[petsc-users] suppress CUDA warning & choose MCA parameter for mpirun during make PETSC_ARCH=arch-linux-c-debug check
Rob Kudyba
rk3199 at columbia.edu
Mon Oct 10 08:12:53 CDT 2022
>
> OK, let's walk back and don't use -DCMAKE_C_COMPILER=/path/to/mpicc
>
Will do
> libompitrace.so.40.30.0 is not the OpenMP library; it is the tracing
> library for OpenMPI, https://github.com/open-mpi/ompi/issues/10036
>
Does that mean I should remove this option in the cmake command?
> In your previous email, there was
>
> /path/to/cmake/cmake-3.22.1-linux-x86_64/bin/cmake -E cmake_link_script
> CMakeFiles/wtm.x.dir/link.txt --verbose=1
> /cm/local/apps/gcc/10.2.0/bin/c++ -isystem -O3 -g -Wall -Wextra -pedantic
> -Wshadow CMakeFiles/wtm.x.dir/src/WTM.cpp.o -o wtm.x
> -Wl,-rpath,/path/to/WTM/build/common/richdem:/path/to/
> gdal-3.3.0/lib:/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_
> support/lib:/path/to/petsc/arch-linux-cxx-debug/lib libwtm.a
> common/richdem/librichdem.so /path/to/gdal-3.3.0/lib/libgdal.so
> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0
> common/fmt/libfmt.a /path/to/petsc/arch-linux-cxx-debug/lib/libpetsc.so
> /usr/bin/ld: CMakeFiles/wtm.x.dir/src/WTM.cpp.o: undefined reference to
> symbol 'ompi_mpi_comm_self'
> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40: error
> adding symbols: DSO missing from command line
>
>
> Let's try to add -lmpi (or /path/to/openmpi-4.1.1_ucx_
> cuda_11.0.3_support/lib/libmpi.so) manually to see if it links
>
> /cm/local/apps/gcc/10.2.0/bin/c++ -isystem -O3 -g -Wall -Wextra -pedantic
> -Wshadow CMakeFiles/wtm.x.dir/src/WTM.cpp.o -o wtm.x
> -Wl,-rpath,/path/to/WTM/build/common/richdem:/path/to/
> gdal-3.3.0/lib:/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_
> support/lib:/path/to/petsc/arch-linux-cxx-debug/lib libwtm.a
> common/richdem/librichdem.so /path/to/gdal-3.3.0/lib/libgdal.so
> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0
> common/fmt/libfmt.a /path/to/petsc/arch-linux-cxx-debug/lib/libpetsc.so
> -lmpi
>
so just adding that to the make command? Sttil seeing linking errors:
make VERBOSE=1 LDFLAGS="-Wl,--copy-dt-needed-entries" -lmpi
/path/to/cmake/cmake-3.22.1-linux-x86_64/bin/cmake -S/path/to/WTM
-B/path/to/WTM/build --check-build-system CMakeFiles/Makefile.cmake 0
/path/to/cmake/cmake-3.22.1-linux-x86_64/bin/cmake -E cmake_progress_start
/path/to/WTM/build/CMakeFiles /path/to/WTM/build//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/path/to/WTM/build'
make -f common/fmt/CMakeFiles/fmt.dir/build.make
common/fmt/CMakeFiles/fmt.dir/depend
make[2]: Entering directory '/path/to/WTM/build'
cd /path/to/WTM/build && /path/to/cmake/cmake-3.22.1-linux-x86_64/bin/cmake
-E cmake_depends "Unix Makefiles" /path/to/WTM /path/to/WTM/common/fmt
/path/to/WTM/build /path/to/WTM/build/common/fmt
/path/to/WTM/build/common/fmt/CMakeFiles/fmt.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/path/to/WTM/build'
make -f common/fmt/CMakeFiles/fmt.dir/build.make
common/fmt/CMakeFiles/fmt.dir/build
make[2]: Entering directory '/path/to/WTM/build'
[ 4%] Building CXX object common/fmt/CMakeFiles/fmt.dir/src/format.cc.o
cd /path/to/WTM/build/common/fmt && /cm/local/apps/gcc/10.2.0/bin/c++
-I/path/to/WTM/common/fmt/include -isystem -std=gnu++11 -MD -MT
common/fmt/CMakeFiles/fmt.dir/src/format.cc.o -MF
CMakeFiles/fmt.dir/src/format.cc.o.d -o CMakeFiles/fmt.dir/src/format.cc.o
-c /path/to/WTM/common/fmt/src/format.cc
[ 8%] Building CXX object common/fmt/CMakeFiles/fmt.dir/src/os.cc.o
