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Subject: Re: [OMPI users] TotalView Memory debugging and OpenMPI
From: Peter Thompson (peter.thompson_at_[hidden])
Date: 2011-05-20 09:27:16


Thanks Ralph. I've seen the messages generated in bugs_at_[hidden], so
I figured something was up! I was going to provide the unified diff,
but then ran into another issue in testing where we immediately ran into
a seq fault, even with this fix. It turns out that a pre-pending of
/lib64 (and maybe /usr/lib64) to LD_LIBRARY_PATH works around that one
though, so I don't think it's directly related, but it threw me off,
along with the beta testing we're doing...

Cheers,
PeterT

Ralph Castain wrote:
> Okay, I finally had time to parse this and fix it. Thanks!
>
> On May 16, 2011, at 1:02 PM, Peter Thompson wrote:
>
>
>> Hmmm? We're not removing the putenv() calls. Just adding a strdup() beforehand, and then calling putenv() with the string duplicated from env[j]. Of course, if the strdup fails, then we bail out.
>> As for why it's suddenly a problem, I'm not quite as certain. The problem we do show is a double free, so someone has already freed that memory used by putenv(), and I do know that while that used to be just flagged as an event before, now we seem to be unable to continue past it. Not sure if that is our change or a library/system change.
>> PeterT
>>
>>
>> Ralph Castain wrote:
>>
>>> On May 16, 2011, at 12:45 PM, Peter Thompson wrote:
>>>
>>>
>>>
>>>> Hi Ralph,
>>>>
>>>> We've had a number of user complaints about this. Since it seems on the face of it that it is a debugger issue, it may have not made it's way back here. Is your objection that the patch basically aborts if it gets a bad value? I could understand that being a concern. Of course, it aborts on TotalView now if we attempt to move forward without this patch.
>>>>
>>>>
>>>>
>>> No - my concern is that you appear to be removing the "putenv" calls. OMPI places some values into the local environment so the user can control behavior. Removing those causes problems.
>>>
>>> What I need to know is why, after it has worked with TV for years, these putenv's are suddenly a problem. Is the problem occurring during shutdown? Or is this something that causes TV to break?
>>>
>>>
>>>
>>>
>>>> I've passed your comment back to the engineer, with a suspicion about the concerns about the abort, but if you have other objections, let me know.
>>>>
>>>> Cheers,
>>>> PeterT
>>>>
>>>>
>>>> Ralph Castain wrote:
>>>>
>>>>
>>>>> That would be a problem, I fear. We need to push those envars into the environment.
>>>>>
>>>>> Is there some particular problem causing what you see? We have no other reports of this issue, and orterun has had that code forever.
>>>>>
>>>>>
>>>>>
>>>>> Sent from my iPad
>>>>>
>>>>> On May 11, 2011, at 2:05 PM, Peter Thompson <peter.thompson_at_[hidden]> wrote:
>>>>>
>>>>>
>>>>>
>>>>>> We've gotten a few reports of problems with memory debugging when using OpenMPI under TotalView. Usually, TotalView will attach tot he processes started after an MPI_Init. However in the case where memory debugging is enabled, things seemed to run away or fail. My analysis showed that we had a number of core files left over from the attempt, and all were mpirun (or orterun) cores. It seemed to be a regression on our part, since testing seemed to indicate this worked okay before TotalView 8.9.0-0, so I filed an internal bug and passed it to engineering. After giving our engineer a brief tutorial on how to build a debug version of OpenMPI, he found what appears to be a problem in the code for orterun.c. He's made a slight change that fixes the issue in 1.4.2, 1.4.3, 1.4.4rc2 and 1.5.3, those being the versions he's tested with so far. He doesn't subscribe to this list that I know of, so I offered to pass this by the group. Of course, I'm not sure if this is exactly the right place to subm
