Compilation Elmer on OpenSUSE 13.2

Discussion about building and installing Elmer

Compilation Elmer on OpenSUSE 13.2

Postby DobesJ88 » 20 Dec 2016, 10:58

Hello to everyone,
I try to compile Elmer software package on the OpenSUSE 13.2 version software.
Start looks good, but after some installation I have got this error:

Code: Select all
Linking Fortran shared library libelmersolver.so
[ 83%] Built target elmersolver
Scanning dependencies of target GebhardtFactors
Scanning dependencies of target Solver_TGT
[ 83%] [ 83%] Building Fortran object fem/src/CMakeFiles/Solver_TGT.dir/Solver.F90.o
Building Fortran object fem/src/CMakeFiles/GebhardtFactors.dir/GebhardtFactors.F90.o
Linking Fortran executable ElmerSolver
libelmersolver.so: undefined reference to `mpi_comm_split_'
collect2: error: ld returned 1 exit status
fem/src/CMakeFiles/Solver_TGT.dir/build.make:89: návod pro cíl „fem/src/ElmerSolver“ selhal
make[2]: *** [fem/src/ElmerSolver] Chyba 1
CMakeFiles/Makefile2:630: návod pro cíl „fem/src/CMakeFiles/Solver_TGT.dir/all“ selhal
make[1]: *** [fem/src/CMakeFiles/Solver_TGT.dir/all] Chyba 2
make[1]: *** Čeká se na nedokončené úlohy…
Linking Fortran executable GebhardtFactors
libelmersolver.so: undefined reference to `mpi_comm_split_'
collect2: error: ld returned 1 exit status
fem/src/CMakeFiles/GebhardtFactors.dir/build.make:99: návod pro cíl „fem/src/GebhardtFactors“ selhal
make[2]: *** [fem/src/GebhardtFactors] Chyba 1
CMakeFiles/Makefile2:587: návod pro cíl „fem/src/CMakeFiles/GebhardtFactors.dir/all“ selhal
make[1]: *** [fem/src/CMakeFiles/GebhardtFactors.dir/all] Chyba 2
Makefile:147: návod pro cíl „all“ selhal
make: *** [all] Chyba 2


If I check the installation I obtain this list:

Code: Select all
# cmake -DWITH_ELMERGUI:BOOL=FALSE -DWITH_MPI:BOOL=FALSE -DCMAKE_INSTALL_PREFIX=../install ../elmerfem
-- The Fortran compiler identification is GNU
-- The C compiler identification is GNU 4.8.3
-- The CXX compiler identification is GNU 4.8.3
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Checking whether GFortran version >= 4.8 -- yes
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE 
-- A library with BLAS API found.
-- A library with BLAS API found.
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- A library with LAPACK API found.
-- Checking whether /usr/bin/gfortran supports PROCEDURE POINTER
-- Checking whether /usr/bin/gfortran supports PROCEDURE POINTER -- yes
-- Checking whether /usr/bin/gfortran supports CONTIGUOUS
-- Checking whether /usr/bin/gfortran supports CONTIGUOUS -- yes
-- Checking whether /usr/bin/gfortran supports EXECUTE_COMMAND_LINE
-- Checking whether /usr/bin/gfortran supports EXECUTE_COMMAND_LINE -- yes
-- Looking for include file inttypes.h
-- Looking for include file inttypes.h - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of long
-- Check size of long - done
-- Found 105 modules from /home/dobes/elmer/elmerfem/fem/src/modules
-- Found 429 tests
-- ------------------------------------------------
--   BLAS library:   /usr/lib64/libblas.so
--   LAPACK library: /usr/lib64/liblapack.so;/usr/lib64/libblas.so
-- ------------------------------------------------
--   Fortran compiler:        /usr/bin/gfortran
--   Fortran flags:            -O2 -g -DNDEBUG
-- ------------------------------------------------
--   C compiler:              /usr/bin/cc
--   C flags:                  -O2 -g -DNDEBUG
-- ------------------------------------------------
--   CXX compiler:            /usr/bin/c++
--   CXX flags:                -O2 -g -DNDEBUG
-- ------------------------------------------------
-- ------------------------------------------------
--   Package filename: elmerfem-8.2-bc737be-20161220_Linux-x86_64
--   Patch version: 8.2-bc737be
-- Configuring done
-- Generating done
-- Build files have been written to: /home/dobes/elmer/build


Where do I found the library with pthread_create?
Many thanks for everyone who helps me with this problem.
DobesJ88
 
Posts: 5
Joined: 18 Dec 2016, 04:22

Re: Compilation Elmer on OpenSUSE 13.2

Postby vencels » 20 Dec 2016, 11:32

You are using Elmer version from git repository which is constantly under development.
Two options:
1) Try to download stable release from https://sourceforge.net/projects/elmerfem/
2) or if you want to use git version then compile with mpi enabled
Code: Select all
-DWITH_MPI=TRUE
vencels
 
Posts: 19
Joined: 20 Sep 2016, 17:05
Location: Latvia

Re: Compilation Elmer on OpenSUSE 13.2

Postby DobesJ88 » 21 Dec 2016, 12:13

Hello,
Many thanks to vencels for the good advice!!! It finally works.

If I check the instalation I occured this error:
Code: Select all
  2/469 Test #139: WinkelPartitionMetisConnect_np8 .......***Failed    2.83 sec
        Start 311: ContactBlunt2Dstick
        Start  13: WinkelPoissonMetisKwayDual


Final results of test:

Code: Select all
99% tests passed, 1 tests failed out of 469

Label Time Summary:
aster        =  23.87 sec
benchmark    = 345.97 sec
contact      = 287.07 sec
eliminate    =   2.27 sec
elmerice     = 662.56 sec
heateq       = 611.18 sec
hutiter      =   6.90 sec
parallel     = 680.80 sec
particle     =  81.67 sec
quick        = 241.30 sec
serial       = 4468.37 sec
slow         = 662.56 sec
threaded     =  21.88 sec
whitney      = 1256.24 sec

Total Test time (real) = 1303.60 sec

The following tests FAILED:
   139 - WinkelPartitionMetisConnect_np8 (Failed)
Errors while running CTest


How can I fix it?

Once again many thanks for your help. If I ask how do you recognize where is the problem?

THX and Merry Xmas.
DobesJ88
 
Posts: 5
Joined: 18 Dec 2016, 04:22

Re: Compilation Elmer on OpenSUSE 13.2

Postby annier » 22 Dec 2016, 10:04

Hi DobesJ88,
The above mentioned fail in ctest or test does not mean an unsuccesful compilation (you don't need to worry on this topic) . you have a successful Elmer compilation or installation in your machine.


Yours Sincerely,
Anil Kunwar
annier
 
Posts: 1043
Joined: 27 Aug 2013, 13:51

Re: Compilation Elmer on OpenSUSE 13.2

Postby DobesJ88 » 22 Dec 2016, 13:51

Hi annier,
many thanks for this information. So I really excited from Elmer software package and from successful instalation on my computer too.

Yours Sincerly,
Josef Dobes
DobesJ88
 
Posts: 5
Joined: 18 Dec 2016, 04:22


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