cd /path/to/WTM/build/common/fmt && /cm/local/apps/gcc/10.2.0/bin/c++
-I/path/to/WTM/common/fmt/include -isystem -std=gnu++11 -MD -MT
common/fmt/CMakeFiles/fmt.dir/src/os.cc.o -MF
CMakeFiles/fmt.dir/src/os.cc.o.d -o CMakeFiles/fmt.dir/src/os.cc.o -c
/path/to/WTM/common/fmt/src/os.cc
[ 12%] Linking CXX static library libfmt.a
cd /path/to/WTM/build/common/fmt &&
/path/to/cmake/cmake-3.22.1-linux-x86_64/bin/cmake -P
CMakeFiles/fmt.dir/cmake_clean_target.cmake
cd /path/to/WTM/build/common/fmt &&
/path/to/cmake/cmake-3.22.1-linux-x86_64/bin/cmake -E cmake_link_script
CMakeFiles/fmt.dir/link.txt --verbose=1
/usr/bin/ar qc libfmt.a CMakeFiles/fmt.dir/src/format.cc.o
CMakeFiles/fmt.dir/src/os.cc.o
/usr/bin/ranlib libfmt.a
make[2]: Leaving directory '/path/to/WTM/build'
[ 12%] Built target fmt
make -f common/richdem/CMakeFiles/richdem.dir/build.make
common/richdem/CMakeFiles/richdem.dir/depend
make[2]: Entering directory '/path/to/WTM/build'
cd /path/to/WTM/build && /path/to/cmake/cmake-3.22.1-linux-x86_64/bin/cmake
-E cmake_depends "Unix Makefiles" /path/to/WTM /path/to/WTM/common/richdem
/path/to/WTM/build /path/to/WTM/build/common/richdem
/path/to/WTM/build/common/richdem/CMakeFiles/richdem.dir/DependInfo.cmake
--color=
make[2]: Leaving directory '/path/to/WTM/build'
make -f common/richdem/CMakeFiles/richdem.dir/build.make
common/richdem/CMakeFiles/richdem.dir/build
make[2]: Entering directory '/path/to/WTM/build'
[ 16%] Building CXX object
common/richdem/CMakeFiles/richdem.dir/src/richdem.cpp.o
cd /path/to/WTM/build/common/richdem && /cm/local/apps/gcc/10.2.0/bin/c++
-Drichdem_EXPORTS -I/path/to/WTM/common/richdem/include
-I/path/to/gdal-3.3.0/include -isystem -fPIC
-DRICHDEM_GIT_HASH=\"3313b290725509d694da1fba83d0f32cca68cc70\"
-DRICHDEM_COMPILE_TIME=\"2022-10-10T13:09:39Z\" -DUSEGDAL -Xpreprocessor
-fopenmp
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40.30.1
-I/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/include -std=gnu++17 -MD
-MT common/richdem/CMakeFiles/richdem.dir/src/richdem.cpp.o -MF
CMakeFiles/richdem.dir/src/richdem.cpp.o.d -o
CMakeFiles/richdem.dir/src/richdem.cpp.o -c
/path/to/WTM/common/richdem/src/richdem.cpp
c++: warning:
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40.30.1:
linker input file unused because linking not done
[ 20%] Building CXX object
common/richdem/CMakeFiles/richdem.dir/src/random.cpp.o
cd /path/to/WTM/build/common/richdem && /cm/local/apps/gcc/10.2.0/bin/c++
-Drichdem_EXPORTS -I/path/to/WTM/common/richdem/include
-I/path/to/gdal-3.3.0/include -isystem -fPIC
-DRICHDEM_GIT_HASH=\"3313b290725509d694da1fba83d0f32cca68cc70\"
-DRICHDEM_COMPILE_TIME=\"2022-10-10T13:09:39Z\" -DUSEGDAL -Xpreprocessor
-fopenmp
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40.30.1
-I/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/include -std=gnu++17 -MD
-MT common/richdem/CMakeFiles/richdem.dir/src/random.cpp.o -MF
CMakeFiles/richdem.dir/src/random.cpp.o.d -o
CMakeFiles/richdem.dir/src/random.cpp.o -c
/path/to/WTM/common/richdem/src/random.cpp
c++: warning:
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40.30.1:
linker input file unused because linking not done
[ 25%] Building CXX object
common/richdem/CMakeFiles/richdem.dir/src/gdal.cpp.o
cd /path/to/WTM/build/common/richdem && /cm/local/apps/gcc/10.2.0/bin/c++
-Drichdem_EXPORTS -I/path/to/WTM/common/richdem/include
-I/path/to/gdal-3.3.0/include -isystem -fPIC
-DRICHDEM_GIT_HASH=\"3313b290725509d694da1fba83d0f32cca68cc70\"
