Problem When Install svFSI by Souce

[Yurui Chen]

Dear developer:

I am installing the svFSI by source. After entering the Prefix_Path with Trilinos, and changing the compiler to gcc & g++, I ran make but met:

CMakeFiles/svFSI.dir/trilinos_linear_solver.cpp.o: In function `trilinos_lhs_create_':
/home/yurui/software/svFSI/svFSI-master/Code/Source/svFSI/trilinos_linear_solver.cpp:162: undefined reference to `Epetra_MpiComm::Epetra_MpiComm(int)'
/home/yurui/software/svFSI/svFSI-master/Code/Source/svFSI/trilinos_linear_solver.cpp:162: undefined reference to `Epetra_MpiComm::~Epetra_MpiComm()'
/home/yurui/software/svFSI/svFSI-master/Code/Source/svFSI/trilinos_linear_solver.cpp:162: undefined reference to `Epetra_MpiComm::~Epetra_MpiComm()'
/usr/local/lib/libepetra.a(Epetra_LAPACK.cpp.o): In function `Epetra_LAPACK::GGSVD(char, char, char, int, int, int, int*, int*, double*, int, double*, int, double*, double*, double*, int, double*, int, double*, int, double*, int*, int*) const':
Epetra_LAPACK.cpp:(.text+0x1485): undefined reference to `dggsvd_'
/usr/local/lib/libepetra.a(Epetra_LAPACK.cpp.o): In function `Epetra_LAPACK::GGSVD(char, char, char, int, int, int, int*, int*, float*, int, float*, int, float*, float*, float*, int, float*, int, float*, int, float*, int*, int*) const':
Epetra_LAPACK.cpp:(.text+0x1565): undefined reference to `sggsvd_'
collect2: error: ld returned 1 exit status
Source/svFSI/CMakeFiles/svFSI.dir/build.make recipe for target 'bin/svFSI' failed
make[2]: *** [bin/svFSI] Error 1
CMakeFiles/Makefile2:440: recipe for target 'Source/svFSI/CMakeFiles/svFSI.dir/all' failed
make[1]: *** [Source/svFSI/CMakeFiles/svFSI.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2

I know this undefined reference to might mean that Epetra is not linked. What's the solution of it?

Thanks,
Yurui

[David Parker]

Hi Yurui,

What OS are you are you trying to build for and what version of LAPACK are you using?

Cheers,
Dave

[Jijo Derick Abraham]

Hai,
I was trying to build svFSI from source code using Trilinos in ubuntu 20.04.
I have just followed the instructions in https://simvascular.github.io/docssvFSI ... urce_build

After running the final 'make' command,
I am also getting similar kind of error.

Code: Select all

/usr/bin/ld: /home/baadalvm/Trilinos_build/lib/libepetra.a(Epetra_LAPACK.cpp.o): in function `E, int, int*, int*, double*, int, double*, int, double*, double*, double*, int, double*, int, do
Epetra_LAPACK.cpp:(.text+0x15a9): undefined reference to `dggsvd_'
/usr/bin/ld: /home/baadalvm/Trilinos_build/lib/libepetra.a(Epetra_LAPACK.cpp.o): in function `E, int, int*, int*, float*, int, float*, int, float*, float*, float*, int, float*, int, float*, 
Epetra_LAPACK.cpp:(.text+0x1689): undefined reference to `sggsvd_'
collect2: error: ld returned 1 exit status
make[5]: *** [Source/svFSI/CMakeFiles/svFSI.dir/build.make:1204: bin/svFSI] Error 1
make[4]: *** [CMakeFiles/Makefile2:403: Source/svFSI/CMakeFiles/svFSI.dir/all] Error 2
make[3]: *** [Makefile:136: all] Error 2
make[2]: *** [CMakeFiles/svFSI.dir/build.make:86: svFSI-prefix/src/svFSI-stamp/svFSI-build] Err
make[1]: *** [CMakeFiles/Makefile2:85: CMakeFiles/svFSI.dir/all] Error 2
make: *** [Makefile:91: all] Error 2

I am having the LAPACK 3.9.0 on my machine.
Please provide suggestions to resolve this error.

[David Parker]

Hi Jijo,

Have a look here https://github.com/SimVascular/svFSI for up-to-date instructions about how to build svFSI.

I believe that you can also just install Trilinos, don't need to build it. See https://ubuntu.pkgs.org/20.04/ubuntu-un ... 4.deb.html

Cheers,
Dave

[Jijo Derick Abraham]

Hi Dave,
As you said, I have tried the latest instruction given in https://github.com/SimVascular/svFSI.
Hence, first I started installing the dependencies as per the instructions in https://github.com/SimVascular/svFSI/bl ... LL-DEPS.md.
I felt there are few typo mistakes in those commands, but they are manageable.
For example,

• in mpich and boost installation cases -p was missing while making the equivalent directory in /opt/

• And in hdf5 installation case

  Code: Select all

  ccmake .. 

  command was missing.

Again these are manageable


However in the case lapack shared and static library installation, I request you to please cross check the installation commands.
Because after installation I am getting empty directories in
/opt/netlib/lapack/3.9.1/shared
and
/opt/netlib/lapack/3.9.1/static

Also when i proceed to installation of hypre, it is not getting installed,
when i tried the

Code: Select all

sudo make install

in the case of hypre, I am getting the following error

Code: Select all

make[1]: Entering directory '/home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/lib'
Building libHYPRE.so ... 
mpicc -shared  -o libHYPRE-2.22.0.so   /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/IJ_mv/*.o* /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/distributed_ls/Euclid/*.o /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/distributed_ls/ParaSails/*.o /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/distributed_ls/pilut/*.o /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/distributed_matrix/*.o* /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/krylov/*.o* /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/matrix_matrix/*.o* /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/multivector/*.o* /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/parcsr_ls/*.o* /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/parcsr_mv/*.o* /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/parcsr_block_mv/*.o* /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/seq_mv/*.o* /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/sstruct_ls/*.o* /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/sstruct_mv/*.o* /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/struct_ls/*.o* /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/struct_mv/*.o* /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/utilities/*.o* /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/blas/*.o* /home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/lapack/*.o*    null -llapack null -lblas -lm           -Wl,-soname,libHYPRE-2.22.0.so -Wl,-z,defs 
gcc: error: null: No such file or directory
gcc: error: null: No such file or directory
Makefile:100: recipe for target 'libHYPRE.so' failed
make[1]: *** [libHYPRE.so] Error 1
make[1]: Leaving directory '/home/jijo/dependencies_for_svfsi/hypre/hypre-2.22.0/src/lib'
Makefile:86: recipe for target 'all' failed
make: *** [all] Error 1

I have tired these installation in both and ubuntu 18.04 and 20.04, I am getting the same error in both.
I think, the the problem is due to lapack only.
Pardon me, If I am wrong.
Please cross check the installation instructions.

Thanks in advance

[David Parker]

Hi Jijo,

The instructions here https://github.com/SimVascular/svFSI/bl ... LL-DEPS.md state that you are encouraged to use package managers such as apt for Ubuntu. You should not be building anything from source except perhaps Trilinos.

Code: Select all

sudo apt update
sudo apt install liblapack-dev
sudo apt install libblas-dev
sudo apt install libopenmpi-dev
sudo apt install openmpi-bin
sudo apt install cmake
sudo apt install cmake-curses-gui

The documentation could use some improvement!

Cheers,
Dave