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Can't find GLIBCXX #9

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jpearl01 opened this issue Jul 5, 2021 · 0 comments
Open

Can't find GLIBCXX #9

jpearl01 opened this issue Jul 5, 2021 · 0 comments

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@jpearl01
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jpearl01 commented Jul 5, 2021 •
edited
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Hello,

I'm trying to install BlastFrost on an older system, but using a newer gcc than the system - however the library being linked is still the system version, not the newer one's libraries. I've tried changing the LD_LIBRARY_PATH to correctly point to the new library, but it still ends up using the older system libraries. Any idea how to force it to use the more recent library during compile time?

(EDIT:) Also have LIBRARY_PATH, and PATH including the new library location.

(blastfrost) [josh@ncb-sv-016 15:42:00 BlastFrost]$ cd build/
(blastfrost) [josh@ncb-sv-016 15:42:03 build]$ cmake ..
-- The C compiler identification is GNU 4.9.1
-- The CXX compiler identification is GNU 4.9.1
-- Check for working C compiler: /opt/gcc_4.9.1/rtf/bin/gcc
-- Check for working C compiler: /opt/gcc_4.9.1/rtf/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /opt/gcc_4.9.1/rtf/bin/c++
-- Check for working CXX compiler: /opt/gcc_4.9.1/rtf/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Configuring done
-- Generating done
-- Build files have been written to: /home/josh/external_bio_programs/BlastFrost/build
(blastfrost) [josh@ncb-sv-016 15:42:07 build]$ make
Scanning dependencies of target bifrost_lib
[  7%] Creating directories for 'bifrost_lib'
[ 14%] No download step for 'bifrost_lib'
[ 21%] No patch step for 'bifrost_lib'
[ 28%] No update step for 'bifrost_lib'
[ 35%] Performing configure step for 'bifrost_lib'
-- The C compiler identification is GNU 4.9.1
-- The CXX compiler identification is GNU 4.9.1
-- Check for working C compiler: /opt/gcc_4.9.1/rtf/bin/gcc
-- Check for working C compiler: /opt/gcc_4.9.1/rtf/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /opt/gcc_4.9.1/rtf/bin/c++
-- Check for working CXX compiler: /opt/gcc_4.9.1/rtf/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
Disabling native architecture compilation (including AVX2)
Build type: Release
Maximum k-mer size: 31
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3")
-- Configuring done
-- Generating done
-- Build files have been written to: /home/josh/external_bio_programs/BlastFrost/bifrost
[ 42%] Performing build step for 'bifrost_lib'
Scanning dependencies of target bifrost_dynamic
[  3%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o
In file included from /home/josh/external_bio_programs/BlastFrost/bifrost/src/CompactedDBG.hpp:24:0,
                 from /home/josh/external_bio_programs/BlastFrost/bifrost/src/Bifrost.cpp:1:
/home/josh/external_bio_programs/BlastFrost/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace
 class BlockedBloomFilter {
       ^
[  6%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o
[ 10%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o
In file included from /home/josh/external_bio_programs/BlastFrost/bifrost/src/BlockedBloomFilter.cpp:1:0:
/home/josh/external_bio_programs/BlastFrost/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace
 class BlockedBloomFilter {
       ^
[ 13%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o
In file included from /home/josh/external_bio_programs/BlastFrost/bifrost/src/CompactedDBG.hpp:24:0,
                 from /home/josh/external_bio_programs/BlastFrost/bifrost/src/ColorSet.hpp:6,
                 from /home/josh/external_bio_programs/BlastFrost/bifrost/src/ColorSet.cpp:1:
/home/josh/external_bio_programs/BlastFrost/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace
 class BlockedBloomFilter {
       ^
[ 17%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o
[ 20%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o
[ 24%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o
[ 27%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o
[ 31%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/Kmer.cpp.o
[ 34%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/KmerIterator.cpp.o
[ 37%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/MinimizerIndex.cpp.o
[ 41%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/TinyBitmap.cpp.o
[ 44%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/UnitigMap.cpp.o
In file included from /home/josh/external_bio_programs/BlastFrost/bifrost/src/CompactedDBG.hpp:24:0,
                 from /home/josh/external_bio_programs/BlastFrost/bifrost/src/UnitigMap.tcc:4,
                 from /home/josh/external_bio_programs/BlastFrost/bifrost/src/UnitigMap.hpp:323,
                 from /home/josh/external_bio_programs/BlastFrost/bifrost/src/UnitigMap.cpp:1:
/home/josh/external_bio_programs/BlastFrost/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace
 class BlockedBloomFilter {
       ^
[ 48%] Building C object src/CMakeFiles/bifrost_dynamic.dir/roaring.c.o
Linking CXX shared library libbifrost.so
[ 48%] Built target bifrost_dynamic
Scanning dependencies of target Bifrost
[ 51%] Building CXX object src/CMakeFiles/Bifrost.dir/Bifrost.cpp.o
In file included from /home/josh/external_bio_programs/BlastFrost/bifrost/src/CompactedDBG.hpp:24:0,
                 from /home/josh/external_bio_programs/BlastFrost/bifrost/src/Bifrost.cpp:1:
/home/josh/external_bio_programs/BlastFrost/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace
 class BlockedBloomFilter {
       ^
Linking CXX executable Bifrost
[ 51%] Built target Bifrost
Scanning dependencies of target bifrost_static
[ 55%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o
In file included from /home/josh/external_bio_programs/BlastFrost/bifrost/src/CompactedDBG.hpp:24:0,
                 from /home/josh/external_bio_programs/BlastFrost/bifrost/src/Bifrost.cpp:1:
/home/josh/external_bio_programs/BlastFrost/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace
 class BlockedBloomFilter {
       ^
[ 58%] Building CXX object src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o
[ 62%] Building CXX object src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o
In file included from /home/josh/external_bio_programs/BlastFrost/bifrost/src/BlockedBloomFilter.cpp:1:0:
/home/josh/external_bio_programs/BlastFrost/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace
 class BlockedBloomFilter {
       ^
[ 65%] Building CXX object src/CMakeFiles/bifrost_static.dir/ColorSet.cpp.o
In file included from /home/josh/external_bio_programs/BlastFrost/bifrost/src/CompactedDBG.hpp:24:0,
                 from /home/josh/external_bio_programs/BlastFrost/bifrost/src/ColorSet.hpp:6,
                 from /home/josh/external_bio_programs/BlastFrost/bifrost/src/ColorSet.cpp:1:
/home/josh/external_bio_programs/BlastFrost/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace
 class BlockedBloomFilter {
       ^
[ 68%] Building CXX object src/CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o
[ 72%] Building CXX object src/CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o
[ 75%] Building CXX object src/CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o
[ 79%] Building CXX object src/CMakeFiles/bifrost_static.dir/GFA_Parser.cpp.o
[ 82%] Building CXX object src/CMakeFiles/bifrost_static.dir/Kmer.cpp.o
[ 86%] Building CXX object src/CMakeFiles/bifrost_static.dir/KmerIterator.cpp.o
[ 89%] Building CXX object src/CMakeFiles/bifrost_static.dir/MinimizerIndex.cpp.o