-DRICHDEM_COMPILE_TIME=\"2022-10-10T13:09:39Z\" -DUSEGDAL -Xpreprocessor
-fopenmp
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40.30.1
-I/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/include -std=gnu++17 -MD
-MT common/richdem/CMakeFiles/richdem.dir/src/gdal.cpp.o -MF
CMakeFiles/richdem.dir/src/gdal.cpp.o.d -o
CMakeFiles/richdem.dir/src/gdal.cpp.o -c
/path/to/WTM/common/richdem/src/gdal.cpp
c++: warning:
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40.30.1:
linker input file unused because linking not done
[ 29%] Building CXX object
common/richdem/CMakeFiles/richdem.dir/src/terrain_generation/terrain_generation.cpp.o
cd /path/to/WTM/build/common/richdem && /cm/local/apps/gcc/10.2.0/bin/c++
-Drichdem_EXPORTS -I/path/to/WTM/common/richdem/include
-I/path/to/gdal-3.3.0/include -isystem -fPIC
-DRICHDEM_GIT_HASH=\"3313b290725509d694da1fba83d0f32cca68cc70\"
-DRICHDEM_COMPILE_TIME=\"2022-10-10T13:09:39Z\" -DUSEGDAL -Xpreprocessor
-fopenmp
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40.30.1
-I/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/include -std=gnu++17 -MD
-MT
common/richdem/CMakeFiles/richdem.dir/src/terrain_generation/terrain_generation.cpp.o
-MF
CMakeFiles/richdem.dir/src/terrain_generation/terrain_generation.cpp.o.d -o
CMakeFiles/richdem.dir/src/terrain_generation/terrain_generation.cpp.o -c
/path/to/WTM/common/richdem/src/terrain_generation/terrain_generation.cpp
c++: warning:
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40.30.1:
linker input file unused because linking not done
[ 33%] Building CXX object
common/richdem/CMakeFiles/richdem.dir/src/terrain_generation/PerlinNoise.cpp.o
cd /path/to/WTM/build/common/richdem && /cm/local/apps/gcc/10.2.0/bin/c++
-Drichdem_EXPORTS -I/path/to/WTM/common/richdem/include
-I/path/to/gdal-3.3.0/include -isystem -fPIC
-DRICHDEM_GIT_HASH=\"3313b290725509d694da1fba83d0f32cca68cc70\"
-DRICHDEM_COMPILE_TIME=\"2022-10-10T13:09:39Z\" -DUSEGDAL -Xpreprocessor
-fopenmp
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40.30.1
-I/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/include -std=gnu++17 -MD
-MT
common/richdem/CMakeFiles/richdem.dir/src/terrain_generation/PerlinNoise.cpp.o
-MF CMakeFiles/richdem.dir/src/terrain_generation/PerlinNoise.cpp.o.d -o
CMakeFiles/richdem.dir/src/terrain_generation/PerlinNoise.cpp.o -c
/path/to/WTM/common/richdem/src/terrain_generation/PerlinNoise.cpp
c++: warning:
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40.30.1:
linker input file unused because linking not done
[ 37%] Linking CXX shared library librichdem.so
cd /path/to/WTM/build/common/richdem &&
/path/to/cmake/cmake-3.22.1-linux-x86_64/bin/cmake -E cmake_link_script
CMakeFiles/richdem.dir/link.txt --verbose=1
/cm/local/apps/gcc/10.2.0/bin/c++ -fPIC -isystem -shared
-Wl,-soname,librichdem.so -o librichdem.so
CMakeFiles/richdem.dir/src/richdem.cpp.o
CMakeFiles/richdem.dir/src/random.cpp.o
CMakeFiles/richdem.dir/src/gdal.cpp.o
CMakeFiles/richdem.dir/src/terrain_generation/terrain_generation.cpp.o
CMakeFiles/richdem.dir/src/terrain_generation/PerlinNoise.cpp.o
-Wl,-rpath,/path/to/gdal-3.3.0/lib:/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib:
/path/to/gdal-3.3.0/lib/libgdal.so
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0
/lib/../lib64/crt1.o: In function `_start':
(.text+0x24): undefined reference to `main'
CMakeFiles/richdem.dir/src/random.cpp.o: In function
`richdem::rand_engine()':
