Make failed at [ 99%] Built target Stokhos_TpetraCrsMatrixMPVectorUnitTest_Serial
Created by: lkkevin
Hi,
I am trying to build Trilinos 12.12.1 for Peridigm on CentOS 7.4. The "make -j 2" failed at 99%] Built target Stokhos_TpetraCrsMatrixMPVectorUnitTest_Serial. I have been working on this issue for a couple day but could not figure out. Please help. Thanks.
#------ These are the prerequisites that i installed on my VM: -----# boost_1_65_1 , cmake-3.10.0-rc5, hdf5-1.10.1, matio-1.5.11, netcdf-c-4.5.0, openmpi-3.0.0, blas 3.8.0, lapack 3.8.0.
#------ This is the CMakeError.log ------# Determining if the pthread_create exist failed with the following output: Change Dir: /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_6fe30/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_6fe30.dir/build.make CMakeFiles/cmTC_6fe30.dir/build
gmake[1]: Entering directory /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp' Building C object CMakeFiles/cmTC_6fe30.dir/CheckSymbolExists.c.o /opt/mpich/bin/mpicc -O3 -DNDEBUG -o CMakeFiles/cmTC_6fe30.dir/CheckSymbolExists.c.o -c /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c Linking C executable cmTC_6fe30 /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_6fe30.dir/link.txt --verbose=1 /opt/mpich/bin/mpicc -O3 -DNDEBUG -rdynamic CMakeFiles/cmTC_6fe30.dir/CheckSymbolExists.c.o -o cmTC_6fe30 /usr/bin/ld: CMakeFiles/cmTC_6fe30.dir/CheckSymbolExists.c.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' /usr/lib64/libpthread.so.0: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status gmake[1]: *** [cmTC_6fe30] Error 1 gmake[1]: Leaving directory /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_6fe30/fast] Error 2
File /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c: /* */ #include <pthread.h>
int main(int argc, char** argv) { (void)argv; #ifndef pthread_create return ((int*)(&pthread_create))[argc]; #else (void)argc; return 0; #endif }
Determining if the function pthread_create exists in the pthreads failed with the following output: Change Dir: /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_59d00/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_59d00.dir/build.make CMakeFiles/cmTC_59d00.dir/build
gmake[1]: Entering directory /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp' Building C object CMakeFiles/cmTC_59d00.dir/CheckFunctionExists.c.o /opt/mpich/bin/mpicc -DCHECK_FUNCTION_EXISTS=pthread_create -O3 -DNDEBUG -o CMakeFiles/cmTC_59d00.dir/CheckFunctionExists.c.o -c /usr/local/share/cmake-3.10/Modules/CheckFunctionExists.c Linking C executable cmTC_59d00 /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_59d00.dir/link.txt --verbose=1 /opt/mpich/bin/mpicc -DCHECK_FUNCTION_EXISTS=pthread_create -O3 -DNDEBUG -rdynamic CMakeFiles/cmTC_59d00.dir/CheckFunctionExists.c.o -o cmTC_59d00 -lpthreads /usr/bin/ld: cannot find -lpthreads collect2: error: ld returned 1 exit status gmake[1]: *** [cmTC_59d00] Error 1 gmake[1]: Leaving directory /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_59d00/fast] Error 2
Performing C++ SOURCE FILE Test HAVE_TEUCHOS_LAPACKLARND failed with the following output:
Change Dir: /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_d5eb7/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_d5eb7.dir/build.make CMakeFiles/cmTC_d5eb7.dir/build
