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Essex_E_
Beginner
80 Views

Pardiso always crashing on Linux

I consistently have Pardiso crash when running on Linux. I've trimmed it down to a relatively simple test case of building a Poisson matrix and solving it with Pardiso.  The same program runs fine on Windows 8 and 10. It segfaults on both Centos 6.7 and Ubuntu 14.04. I assume I'm doing something wrong, but I can't tell what.

I'm building and testing on Centos 6.7 (upgraded from 6.5, not originally installed as 6.7).  I'm using g++ 4.8.2.  I put a fresh install of MKL from "parallel_studio_xe_2016_composer_edition_for_cpp_update2.tgz" into my home directory. I'm intentionally using the TBB version of MKL, and not using OpenMP at all. When I started working on this, I was using OpenMP and Pardiso was still crashing in OpenMP instead of TBB.

GDB shows the segfault is during Pardiso phase 11, inside some tbbmalloc stuff.

Full Source file: https://drive.google.com/open?id=0B1-EScYNsy0uTDZNX2Etck9NM1U

Makefile: https://drive.google.com/file/d/0B1-EScYNsy0uNEZLQmx5dl80ZUk/view?usp=sharing

Lots of console output, versions, make, gdb, ldd: https://drive.google.com/file/d/0B1-EScYNsy0uTjFqU2lyQTVjdUU/view?usp=sharing

Any suggestions on what I should look at?

-Essex

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4 Replies
Gennady_F_Intel
Moderator
80 Views

Essex, could you please check if the problem exists with the latest version of MKL we released a couple of days ago? This is version 11.3 update 3. The similar issue has been fixed into this update. Thanks. 

Essex_E_
Beginner
80 Views

Thank you very much for your response.

I have just installed update 3 (parallel_studio_xe_2016_composer_edition_for_cpp_update3.tgz).  I had to run install.sh twice. On the first install, mkl_tbb_thread.lib was missing, so I re-ran the installer to modify the installation and add TBB support to MKL.

My test program now runs without crashing, but it's only running a single thread. Running fine on a single thread is not new. It used to do that already. The segfault is in some parallel section. Unfortunately, I can't figure out how to get it to run with more threads. Changing the TBB_NUM_THREADS environment variable and calling mkl_set_num_threads(16) don't change anything. It used to just do it automatically.

If I switch from linking with mkl_tbb_thread.a to linking with mkl_intel_thread.a and libiomp5.a, then it runs with 4 threads and doesn't crash. If need be, I guess I can work with this, but the rest of my application is threaded with TBB. Are there correctness problems from using mkl_intel_thread in a TBB-parallelized application?

Roman_A_Intel
Employee
80 Views

Hi Essex,

Actually, there is no way to set number of threads for TBB. In case of TBB threading Pardiso automatically detects the number of threads. Also if you set msglvl = 1 then you will see that number of threads always equal to 1 in case of TBB, but in fact Pardiso runs on multiple threads. The correct output in case of msglvl=1 will be fixed in one of the following releases.

Regards, Roman

Essex_E_
Beginner
80 Views

Okay, I see what you're saying.  The verbose output was saying things like "Parallel Direct Factorization is running on 1 OpenMP" and I interpreted this to mean that it's running on 1 thread, since there is no other output about threading. But if I watch the process in "top", that I see it's running 400% CPU (on my 4-core virtual machine).

To recap, 

On 11.3 update 2, I always segfault, due to some sort of bug in MKL.

On 11.3 update 3, using mkl_tbb_thread.a, the verbose Pardiso output doesn't say how many threads it used and reports it's only using 1 (irrelevant) OpenMP thread. I was confused by this, but "top" reveals it's working fine.

I think this is all resolved. Thanks.

 

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