random.cpp:(.text+0x45): undefined reference to `omp_get_thread_num'
CMakeFiles/richdem.dir/src/random.cpp.o: In function
`richdem::seed_rand(unsigned long)':
random.cpp:(.text+0xb6): undefined reference to `GOMP_parallel'
CMakeFiles/richdem.dir/src/random.cpp.o: In function
`richdem::uniform_rand_int(int, int)':
random.cpp:(.text+0x10c): undefined reference to `omp_get_thread_num'
CMakeFiles/richdem.dir/src/random.cpp.o: In function
`richdem::uniform_rand_real(double, double)':
random.cpp:(.text+0x1cb): undefined reference to `omp_get_thread_num'
CMakeFiles/richdem.dir/src/random.cpp.o: In function
`richdem::normal_rand(double, double)':
random.cpp:(.text+0x29e): undefined reference to `omp_get_thread_num'
CMakeFiles/richdem.dir/src/random.cpp.o: In function
`richdem::seed_rand(unsigned long) [clone ._omp_fn.0]':
random.cpp:(.text+0x4a3): undefined reference to `GOMP_critical_start'
random.cpp:(.text+0x4b1): undefined reference to `GOMP_critical_end'
random.cpp:(.text+0x4c3): undefined reference to `omp_get_thread_num'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Comm_rank'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Get_address'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Comm_get_name'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Add_error_string'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Type_get_name'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Abort'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Alloc_mem'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Isend'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Barrier'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Allgather'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Reduce'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Send'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Init'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Type_size'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Accumulate'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Add_error_class'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Finalize'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Allgatherv'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Bcast'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Recv'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Request_free'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Allreduce'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `ompi_mpi_comm_world'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Sendrecv'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Add_error_code'
/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
undefined reference to `PMPI_Win_get_name'
collect2: error: ld returned 1 exit status
make[2]: *** [common/richdem/CMakeFiles/richdem.dir/build.make:163:
common/richdem/librichdem.so] Error 1
make[2]: Leaving directory '/path/to/WTM/build'
make[1]: *** [CMakeFiles/Makefile2:306:
common/richdem/CMakeFiles/richdem.dir/all] Error 2
make[1]: Leaving directory '/path/to/WTM/build'
make: *** [Makefile:136: all] Error 2
> On Sun, Oct 9, 2022 at 9:28 PM Rob Kudyba <rk3199 at columbia.edu> wrote:
>
>> I did have -DMPI_CXX_COMPILER set, so I added -DCMAKE_C_COMPILER and now
>> get these errors:
>>
>> [ 25%] Linking CXX shared library librichdem.so
>> /lib/../lib64/crt1.o: In function `_start':
>> (.text+0x24): undefined reference to `main'
>> CMakeFiles/richdem.dir/src/random.cpp.o: In function
>> `richdem::rand_engine()':