gmake[1]: Entering directory /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp' Building CXX object CMakeFiles/cmTC_d5eb7.dir/src.cxx.o /opt/mpich/bin/mpicxx -O2 -std=c++11 -pedantic -ftrapv -Wall -Wno-long-long -std=c++11 -DHAVE_TEUCHOS_LAPACKLARND -O3 -DNDEBUG -o CMakeFiles/cmTC_d5eb7.dir/src.cxx.o -c /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp/src.cxx /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp/src.cxx: In function ‘int main()’: /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp/src.cxx:12:38: warning: narrowing conversion of ‘0.0’ from ‘double’ to ‘int’ inside { } [-Wnarrowing] int seed[4] = { 0.0, 0.0, 0.0, 1.0 }; ^ /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp/src.cxx:12:38: warning: narrowing conversion of ‘0.0’ from ‘double’ to ‘int’ inside { } [-Wnarrowing] /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp/src.cxx:12:38: warning: narrowing conversion of ‘0.0’ from ‘double’ to ‘int’ inside { } [-Wnarrowing] /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp/src.cxx:12:38: warning: narrowing conversion of ‘1.0e+0’ from ‘double’ to ‘int’ inside { } [-Wnarrowing] Linking CXX executable cmTC_d5eb7 /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_d5eb7.dir/link.txt --verbose=1 /opt/mpich/bin/mpicxx -O2 -std=c++11 -pedantic -ftrapv -Wall -Wno-long-long -std=c++11 -DHAVE_TEUCHOS_LAPACKLARND -O3 -DNDEBUG -rdynamic CMakeFiles/cmTC_d5eb7.dir/src.cxx.o -o cmTC_d5eb7 -Wl,-rpath,/opt/lib/LAPACK /opt/lib/LAPACK/liblapack.so CMakeFiles/cmTC_d5eb7.dir/src.cxx.o: In function main':
src.cxx:(.text.startup+0x22): undefined reference to dlarnd_' collect2: error: ld returned 1 exit status gmake[1]: *** [cmTC_d5eb7] Error 1 gmake[1]: Leaving directory /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_d5eb7/fast] Error 2
Return value: 1 Source file was:
#define F77_BLAS_MANGLE(name,NAME) name ## _
#define DLARND_F77 F77_BLAS_MANGLE(dlarnd,DLARND)
extern "C" { double DLARND_F77(const int* idist, int* seed); }
int main() {
const int idist = 1; int seed[4] = { 0.0, 0.0, 0.0, 1.0 };
double val = DLARND_F77(&idist, seed);
return (val < 0.0 ? 1 : 0); }
Performing C++ SOURCE FILE Test HAVE_CXX_PRAGMA_WEAK failed with the following output: Change Dir: /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_32f82/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_32f82.dir/build.make CMakeFiles/cmTC_32f82.dir/build
gmake[1]: Entering directory /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp' Building CXX object CMakeFiles/cmTC_32f82.dir/src.cxx.o /opt/mpich/bin/mpicxx -O2 -std=c++11 -pedantic -ftrapv -Wall -Wno-long-long -std=c++11 -DHAVE_CXX_PRAGMA_WEAK -O3 -DNDEBUG -o CMakeFiles/cmTC_32f82.dir/src.cxx.o -c /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp/src.cxx Linking CXX executable cmTC_32f82 /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_32f82.dir/link.txt --verbose=1 /opt/mpich/bin/mpicxx -O2 -std=c++11 -pedantic -ftrapv -Wall -Wno-long-long -std=c++11 -DHAVE_CXX_PRAGMA_WEAK -O3 -DNDEBUG -rdynamic CMakeFiles/cmTC_32f82.dir/src.cxx.o -o cmTC_32f82 CMakeFiles/cmTC_32f82.dir/src.cxx.o: In function main':
src.cxx:(.text.startup+0x1c): undefined reference to A::theFunction()' collect2: error: ld returned 1 exit status gmake[1]: *** [cmTC_32f82] Error 1 gmake[1]: Leaving directory /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_32f82/fast] Error 2
Source file was:
#include
namespace A { // theFunction never gets defined, because we // don't link with a library that defines it. // That's OK, because it's weak linkage. #pragma weak theFunction extern void theFunction (); }
int main() { std::cout << "Hi! I am main." << std::endl; if (A::theFunction != NULL) { // Should never be called, since we don't link // with a library that defines A::theFunction. A::theFunction (); } return 0; }
Determining if the function dggsvd3 exists failed with the following output:
Change Dir: /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_a3af9/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_a3af9.dir/build.make CMakeFiles/cmTC_a3af9.dir/build
