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  • #1

    GPU blast setup

    Facing problem in configuring GPU blast, getting following error, please help me to setup GPUE blast.

    System configuration:
    RAM: 7.7 GiB
    Processor" Intel® Core™ i5-3470 CPU @ 3.20GHz × 4
    Graphics: GeForce GTX 1050 Ti/PCIe/SSE2
    os: 64-bit


    Error Part:

    /usr/bin/g++ -c -g -D_DEBUG -DNCBI_WITHOUT_MT -I/home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/UNKNOWN000-Debug64/inc -I/home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/src/corelib/ncbiexpt.cpp -o ncbiexpt.o
    In file included from /usr/include/c++/5/backward/strstream:50:0,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbistre.hpp:86,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbi_stack.hpp:35,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbidiag.hpp:43,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbiexpt.hpp:42,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/src/corelib/ncbiexpt.cpp:40:
    /usr/include/c++/5/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
    #warning \
    ^
    /usr/bin/g++ -c -g -D_DEBUG -DNCBI_WITHOUT_MT -I/home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/UNKNOWN000-Debug64/inc -I/home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/src/corelib/ncbifile.cpp -o ncbifile.o
    In file included from /usr/include/c++/5/backward/strstream:50:0,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbistre.hpp:86,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbi_stack.hpp:35,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbidiag.hpp:43,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbiexpt.hpp:42,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/tempstr.hpp:38,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbistr.hpp:38,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbistd.hpp:37,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbitime.hpp:59,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbi_system.hpp:36,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbifile.hpp:46,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/src/corelib/ncbifile.cpp:33:
    /usr/include/c++/5/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
    #warning \
    ^
    In file included from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/tempstr.hpp:39:0,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbistr.hpp:38,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbistd.hpp:37,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbitime.hpp:59,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbi_system.hpp:36,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbifile.hpp:46,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/src/corelib/ncbifile.cpp:33:
    /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbimisc.hpp: In instantiation of ‘static void ncbi::CDeleter<X>:elete(X*) [with X = char]’:
    /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbimisc.hpp:536:17: required from ‘void ncbi::AutoPtr<X, Del>::reset(ncbi::AutoPtr<X, Del>::element_type*, EOwnership) [with X = char; Del = ncbi::CDeleter<char>; ncbi::AutoPtr<X, Del>::element_type = char; EOwnership = ENcbiOwnership]’
    /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbimisc.hpp:488:14: required from ‘ncbi::AutoPtr<X, Del>::~AutoPtr() [with X = char; Del = ncbi::CDeleter<char>]’
    /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/src/corelib/ncbifile.cpp:5438:68: required from here
    /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbimisc.hpp:418:11: error: ‘free’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
    { free(object); }
    ^
    In file included from /usr/include/c++/5/cstdlib:72:0,
    from /usr/include/c++/5/bits/stl_algo.h:59,
    from /usr/include/c++/5/algorithm:62,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/tempstr.hpp:41,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbistr.hpp:38,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbistd.hpp:37,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbitime.hpp:59,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbi_system.hpp:36,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/include/corelib/ncbifile.hpp:46,
    from /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/src/corelib/ncbifile.cpp:33:
    /usr/include/stdlib.h:483:13: note: ‘void free(void*)’ declared here, later in the translation unit
    extern void free (void *__ptr) __THROW;
    ^
    /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/UNKNOWN000-Debug64/build/Makefile.rules:26: recipe for target 'ncbifile.o' failed
    make[3]: *** [ncbifile.o] Error 1
    make[3]: Leaving directory '/home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/UNKNOWN000-Debug64/build/corelib'
    FAILED: src/corelib/Makefile.corelib.lib
    make[3]: Entering directory '/home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/UNKNOWN000-Debug64/build/corelib'
    /bin/rm -f libxncbi.a .xncbi.dep .libxncbi.a.stamp
    /bin/rm -f /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/UNKNOWN000-Debug64/lib/libxncbi.a /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/UNKNOWN000-Debug64/status/.xncbi.dep \
    /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/UNKNOWN000-Debug64/lib/libxncbi-static.a /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/UNKNOWN000-Debug64/status/.xncbi-static.dep
    make[3]: Leaving directory '/home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/UNKNOWN000-Debug64/build/corelib'
    /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/src/build-system/Makefile.meta_l:238: recipe for target 'all.nonusr' failed
    make[2]: *** [all.nonusr] Error 2
    make[2]: Leaving directory '/home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/UNKNOWN000-Debug64/build/corelib'
    /home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/src/build-system/Makefile.meta_r:39: recipe for target 'all_r.real' failed
    make[1]: *** [all_r.real] Error 5
    make[1]: Leaving directory '/home/md11060/Downloads/ncbi-blast-2.2.28+_1/c++/UNKNOWN000-Debug64/build'
    Makefile:23: recipe for target 'all' failed
    make: *** [all] Error 2
    Tags: None
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