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undefined reference to symbol 'MPI_Rsend' and error adding symbols: DSO missing from command line #34

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sun51027 opened this issue Jun 30, 2023 · 9 comments
Open

undefined reference to symbol 'MPI_Rsend' and error adding symbols: DSO missing from command line #34

sun51027 opened this issue Jun 30, 2023 · 9 comments

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@sun51027
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Hi
I have problems with "make" files.
I follow the guide in Stellarator-Tools, and cmake runs well.
While when compiling ("make"), error occurred:

/usr/bin/ld: /home/linshih/Library/scalapack/build/lib/libscalapack.a(BI_Rsend.c.o): undefined reference to symbol 'MPI_Rsend'
/home/linshih/Library/openmpi-4.1.5/lib/libmpi.so: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
_deps/parvmec-build/CMakeFiles/xvmec.dir/build.make:106: recipe for target '_deps/parvmec-build/xvmec' failed
make[2]: *** [_deps/parvmec-build/xvmec] Error 1
CMakeFiles/Makefile2:929: recipe for target '_deps/parvmec-build/CMakeFiles/xvmec.dir/all' failed
make[1]: *** [_deps/parvmec-build/CMakeFiles/xvmec.dir/all] Error 2
Makefile:145: recipe for target 'all' failed
make: *** [all] Error 2.

Does it matter with my environment setting?
I've downloaded latest version SCALAPACK and OpenMPI and point them into correct paths, so cmake runs well. But I still don't understand what I should do to deal with this.
Thanks!
@cianciosa
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cianciosa commented Jun 30, 2023 via email

@sun51027
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Hi I tried make VERBOSE=1
I still don't know what exactly the problems are.

[ 98%] Linking Fortran executable xvmec
cd /home/linshih/testspace/Stellarator-Tools/build/_deps/parvmec-build && /home/linshih/cmake-3.26.4-linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/xvmec.dir/link.txt --verbose=1
/usr/bin/gfortran -Wl,-rpath -Wl,/usr/lib/openmpi/lib -Wl,--enable-new-dtags -L/usr/lib/openmpi/lib -pthread CMakeFiles/xvmec.dir/Sources/TimeStep/vmec.f.o -o xvmec  -Wl,-rpath,/home/linshih/Library/openmpi-4.1.5/lib: libvmec.a ../libstell-build/libstell.a /home/linshih/Library/openmpi-4.1.5/lib/libmpi_usempif08.so /home/linshih/Library/openmpi-4.1.5/lib/libmpi_usempi_ignore_tkr.so /home/linshih/Library/openmpi-4.1.5/lib/libmpi_mpifh.so /home/linshih/Library/openmpi-4.1.5/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libnetcdff.so /usr/lib/x86_64-linux-gnu/libnetcdf.so /home/linshih/Library/scalapack/build/lib/libscalapack.a /usr/lib/libblas.so /usr/lib/liblapack.so
/usr/bin/ld: /home/linshih/Library/scalapack/build/lib/libscalapack.a(BI_Rsend.c.o): undefined reference to symbol 'MPI_Rsend'
/home/linshih/Library/openmpi-4.1.5/lib/libmpi.so: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
_deps/parvmec-build/CMakeFiles/xvmec.dir/build.make:106: recipe for target '_deps/parvmec-build/xvmec' failed

Is it possible that the gfortran or other lib like mpi too old so it fails?
I guessed "openmpi" in my /usr/lib/ could be obsolete, so I installed the latest version openmpi-4.5.1 in my home directory lest affect other users on the server.
(I've done this cmake -DCMAKE_PREFIX_PATH=/home/linshih/Library/openmpi-4.1.5/lib)
Thank you!

@cianciosa
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I think the problem is the order that the MPI and Scalapack libraries are being linked. In the LIBSTELL/CMakeLists.txt file change

target_link_libraries (stell

                       PUBLIC

                       $<$<BOOL:${MPI_Fortran_FOUND}>:MPI::MPI_Fortran>
                       $<$<BOOL:${NetCDF_FOUND}>:NetCDF::NetCDF>
                       $<$<BOOL:${SCALAPACK_FOUND}>:SCALAPACK::SCALAPACK>
                       $<$<AND:$<BOOL:${BLAS_FOUND}>,$<VERSION_GREATER_EQUAL:${CMAKE_VERSION},3.18>>:BLAS::BLAS>
                       $<$<AND:$<BOOL:${LAPACK_FOUND}>,$<VERSION_GREATER_EQUAL:${CMAKE_VERSION},3.18>>:LAPACK::LAPACK>
                       $<$<AND:$<BOOL:${BLAS_FOUND}>,$<VERSION_LESS:${CMAKE_VERSION},3.18>>:${BLAS_LIBRARIES}>
                       $<$<AND:$<BOOL:${LAPACK_FOUND}>,$<VERSION_LESS:${CMAKE_VERSION},3.18>>:${LAPACK_LIBRARIES}>
)