gmake[1]: Entering directory /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp' Building C object CMakeFiles/cmTC_a3af9.dir/CheckFunctionExists.c.o /opt/mpich/bin/mpicc -DCHECK_FUNCTION_EXISTS=dggsvd3 -O3 -DNDEBUG -o CMakeFiles/cmTC_a3af9.dir/CheckFunctionExists.c.o -c /usr/local/share/cmake-3.10/Modules/CheckFunctionExists.c Linking C executable cmTC_a3af9 /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_a3af9.dir/link.txt --verbose=1 /opt/mpich/bin/mpicc -DCHECK_FUNCTION_EXISTS=dggsvd3 -O3 -DNDEBUG -rdynamic CMakeFiles/cmTC_a3af9.dir/CheckFunctionExists.c.o -o cmTC_a3af9 -L/opt/lib/BLAS -Wl,-rpath,/opt/lib/LAPACK:/opt/lib/BLAS /opt/lib/LAPACK/liblapack.so -lblas CMakeFiles/cmTC_a3af9.dir/CheckFunctionExists.c.o: In function main':
CheckFunctionExists.c:(.text.startup+0xc): undefined reference to dggsvd3' collect2: error: ld returned 1 exit status gmake[1]: *** [cmTC_a3af9] Error 1 gmake[1]: Leaving directory /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_a3af9/fast] Error 2
Determining if the function DGGSVD3 exists failed with the following output: Change Dir: /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_1a133/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_1a133.dir/build.make CMakeFiles/cmTC_1a133.dir/build
gmake[1]: Entering directory /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp' Building C object CMakeFiles/cmTC_1a133.dir/CheckFunctionExists.c.o /opt/mpich/bin/mpicc -DCHECK_FUNCTION_EXISTS=DGGSVD3 -O3 -DNDEBUG -o CMakeFiles/cmTC_1a133.dir/CheckFunctionExists.c.o -c /usr/local/share/cmake-3.10/Modules/CheckFunctionExists.c Linking C executable cmTC_1a133 /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_1a133.dir/link.txt --verbose=1 /opt/mpich/bin/mpicc -DCHECK_FUNCTION_EXISTS=DGGSVD3 -O3 -DNDEBUG -rdynamic CMakeFiles/cmTC_1a133.dir/CheckFunctionExists.c.o -o cmTC_1a133 -L/opt/lib/BLAS -Wl,-rpath,/opt/lib/LAPACK:/opt/lib/BLAS /opt/lib/LAPACK/liblapack.so -lblas CMakeFiles/cmTC_1a133.dir/CheckFunctionExists.c.o: In function main':
CheckFunctionExists.c:(.text.startup+0xc): undefined reference to DGGSVD3' collect2: error: ld returned 1 exit status gmake[1]: *** [cmTC_1a133] Error 1 gmake[1]: Leaving directory /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_1a133/fast] Error 2
Determining if the function DGGSVD3_ exists failed with the following output: Change Dir: /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_6f85a/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_6f85a.dir/build.make CMakeFiles/cmTC_6f85a.dir/build
gmake[1]: Entering directory /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp' Building C object CMakeFiles/cmTC_6f85a.dir/CheckFunctionExists.c.o /opt/mpich/bin/mpicc -DCHECK_FUNCTION_EXISTS=DGGSVD3_ -O3 -DNDEBUG -o CMakeFiles/cmTC_6f85a.dir/CheckFunctionExists.c.o -c /usr/local/share/cmake-3.10/Modules/CheckFunctionExists.c Linking C executable cmTC_6f85a /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_6f85a.dir/link.txt --verbose=1 /opt/mpich/bin/mpicc -DCHECK_FUNCTION_EXISTS=DGGSVD3_ -O3 -DNDEBUG -rdynamic CMakeFiles/cmTC_6f85a.dir/CheckFunctionExists.c.o -o cmTC_6f85a -L/opt/lib/BLAS -Wl,-rpath,/opt/lib/LAPACK:/opt/lib/BLAS /opt/lib/LAPACK/liblapack.so -lblas CMakeFiles/cmTC_6f85a.dir/CheckFunctionExists.c.o: In function main':
CheckFunctionExists.c:(.text.startup+0xc): undefined reference to DGGSVD3_' collect2: error: ld returned 1 exit status gmake[1]: *** [cmTC_6f85a] Error 1 gmake[1]: Leaving directory /root/Downloads/trilinos-12.12.1-Source/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_6f85a/fast] Error 2
#----- and this is when the"make -j2" kicked out -----#
.......
