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September 20, 2014 at 10:27 am #1990
Anonymous
Dear all, I keep having problems compiling Rosetta 3.5 on our university cluster. First, I edited site.settings so scons finds mpicc and mpicxx
import os
settings = {
"site" : {
"prepends" : {
"program_path" : os.environ["PATH"].split(":"),
"include_path" : os.environ["INCLUDE"].split(":"),
"library_path" : os.environ["LD_LIBRARY_PATH"].split(":"),
},
"appends" : {
},
"overrides" : {
"cxx": "/opt/openmpi/1.7.3/gcc/bin/mpicxx",
"cc": "/opt/openmpi/1.7.3/gcc/bin/mpiCC",
},
"removes" : {
},
},
}
Now when compiling with gcc (./scons.py mode= release extras=mpi bin) after some minutes I get the following error:
external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:98610: error: invalid use of incomplete type 'sruct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:98613: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:98614: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:98617: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c: In function 'Bitmask codeOneLoopStart(WhereInfo*, int, u16, Bitmask)': external/dbio/sqlite3/sqlite3.c:98691: error: cannot convert 'SrcList::SrcList_item*' to 'SrcList_item*' in assignment external/dbio/sqlite3/sqlite3.c:98692: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:98714: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:98714: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:98729: error: cannot convert 'sqlite3_index_info::sqlite3_index_constraint_usage*' to 'sqlite3_index_constraint_usage*' in initialization external/dbio/sqlite3/sqlite3.c:98731: error: cannot convert 'sqlite3_index_info::sqlite3_index_constraint*' to 'const sqlite3_index_constraint*' in initialization external/dbio/sqlite3/sqlite3.c:98737: error: invalid use of incomplete type 'struct sqlite3_index_constraint_usage' external/dbio/sqlite3/sqlite3.c:98728: error: forward declaration of 'struct sqlite3_index_constraint_usage' external/dbio/sqlite3/sqlite3.c:98737: error: invalid use of incomplete type 'struct sqlite3_index_constraint_usage' external/dbio/sqlite3/sqlite3.c:98728: error: forward declaration of 'struct sqlite3_index_constraint_usage' external/dbio/sqlite3/sqlite3.c:98738: error: invalid use of incomplete type 'struct sqlite3_index_constraint' external/dbio/sqlite3/sqlite3.c:98730: error: forward declaration of 'struct sqlite3_index_constraint' external/dbio/sqlite3/sqlite3.c:98738: error: invalid use of incomplete type 'const struct sqlite3_index_constraint' external/dbio/sqlite3/sqlite3.c:98730: error: forward declaration of 'const struct sqlite3_index_constraint' external/dbio/sqlite3/sqlite3.c:98751: error: invalid use of incomplete type 'struct sqlite3_index_constraint_usage' external/dbio/sqlite3/sqlite3.c:98728: error: forward declaration of 'struct sqlite3_index_constraint_usage' external/dbio/sqlite3/sqlite3.c:98751: error: invalid use of incomplete type 'struct sqlite3_index_constraint_usage' external/dbio/sqlite3/sqlite3.c:98728: error: forward declaration of 'struct sqlite3_index_constraint_usage' external/dbio/sqlite3/sqlite3.c:98752: error: invalid use of incomplete type 'struct sqlite3_index_constraint' external/dbio/sqlite3/sqlite3.c:98730: error: forward declaration of 'struct sqlite3_index_constraint' external/dbio/sqlite3/sqlite3.c:98752: error: invalid use of incomplete type 'const struct sqlite3_index_constraint' external/dbio/sqlite3/sqlite3.c:98730: error: forward declaration of 'const struct sqlite3_index_constraint' external/dbio/sqlite3/sqlite3.c:99161: error: invalid conversion from 'void*' to 'SrcList*' external/dbio/sqlite3/sqlite3.c:99166: error: invalid application of 'sizeof' to incomplete type 'SrcList_item' external/dbio/sqlite3/sqlite3.c:99167: error: cannot convert 'SrcList::SrcList_item [1]' to 'SrcList_item*' in assignment external/dbio/sqlite3/sqlite3.c:99169: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:99208: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c: In function 'WhereInfo* sqlite3WhereBegin(Parse*, SrcList*, Expr*, ExprList**, u16)': external/dbio/sqlite3/sqlite3.c:99486: error: invalid conversion from 'void*' to 'WhereInfo*' external/dbio/sqlite3/sqlite3.c:99584: error: cannot convert 'SrcList::SrcList_item [1]' to 'SrcList_item*' in assignment external/dbio/sqlite3/sqlite3.c:99649: error: cannot convert 'SrcList::SrcList_item*' to 'SrcList_item*' in assignment external/dbio/sqlite3/sqlite3.c:99649: error: cannot increment a pointer to incomplete type 'SrcList_item' external/dbio/sqlite3/sqlite3.c:99654: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:99656: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:99663: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:99669: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:99714: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:99803: error: cannot convert 'SrcList::SrcList_item*' to 'SrcList_item*' in assignment external/dbio/sqlite3/sqlite3.c:99804: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:99805: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:99814: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:99821: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:99825: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:99829: error: invalid conversion from 'void*' to 'const char*' external/dbio/sqlite3/sqlite3.c:99829: error: initializing argument 3 of 'void sqlite3VdbeChangeP4(Vdbe*, int, const char*, int)' external/dbio/sqlite3/sqlite3.c:99851: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c: In function 'void sqlite3WhereEnd(WhereInfo*)': external/dbio/sqlite3/sqlite3.c:99957: error: cannot convert 'WhereLevel::
