Deal.II does not pass quick tests after installation

[deal.II newbie]

Hi! I am a newbie to Deal.II. After the installation, I typed the command make test for running the quick tests. But all four tests failed out of four. The reason listed below in the quicktests.log is the same for all 4 tests. I would like to ask if anyone could please help indicate what the error is and how to fix it? Any help or hints would be much appreciated! Thank you very much in advance!

The error is the same for all 4 tests as follows,

Scanning dependencies of target tbb.debug

[100%] Building CXX object tests/quick_tests/CMakeFiles/tbb.debug.dir/tbb.cc.o

/root/dealii-8.4.1/tests/quick_tests/tbb.cc:49:6: warning: unused parameter ‘scratch’ [-Wunused-parameter]

Linking CXX executable tbb.debug

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_mutexattr_destroy'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_join'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_detach'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_barrier_wait'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_mutexattr_settype'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_mutex_trylock'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_barrier_init'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `sem_wait'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `sem_init'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_getspecific'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_setspecific'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `sem_destroy'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_create'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_key_delete'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_key_create'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_mutexattr_init'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_attr_getstack'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_barrier_destroy'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `sem_post'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_getattr_np'

../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_attr_setstacksize'

collect2: error: ld returned 1 exit status

gmake[7]: *** [tests/quick_tests/tbb.debug] Error 1

gmake[6]: *** [tests/quick_tests/CMakeFiles/tbb.debug.dir/all] Error 2

gmake[5]: *** [tests/quick_tests/CMakeFiles/tbb.debug.run.dir/rule] Error 2

gmake[4]: *** [tbb.debug.run] Error 2

[David Wells]

Hi there,

Well that is something I have not seen before: it looks like it did not link correctly to your copy of libpthread.so. To confirm this, could you run

ldd build-directory/lib/libdeal_II.so

(where build-directory is whereever you compiled the library)

and see if it did not find a particular library.

Since it looks like the library is in '/root/': did you compile this as root? If so weird things can happen; you should build it as an unprivileged user.

Thanks,
David Wells

[Thien Binh Nguyen]

Dear Mr. Wells, 

Thank you very much for your prompt response, and I am also sorry for my late reply!

When ldd either to libdeal_II.so or libdeal_II.g.so, I received the following messages

As you noticed, I compiled Deal.II with root privilege. I was trying to re-installed and complied Deal.II with my own account. But I still got the same error messages.

Thank you very much!

Yours sincerely,

Nguyen Thien Binh

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[David Wells]

Mr. Nguyen,

Not a problem; I hope that I can help :)

That is odd; it doesn't seem to have linked (or tried to link) against libpthread at all. This implies that (since it compiled successfully) it never tried to link with libpthread. Would you please post the file detailed.log (should be in your build directory)? Mine specifies the variable THREAD_LINKER_FLAGS; I suspect that variable is not correct in your copy.

Thanks,

David Wells

[Thien Binh Nguyen]

Dear Mr. Wells,

Thanks for your help again!

I would like to send you the detailed.log as well as summary.log and quicktests.log. Could you please have a check on the attachment?

I hope these will give some information about the error.

Yours sincerely,

Nguyen Thien Binh

[David Wells]

Mr. Nguyen,

Well, this is awkward. I looked over your files carefully and I see nothing unusual in the configuration. CMake definitely, at some point, recognizes that it needs to link against libpthread but it never seems to do it. I really hope that we can figure this out because it is probably a bug in our CMake code.

I think that one way to get around this temporarily would be to compile the library without threads, i.e., compile it with the flag -DDEAL_II_WITH_THREADS=OFF. That should let you compile the library but you won't be able to use threads (bad, but better than nothing).

I am running out of explanations for this error. Would you humor me and check that you do have /usr/lib/libpthread.so or /usr/lib64/libpthread.so on your system? Perhaps the libraries are in some strange place that CMake cannot find.

Thanks,
David Wells

[David Wells]

Someone with administrative priviledges: the last message also has a picture in it with an IP address. Could you delete that too?

[Jean-Paul Pelteret]

Thanks for pointing that out David, I didn't see the picture in the reply. Since I can't edit the posts themselves, I've duplicated the post here and those that required "censoring". Nguyen's message follows:

---------------

Dear Mr. Wells,

I am sorry but if you would please kindly delete the attached figure in the previous mail and replace it with the following?

This is because the previous one contains our machine's IP address. Since all these messages are supposed to be on public in Deal.II community, I think it would be better such information is not shown in cases of any unexpected problems.

[David Wells]

Thank you JP :)

Did you try compiling the library without threads?

I believe you said earlier that you were using centOS. What is the exact version information of your operating system?

Thanks,

David Wells

On Mon, Jul 11, 2016 at 2:29 PM, Jean-Paul Pelteret <jppel...@gmail.com> wrote:

Thanks for pointing that out David, I didn't see the picture in the reply. Since I can't edit the posts themselves, I've duplicated the post here and those that required "censoring". Nguyen's message follows:

---------------

Dear Mr. Wells,

I am sorry but if you would please kindly delete the attached figure in the previous mail and replace it with the following?

This is because the previous one contains our machine's IP address. Since all these messages are supposed to be on public in Deal.II community, I think it would be better such information is not shown in cases of any unexpected problems.

Thank you very much!

Yours sincerely,

Nguyen Thien Binh

--

[Thien Binh Nguyen]

Thank you very much Mr. Pelteret for handling the case!

Mr. Wells,

I have tried compiling the library without using pthreads. The quicktests are now passed successfully

For the other question, we have CentOS 5.3 installed in our machine. But I have installed necessary packages for Deal.II, i.e. CMake 2.8.10.2, GNU make 3.81, as well as gcc 4.7.2 and the other ones.

Thank you very much!

Yours sincerely,

Nguyen Thien Binh

[David Wells]

I do not understand why we were not able to link successfully with pthreads; I'll try to get a copy of centOS 5.3 at some point and see if I can reproduce this. Either way I am glad that we could get you set up correctly :)

[Thien Binh Nguyen]

Dear Mr. Wells,

Thank you very much for all of your help! I really appreciate it!

It seems that the cause of this problem is due to CentOS 5.3 because when I tried installing Deal.II into another cluster with newer CentOS 6.3, we did not experience the problem, and all the quicktests passed successfully without turning off pthreads.

If there is a way to enable pthreads for Deal.II for CentOS 5.3, could you please share the information with me?

Thanks a lot once again!

Yours sincerely,

Nguyen Thien Binh