[ 99%] Linking CXX executable Stokhos_KokkosCrsMatrixMPVectorUnitTest_Serial.exe
[ 99%] Built target Stokhos_KokkosCrsMatrixMPVectorUnitTest_Serial
Scanning dependencies of target Stokhos_KokkosViewMPVectorUnitTest_Serial
[ 99%] Building CXX object packages/stokhos/test/UnitTest/CMakeFiles/Stokhos_KokkosViewMPVectorUnitTest_Serial.dir/Stokhos_KokkosViewMPVectorUnitTest_Serial.cpp.o
In file included from /root/Downloads/trilinos-12.12.1-Source/packages/muelu/adapters/tpetra/MueLu_CreateTpetraPreconditioner.hpp:10:0,
from /root/Downloads/trilinos-12.12.1-Source/packages/stokhos/test/UnitTest/Stokhos_TpetraCrsMatrixMPVectorUnitTest.hpp:77,
from /root/Downloads/trilinos-12.12.1-Source/packages/stokhos/test/UnitTest/Stokhos_TpetraCrsMatrixMPVectorUnitTest_Serial.cpp:46:
/root/Downloads/trilinos-12.12.1-Source/packages/xpetra/src/CrsMatrix/Xpetra_TpetraBlockCrsMatrix.hpp: In instantiation of ‘void Xpetra::TpetraBlockCrsMatrix<Scalar, LocalOrdinal, GlobalOrdinal, Node>::getLocalDiagOffsets(Teuchos::ArrayRCP&) const [with Scalar = Sacado::MP::Vector<Stokhos::StaticFixedStorage<int, double, 16, Kokkos::Serial> >; LocalOrdinal = int; GlobalOrdinal = int; Node = Kokkos::Compat::KokkosDeviceWrapperNodeKokkos::Serial]’:
/root/Downloads/trilinos-12.12.1-Source/packages/stokhos/test/UnitTest/Stokhos_TpetraCrsMatrixMPVectorUnitTest_Serial.cpp:71:1: required from here
/root/Downloads/trilinos-12.12.1-Source/packages/xpetra/src/CrsMatrix/Xpetra_TpetraBlockCrsMatrix.hpp:343:7: warning: ‘void Tpetra::Experimental::BlockCrsMatrix<S, LO, GO, N>::getLocalDiagOffsets(Teuchos::ArrayRCP&) const [with Scalar = Sacado::MP::Vector<Stokhos::StaticFixedStorage<int, double, 16, Kokkos::Serial> >; LO = int; GO = int; Node = Kokkos::Compat::KokkosDeviceWrapperNodeKokkos::Serial]’ is deprecated (declared at /root/Downloads/trilinos-12.12.1-Source/packages/tpetra/core/src/Tpetra_Experimental_BlockCrsMatrix_def.hpp:1062) [-Wdeprecated-declarations]
mtx_->getLocalDiagOffsets(offsets);
^
[ 99%] Linking CXX executable Stokhos_KokkosViewMPVectorUnitTest_Serial.exe
[ 99%] Built target Stokhos_KokkosViewMPVectorUnitTest_Serial
Scanning dependencies of target Stokhos_SacadoMPVectorCommTests
[ 99%] Building CXX object packages/stokhos/test/UnitTest/CMakeFiles/Stokhos_SacadoMPVectorCommTests.dir/Stokhos_SacadoMPVectorCommTests.cpp.o
[ 99%] Linking CXX executable Stokhos_SacadoMPVectorCommTests.exe
[ 99%] Built target Stokhos_SacadoMPVectorCommTests
Scanning dependencies of target Stokhos_SDMUtilsUnitTest
[ 99%] Building CXX object packages/stokhos/test/UnitTest/CMakeFiles/Stokhos_SDMUtilsUnitTest.dir/Stokhos_SDMUtilsUnitTest.cpp.o
[ 99%] Linking CXX executable Stokhos_SDMUtilsUnitTest.exe
