Question: Kmergenie compilation problem
1
gravatar for yvan.wenger
14 months ago by
yvan.wenger20
yvan.wenger20 wrote:

Hello,

I would like to try kmergenie, but I can't compile (actually on my machine, Ubuntu 14.04.4 LTS, there is no problem, but on the server I would like to install it I get this error:

g++ -o minia/Pool.o -c minia/Pool.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread  -D_largeint -DKMER_PRECISION=4
g++ -o minia/Bank.o -c minia/Bank.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread  -D_largeint -DKMER_PRECISION=4
g++ -o minia/Hash16.o -c minia/Hash16.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread  -D_largeint -DKMER_PRECISION=4
g++ -o minia/Bloom.o -c minia/Bloom.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread  -D_largeint -DKMER_PRECISION=4
g++ -o minia/Kmer.o -c minia/Kmer.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread  -D_largeint -DKMER_PRECISION=4
g++ -o minia/Utils.o -c minia/Utils.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread  -D_largeint -DKMER_PRECISION=4
g++ -o minia/LinearCounter.o -c minia/LinearCounter.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread  -D_largeint -DKMER_PRECISION=4
g++ -o minia/LargeInt.o -c minia/LargeInt.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread  -D_largeint -DKMER_PRECISION=4
g++ -o minia/MultiConsumer.o -c minia/MultiConsumer.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread  -D_largeint -DKMER_PRECISION=4
g++ -o minia/Hashing.o -c minia/Hashing.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread  -D_largeint -DKMER_PRECISION=4
g++ -o specialk minia/Pool.o minia/Bank.o minia/Hash16.o minia/Bloom.o minia/Kmer.o minia/Utils.o minia/LinearCounter.o minia/LargeInt.o minia/MultiConsumer.o minia/Hashing.o main.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread  -D_largeint -DKMER_PRECISION=4 -L/opt/rh/devtoolset-2/root/usr/lib64 -L/opt/rh/devtoolset-2/root/usr/lib -lz -DSVN_REV=1.7016
minia/Bank.o:Bank.cpp:function Bank::open_stream(int): error: undefined reference to 'gzopen64'
minia/Bank.o:Bank.cpp:function Bank::init(char**, int): error: undefined reference to 'gzopen64'
minia/Bank.o:Bank.cpp:function Bank::estimate_kmers_volume(int): error: undefined reference to 'gztell64'
minia/Bank.o:Bank.cpp:function Bank::estimate_kmers_volume(int): error: undefined reference to 'gztell64'
minia/Bank.o:Bank.cpp:function Bank::estimate_nb_reads(): error: undefined reference to 'gztell64'
minia/Bank.o:Bank.cpp:function Bank::estimate_nb_reads(): error: undefined reference to 'gztell64'
minia/Bank.o:Bank.cpp:function Bank::load_position(): error: undefined reference to 'gzseek64'
collect2: error: ld returned 1 exit status
make: *** [specialk] Error 1

Theoretically dependencies are met...

Currently Loaded Modules:
  1) GCC/4.9.3-2.25                 7) ScaLAPACK/2.0.2-OpenBLAS-0.2.15-LAPACK-3.6.0  13) Java/1.8.0_72    19) HDF5/1.8.16     25) bzip2/1.0.6     31) GCCcore/4.9.3                    37) impi/5.1.2.150
  2) numactl/2.0.11                 8) ncurses/6.0                                   14) Tcl/8.6.4        20) netCDF/4.3.3.1  26) gettext/0.19.6  32) ifort/2016.1.150-GCC-4.9.3-2.25  38) python/33
  3) hwloc/1.11.2                   9) libreadline/6.3                               15) Tk/8.6.4-no-X11  21) expat/2.1.0     27) XZ/5.2.2        33) iimpi/8.1.5-GCC-4.9.3-2.25
  4) OpenMPI/1.10.2                10) libpng/1.6.21                                 16) cURL/7.47.0      22) GDAL/2.0.2      28) PCRE/8.38       34) binutils/2.25
  5) OpenBLAS/0.2.15-LAPACK-3.6.0  11) NASM/2.11.08                                  17) libxml2/2.9.3    23) PROJ/4.9.2      29) R/3.3.1         35) zlib/1.2.8
  6) FFTW/3.3.4                    12) libjpeg-turbo/1.4.2                           18) Szip/2.1         24) GMP/6.1.0       30) gcc/devtoolset  36) icc/2016.1.150-GCC-4.9.3-2.25
kmergenie next-gen assembly • 539 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by yvan.wenger20

Do you have the zlib-devel package installed?

This thread may be also of interest, if you do.

ADD REPLYlink modified 14 months ago • written 14 months ago by genomax33k

Sorry, I didn't reply the right way...

