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HYPHY Package >> HyPhy bugs >> error in compilation http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1220516645 Message started by luis on Sep 4th, 2008 at 1:24am |
Title: error in compilation Post by luis on Sep 4th, 2008 at 1:24am
error in compilation
./build.sh MPI Linux Checking for curl Curl seems to be present +-----------------------------------------------------------+ |Building a single-threaded HYPHYKernelMPI for MPI | +-----------------------------------------------------------+ COMPILER=g++, gcc COMPILER_FLAGS= -w -c -fsigned-char -O3 -fpermissive -I/home/jlacosta/Download/programas/HYPHY_Source/Source -I/home/jlacosta/Download/programas/HYPHY_Source/Source/SQLite -D INTPTR_TYPE=long -D __UNIX__ -D __HYPHYMPI__ File baseobj.cpp is up to date File batchlan2.cpp is up to date File batchlan.cpp is up to date File bgm.cpp is up to date File calcnode.cpp is up to date File category.cpp is up to date File error.cpp is up to date File fisher_exact.cpp is up to date File HYNetInterface.cpp is up to date File hyphyunixutils.cpp is up to date File likefunc.cpp is up to date File list.cpp is up to date File matrix.cpp is up to date File Net.cpp is up to date File nexus.cpp is up to date File parser2.cpp is up to date File parser.cpp is up to date File polynoml.cpp is up to date File regex.cpp is up to date File scfg.cpp is up to date File sequence.cpp is up to date File site.cpp is up to date File strings.cpp is up to date File main-unix.cxx is up to date SQLite File attach.c is up to date SQLite File auth.c is up to date SQLite File btree.c is up to date SQLite File btree_rb.c is up to date SQLite File build.c is up to date SQLite File copy.c is up to date SQLite File delete.c is up to date SQLite File expr.c is up to date SQLite File func.c is up to date SQLite File hash.c is up to date SQLite File insert.c is up to date SQLite File main.c is up to date SQLite File opcodes.c is up to date SQLite File os.c is up to date SQLite File pager.c is up to date SQLite File parse.c is up to date SQLite File pragma.c is up to date SQLite File printf.c is up to date SQLite File random.c is up to date SQLite File select.c is up to date SQLite File table.c is up to date SQLite File tokenize.c is up to date SQLite File trigger.c is up to date SQLite File update.c is up to date SQLite File util.c is up to date SQLite File vacuum.c is up to date SQLite File vdbe.c is up to date SQLite File where.c is up to date Linking HYPHYMPI g++ -w -fsigned-char -o HYPHYMPI obj_MPI/attach.c.o obj_MPI/auth.c.o obj_MPI/baseobj.cpp.o obj_MPI/batchlan2.cpp.o obj_MPI/batchlan.cpp.o obj_MPI/bgm.cpp.o obj_MPI/btree.c.o obj_MPI/btree_rb.c.o obj_MPI/build.c.o obj_MPI/calcnode.cpp.o obj_MPI/category.cpp.o obj_MPI/copy.c.o obj_MPI/delete.c.o obj_MPI/error.cpp.o obj_MPI/expr.c.o obj_MPI/fisher_exact.cpp.o obj_MPI/func.c.o obj_MPI/hash.c.o obj_MPI/HYNetInterface.cpp.o obj_MPI/hyphyunixutils.cpp.o obj_MPI/insert.c.o obj_MPI/likefunc.cpp.o obj_MPI/list.cpp.o obj_MPI/main.c.o obj_MPI/main-unix.cxx.o obj_MPI/matrix.cpp.o obj_MPI/Net.cpp.o obj_MPI/nexus.cpp.o obj_MPI/opcodes.c.o obj_MPI/os.c.o obj_MPI/pager.c.o obj_MPI/parse.c.o obj_MPI/parser2.cpp.o obj_MPI/parser.cpp.o obj_MPI/polynoml.cpp.o obj_MPI/pragma.c.o obj_MPI/printf.c.o obj_MPI/random.c.o obj_MPI/regex.cpp.o obj_MPI/scfg.cpp.o obj_MPI/select.c.o obj_MPI/sequence.cpp.o obj_MPI/site.cpp.o obj_MPI/strings.cpp.o obj_MPI/table.c.o obj_MPI/tokenize.c.o obj_MPI/trigger.c.o obj_MPI/update.c.o obj_MPI/util.c.o obj_MPI/vacuum.c.o obj_MPI/vdbe.c.o obj_MPI/where.c.o -lssl -lcrypto -lcurl -lm obj_MPI/baseobj.cpp.o: In function `GlobalShutdown()': baseobj.cpp:(.text+0x672): undefined