[ 93%] Building CXX object src/CMakeFiles/bifrost_static.dir/TinyBitmap.cpp.o
[ 96%] Building CXX object src/CMakeFiles/bifrost_static.dir/UnitigMap.cpp.o
In file included from /home/josh/external_bio_programs/BlastFrost/bifrost/src/CompactedDBG.hpp:24:0,
                 from /home/josh/external_bio_programs/BlastFrost/bifrost/src/UnitigMap.tcc:4,
                 from /home/josh/external_bio_programs/BlastFrost/bifrost/src/UnitigMap.hpp:323,
                 from /home/josh/external_bio_programs/BlastFrost/bifrost/src/UnitigMap.cpp:1:
/home/josh/external_bio_programs/BlastFrost/bifrost/src/BlockedBloomFilter.hpp:27:7: warning: ‘BlockedBloomFilter’ has a field ‘BlockedBloomFilter::fast_div_’ whose type uses the anonymous namespace
 class BlockedBloomFilter {
       ^
[100%] Building C object src/CMakeFiles/bifrost_static.dir/roaring.c.o
Linking CXX static library libbifrost.a
[100%] Built target bifrost_static
[ 50%] No install step for 'bifrost_lib'
[ 57%] Completed 'bifrost_lib'
[ 57%] Built target bifrost_lib
Scanning dependencies of target BlastFrost
[ 64%] Building CXX object CMakeFiles/BlastFrost.dir/src/BlastFrost.cpp.o
[ 71%] Building CXX object CMakeFiles/BlastFrost.dir/src/BubbleExplorer.cpp.o
[ 78%] Building CXX object CMakeFiles/BlastFrost.dir/src/QuerySearch.cpp.o
[ 85%] Building CXX object CMakeFiles/BlastFrost.dir/src/SubGraphTraverser.cpp.o
[ 92%] Building CXX object CMakeFiles/BlastFrost.dir/src/UnionFind.cpp.o
[100%] Building CXX object CMakeFiles/BlastFrost.dir/src/UnitigData.cpp.o
Linking CXX executable BlastFrost
[100%] Built target BlastFrost
(blastfrost) [josh@ncb-sv-016 15:44:17 build]$ ./BlastFrost
**./BlastFrost: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.5' not found (required by ./BlastFrost)
./BlastFrost: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found (required by ./BlastFrost)
./BlastFrost: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.17' not found (required by ./BlastFrost)
./BlastFrost: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by ./BlastFrost)
./BlastFrost: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by ./BlastFrost)**
(blastfrost) [josh@ncb-sv-016 15:44:23 build]$ echo $LD_LIBRARY_PATH
/opt/gcc_4.9.1/rtf/lib:/usr/lib64
(blastfrost) [josh@ncb-sv-016 15:44:29 build]$ strings /opt/gcc_4.9.1/rtf/lib/libstdc++.so.6 |grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_FORCE_NEW
GLIBCXX_DEBUG_MESSAGE_LENGTH
(blastfrost) [josh@ncb-sv-016 15:44:42 build]$
(blastfrost) [josh@ncb-sv-016 15:44:42 build]$ strings /usr/lib64/libstdc++.so.6 |grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_FORCE_NEW
GLIBCXX_DEBUG_MESSAGE_LENGTH
EDIT:
(blastfrost) [josh@ncb-sv-016 15:58:03 build]$ echo $LIBRARY_PATH
/opt/gcc_4.9.1/rtf/lib
(blastfrost) [josh@ncb-sv-016 15:58:57 build]$ echo $PATH
/home/josh/miniconda3/envs/blastfrost/bin:/opt/pacbio/smrtlink/smrtcmds/bin:/home/josh/miniconda3/bin/aws_completer:/opt/R/R-3.3.3/bin:/home/josh/.rvm/gems/ruby-2.3.5/bin:/home/josh/.rvm/gems/ruby-2.3.5@global/bin:/home/josh/.rvm/rubies/ruby-2.3.5/bin:/home/josh/miniconda3/condabin:/home/josh/miniconda2/bin:/home/josh/.linuxbrew/bin:/home/josh/miniconda2/bin:/usr/share/gridengine/bin/lx26-amd64:/usr/lib64/qt-3.3/bin:/usr/NX/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/pssc/bin:/opt/openmpi/bin:/opt/torque/bin:/opt/torque/sbin:/opt/mpich2/bin:/home/josh/.rvm/bin:/opt/openmpi/bin:/opt/pacbio/smrtlink/smrtcmds/bin:/home/josh/bin/bin:/home/josh/edirect:/home/josh/bin:/home/josh/external_bio_programs/prokka-1.11/bin:/opt/hmmer-3.1b2/binaries:/opt/rnammer-1.2:/opt/smrttools/smrtlink/install/smrtlink-fromsrc_4.0.0.190159+190159-190159-189856-189856-189856/bundles/smrttools/install/smrttools-fromsrc_4.0.0.190159/smrtcmds/bin:/usr/local/emboss/bin:/opt/gcc_4.9.1/rtf/lib
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@jpearl01