TEST FAILS RUNNING "make test" AFTER SUCCESSFUL DEALII INSTALLATION

[Joseph Ofosu]

I had the following error messages on screening after running 'make test' post dealII installation:

[100%] Built target deal_II.g

Linking CXX executable step.debug

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_realloc'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_free'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_time'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_calloc'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_config'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_malloc'

collect2: error: ld returned 1 exit status

make[7]: *** [tests/quick_tests/step.debug] Error 1

make[6]: *** [tests/quick_tests/CMakeFiles/step.debug.dir/all] Error 2

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

make[4]: *** [step.debug.run] Error 2

step.debug: ******    BUILD failed    *******

[100%] Built target deal_II

Linking CXX executable step.release

../../lib/libdeal_II.so.8.2.1: undefined reference to `SuiteSparse_realloc'

../../lib/libdeal_II.so.8.2.1: undefined reference to `SuiteSparse_free'

../../lib/libdeal_II.so.8.2.1: undefined reference to `SuiteSparse_time'

../../lib/libdeal_II.so.8.2.1: undefined reference to `SuiteSparse_calloc'

../../lib/libdeal_II.so.8.2.1: undefined reference to `SuiteSparse_config'

../../lib/libdeal_II.so.8.2.1: undefined reference to `SuiteSparse_malloc'

collect2: error: ld returned 1 exit status

make[7]: *** [tests/quick_tests/step.release] Error 1

make[6]: *** [tests/quick_tests/CMakeFiles/step.release.dir/all] Error 2

make[5]: *** [tests/quick_tests/CMakeFiles/step.release.run.dir/rule] Error 2

make[4]: *** [step.release.run] Error 2

step.release: ******    BUILD failed    *******

[100%] Built target deal_II.g

Linking CXX executable affinity.debug

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_realloc'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_free'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_time'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_calloc'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_config'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_malloc'

collect2: error: ld returned 1 exit status

make[7]: *** [tests/quick_tests/affinity.debug] Error 1

make[6]: *** [tests/quick_tests/CMakeFiles/affinity.debug.dir/all] Error 2

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

make[4]: *** [affinity.debug.run] Error 2

affinity.debug: ******    BUILD failed    *******

[ 98%] Built target deal_II.g

Linking CXX executable tbb.debug

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_realloc'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_free'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_time'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_calloc'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_config'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_malloc'

collect2: error: ld returned 1 exit status

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

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

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

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

tbb.debug: ******    BUILD failed    *******

I also did run: export OMP_NUM_THREADS=1

BUT THE ABOVE ERRORS WERE REPEATED AGAIN.

How can I address this. Thanks.

[Bruno Turcksin]

Joseph,

please send me the file detailed.log deal.II cannot find SuiteSparse which is the same problem that you had with Trilinos. Do you know if Trilinos works correctly ?

Best,

Bruno

[Joseph Ofosu]

Bruno, 

Thanks for the quick response.

Honestly, I could successfully install Trilinos, however I am unable to tell if it works fine.

I have attached the quicktests.log to this response.

Bruno, should I do a fresh installation for both Trillinos and DealII? If so, what is the best way to uninstall Trilinos?

Thanks.

[Bruno Turcksin]

On 04/17/2015 03:24 PM, Joseph Ofosu wrote:
> I have attached the quicktests.log to this response.

This is not what I need. In the directory where you have built deal.II,
there is a file called detailed.log. I need it to see if suitesparse was
picked up by Trilinos or by deal.II

> Bruno, should I do a fresh installation for both Trillinos and DealII?
> If so, what is the best way to uninstall Trilinos

This may help. The best way to uninstall Trilinos and deal.II is to
delete the directories where you built them and start from scratch. Make
sure you save somewhere the configuration you used for Trilinos and deal.II.

Best,

Bruno

[Joseph Ofosu]

Okay, 

I am very sorry for sending the wrong file.

This is the right file. It is attached to this response.

I think with dealII it quite straight-forward to do a re-install without any rigorous configurations. Unfortunately, I can not say same for Trilinos.

[Bruno Turcksin]

On 04/17/2015 03:44 PM, Joseph Ofosu wrote:
>
> I think with dealII it quite straight-forward to do a re-install
> without any rigorous configurations. Unfortunately, I can not say same
> for Trilinos.
>

If you do a fresh install of deal.II with the same configuration, it
should work. I think the problem here is that you have some old
configuration that have been cached by cmake. However, in this
configuration p4est and trilinos are turned off. I don't know if it is
what you wanted.

Bruno

[Joseph Ofosu]

Thanks Bruno,

How do I get rid of those old configurations?

Secondly, is it possible to do a fresh installation with trilinos turned

[Joseph Ofosu]

Thanks Bruno,

How do I get rid of those old configurations?

I meant that:

Secondly, is it possible to do a fresh installation with trilinos turned ON?

Thanks.

On Saturday, 18 April 2015 05:52:58 UTC+9, Bruno Turcksin wrote:

[Bruno Turcksin]

On 04/17/2015 04:06 PM, Joseph Ofosu wrote:
> How do I get rid of those old configurations?

Unfortunately, the safest method is to delete the directory where you
have built deal.II

> I meant that:
> Secondly, is it possible to do a fresh installation with trilinos
> turned ON?

