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ORNL-Fusion / PARVMEC

3D Equilibrium Solver
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undefined reference to symbol 'MPI_Rsend' and error adding symbols: DSO missing from command line #34

Open sun51027 opened 1 year ago

sun51027 commented 1 year ago

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 commented 1 year ago

To help debug this, you can run the make file with

make VERBOSE=1

to see the command that is sent to the compiler. But it looks like it’s missing the mpi library when linking the final executables.

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From: sun51027 @.> Sent: Friday, June 30, 2023 2:49:13 AM To: ORNL-Fusion/PARVMEC @.> Cc: Subscribed @.***> Subject: [EXTERNAL] [ORNL-Fusion/PARVMEC] undefined reference to symbol 'MPI_Rsend' and error adding symbols: DSO missing from command line (Issue #34)

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!

— Reply to this email directly, view it on GitHubhttps://urldefense.us/v2/url?u=https-3A__github.com_ORNL-2DFusion_PARVMEC_issues_34&d=DwMCaQ&c=v4IIwRuZAmwupIjowmMWUmLasxPEgYsgNI-O7C4ViYc&r=jHzqd7h8AUyesPAQHKZPYGMox50RMWt0Xdplk3LbqH8&m=sU9qeKDNGWlIW5Rl4uD8EjaXXvX9_J79BYAxeiimL1pyAreYaydTAtvjrl-TfSN5&s=6QKf-irONVGb3vJyREtyUt7EvkFmgeix1FSBrtxSdkU&e=, or unsubscribehttps://urldefense.us/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ADAPYD7ZIBSZNPIJD26CGMLXNZZGTANCNFSM6AAAAAAZZN3NKI&d=DwMCaQ&c=v4IIwRuZAmwupIjowmMWUmLasxPEgYsgNI-O7C4ViYc&r=jHzqd7h8AUyesPAQHKZPYGMox50RMWt0Xdplk3LbqH8&m=sU9qeKDNGWlIW5Rl4uD8EjaXXvX9_J79BYAxeiimL1pyAreYaydTAtvjrl-TfSN5&s=tv2cx_wrpGpfYTkXFblcCEOTeJcDnudlL5FlA58pd9E&e=. You are receiving this because you are subscribed to this thread.Message ID: @.***>

sun51027 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

The error that you’re seeing is only in one of the test utilities and is not needed for compiling just VMEC if you run

make help

You can get a list of targets you can build

make xvmec

will build just the VMEC tool and it’s associated dependencies and should avoid the problem until I can up load a fix.

Mark

On Jul 2, 2023, at 4:09 AM, sun51027 @.**@.>> wrote:

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!

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sun51027 commented 1 year ago

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 commented 1 year ago

The test utilities are only for the ci_test. I did some digging and this looks like a bug in the gnu compiler that was fixed in a later version. If you want to run some test cases, there are example vmec cases in

PARVMEC/Testing/tests

On Jul 12, 2023, at 3:18 AM, sun51027 @.**@.>> wrote:

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!

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