reference to `ompi_mpi_comm_world' baseobj.cpp:(.text+0x681): undefined reference to `MPI_Comm_rank' baseobj.cpp:(.text+0x68b): undefined reference to `ompi_mpi_comm_world' baseobj.cpp:(.text+0x690): undefined reference to `MPI_Comm_size' baseobj.cpp:(.text+0x6b8): undefined reference to `SEEK_END' baseobj.cpp:(.text+0x71e): undefined reference to `MPI_Finalize' baseobj.cpp:(.text+0x765): undefined reference to `MPI_Finalize' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Set_name(char const*)': baseobj.cpp:(.text._ZN3MPI8Datatype8Set_nameEPKc[MPI::Datatype::Set_name(char const*)]+0x5): undefined reference to `MPI_Type_set_name' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Set_attr(int, void const*)': baseobj.cpp:(.text._ZN3MPI8Datatype8Set_attrEiPKv[MPI::Datatype::Set_attr(int, void const*)]+0x5): undefined reference to `MPI_Type_set_attr' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Get_name(char*, int&) const': baseobj.cpp:(.text._ZNK3MPI8Datatype8Get_nameEPcRi[MPI::Datatype::Get_name(char*, int&) const]+0x5): undefined reference to `MPI_Type_get_name' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Get_envelope(int&, int&, int&, int&) const': baseobj.cpp:(.text._ZNK3MPI8Datatype12Get_envelopeERiS1_S1_S1_[MPI::Datatype::Get_envelope(int&, int&, int&, int&) const]+0x5): undefined reference to `MPI_Type_get_envelope' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Get_contents(int, int, int, int*, long*, MPI::Datatype*) const': baseobj.cpp:(.text._ZNK3MPI8Datatype12Get_contentsEiiiPiPlPS0_[MPI::Datatype::Get_contents(int, int, int, int*, long*, MPI::Datatype*) const]+0x67): undefined reference to `MPI_Type_get_contents' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Get_attr(int, void*) const': baseobj.cpp:(.text._ZNK3MPI8Datatype8Get_attrEiPv[MPI::Datatype::Get_attr(int, void*) const]+0xe): undefined reference to `MPI_Type_get_attr' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Delete_attr(int)': baseobj.cpp:(.text._ZN3MPI8Datatype11Delete_attrEi[MPI::Datatype::Delete_attr(int)]+0x5): undefined reference to `MPI_Type_delete_attr' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Dup() const': baseobj.cpp:(.text._ZNK3MPI8Datatype3DupEv[MPI::Datatype::Dup() const]+0x15): undefined reference to `MPI_Type_dup' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Create_subarray(int, int const*, int const*, int const*, int) const': baseobj.cpp:(.text._ZNK3MPI8Datatype15Create_subarrayEiPKiS2_S2_i[MPI::Datatype::Create_subarray(int, int const*, int const*, int const*, int) const]+0x29): undefined reference to `MPI_Type_create_subarray' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Pack_size(int, MPI::Comm const&) const': baseobj.cpp:(.text._ZNK3MPI8Datatype9Pack_sizeEiRKNS_4CommE[MPI::Datatype::Pack_size(int, MPI::Comm const&) const]+0x16): undefined reference to `MPI_Pack_size' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Unpack(void const*, int, void*, int, int&, MPI::Comm const&) const': baseobj.cpp:(.text._ZNK3MPI8Datatype6UnpackEPKviPviRiRKNS_4CommE[MPI::Datatype::Unpack(void const*, int, void*, int, int&, MPI::Comm const&) const]+0x1e): undefined reference to `MPI_Unpack' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Pack(void const*, int, void*, int, int&, MPI::Comm const&) const': baseobj.cpp:(.text._ZNK3MPI8Datatype4PackEPKviPviRiRKNS_4CommE[MPI::Datatype::Pack(void const*, int, void*, int, int&, MPI::Comm const&) const]+0x1b): undefined reference to `MPI_Pack' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Commit()': baseobj.cpp:(.text._ZN3MPI8Datatype6CommitEv[MPI::Datatype::Commit()]+0x5): undefined reference to `MPI_Type_commit' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Get_true_extent(long&, long&) const': baseobj.cpp:(.text._ZNK3MPI8Datatype15Get_true_extentERlS1_[MPI::Datatype::Get_true_extent(long&, long&) const]+0x5): undefined reference to `MPI_Type_get_true_extent' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Get_extent(long&, long&) const': baseobj.cpp:(.text._ZNK3MPI8Datatype10Get_extentERlS1_[MPI::Datatype::Get_extent(long&, long&) const]+0x5): undefined reference to `MPI_Type_get_extent' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Get_size() const': baseobj.cpp:(.text._ZNK3MPI8Datatype8Get_sizeEv[MPI::Datatype::Get_size() const]+0xe): undefined reference to `MPI_Type_size' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Create_resized(long, long) const': baseobj.cpp:(.text._ZNK3MPI8Datatype14Create_resizedEll[MPI::Datatype::Create_resized(long, long) const]+0x1e): undefined reference to `MPI_Type_create_resized' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Create_indexed_block(int, int, int const*) const': baseobj.cpp:(.text._ZNK3MPI8Datatype20Create_indexed_blockEiiPKi[MPI::Datatype::Create_indexed_block(int, int, int const*) const]+0x1b): undefined reference to `MPI_Type_create_indexed_block' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Create_hvector(int, int, long) const': baseobj.cpp:(.text._ZNK3MPI8Datatype14Create_hvectorEiil[MPI::Datatype::Create_hvector(int, int, long) const]+0x1b): undefined reference to `MPI_Type_create_hvector' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Create_hindexed(int, int const*, long const*) const': baseobj.cpp:(.text._ZNK3MPI8Datatype15Create_hindexedEiPKiPKl[MPI::Datatype::Create_hindexed(int, int const*, long const*) const]+0x1d): undefined reference to `MPI_Type_create_hindexed' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Create_indexed(int, int const*, int const*) const': baseobj.cpp:(.text._ZNK3MPI8Datatype14Create_indexedEiPKiS2_[MPI::Datatype::Create_indexed(int, int const*, int const*) const]+0x1d): undefined reference to `MPI_Type_indexed' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Create_vector(int, int, int) const': baseobj.cpp:(.text._ZNK3MPI8Datatype13Create_vectorEiii[MPI::Datatype::Create_vector(int, int, int) const]+0x1b): undefined reference to `MPI_Type_vector' obj_MPI/baseobj.cpp.o: In function `MPI::Datatype::Create_contiguous(int) const': baseobj.cpp:(.text._ZNK3MPI8Datatype17Create_contiguousEi[MPI::Datatype::Create_contiguous(int) const]+0x14): undefined reference to `MPI_Type_contiguous' obj_MPI/baseobj.cpp.o: In function `MPI::Prequest::Start()': baseobj.cpp:(.text._ZN3MPI8Prequest5StartEv[MPI::Prequest::Start()]+0x5): undefined reference to `MPI_Start' obj_MPI/baseobj.cpp.o: In function `MPI::Grequest::Complete()': baseobj.cpp:(.text._ZN3MPI8Grequest8CompleteEv[MPI::Grequest::Complete()]+0x5): undefined reference to `MPI_Grequest_complete' obj_MPI/baseobj |
Title: Re: error in compilation Post by Sergei on Sep 4th, 2008 at 7:31am
Dear Luis,
Your MPI libraries are not being found. Edit the build script (build.sh) and replace COMPILER="g++" with COMPILER="mpic++" (and similarly for COMPILER_C="mpicc") I assume your system has those wrappers for MPI. If not, look for libmpich.* in your system library paths and add -L/path/to/libmpich into the LINKER_FLAGS variable inside build.sh Cheers, Sergei |
Title: Re: error in compilation Post by luis on Sep 8th, 2008 at 3:36pm
run ./HYPHYMPI and show error
./HYPHYMPI: Symbol `ompi_mpi_comm_world' has different size in shared object, consider re-linking ./HYPHYMPI: symbol lookup error: ./HYPHYMPI: undefined symbol: SEEK_SET ?? |
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