>> random.cpp:(.text+0x45): undefined reference to `omp_get_thread_num'
>> CMakeFiles/richdem.dir/src/random.cpp.o: In function
>> `richdem::seed_rand(unsigned long)':
>> random.cpp:(.text+0xb6): undefined reference to `GOMP_parallel'
>> CMakeFiles/richdem.dir/src/random.cpp.o: In function
>> `richdem::uniform_rand_int(int, int)':
>> random.cpp:(.text+0x10c): undefined reference to `omp_get_thread_num'
>> CMakeFiles/richdem.dir/src/random.cpp.o: In function
>> `richdem::uniform_rand_real(double, double)':
>> random.cpp:(.text+0x1cb): undefined reference to `omp_get_thread_num'
>> CMakeFiles/richdem.dir/src/random.cpp.o: In function
>> `richdem::normal_rand(double, double)':
>> random.cpp:(.text+0x29e): undefined reference to `omp_get_thread_num'
>> CMakeFiles/richdem.dir/src/random.cpp.o: In function
>> `richdem::seed_rand(unsigned long) [clone ._omp_fn.0]':
>> random.cpp:(.text+0x4a3): undefined reference to `GOMP_critical_start'
>> random.cpp:(.text+0x4b1): undefined reference to `GOMP_critical_end'
>> random.cpp:(.text+0x4c3): undefined reference to `omp_get_thread_num'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Comm_rank'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Get_address'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Comm_get_name'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Add_error_string'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Type_get_name'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Abort'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Alloc_mem'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Isend'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Barrier'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Allgather'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Reduce'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Send'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Init'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Type_size'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Accumulate'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Add_error_class'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Finalize'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Allgatherv'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Bcast'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Recv'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Request_free'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Allreduce'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `ompi_mpi_comm_world'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Sendrecv'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Add_error_code'
>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0:
>> undefined reference to `PMPI_Win_get_name'
>> collect2: error: ld returned 1 exit status
>> make[2]: *** [common/richdem/CMakeFiles/richdem.dir/build.make:163:
>> common/richdem/librichdem.so] Error 1
>> make[1]: *** [CMakeFiles/Makefile2:306:
>> common/richdem/CMakeFiles/richdem.dir/all] Error 2
>> make: *** [Makefile:136: all] Error 2
>>
>> I took a guess at using -DOpenMP_libomp_LIBRARY="/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0"
>> as
>> as otherwise I'd get:
>> CMake Error at
>> /path/to/cmake/cmake-3.22.1-linux-x86_64/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:230
>> (message):
>> Could NOT find OpenMP_CXX (missing: OpenMP_libomp_LIBRARY
>> OpenMP_libomp_LIBRARY) (found version "4.5")
>>
>> So perhaps that's the real problem?