You probably want to add something like this to your configuration:
-D DEAL_II_WITH_MPI=ON \
-D DEAL_II_WITH_P4ST=ON \
-D P4EST_DIR=/path/to/p4est \
-D DEAL_II_WITH_TRILINOS=ON \
-D TRILINOS_DIR=/path/to/trilinos

You need p4est to use mpi in deal.II There is a script that will install
p4est for you: https://dealii.org/8.2.1/external-libs/p4est.html

Bruno

[Matthias Maier]

Bruno,

I have seen this kind of error so far when someone tries to link against
a static (often local) suitesparse configuration without -fpic. In this
case deal.II cmake configuration drops libsuitesparse_config.a because
it cannot link against it with a shared library (which is a bugfix for a
bunch of Ubuntu versions...)

Best,
Matthias

[Joseph Ofosu]

Hi Bruno,

I did as you advised, but I still had the same errors. Thus I have decided to delete build directory of Trilinos and re-install again

without using the whole package of suitesparse except Umfpack and other libraries.

After which I will try and re-install dealii once more.

[Matthias Maier]

Hi,

please post your current detailed.log.

Best,
Matthias

[Joseph Ofosu]

Hi Matthias,

I have attached the detailed.log file here.

Thanks a lot.

[Joseph Ofosu]

Hello Matthias,

I performed the configuration of Suitesparse with '-fPIC' flag yet the problem was not resolved.

[Joseph Ofosu]

Hello Bruno and Matthias,

I did a fresh install of Suitesparse, Trilinos and Dealii and yet the problem persists.

I think some of the header files, which I didn't configure in the second build of Trilinos are still in my /usr/local/include path.

This is a summary of the test results:

0% tests passed, 6 tests failed out of 6

Total Test time (real) =  83.41 sec

The following tests FAILED:

 1 - step.debug (Failed)

 2 - step.release (Failed)

 3 - affinity.debug (Failed)

 4 - mpi.debug (Failed)

 5 - tbb.debug (Failed)

 6 - p4est.debug (Failed)

And each of them had this appearance:

Linking CXX executable tbb.debug

/usr/local/lib/libumfpack.5.7.1.a(umfpack_gn_tictoc.o): In function `umfpack_tic':

umfpack_tictoc.c:(.text+0x5): undefined reference to `SuiteSparse_time'

/usr/local/lib/libumfpack.5.7.1.a(umfpack_gn_tictoc.o): In function `umfpack_toc':

umfpack_tictoc.c:(.text+0x25): undefined reference to `SuiteSparse_time'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_realloc'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_free'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_config'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_malloc'

../../lib/libdeal_II.g.so.8.2.1: undefined reference to `SuiteSparse_calloc'

collect2: error: ld returned 1 exit status

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

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

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

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

I have attached both the detailed.log and quicktests.log files here.

Thanks for assisting me.

[Matthias Maier]

Am 19. Apr 2015, 11:40 schrieb Joseph Ofosu <amp...@gmail.com>:

> Hello Matthias,
>
> I performed the configuration of Suitesparse with '-fPIC' flag yet the
> problem was not resolved.

Have you tried to build Suitesparse as shared libraries? This should
resolve most of the problems that might be the cause of your link
failure.

Best,
Matthias

[Joseph Ofosu]

Hi Matthias,

Thanks for the response.

does shared libraries mean configuring the CFLAGS with the 'fPIC' options?

If yes, then I did that.

[Matthias Maier]

> does shared libraries mean configuring the CFLAGS with the 'fPIC' options?

No, it means that it should create shared libraries "libumfpack.so"
instead of static archives "libumfpack.a". The suitesparse build system
should have a configure switch for that.

Shared libraries have the advantage that they store (part) of their link
interface - especially libsuitsparseconfig.(a|so) should then be
automatically picked up by your dynamic loader.

Best,
Matthias

[Joseph Ofosu]

Thanks Matthias,

For further assistance I have attached the config.mk file for suitesparse which I did use.

[Joseph Ofosu]

Sorry Matthias,

The file did not upload. I have attached it now.

Thanks.

Joseph.

[Joseph Ofosu]

SUBJECT:: SUCCESSFUL INSTALLATION OF TRILINOS  AND DEALII WITH SUCCESSFUL BUILT TESTS

DEAR MATTHIAS AND BRUNO,

Matthias as you rightly said, the issue/ problem is with the fact that suitesparse is unable to output a shared library file, except a static one. 

Thus I found this piece of commands on the bug-fix issue of Suitesparse and I used it. Here it is:

sudo add-apt-repository ppa:bzindovic/suitesparse-bugfix-1319687
sudo apt-get update
sudo apt-get install libsuitesparse-dev

Although useful, the above does not provide all the umfpack header files needed to install trilinos. 
Thus I did a separate install of UMFPACK alone. This is automatically packaged with the Suitesparse download.

After which I installed Trilinos and Dealii and built with the following output:

Test project /home/ofosu-kesan2/Projects/dealii-build/tests/quick_tests
Start 1: step.debug
1/6 Test #1: step.debug ....................... Passed 10.92 sec
Start 2: step.release
2/6 Test #2: step.release ..................... Passed 9.01 sec
Start 3: affinity.debug
3/6 Test #3: affinity.debug ................... Passed 9.07 sec
Start 4: mpi.debug
4/6 Test #4: mpi.debug ........................ Passed 11.29 sec
Start 5: tbb.debug
5/6 Test #5: tbb.debug ........................ Passed 9.16 sec
Start 6: p4est.debug
6/6 Test #6: p4est.debug ...................... Passed 10.57 sec


100% tests passed, 0 tests failed out of 6


Total Test time (real) = 60.01 sec
Built target test

Thanks for your kind assistance always. I am so grateful!!!

Ofosu Joseph.