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Subject: Re: [OMPI users] Segfault on any MPI communication on head node
From: Ralph Castain (rhc.openmpi_at_[hidden])
Date: 2011-10-03 20:28:33


That means you have mismatched installations around - one configured as debug, and one not. They have to match.

Sent from my iPad

On Oct 3, 2011, at 2:44 PM, Phillip Vassenkov <phillip.vassenkov_at_[hidden]> wrote:

> 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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