Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • #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
Previous template Next

Latest Articles

Collapse
  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM
  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
View All

ad_right_rmr

Collapse

News

Collapse
Topics Statistics Last Post
Cancer Metastasis: A Deep Dive into Cellular Plasticity by seqadmin
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
18 views
0 likes
 Last Post seqadmin
by seqadmin
04-11-2024, 12:08 PM  
Proteogenomic Profiles Offer New Clues in Prostate Cancer by seqadmin
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
22 views
0 likes
 Last Post seqadmin
by seqadmin
04-10-2024, 10:19 PM  
Novel Diagnostic Assay Enhances Ovarian Cancer Detection by seqadmin
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
16 views
0 likes
 Last Post seqadmin
by seqadmin
04-10-2024, 09:21 AM  
Evolutionary Dynamics of Centromeres: A Comparative Genomic Analysis by seqadmin
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
47 views
0 likes
 Last Post seqadmin
by seqadmin
04-04-2024, 09:00 AM  
View All
Working...
X