CMakeFiles/Stokhos_SDMUtilsUnitTest.dir/Stokhos_SDMUtilsUnitTest.cpp.o: In function void Stokhos::CPQR_Householder<int, double>(Teuchos::SerialDenseMatrix<int, double> const&, Teuchos::SerialDenseMatrix<int, double>&, Teuchos::SerialDenseMatrix<int, double>&, Teuchos::Array<int>&)': Stokhos_SDMUtilsUnitTest.cpp:(.text._ZN7Stokhos16CPQR_HouseholderIidEEvRKN7Teuchos17SerialDenseMatrixIT_T0_EERS5_S8_RNS1_5ArrayIS3_EE[_ZN7Stokhos16CPQR_HouseholderIidEEvRKN7Teuchos17SerialDenseMatrixIT_T0_EERS5_S8_RNS1_5ArrayIS3_EE]+0x16c): undefined reference to dgeqpf_'
collect2: error: ld returned 1 exit status
make[2]: *** [packages/stokhos/test/UnitTest/Stokhos_SDMUtilsUnitTest.exe] Error 1
make[1]: *** [packages/stokhos/test/UnitTest/CMakeFiles/Stokhos_SDMUtilsUnitTest.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
In file included from /root/Downloads/trilinos-12.12.1-Source/build/packages/muelu/src/MueLu_VariableDofLaplacianFactory.hpp:2:0,
from /root/Downloads/trilinos-12.12.1-Source/packages/muelu/src/Interface/MueLu_FactoryFactory_decl.hpp:146,
from /root/Downloads/trilinos-12.12.1-Source/build/packages/muelu/src/Interface/MueLu_FactoryFactory.hpp:1,
from /root/Downloads/trilinos-12.12.1-Source/packages/muelu/src/Interface/MueLu_ParameterListInterpreter_def.hpp:73,
from /root/Downloads/trilinos-12.12.1-Source/build/packages/muelu/src/Interface/MueLu_ParameterListInterpreter.hpp:2,
from /root/Downloads/trilinos-12.12.1-Source/packages/muelu/adapters/tpetra/MueLu_CreateTpetraPreconditioner.hpp:22,
from /root/Downloads/trilinos-12.12.1-Source/packages/stokhos/test/UnitTest/Stokhos_TpetraCrsMatrixMPVectorUnitTest.hpp:77,
from /root/Downloads/trilinos-12.12.1-Source/packages/stokhos/test/UnitTest/Stokhos_TpetraCrsMatrixMPVectorUnitTest_Serial.cpp:46:
/root/Downloads/trilinos-12.12.1-Source/packages/muelu/src/Interface/../Graph/MueLu_VariableDofLaplacianFactory_def.hpp: In member function ‘void MueLu::VariableDofLaplacianFactory<Scalar, LocalOrdinal, GlobalOrdinal, Node>::Build(MueLu::VariableDofLaplacianFactory<Scalar, LocalOrdinal, GlobalOrdinal, Node>::Level&) const [with Scalar = Sacado::MP::Vector<Stokhos::StaticFixedStorage<int, double, 16, Kokkos::Serial> >; LocalOrdinal = int; GlobalOrdinal = int; Node = Kokkos::Compat::KokkosDeviceWrapperNodeKokkos::Serial; MueLu::VariableDofLaplacianFactory<Scalar, LocalOrdinal, GlobalOrdinal, Node>::Level = MueLu::Level]’:
/root/Downloads/trilinos-12.12.1-Source/packages/muelu/src/Interface/../Graph/MueLu_VariableDofLaplacianFactory_def.hpp:256:16: warning: ‘blockRow’ may be used uninitialized in this function [-Wmaybe-uninitialized]
amalgRowPtr[blockRow+1] = newNzs;
^
[ 99%] Linking CXX executable Stokhos_TpetraCrsMatrixMPVectorUnitTest_Serial.exe
[ 99%] Built target Stokhos_TpetraCrsMatrixMPVectorUnitTest_Serial
make: *** [all] Error 2
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