installation issue: error: undefined reference to '__wrap_memcpy'

[MichelMoser]

hi,

I am trying to compile edyeet and run into some problems with the --wrap=memcpy option.

install commands:

 module load zlib/1.2.11-GCCcore-8.3.0
 module load Boost/1.71.0-gompi-2019b
 module load GCC/8.3.0
cd edyeet
./bootstrap.sh
 ./configure --prefix=$PWD --with-boost=/cluster/software/Boost/1.71.0-gompi-2019b/
make

output:

checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking boost/math/distributions/binomial.hpp usability... yes
checking boost/math/distributions/binomial.hpp presence... yes
checking for boost/math/distributions/binomial.hpp... yes
configure: creating ./config.status
config.status: creating Makefile

#make
g++ -O3 -DNDEBUG -g -std=c++14 -Wno-deprecated-declarations -Isrc -I /cluster/software/Boost/1.71.0-gompi-2019b//include -include src/common/memcpyLink.h -Wl,--wrap=memcpy -DUSE_BOOST src/yeet/yeet_main.cpp -o edyeet /cluster/software/Boost/1.71.0-gompi-2019b//lib/libboost_math_c99.a -lstdc++ -lz -lm -lpthread
/net/10.222.0.31/projects01/Orion/cluster/software/GCCcore/8.3.0/include/c++/8.3.0/bits/stl_algobase.h:368: error: undefined reference to '__wrap_memcpy'
/net/10.222.0.31/projects01/Orion/cluster/software/GCCcore/8.3.0/include/c++/8.3.0/bits/stl_algobase.h:368: error: undefined reference to '__wrap_memcpy'
/net/10.222.0.31/projects01/Orion/cluster/software/GCCcore/8.3.0/include/c++/8.3.0/bits/stl_algobase.h:368: error: undefined reference to '__wrap_memcpy'
/net/10.222.0.31/projects01/Orion/cluster/software/GCCcore/8.3.0/include/c++/8.3.0/bits/char_traits.h:352: error: undefined reference to '__wrap_memcpy'
collect2: error: ld returned 1 exit status
make: *** [edyeet] Error 1

I tried augmenting the src/common/memcpyLink.h file according to a similar issue in MashMap: https://github.com/marbl/MashMap/issues/10 but resulting binary is not responding.

Help would be appreciated.

Thanks, Michel

[ekg]

I haven't compiled with boost. Can you figure out how to disable that aspect of the build?

On Thu, Nov 5, 2020, 10:25 MichelMoser notifications@github.com wrote:

hi,

I am trying to compile edyeet and run into some problems with the --wrap=memcpy option.

install commands:

module load zlib/1.2.11-GCCcore-8.3.0 module load Boost/1.71.0-gompi-2019b module load GCC/8.3.0 cd edyeet ./bootstrap.sh ./configure --prefix=$PWD --with-boost=/cluster/software/Boost/1.71.0-gompi-2019b/ make

output:

checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking boost/math/distributions/binomial.hpp usability... yes checking boost/math/distributions/binomial.hpp presence... yes checking for boost/math/distributions/binomial.hpp... yes configure: creating ./config.status config.status: creating Makefile

make

g++ -O3 -DNDEBUG -g -std=c++14 -Wno-deprecated-declarations -Isrc -I /cluster/software/Boost/1.71.0-gompi-2019b//include -include src/common/memcpyLink.h -Wl,--wrap=memcpy -DUSE_BOOST src/yeet/yeet_main.cpp -o edyeet /cluster/software/Boost/1.71.0-gompi-2019b//lib/libboost_math_c99.a -lstdc++ -lz -lm -lpthread /net/10.222.0.31/projects01/Orion/cluster/software/GCCcore/8.3.0/include/c++/8.3.0/bits/stl_algobase.h:368: error: undefined reference to 'wrap_memcpy' /net/10.222.0.31/projects01/Orion/cluster/software/GCCcore/8.3.0/include/c++/8.3.0/bits/stl_algobase.h:368: error: undefined reference to 'wrap_memcpy' /net/10.222.0.31/projects01/Orion/cluster/software/GCCcore/8.3.0/include/c++/8.3.0/bits/stl_algobase.h:368: error: undefined reference to 'wrap_memcpy' /net/10.222.0.31/projects01/Orion/cluster/software/GCCcore/8.3.0/include/c++/8.3.0/bits/char_traits.h:352: error: undefined reference to 'wrap_memcpy' collect2: error: ld returned 1 exit status make: *** [edyeet] Error 1

I tried augmenting the src/common/memcpyLink.h file according to a similar issue in MashMap: marbl/MashMap#10 https://github.com/marbl/MashMap/issues/10 but resulting binary is not responding.

Help would be appreciated.