>>
>> On Sun, Oct 9, 2022 at 9:31 PM Junchao Zhang <junchao.zhang at gmail.com>
>> wrote:
>>
>>> In the last link step to generate the executable
>>> /cm/local/apps/gcc/10.2.0/bin/c++ -isystem -O3 -g -Wall -Wextra
>>> -pedantic -Wshadow CMakeFiles/wtm.x.dir/src/WTM.cpp.o -o wtm.x
>>> -Wl,-rpath,/path/to/WTM/build/common/richdem:/path/to/
>>> gdal-3.3.0/lib:/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_
>>> support/lib:/path/to/petsc/arch-linux-cxx-debug/lib libwtm.a
>>> common/richdem/librichdem.so /path/to/gdal-3.3.0/lib/libgdal.so
>>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0
>>> common/fmt/libfmt.a /path/to/petsc/arch-linux-cxx-debug/lib/libpetsc.so
>>>
>>> I did not find -lmpi to link in the mpi library. You can try to use cmake
>>> -DCMAKE_C_COMPILER=/path/to/mpicc -DCMAKE_CXX_COMPILER=/path/to/mpicxx to
>>> build your code
>>>
>>> On Sat, Oct 8, 2022 at 9:32 PM Rob Kudyba <rk3199 at columbia.edu> wrote:
>>>
>>>> Perhaps we can back one step:
>>>>> Use your mpicc to build a "hello world" mpi test, then run it on a
>>>>> compute node (with GPU) to see if it works.
>>>>> If no, then your MPI environment has problems;
>>>>> If yes, then use it to build petsc (turn on petsc's gpu support,
>>>>> --with-cuda --with-cudac=nvcc), and then your code.
>>>>> --Junchao Zhang
>>>>
>>>> OK tried this just to eliminate that the CUDA-capable OpenMPI is a
>>>> factor:
>>>> ./configure --with-debugging=0 --with-cmake=true --with-mpi=true
>>>> --with-mpi-dir=/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support --with-fc=0
>>>> --with-cuda=1
>>>> [..]
>>>> cuda:
>>>> Version: 11.7
>>>> Includes: -I/path/to/cuda11.7/toolkit/11.7.1/include
>>>> Libraries: -Wl,-rpath,/path/to/cuda11.7/toolkit/11.7.1/lib64
>>>> -L/cm/shared/apps/cuda11.7/toolkit/11.7.1/lib64
>>>> -L/path/to/cuda11.7/toolkit/11.7.1/lib64/stubs -lcudart -lnvToolsExt
>>>> -lcufft -lcublas -lcusparse -lcusolver -lcurand -lcuda
>>>> CUDA SM 75
>>>> CUDA underlying compiler:
>>>> CUDA_CXX="/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/bin"/mpicxx
>>>> CUDA underlying compiler flags: CUDA_CXXFLAGS=
>>>> CUDA underlying linker libraries: CUDA_CXXLIBS=
>>>> [...]
>>>> Configure stage complete. Now build PETSc libraries with:
>>>> make PETSC_DIR=/path/to/petsc PETSC_ARCH=arch-linux-c-opt all
>>>>
>>>> C++ compiler version: g++ (GCC) 10.2.0
>>>> Using C++ compiler to compile PETSc
>>>> -----------------------------------------
>>>> Using C/C++ linker:
>>>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/bin/mpicxx
>>>> Using C/C++ flags: -Wall -Wwrite-strings -Wno-strict-aliasing
>>>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector
>>>> -fvisibility=hidden -g -O0
>>>> -----------------------------------------
>>>> Using system modules:
>>>> shared:slurm/20.02.6:DefaultModules:openmpi/gcc/64/4.1.1_cuda_11.0.3_aware:gdal/3.3.0:cmake/3.22.1:cuda11.7/toolkit/11.7.1:openblas/dynamic/0.3.7:gcc/10.2.0
>>>> Using mpi.h: # 1
>>>> "/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/include/mpi.h" 1
>>>> -----------------------------------------
>>>> Using libraries: -Wl,-rpath,/path/to/petsc/arch-linux-cxx-debug/lib
>>>> -L/path/to/petsc/arch-linux-cxx-debug/lib -lpetsc -lopenblas -lm -lX11
>>>> -lquadmath -lstdc++ -ldl
>>>> ------------------------------------------
>>>> Using mpiexec: mpiexec -mca orte_base_help_aggregate 0 -mca pml ucx
>>>> --mca btl '^openib'
>>>> ------------------------------------------
>>>> Using MAKE: /path/to/petsc/arch-linux-cxx-debug/bin/make
>>>> Using MAKEFLAGS: -j24 -l48.0 --no-print-directory -- MPIEXEC=mpiexec\
>>>> -mca\ orte_base_help_aggregate\ 0\ \ -mca\ pml\ ucx\ --mca\ btl\ '^openib'
>>>> PETSC_ARCH=arch-linux-cxx-debug PETSC_DIR=/path/to/petsc
>>>> ==========================================
>>>> make[3]: Nothing to be done for 'libs'.