# Wrapped for easier reading
$ module show zlib
/opt/ebmodules/all/Compiler/GCCcore/4.9.3/zlib/1.2.8.lua:

help([[zlib is designed to be a free, general-purpose, legally unencumbered -- \
that is, not covered by any patents -- lossless data-compression library for use \
on virtually any computer hardware and operating system. - Homepage: \
http://www.zlib.net/]]) whatis("Description: zlib is designed to be a free, \
general-purpose, legally unencumbered -- that is, not covered by any \
patents -- lossless data-compression library for use on virtually any \
computer hardware and operating system. - Homepage: \
http://www.zlib.net/") conflict("zlib") \
prepend_path("CPATH","/opt/ebsofts/Compiler/GCCcore/4.9.3/zlib/1.2.8/include") \
prepend_path("LD_LIBRARY_PATH","/opt/ebsofts/Compiler/GCCcore/4.9.3/zlib/1.2.8/lib") \ prepend_path("LIBRARY_PATH","/opt/ebsofts/Compiler/GCCcore/4.9.3/zlib/1.2.8/lib") \ prepend_path("MANPATH","/opt/ebsofts/Compiler/GCCcore/4.9.3/zlib/1.2.8/share/man") \
prepend_path("PKG_CONFIG_PATH","/opt/ebsofts/Compiler/GCCcore/4.9.3/zlib/1.2.8/lib/pkgconfig") \ setenv("EBROOTZLIB","/opt/ebsofts/Compiler/GCCcore/4.9.3/zlib/1.2.8") setenv("EBVERSIONZLIB","1.2.8") \
setenv("EBDEVELZLIB","/opt/ebsofts/Compiler/GCCcore/4.9.3/zlib/1.2.8/easybuild/Compiler-GCCcore-4.9.3-zlib-1.2.8-easybuild-devel")
ADD REPLYlink modified 14 months ago by Ram12k • written 14 months ago by yvan.wenger20

What do you get with echo $LD_LIBRARY_PATH?

I think these two locations don't seem to have the zlib files (-L/opt/rh/devtoolset-2/root/usr/lib64 -L/opt/rh/devtoolset-2/root/usr/lib). Can you edit the Makefile for minia and add the location for your zlib files with another -L /opt/ebsofts/Compiler/GCCcore/4.9.3/zlib/1.2.8/lib)? Or you could append this directory to your LD_LIBRARY_PATH as an alternative.

ADD REPLYlink modified 14 months ago • written 14 months ago by genomax33k

Great, here is what I get:

# Wrapped for easier reading
[wengery@login1 ~]$ echo $LD_LIBRARY_PATH

echo $LD_LIBRARY_PATH

/opt/ebsofts/Core/zlib/1.2.8/lib:\
/opt/intel/composer_xe_2015.0.090/compiler/lib/intel64:\
/opt/intel/mic/coi/host-linux-release/lib:\
/opt/intel/mic/myo/lib:/opt/intel/composer_xe_2015.0.090/mpirt/lib/intel64:\
/opt/intel/composer_xe_2015.0.090/compiler/lib/intel64:/opt/intel/composer_xe_2015.0.090/ipp/lib/intel64:\
/opt/intel/mic/coi/host-linux-release/lib:/opt/intel/mic/myo/lib:\
/opt/intel/composer_xe_2015.0.090/compiler/lib/intel64:\
/opt/intel/composer_xe_2015.0.090/mkl/lib/intel64:\
/opt/intel/composer_xe_2015.0.090/tbb/lib/intel64/gcc4.4

I do not see a makefile in the minia directory, and if I need to add the location for the zlib file to the main makefile, how shoud I do it? I am not really an expert...

ADD REPLYlink modified 14 months ago by Ram12k • written 14 months ago by yvan.wenger20

Can you try

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/ebsofts/Compiler/GCCcore/4.9.3/zlib/1.2.8/lib

What files are in /opt/ebsofts/Compiler/GCCcore/4.9.3/zlib/1.2.8/lib?

ADD REPLYlink modified 14 months ago • written 14 months ago by genomax33k

The files in /opt/ebsofts/Compiler/GCCcore/4.9.3/zlib/1.2.8/lib are

libz.a
libz.so -> libz.so.1.2.8
libz.so.1.2.8
libz.so.1.2.8
pkgconfig

I added

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/ebsofts/Compiler/GCCcore/4.9.3/zlib/1.2.8/lib

at the beginning of the makefile, but still get the same error.

ADD REPLYlink modified 14 months ago by genomax33k • written 14 months ago by yvan.wenger20

Issue the export command on the command line (don't add it to the makefile).

ADD REPLYlink modified 14 months ago • written 14 months ago by genomax33k
1

Still the same error. But I tested on another account on the same cluster, and it worked perfectly. So the issue must be specifically related to my account. I will try to sort things out and post here what was wrong.

Many thanks for you help !

ADD REPLYlink written 14 months ago by yvan.wenger20
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