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error in compilation (Read 24776 times)
luis
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error in compilation
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:Cheesyatatype::Set_name(char const*)':
baseobj.cpp:(.text._ZN3MPI8Datatype8Set_nameEPKc[MPI:Cheesyatatype::Set_name(char const*)]+0x5): undefined reference to `MPI_Type_set_name'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Set_attr(int, void const*)':
baseobj.cpp:(.text._ZN3MPI8Datatype8Set_attrEiPKv[MPI:Cheesyatatype::Set_attr(int, void const*)]+0x5): undefined reference to `MPI_Type_set_attr'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Get_name(char*, int&) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype8Get_nameEPcRi[MPI:Cheesyatatype::Get_name(char*, int&) const]+0x5): undefined reference to `MPI_Type_get_name'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Get_envelope(int&, int&, int&, int&) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype12Get_envelopeERiS1_S1_S1_[MPI:Cheesyatatype::Ge
t_envelope(int&, int&, int&, int&) const]+0x5): undefined reference to `MPI_Type_get_envelope'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Get_contents(int, int, int, int*, long*, MPI:Cheesyatatype*) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype12Get_contentsEiiiPiPlPS0_[MPI:Cheesyatatype::Ge
t_contents(int, int, int, int*, long*, MPI:Cheesyatatype*) const]+0x67): undefined reference to `MPI_Type_get_contents'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Get_attr(int, void*) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype8Get_attrEiPv[MPI:Cheesyatatype::Get_attr(int, void*) const]+0xe): undefined reference to `MPI_Type_get_attr'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype:Cheesyelete_attr(int)':
baseobj.cpp:(.text._ZN3MPI8Datatype11Delete_attrEi[MPI:Cheesyatatype:Cheesyelete_attr(int)]+0x5): undefined reference to `MPI_Type_delete_attr'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype:Cheesyup() const':
baseobj.cpp:(.text._ZNK3MPI8Datatype3DupEv[MPI:Cheesyatatype:Cheesyup() const]+0x15): undefined reference to `MPI_Type_dup'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Create_subarray(int, int const*, int const*, int const*, int) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype15Create_subarrayEiPKiS2_S2_i[MPI:Cheesyatatype:
: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:Cheesyatatype:Tongueack_size(int, MPI::Comm const&) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype9Pack_sizeEiRKNS_4CommE[MPI:Cheesyatatype:Tongueack_
size(int, MPI::Comm const&) const]+0x16): undefined reference to `MPI_Pack_size'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Unpack(void const*, int, void*, int, int&, MPI::Comm const&) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype6UnpackEPKviPviRiRKNS_4CommE[MPI:Cheesyatatype::
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:Cheesyatatype:Tongueack(void const*, int, void*, int, int&, MPI::Comm const&) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype4PackEPKviPviRiRKNS_4CommE[MPI:Cheesyatatype:Tonguea
ck(void const*, int, void*, int, int&, MPI::Comm const&) const]+0x1b): undefined reference to `MPI_Pack'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Commit()':
baseobj.cpp:(.text._ZN3MPI8Datatype6CommitEv[MPI:Cheesyatatype::Commit()]+0x5): undefined reference to `MPI_Type_commit'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Get_true_extent(long&, long&) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype15Get_true_extentERlS1_[MPI:Cheesyatatype::Get_t
rue_extent(long&, long&) const]+0x5): undefined reference to `MPI_Type_get_true_extent'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Get_extent(long&, long&) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype10Get_extentERlS1_[MPI:Cheesyatatype::Get_extent(long&, long&) const]+0x5): undefined reference to `MPI_Type_get_extent'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Get_size() const':
baseobj.cpp:(.text._ZNK3MPI8Datatype8Get_sizeEv[MPI:Cheesyatatype::Get_size() const]+0xe): undefined reference to `MPI_Type_size'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Create_resized(long, long) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype14Create_resizedEll[MPI:Cheesyatatype::Create_resized(long, long) const]+0x1e): undefined reference to `MPI_Type_create_resized'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Create_indexed_block(int, int, int const*) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype20Create_indexed_blockEiiPKi[MPI:Cheesyatatype::
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:Cheesyatatype::Create_hvector(int, int, long) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype14Create_hvectorEiil[MPI:Cheesyatatype::Create_hvector(int, int, long) const]+0x1b): undefined reference to `MPI_Type_create_hvector'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Create_hindexed(int, int const*, long const*) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype15Create_hindexedEiPKiPKl[MPI:Cheesyatatype::Cre
ate_hindexed(int, int const*, long const*) const]+0x1d): undefined reference to `MPI_Type_create_hindexed'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Create_indexed(int, int const*, int const*) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype14Create_indexedEiPKiS2_[MPI:Cheesyatatype::Crea
te_indexed(int, int const*, int const*) const]+0x1d): undefined reference to `MPI_Type_indexed'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Create_vector(int, int, int) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype13Create_vectorEiii[MPI:Cheesyatatype::Create_vector(int, int, int) const]+0x1b): undefined reference to `MPI_Type_vector'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Create_contiguous(int) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype17Create_contiguousEi[MPI:Cheesyatatype::Create_contiguous(int) const]+0x14): undefined reference to `MPI_Type_contiguous'
obj_MPI/baseobj.cpp.o: In function `MPI:Tonguerequest::Start()':
baseobj.cpp:(.text._ZN3MPI8Prequest5StartEv[MPI:Tonguerequest::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
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Sergei
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Re: error in compilation
Reply #1 - 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
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luis
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Re: error in compilation
Reply #2 - 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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Sergei
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Re: error in compilation
Reply #3 - Sep 8th, 2008 at 3:55pm
 
Dear Luis,

No idea what the first error means. Try googling the error for your specific MPI distribution. As far as SEEK_SET goes, take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login
This is a known issue with the MPICH implementation.

Cheers,
Sergei
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Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego
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