:: ::InLoop*' to 'InLoop*' in assignment external/dbio/sqlite3/sqlite3.c:99957: error: cannot decrement a pointer to incomplete type 'InLoop' external/dbio/sqlite3/sqlite3.c:99958: error: invalid use of incomplete type 'struct InLoop' external/dbio/sqlite3/sqlite3.c:99954: error: forward declaration of 'struct InLoop' external/dbio/sqlite3/sqlite3.c:99959: error: invalid use of incomplete type 'struct InLoop' external/dbio/sqlite3/sqlite3.c:99954: error: forward declaration of 'struct InLoop' external/dbio/sqlite3/sqlite3.c:99959: error: invalid use of incomplete type 'struct InLoop' external/dbio/sqlite3/sqlite3.c:99954: error: forward declaration of 'struct InLoop' external/dbio/sqlite3/sqlite3.c:99960: error: invalid use of incomplete type 'struct InLoop' external/dbio/sqlite3/sqlite3.c:99954: error: forward declaration of 'struct InLoop' external/dbio/sqlite3/sqlite3.c:99994: error: cannot convert 'SrcList::SrcList_item*' to 'SrcList_item*' in initialization external/dbio/sqlite3/sqlite3.c:99995: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:100003: error: invalid use of incomplete type 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c:10825: error: forward declaration of 'struct SrcList_item' external/dbio/sqlite3/sqlite3.c: At global scope: external/dbio/sqlite3/sqlite3.c:100099: error: expected unqualified-id before '!' token external/dbio/sqlite3/sqlite3.c: In function 'void yy_reduce(yyParser*, int)': external/dbio/sqlite3/sqlite3.c:102478: error: invalid conversion from 'void*' to 'SrcList*' external/dbio/sqlite3/sqlite3.c:102762: error: expected unqualified-id before '!' token external/dbio/sqlite3/sqlite3.c:102762: error: expected ';' before '!' token external/dbio/sqlite3/sqlite3.c:102766: error: expected unqualified-id before '!' token external/dbio/sqlite3/sqlite3.c:102766: error: expected ';' before '!' token external/dbio/sqlite3/sqlite3.c:102774: error: expected unqualified-id before '!' token external/dbio/sqlite3/sqlite3.c:102774: error: expected ')' before '!' token external/dbio/sqlite3/sqlite3.c:102787: error: expected unqualified-id before '!' token external/dbio/sqlite3/sqlite3.c:102787: error: expected ')' before '!' token external/dbio/sqlite3/sqlite3.c: In function 'int sqlite3_complete16(const void*)': external/dbio/sqlite3/sqlite3.c:104562: error: invalid conversion from 'const void*' to 'const char*' external/dbio/sqlite3/sqlite3.c: At global scope: external/dbio/sqlite3/sqlite3.c:104737: error: redefinition of 'char* sqlite3_temp_directory' external/dbio/sqlite3/sqlite3.c:4585: error: 'char* sqlite3_temp_directory' previously declared here external/dbio/sqlite3/sqlite3.c: In function 'int createCollation(sqlite3*, const char*, u8, u8, void*, int (*)(void*, int, const void*, int, const void*), void(*)(void*))': external/dbio/sqlite3/sqlite3.c:106252: error: invalid conversion from 'void*' to 'CollSeq*' external/dbio/sqlite3/sqlite3.c: In function 'int openDatabase(const char*, sqlite3**, unsigned int, const char*)': external/dbio/sqlite3/sqlite3.c:106456: error: invalid conversion from 'void*' to 'sqlite3*' external/dbio/sqlite3/sqlite3.c:106540: warning: deprecated conversion from string constant to 'char*' external/dbio/sqlite3/sqlite3.c:106542: warning: deprecated conversion from string constant to 'char*' external/dbio/sqlite3/sqlite3.c: In function 'int sqlite3_open16(const void*, sqlite3**)': external/dbio/sqlite3/sqlite3.c:106672: error: invalid conversion from 'const void*' to 'const char*' scons: *** [build/external/release/linux/2.6/64/x86/gcc/4.4/mpi/dbio/sqlite3/sqlite3.os] Error 1 scons: building terminated because of errors. Actually this is not the whole error log but the last part of it. Could you help me with this one?
Regards, Jan
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September 22, 2014 at 3:28 pm #10293
Anonymous
I’m guessing that your mpi complier is having an issue with the way we’ve set up the compiler commandlines.
Scons should print out the exact commandline that it’s using prior to executing it. What does it look like on your system? Is it running the /opt/openmpi/1.7.3/gcc/bin/mpiCC compiler (for the sqlite3 files)? If you run it manually, does it give the same error? What if you change all the “-isystem”s to just “-I”?
Also, just to confirm, what happens when you run
/opt/openmpi/1.7.3/gcc/bin/mpicxx –version
and
/opt/openmpi/1.7.3/gcc/bin/mpiCC –version
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