Thanks, Michel

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[MichelMoser]

i switched to GSL, but same error occurs.

make
g++ -O3 -DNDEBUG -g -std=c++14 -Wno-deprecated-declarations -Isrc -I /cluster/software/GSL/2.5-GCC-7.3.0-2.30//include -include src/common/memcpyLink.h -Wl,--wrap=memcpy  src/yeet/yeet_main.cpp -o edyeet -L/cluster/software/GSL/2.5-GCC-7.3.0-2.30//lib -lgsl -lgslcblas -lstdc++ -lz -lm -lpthread
/net/10.222.0.31/projects01/Orion/cluster/software/GCCcore/7.3.0/include/c++/7.3.0/bits/char_traits.h:350: error: undefined reference to '__wrap_memcpy'
src/common/edlib.hxx:1364: error: undefined reference to '__wrap_memcpy'
src/common/edlib.hxx:1365: error: undefined reference to '__wrap_memcpy'
src/common/edlib.hxx:307: error: undefined reference to '__wrap_memcpy'
collect2: error: ld returned 1 exit status
make: *** [edyeet] Error 1

Should GCC version match the version mentioned in src/common/memcpyLink.h?

cat src/common/memcpyLink.h

/**
 * @file    memcpyLink.h
 * @author  Chirag Jain <cjain7@gatech.edu>
 */

__asm__(".symver memcpy,memcpy@GLIBC_2.2.5");

[ekg]

Uh oh. I wonder if that's the problem. Would you please check if setting the correct GCC version here fixes the build?

On Thu, Nov 5, 2020, 11:34 MichelMoser notifications@github.com wrote:

i switched to GSL, but same error occurs.

make g++ -O3 -DNDEBUG -g -std=c++14 -Wno-deprecated-declarations -Isrc -I /cluster/software/GSL/2.5-GCC-7.3.0-2.30//include -include src/common/memcpyLink.h -Wl,--wrap=memcpy src/yeet/yeet_main.cpp -o edyeet -L/cluster/software/GSL/2.5-GCC-7.3.0-2.30//lib -lgsl -lgslcblas -lstdc++ -lz -lm -lpthread /net/10.222.0.31/projects01/Orion/cluster/software/GCCcore/7.3.0/include/c++/7.3.0/bits/char_traits.h:350: error: undefined reference to 'wrap_memcpy' src/common/edlib.hxx:1364: error: undefined reference to '__wrap_memcpy' src/common/edlib.hxx:1365: error: undefined reference to 'wrap_memcpy' src/common/edlib.hxx:307: error: undefined reference to '__wrap_memcpy' collect2: error: ld returned 1 exit status make: *** [edyeet] Error 1

Should GCC version match the version mentioned in src/common/memcpyLink.h?

cat src/common/memcpyLink.h

/**

• @file memcpyLink.h
• @author Chirag Jain cjain7@gatech.edu */

asm(".symver memcpy,memcpy@GLIBC_2.2.5");

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[MichelMoser]

hmm, no this did not solve the problem.

Could you share your compilation settings and commands for edyeet? So i can maybe backtrack the error.

I am on a Centos 7.8 node on a cluster. Maybe using a container would be better?

[MichelMoser]

tried building the container based on the Dockerfile at pggb repo.

edyeet compiled successfully, but smoothxg is missing some files. probably some error introduced in the latest push?

[subwaystation]

Hi Michel, thanks for reporting that the current Dockerfile of pggb is broken. Currently taking a look at it.

[MichelMoser]

great, thank you!

[subwaystation]

Was able to reproduce you the issue locally. Now trying a fix.

[subwaystation]

The Dockerfile in current master of pggb should work now. I tested it locally and in a Ubuntu VM. Please try it out :) Or just wait, until the container was built.

[MichelMoser]

great, we will test and report back

[MichelMoser]

successfully built the container and ran the test dataset of pggb. Thank you very much!

[MichelMoser]

actually, smoothxg is failing because its missing an output option -o which can not be set within pggb

[seqwish::links] 0.439 links derived
[seqwish::gfa] 0.439 writing graph
[seqwish::gfa] 0.473 done
seqwish -t 16 -s /mnt/users/michelmo/tools/pggb/data/HLA/DRB1-3123.fa.gz -p /mnt/users/michelmo/tools/pggb/data/HLA/DRB1-3123.fa.gz.pggb-s3000-p70-n10-a70-K16-k8-w10000-j5000-e5000.paf -k 8 -g /mnt/users/michelmo/tools/pggb/data/HLA/DRB1-3123.fa.gz.pggb-s3000-p70-n10-a70-K16-k8-w10000-j5000-e5000.seqwish.gfa -P
0.33s user 0.19s system 90% cpu 0.59s total 26144Kb max memory
[smoothxg::main] error: Please specify an output file with -o/--smoothed-out
Command exited with non-zero status 1
smoothxg -t 16 -g /mnt/users/michelmo/tools/pggb/data/HLA/DRB1-3123.fa.gz.pggb-s3000-p70-n10-a70-K16-k8-w10000-j5000-e5000.seqwish.gfa -w 10000 -j 5000 -e 5000 -l 10000 -m /mnt/users/michelmo/tools/pggb/data/HLA/DRB1-3123.fa.gz.pggb-s3000-p70-n10-a70-K16-k8-w10000-j5000-e5000.smooth.maf -s /mnt/users/michelmo/tools/pggb/data/HLA/DRB1-3123.fa.gz.pggb-s3000-p70-n10-a70-K16-k8-w10000-j5000-e5000.consensus -a -C 10,100,1000,10000
0.00s user 0.05s system 96% cpu 0.05s total 2484Kb max memory

so smoothxg currently has to be run as a separate final step. But that's no big issue

[subwaystation]

Hmm, it should work. We set -o https://github.com/pangenome/pggb/blob/c3cfcc9e4468928d8ca43cae759577cdb6e9d1d6/pggb#L196.

[subwaystation]

Could it be that you didn't check out the latest master? Not sure, how I could reproduce your error.

[koolhazz]

-O2 ?