>>>> =========================================
>>>> Now to check if the libraries are working do:
>>>> make PETSC_DIR=/path/to/petsc PETSC_ARCH=arch-linux-cxx-debug check
>>>> =========================================
>>>> [me at xxx petsc]$ make PETSC_DIR=/path/to/petsc
>>>> PETSC_ARCH=arch-linux-cxx-debug MPIEXEC="mpiexec -mca
>>>> orte_base_help_aggregate 0 -mca pml ucx --mca btl '^openib'" check
>>>> Running check examples to verify correct installation
>>>> Using PETSC_DIR=/path/to/petsc and PETSC_ARCH=arch-linux-cxx-debug
>>>> C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI
>>>> process
>>>> C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI
>>>> processes
>>>>
>>>> ./bandwidthTest
>>>> [CUDA Bandwidth Test] - Starting...
>>>> Running on...
>>>>
>>>> Device 0: Quadro RTX 8000
>>>> Quick Mode
>>>>
>>>> Host to Device Bandwidth, 1 Device(s)
>>>> PINNED Memory Transfers
>>>> Transfer Size (Bytes) Bandwidth(GB/s)
>>>> 32000000 12.3
>>>>
>>>> Device to Host Bandwidth, 1 Device(s)
>>>> PINNED Memory Transfers
>>>> Transfer Size (Bytes) Bandwidth(GB/s)
>>>> 32000000 13.2
>>>>
>>>> Device to Device Bandwidth, 1 Device(s)
>>>> PINNED Memory Transfers
>>>> Transfer Size (Bytes) Bandwidth(GB/s)
>>>> 32000000 466.2
>>>>
>>>> Result = PASS
>>>>
>>>> On Sat, Oct 8, 2022 at 7:56 PM Barry Smith <bsmith at petsc.dev> wrote:
>>>>
>>>>>
>>>>> True, but when users send reports back to us they will never have
>>>>> used the VERBOSE=1 option, so it requires one more round trip of email to
>>>>> get this additional information.
>>>>>
>>>>> > On Oct 8, 2022, at 6:48 PM, Jed Brown <jed at jedbrown.org> wrote:
>>>>> >
>>>>> > Barry Smith <bsmith at petsc.dev> writes:
>>>>> >
>>>>> >> I hate these kinds of make rules that hide what the compiler is
>>>>> doing (in the name of having less output, I guess) it makes it difficult to
>>>>> figure out what is going wrong.
>>>>> >
>>>>> > You can make VERBOSE=1 with CMake-generated makefiles.