it patches, but I'm sure you'd tell me where to put it if I'm in the wrong here. It's a short patch, so I'll cut and paste it, and attach as well, since cut and paste can do weird things to formatting.
>>>>>>
>>>>>> Credit goes to Ariel Burton for this patch. Of course he used TotalVIew to find this ;-) It shows up if you do 'mpirun -tv -np 4 ./foo' or 'totalview mpirun -a -np 4 ./foo'
>>>>>>
>>>>>> Cheers,
>>>>>> PeterT
>>>>>>
>>>>>>
>>>>>> more ~/patches/anbs-patch
>>>>>> *** orte/tools/orterun/orterun.c 2010-04-13 13:30:34.000000000 -0400
>>>>>> --- /home/anb/packages/openmpi-1.4.2/linux-x8664-iwashi/installation/bin/../../.
>>>>>> ./src/openmpi-1.4.2/orte/tools/orterun/orterun.c 2011-05-09 20:28:16.5881
>>>>>> 83000 -0400
>>>>>> ***************
>>>>>> *** 1578,1588 ****
>>>>>> }
>>>>>> if (NULL != env) {
>>>>>> size1 = opal_argv_count(env);
>>>>>> for (j = 0; j < size1; ++j) {
>>>>>> ! putenv(env[j]);
>>>>>> }
>>>>>> }
>>>>>> /* All done */
>>>>>> --- 1578,1600 ----
>>>>>> }
>>>>>> if (NULL != env) {
>>>>>> size1 = opal_argv_count(env);
>>>>>> for (j = 0; j < size1; ++j) {
>>>>>> ! /* Use-after-Free error possible here. putenv does not copy
>>>>>> ! the string passed to it, and instead stores only the pointer.
>>>>>> ! env[j] may be freed later, in which case the pointer
>>>>>> ! in environ will now be left dangling into a deallocated
>>>>>> ! region.
>>>>>> ! So we make a copy of the variable.
>>>>>> ! */
>>>>>> ! char *s = strdup(env[j]);
>>>>>> !
>>>>>> ! if (NULL == s) {
>>>>>> ! return OPAL_ERR_OUT_OF_RESOURCE;
>>>>>> ! }
>>>>>> ! putenv(s);
>>>>>> }
>>>>>> }
>>>>>> /* All done */
>>>>>>
>>>>>> *** orte/tools/orterun/orterun.c 2010-04-13 13:30:34.000000000 -0400
>>>>>> --- /home/anb/packages/openmpi-1.4.2/linux-x8664-iwashi/installation/bin/../../../src/openmpi-1.4.2/orte/tools/orterun/orterun.c 2011-05-09 20:28:16.588183000 -0400
>>>>>> ***************
>>>>>> *** 1578,1588 ****
>>>>>> }
>>>>>>
>>>>>> if (NULL != env) {
>>>>>> size1 = opal_argv_count(env);
>>>>>> for (j = 0; j < size1; ++j) {
>>>>>> ! putenv(env[j]);
>>>>>> }
>>>>>> }
>>>>>>
>>>>>> /* All done */
>>>>>>
>>>>>> --- 1578,1600 ----
>>>>>> }
>>>>>>
>>>>>> if (NULL != env) {
>>>>>> size1 = opal_argv_count(env);
>>>>>> for (j = 0; j < size1; ++j) {
>>>>>> ! /* Use-after-Free error possible here. putenv does not copy
>>>>>> ! the string passed to it, and instead stores only the pointer.
>>>>>> ! env[j] may be freed later, in which case the pointer
>>>>>> ! in environ will now be left dangling into a deallocated
>>>>>> ! region.
>>>>>> ! So we make a copy of the variable.
>>>>>> ! */
>>>>>> ! char *s = strdup(env[j]);
>>>>>> ! ! if (NULL == s) {
>>>>>> ! return OPAL_ERR_OUT_OF_RESOURCE;
>>>>>> ! }
>>>>>> ! putenv(s);
>>>>>> }
>>>>>> }
>>>>>>
>>>>>> /* All done */
>>>>>>
>>>>>> _______________________________________________
>>>>>> users mailing list
>>>>>> users_at_[hidden]
>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>>>
>>>>>>
>>>
>>>
>
>