc_start_main+0xfd)
>>>>>>>>> [0x34a841ee5d]
>>>>>>>>> [pastec:19917] [13] ./b.out() [0x400919]
>>>>>>>>> [pastec:19917] *** End of error message ***
>>>>>>>>> [pastec.gtri.gatech.edu:19913] [[18526,0],0]-[[18526,1],1]
>>>>>>>>> mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104)
>>>>>>>>> --------------------------------------------------------------------------
>>>>>>>>>
>>>>>>>>> mpirun noticed that process rank 1 with PID 19917 on node
>>>>>>>>> pastec.gtri.gatech.edu exited on signal 11 (Segmentation fault).
>>>>>>>>> --------------------------------------------------------------------------
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
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