to

target_link_libraries (stell

                       PUBLIC

                       $<$<BOOL:${NetCDF_FOUND}>:NetCDF::NetCDF>
                       $<$<BOOL:${SCALAPACK_FOUND}>:SCALAPACK::SCALAPACK>
                       $<$<BOOL:${MPI_Fortran_FOUND}>:MPI::MPI_Fortran>
                       $<$<AND:$<BOOL:${BLAS_FOUND}>,$<VERSION_GREATER_EQUAL:${CMAKE_VERSION},3.18>>:BLAS::BLAS>
                       $<$<AND:$<BOOL:${LAPACK_FOUND}>,$<VERSION_GREATER_EQUAL:${CMAKE_VERSION},3.18>>:LAPACK::LAPACK>
                       $<$<AND:$<BOOL:${BLAS_FOUND}>,$<VERSION_LESS:${CMAKE_VERSION},3.18>>:${BLAS_LIBRARIES}>
                       $<$<AND:$<BOOL:${LAPACK_FOUND}>,$<VERSION_LESS:${CMAKE_VERSION},3.18>>:${LAPACK_LIBRARIES}>
)

and see if that fixes things.

@sun51027
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sun51027 commented Jul 2, 2023

Thank you so much! This fixed DSO missing problem, and passed "Linking Fortran executable xvmec" .
But another problem occurred:

[ 98%] Linking Fortran executable xvmec
[ 98%] Built target xvmec
[ 98%] Building CXX object _deps/parvmec-build/CMakeFiles/xwout_diff.dir/Testing/test_utilities/wout_diff.cpp.o
[ 98%] Building CXX object _deps/parvmec-build/CMakeFiles/xwout_diff.dir/Testing/test_utilities/vmec_test_commandline_parser.cpp.o
/home/linshih/testspace/Stellarator-Tools/PARVMEC/Testing/test_utilities/vmec_test_commandline_parser.cpp:15:74: error: specialization of ‘template<class TYPE> TYPE vmec_test::commandline_parser::get(const string&) const’ in different namespace [-fpermissive]
 vmec_test::commandline_parser::get<std::string> (const std::string &key) const {
                                                                          ^
In file included from /home/linshih/testspace/Stellarator-Tools/PARVMEC/Testing/test_utilities/vmec_test_commandline_parser.cpp:6:0:
/home/linshih/testspace/Stellarator-Tools/PARVMEC/Testing/test_utilities/vmec_test_commandline_parser.hpp:99:14: error:   from definition of ‘template<class TYPE> TYPE vmec_test::commandline_parser::get(const string&) const’ [-fpermissive]
         TYPE get(const std::string &key) const {
              ^
_deps/parvmec-build/CMakeFiles/xwout_diff.dir/build.make:89: recipe for target '_deps/parvmec-build/CMakeFiles/xwout_diff.dir/Testing/test_utilities/vmec_test_commandline_parser.cpp.o' failed

Does this relate to my environment setting?
Thank you again!

@cianciosa cianciosa mentioned this issue Jul 2, 2023
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@cianciosa
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No that's just a coding error on my part. What compiler, version of that compiler, and platform are you trying to build on?

@sun51027
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sun51027 commented Jul 2, 2023

Compiler:
The Fortran compiler identification is GNU 5.4.0

I use the server of our instituite, it is ubuntu:

No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 16.04.7 LTS
Release:	16.04

Other information
Found OpenMP_C: -fopenmp (found version "4.0")
Found OpenMP_CXX: -fopenmp (found version "4.0")
Found OpenMP_Fortran: -fopenmp (found version "4.0")
Found OpenMP: TRUE (found version "4.0")
Found NetCDF: /usr/lib/x86_64-linux-gnu/libnetcdf.so (found version "4.4.0")
Found SCALAPACK: /home/linshih/Library/scalapack/build/lib/libscalapack.a
Found MPI_C: /home/linshih/Library/openmpi-4.1.5/lib/libmpi.so (found version "3.1")
Found MPI_CXX: /home/linshih/Library/openmpi-4.1.5/lib/libmpi.so (found version "3.1")
Found MPI_Fortran: /home/linshih/Library/openmpi-4.1.5/lib/libmpi_usempif08.so (found version "3.1")
Found MPI: TRUE (found version "3.1")

Thank you!

@cianciosa
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cianciosa commented Jul 5, 2023 via email

@sun51027
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I would also like to have a test run, so if test utilities are able to run, this may help me a lot.
Thank you so much!

@cianciosa
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cianciosa commented Jul 12, 2023 via email

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@cianciosa @sun51027