>>>>>
>>>>
>>>>
>>>>> Anyways, either some of the MPI libraries are missing from the link
>>>>> line or they are in the wrong order and thus it is not able to search them
>>>>> properly. Here is a bunch of discussions on why that error message can
>>>>> appear
>>>>> https://stackoverflow.com/questions/19901934/libpthread-so-0-error-adding-symbols-dso-missing-from-command-line
>>>>>
>>>>
>>>>
>>>> Still same but more noise and I have been using the suggestion of
>>>> LDFLAGS="-Wl,--copy-dt-needed-entries" along with make:
>>>> make[2]: Entering directory '/path/to/WTM/build'
>>>> cd /path/to/WTM/build &&
>>>> /path/to/cmake/cmake-3.22.1-linux-x86_64/bin/cmake -E cmake_depends "Unix
>>>> Makefiles" /path/to/WTM /path/to/WTM /path/to/WTM/build /path/to/WTM/build
>>>> /path/to/WTM/build/CMakeFiles/wtm.x.dir/DependInfo.cmake --color=
>>>> make[2]: Leaving directory '/path/to/WTM/build'
>>>> make -f CMakeFiles/wtm.x.dir/build.make CMakeFiles/wtm.x.dir/build
>>>> make[2]: Entering directory '/path/to/WTM/build'
>>>> [ 66%] Building CXX object CMakeFiles/wtm.x.dir/src/WTM.cpp.o
>>>> /cm/local/apps/gcc/10.2.0/bin/c++
>>>> -I/path/to/WTM/common/richdem/include -I/path/to/gdal-3.3.0/include
>>>> -I/path/to/WTM/common/fmt/include -isystem
>>>> /path/to/petsc/arch-linux-cxx-debug/include -isystem /path/to/petsc/include
>>>> -isystem -O3 -g -Wall -Wextra -pedantic -Wshadow -Wfloat-conversion -Wall
>>>> -Wextra -pedantic -Wshadow -DRICHDEM_GIT_HASH=\"xxx\"
>>>> -DRICHDEM_COMPILE_TIME=\"2022-10-09T02:21:11Z\" -DUSEGDAL -Xpreprocessor
>>>> -fopenmp
>>>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40.30.1
>>>> -I/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/include -std=gnu++2a -MD
>>>> -MT CMakeFiles/wtm.x.dir/src/WTM.cpp.o -MF
>>>> CMakeFiles/wtm.x.dir/src/WTM.cpp.o.d -o CMakeFiles/wtm.x.dir/src/WTM.cpp.o
>>>> -c /path/to/WTM/src/WTM.cpp
>>>> c++: warning:
>>>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40.30.1:
>>>> linker input file unused because linking not done
>>>> [ 70%] Linking CXX executable wtm.x
>>>> /path/to/cmake/cmake-3.22.1-linux-x86_64/bin/cmake -E cmake_link_script
>>>> CMakeFiles/wtm.x.dir/link.txt --verbose=1
>>>> /cm/local/apps/gcc/10.2.0/bin/c++ -isystem -O3 -g -Wall -Wextra
>>>> -pedantic -Wshadow CMakeFiles/wtm.x.dir/src/WTM.cpp.o -o wtm.x
>>>> -Wl,-rpath,/path/to/WTM/build/common/richdem:/path/to/gdal-3.3.0/lib:/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib:/path/to/petsc/arch-linux-cxx-debug/lib
>>>> libwtm.a common/richdem/librichdem.so /path/to/gdal-3.3.0/lib/libgdal.so
>>>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0
>>>> common/fmt/libfmt.a /path/to/petsc/arch-linux-cxx-debug/lib/libpetsc.so
>>>> /usr/bin/ld: CMakeFiles/wtm.x.dir/src/WTM.cpp.o: undefined reference to
>>>> symbol 'ompi_mpi_comm_self'
>>>> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40: error
>>>> adding symbols: DSO missing from command line
>>>> collect2: error: ld returned 1 exit status
>>>> make[2]: *** [CMakeFiles/wtm.x.dir/build.make:103: wtm.x] Error 1
>>>> make[2]: Leaving directory '/path/to/WTM/build'
>>>> make[1]: *** [CMakeFiles/Makefile2:225: CMakeFiles/wtm.x.dir/all] Error
>>>> 2
>>>> make[1]: Leaving directory '/path/to/WTM/build'
>>>> make: *** [Makefile:136: all] Error 2
>>>>
>>>> Anything stick out?
>>>>
>>>
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